Co-reporter:Peizhi Zhu, Jiadi Xu, Nadder Sahar, Michael D. Morris, David H. Kohn and Ayyalusamy Ramamoorthy
Journal of the American Chemical Society December 2, 2009 Volume 131(Issue 47) pp:17064-17065
Publication Date(Web):November 6, 2009
DOI:10.1021/ja9081028
Understanding the structure and structural changes of bone, a highly heterogeneous material with a complex hierarchical architecture, continues to be a significant challenge even for high-resolution solid-state NMR spectroscopy. While it is known that dehydration affects mechanical properties of bone by decreasing its strength and toughness, the underlying structural mechanism at the atomic level is unknown. Solid-state NMR spectroscopy, controlled dehydration, and H/D exchange were used for the first time to reveal the structural changes of an intact piece of bovine cortical bone. 1H spectra were used to monitor the dehydration of the bone inside the rotor, and high-resolution 13C chemical shift spectra obtained under magic-angle spinning were used evaluate the dehydration-induced conformational changes in the bone. The experiments revealed the slow denaturation of collagen due to dehydration while the trans-Xaa-Pro conformation in collagen remained unchanged. Our results suggest that glycosaminoglycans in the collagen fiber and mineral interface may chelate with a Ca2+ ion present on the surface of the mineral through sulfate or carboxylate groups. These results provide insights into the role of water molecules in the bone structure and shed light on the relationship between the structure and mechanics of bone.
Co-reporter:Rongchun Zhang, Kamal H. Mroue, and Ayyalusamy Ramamoorthy
Accounts of Chemical Research April 18, 2017 Volume 50(Issue 4) pp:1105-1105
Publication Date(Web):March 29, 2017
DOI:10.1021/acs.accounts.7b00082
ConspectusProtons are vastly abundant in a wide range of exciting macromolecules and thus can be a powerful probe to investigate the structure and dynamics at atomic resolution using solid-state NMR (ssNMR) spectroscopy. Unfortunately, the high signal sensitivity, afforded by the high natural-abundance and high gyromagnetic ratio of protons, is greatly compromised by severe line broadening due to the very strong 1H–1H dipolar couplings. As a result, protons are rarely used, in spite of the desperate need for enhancing the sensitivity of ssNMR to study a variety of systems that are not amenable for high resolution investigation using other techniques including X-ray crystallography, cryo-electron microscopy, and solution NMR spectroscopy. Thanks to the remarkable improvement in proton spectral resolution afforded by the significant advances in magic-angle-spinning (MAS) probe technology, 1H ssNMR spectroscopy has recently attracted considerable attention in the structural and dynamics studies of various molecular systems. However, it still remains a challenge to obtain narrow 1H spectral lines, especially from proteins, without resorting to deuteration.In this Account, we review recent proton-based ssNMR strategies that have been developed in our laboratory to further improve proton spectral resolution without resorting to chemical deuteration for the purposes of gaining atomistic-level insights into molecular structures of various crystalline solid systems, using small molecules and peptides as illustrative examples. The proton spectral resolution enhancement afforded by the ultrafast MAS frequencies up to 120 kHz is initially discussed, followed by a description of an ensemble of multidimensional NMR pulse sequences, all based on proton detection, that have been developed to obtain in-depth information from dipolar couplings and chemical shift anisotropy (CSA). Simple single channel multidimensional proton NMR experiments could be performed to probe the proximity of protons for structure determination using 1H–1H dipolar couplings and to evaluate the changes in chemical environments as well as the relative orientation to the external magnetic field using proton CSA. Due to the boost in signal sensitivity enabled by proton detection under ultrafast MAS, by virtue of high proton natural abundance and gyromagnetic ratio, proton-detected multidimensional experiments involving low-γ nuclei can now be accomplished within a reasonable time, while the higher dimension also offers additional resolution enhancement. In addition, the application of proton-based ssNMR spectroscopy under ultrafast MAS in various challenging and crystalline systems is also presented. Finally, we briefly discuss the limitations and challenges pertaining to proton-based ssNMR spectroscopy under ultrafast MAS conditions, such as the presence of high-order dipolar couplings, friction-induced sample heating, and limited sample volume. Although there are still a number of challenges that must be circumvented by further developments in radio frequency pulse sequences, MAS probe technology and approaches to prepare NMR-friendly samples, proton-based ssNMR has already gained much popularity in various research domains, especially in proteins where uniform or site-selective deuteration can be relatively easily achieved. In addition, implementation of the recently developed fast data acquisition approaches would also enable further developments in the design and applications of proton-based ultrafast MAS multidimensional ssNMR techniques.
Co-reporter:Dr. Thirupathi Ravula;Dr. Sudheer Kumar Ramadugu;Giacomo Di Mauro; Ayyalusamy Ramamoorthy
Angewandte Chemie 2017 Volume 129(Issue 38) pp:11624-11628
Publication Date(Web):2017/09/11
DOI:10.1002/ange.201705569
AbstractPolymer-based nanodiscs are valuable tools in biomedical research that can offer a detergent-free solubilization of membrane proteins maintaining their native lipid environment. Herein, we introduce a novel ca. 1.6 kDa SMA-based polymer with styrene:maleic acid moieties that can form nanodiscs containing a planar lipid bilayer which are useful to reconstitute membrane proteins for structural and functional studies. The physicochemical properties and the mechanism of formation of polymer-based nanodiscs are characterized by light scattering, NMR, FT-IR, and TEM. A remarkable feature is that nanodiscs of different sizes, from nanometer to sub-micrometer diameter, can be produced by varying the lipid-to-polymer ratio. The small-size nanodiscs (up to ca. 30 nm diameter) can be used for solution NMR spectroscopy studies whereas the magnetic-alignment of macro-nanodiscs (diameter of > ca. 40 nm) can be exploited for solid-state NMR studies on membrane proteins.
Co-reporter:Shruti Mukherjee;Rajiv K. Kar;Ravi Prakash Reddy Nanga;Kamal H. Mroue;Anirban Bhunia
Physical Chemistry Chemical Physics 2017 vol. 19(Issue 29) pp:19289-19299
Publication Date(Web):2017/07/26
DOI:10.1039/C7CP01941F
Multidrug resistance against the existing antibiotics is one of the most challenging threats across the globe. Antimicrobial peptides (AMPs), in this regard, are considered to be one of the effective alternatives that can overcome bacterial resistance. MSI-594, a 24-residue linear alpha-helical cationic AMP, has been shown to function via the carpet mechanism to disrupt bacterial membrane systems. To better understand the role of lipid composition in the function of MSI-594, in the present study, eight different model membrane systems have been studied using accelerated molecular dynamics (aMD) simulations. The simulated results are helpful in discriminating the particular effects of cationic MSI-594 against zwitterionic POPC, anionic POPG and POPS, and neutral POPE lipid moieties. Additionally, the effects of various heterogeneous POPC/POPG (7 : 3), POPC/POPS (7 : 3), and POPG/POPE (1 : 3 and 3 : 1) bilayer systems on the dynamic interaction of MSI-594 have also been investigated. The effect on the lipid bilayer due to the interaction with the peptide is characterized by lipid acyl-chain order, membrane thickness, and acyl-chain dynamics. Our simulation results show that the lipid composition affects the membrane interaction of MSI-594, suggesting that membrane selectivity is crucial to its mechanism of action. The results reported in this study are helpful to obtain accurate atomistic-level information governing MSI-594 and its membrane disruptive antimicrobial mechanism of action, and to design next generation potent antimicrobial peptides.
Co-reporter:Venkata Sudheer Kumar Ramadugu;Giacomo Maria Di Mauro;Thirupathi Ravula
Chemical Communications 2017 vol. 53(Issue 78) pp:10824-10826
Publication Date(Web):2017/09/28
DOI:10.1039/C7CC06409H
Polymer lipid nanodiscs have enabled some exciting structural biology and nanobiotechnology applications. The use of a small molecular weight polymer (SMA-EA) has been demonstrated to dramatically increase the size of nanodiscs (up to ∼60 nm diameter). Here, we report the first demonstration of the formation of macro-nanodiscs for a variety of lipids, and solid-state NMR experiments utilizing their magnetic-alignment properties.
Co-reporter:Thirupathi Ravula;Carlo Barnaba;Mukesh Mahajan;G. M. Anantharamaiah;Sang-Choul Im;Lucy Waskell
Chemical Communications 2017 vol. 53(Issue 95) pp:12798-12801
Publication Date(Web):2017/11/28
DOI:10.1039/C7CC07520K
Heme's spin-multiplicity is key in determining the enzymatic function of cytochrome P450 (cytP450). The origin of the low-spin state in ferric P450 is still under debate. Here, we report the first experimental demonstration of P450's membrane interaction altering its spin equilibrium which is accompanied by a stronger affinity for cytochrome b5. These results highlight the importance of lipid membrane for the function of P450.
Co-reporter:Dr. Hyuck Jin Lee;Dr. Kyle J. Korshavn;Younwoo Nam;Juhye Kang;Thomas J. Paul;Dr. Richard A. Kerr;Dr. Il Seung Youn;Dr. Mehmet Ozbil; Dr. Kwang S. Kim; Dr. Bron T. Ruotolo; Dr. Rajeev Prabhakar; Dr. Ayyalusamy Ramamoorthy; Dr. Mi Hee Lim
Chemistry - A European Journal 2017 Volume 23(Issue 11) pp:2706-2715
Publication Date(Web):2017/02/21
DOI:10.1002/chem.201605401
AbstractTo elucidate the involvement of individual and inter-related pathological factors [i.e., amyloid-β (Aβ), metals, and oxidative stress] in the pathogenesis of Alzheimer's disease (AD), chemical tools have been developed. Characteristics required for such tool construction, however, have not been clearly identified; thus, the optimization of available tools or new design has been limited. Here, key structural properties and mechanisms that can determine tools’ regulatory reactivities with multiple pathogenic features found in AD are reported. A series of small molecules was built up through rational structural selection and variations onto the framework of a tool useful for in vitro and in vivo metal–Aβ investigation. Variations include: (i) location and number of an Aβ interacting moiety; (ii) metal binding site; and (iii) denticity and structural flexibility. Detailed biochemical, biophysical, and computational studies were able to provide a foundation of how to originate molecular formulas to devise chemical tools capable of controlling the reactivities of various pathological components through distinct mechanisms. Overall, this multidisciplinary investigation illustrates a structure–mechanism-based strategy of tool invention for such a complicated brain disease.
Co-reporter:Amit S. Pithadia, Anirban Bhunia, Rajendran Sribalan, Vediappen Padmini, Carol A. Fierke and Ayyalusamy Ramamoorthy
Chemical Communications 2016 vol. 52(Issue 5) pp:942-945
Publication Date(Web):13 Nov 2015
DOI:10.1039/C5CC07792C
The deposition of aggregates of human islet amyloid polypeptide (hIAPP) has been correlated with the death of β-cells in type II diabetes mellitus. The actual molecular mechanism of cell death remains largely unknown; however, it has been postulated that the process of aggregation from monomeric hIAPP is closely involved. A possible cause of cellular toxicity may be through the disruption of structural integrity of the cell membrane by IAPP. Herein, a water-soluble curcumin derivative, CurDAc, is used to investigate the mitigation of hIAPP aggregation in the absence and presence of lipid membrane.
Co-reporter:Kyle J. Korshavn, Anirban Bhunia, Mi Hee Lim and Ayyalusamy Ramamoorthy
Chemical Communications 2016 vol. 52(Issue 5) pp:882-885
Publication Date(Web):06 Nov 2015
DOI:10.1039/C5CC08634E
Aggregation at the neuronal cell membrane's lipid bilayer surface is implicated in amyloid-β (Aβ) toxicity associated with Alzheimer's disease; however, structural and mechanistic insights into the process remain scarce. We have identified a conserved binding mode of Aβ40 on lipid bilayer surfaces with a conserved helix containing the self-recognition site (K16-E22).
Co-reporter:Kamal H. Mroue, Jiadi Xu, Peizhi Zhu, Michael D. Morris and Ayyalusamy Ramamoorthy
Physical Chemistry Chemical Physics 2016 vol. 18(Issue 28) pp:18687-18691
Publication Date(Web):29 Jun 2016
DOI:10.1039/C6CP03506J
Using 1H-based magic angle spinning solid-state NMR spectroscopy, we report an atomistic-level characterization of triglycerides in compact cortical bone. By suppressing contributions from immobile molecules present in bone, we show that a 1H-based constant-time uniform-sign cross-peak (CTUC) two-dimensional COSY-type experiment that correlates the chemical shifts of protons can selectively detect a mobile triglyceride layer as the main component of small lipid droplets embedded on the surface of collagen fibrils. High sensitivity and resolution afforded by this NMR approach could be potentially utilized to investigate the origin of triglycerides and their pathological roles associated with bone fractures, diseases, and aging.
Co-reporter:Meng Zhang;Rui Huang;Dr. Rose Ackermann;Dr. Sang-Choul Im; Lucy Waskell; Anna Schwendeman; Ayyalusamy Ramamoorthy
Angewandte Chemie 2016 Volume 128( Issue 14) pp:4573-4575
Publication Date(Web):
DOI:10.1002/ange.201600073
Abstract
Cytochrome P450s (P450s) are a superfamily of enzymes responsible for the catalysis of a wide range of substrates. Dynamic interactions between full-length membrane-bound P450 and its redox partner cytochrome b5 (cytb5) have been found to be important for the enzymatic activity of P450. However, the stability of the circa 70 kDa membrane-bound complex in model membranes renders high-resolution structural NMR studies particularly difficult. To overcome these challenges, reconstitution of the P450–cytb5 complex in peptide-based nanodiscs, containing no detergents, has been demonstrated, which are characterized by size exclusion chromatography and NMR spectroscopy. In addition, NMR experiments are used to identify the binding interface of the P450–cytb5 complex in the nanodisc. This is the first successful demonstration of a protein–protein complex in a nanodisc using NMR structural studies and should be useful to obtain valuable structural information on membrane-bound protein complexes.
Co-reporter:Meng Zhang;Rui Huang;Dr. Rose Ackermann;Dr. Sang-Choul Im; Lucy Waskell; Anna Schwendeman; Ayyalusamy Ramamoorthy
Angewandte Chemie International Edition 2016 Volume 55( Issue 14) pp:4497-4499
Publication Date(Web):
DOI:10.1002/anie.201600073
Abstract
Cytochrome P450s (P450s) are a superfamily of enzymes responsible for the catalysis of a wide range of substrates. Dynamic interactions between full-length membrane-bound P450 and its redox partner cytochrome b5 (cytb5) have been found to be important for the enzymatic activity of P450. However, the stability of the circa 70 kDa membrane-bound complex in model membranes renders high-resolution structural NMR studies particularly difficult. To overcome these challenges, reconstitution of the P450–cytb5 complex in peptide-based nanodiscs, containing no detergents, has been demonstrated, which are characterized by size exclusion chromatography and NMR spectroscopy. In addition, NMR experiments are used to identify the binding interface of the P450–cytb5 complex in the nanodisc. This is the first successful demonstration of a protein–protein complex in a nanodisc using NMR structural studies and should be useful to obtain valuable structural information on membrane-bound protein complexes.
Co-reporter:U.S. Sudheendra, Vishnu Dhople, Aritreyee Datta, Rajiv K. Kar, Charles E. Shelburne, Anirban Bhunia, Ayyalusamy Ramamoorthy
European Journal of Medicinal Chemistry 2015 Volume 91() pp:91-99
Publication Date(Web):16 February 2015
DOI:10.1016/j.ejmech.2014.08.021
•Underlining structural motifs of HβD-3 analogs designed for antimicrobial activity.•Elucidation of conformational details with lipid vesicles and lipopolysaccharides.•Cell membrane permeabilizing ability of HβD-3 analogs in phospholipid vesicles.•Activity of HβD-3 analogs against bacterial cell and human erythrocytes.•Role of charged terminal residues found to enhance the activity profile.Human beta defensin-3 (HβD-3) is a host-defense protein exhibiting antibacterial activity towards both Gram-negative and Gram-positive bacteria. There is considerable interest in the function of this protein due to its increased salt tolerance and activity against Gram-positive Staphylococcus aureus. In this study, analogs of HβD-3 devoid of N and C terminal regions are investigated to determine the influence of specific structural motif on antimicrobial activity and selectivity between Gram-positive and Gram-negative bacteria. Circular dichroism, fluorescence and solid-state NMR experiments have been used to investigate the conformation and mode of action of HβD3 analogs with various model membranes to mimic bacterial inner and outer membranes and also mammalian membranes. Our studies specifically focused on determining four major characteristics: (i) interaction of HβD3 analogs with phospholipid vesicles composed of zwitterionic PC or anionic PE:PG vesicles and LPS; (ii) conformation of HβD3-peptide analogs in the presence of PC or PE:PG vesicles; (iii) ability of HβD3 analogs to permeate phospholipid vesicles composed of PC or PE:PG; and (iv) activities on bacteria cells and erythrocytes. Our results infer that the linear peptide L25P and its cyclic form C25P are more active than L21P and C21P analogs. However, they are less active than the parent peptide, thus pointing towards the importance of the N terminal domain in its biological activity. The variation in the activities of L21P/C21P and L25P/C25P also suggest the importance of the positively charged residues at the C terminus in providing selectivity particularly to Gram-negative bacteria.
Co-reporter:Dong-Kuk Lee, Anirban Bhunia, Samuel A. Kotler, and Ayyalusamy Ramamoorthy
Biochemistry 2015 Volume 54(Issue 10) pp:1897-1907
Publication Date(Web):February 25, 2015
DOI:10.1021/bi501418m
Multidrug resistance against the existing antibiotics is becoming a global threat, and any potential drug that can be designed using cationic antimicrobial peptides (AMP) could be an alternate solution to alleviate this existing problem. The mechanism of action of killing bacteria by an AMP differs drastically in comparison to that of small molecule antibiotics. The main target of AMPs is to interact with the lipid bilayer of the cell membrane and disrupt it to kill bacteria. Consequently, the modes of membrane interaction that lead to the selectivity of an AMP are very important to understand. Here, we have used different membrane compositions, such as negatively charged, zwitterionic, or mixed large unilamellar vesicles (LUVs), to study the interaction of four different synthetically designed cationic, linear antimicrobial peptides: MSI-78 (commercially known as pexiganan), MSI-367, MSI-594, and MSI-843. Our solid-state nuclear magnetic resonance (NMR) experiments confirmed that the MSI peptides fragmented LUVs through a detergent-like carpet mechanism depending on the amino acid sequence of the MSI peptide and/or the membrane composition of LUVs. Interestingly, the fragmented lipid aggregates such as SUVs or micelles are sufficiently small to produce an isotropic peak in the 31P NMR spectrum. These fragmented lipid aggregates contain only MSI peptides bestowed with lipid molecules as confirmed by NMR in conjunction with circular dichroism spectroscopy. Our results also demonstrate that cholesterol, which is present only in the eukaryotic cell membrane, inhibits the MSI-induced fragmentation of LUVs, suggesting that the MSI peptides can discriminate the bacteria and the eukaryotic cell membranes, and this selectivity could be used for further development of novel antibiotics.
Co-reporter:Nirbhay S. Jain, Ulrich H.N. Dürr, Ayyalusamy Ramamoorthy
Chinese Chemical Letters 2015 Volume 26(Issue 4) pp:407-415
Publication Date(Web):April 2015
DOI:10.1016/j.cclet.2015.03.001
Metabolomics is an emerging field dealing with the measurement and interpretation of small molecular byproducts of biochemical processes, or metabolites, which can be used to generate profiles from biological samples. Promising for use in pathophysiology, metabolomic profiles give the immediate biological state of a sample. These profiles are altered in diseases and are detectable in biological samples, such as tissue, blood, urine, saliva, and others. Most remarkably, metabolic profiles usually are altered before symptoms appear in a patient. For this reason, metabolomics has potential as a reliable method for an early diagnosis of diseases through disease biomarker identification. This application is most prevalent in cancer, such as head and neck cancer (HNC). Metabolomic studies offer avenues to improve on current medical techniques through the application of mass spectrometry (MS), nuclear magnetic resonance spectroscopy (NMR), and statistical analysis to determine better biomarkers than those currently known. In this review, we discuss the use of MS and NMR tools for detecting biomarkers in tissue and fluid samples, and the appropriateness of metabolomics in analyzing cancer. Advantages, disadvantages, and recent studies on metabolomic profiling techniques in HNC analysis are also discussed herein.Metabolomics is an emerging field dealing with the measurement and interpretation of small molecular byproducts of biochemical processes, or metabolites, which can be used to generate profiles from biological samples. In this review, we discuss the application of metabolomic methodologies to the study of head and neck cancer.
Co-reporter:Kazutoshi Yamamoto, Paige Pearcy, Dong-Kuk Lee, Changsu Yu, Sang-Choul Im, Lucy Waskell, and Ayyalusamy Ramamoorthy
Langmuir 2015 Volume 31(Issue 4) pp:1496-1504
Publication Date(Web):January 7, 2015
DOI:10.1021/la5043876
Three-dimensional structure determination of membrane proteins is important to fully understand their biological functions. However, obtaining a high-resolution structure has been a major challenge mainly due to the difficulties in retaining the native folding and function of membrane proteins outside of the cellular membrane environment. These challenges are acute if the protein contains a large soluble domain, as it needs bulk water unlike the transmembrane domains of an integral membrane protein. For structural studies on such proteins either by nuclear magnetic resonance (NMR) spectroscopy or X-ray crystallography, bicelles have been demonstrated to be superior to conventional micelles, yet their temperature restrictions attributed to their thermal instabilities are a major disadvantage. Here, we report an approach to overcome this drawback through searching for an optimum combination of bicellar compositions. We demonstrate that bicelles composed of 1,2-didecanoyl-sn-glycero-3-phosphocholine (DDPC) and 1,2-diheptanoyl-sn-glycero-3-phosphocholin (DHepPC), without utilizing additional stabilizing chemicals, are quite stable and are resistant to temperature variations. These temperature-resistant bicelles have a robust bicellar phase and magnetic alignment over a broad range of temperatures, between −15 and 80 °C, retain the native structure of a membrane protein, and increase the sensitivity of solid-state NMR experiments performed at low temperatures. Advantages of two-dimensional separated-local field (SLF) solid-state NMR experiments at a low temperature are demonstrated on magnetically aligned bicelles containing an electron carrier membrane protein, cytochrome b5. Morphological information on different DDPC-based bicellar compositions, varying q ratio/size, and hydration levels obtained from 31P NMR experiments in this study is also beneficial for a variety of biophysical and spectroscopic techniques, including solution NMR and magic-angle-spinning (MAS) NMR for a wide range of temperatures.
Co-reporter:Rongchun Zhang, Joshua Damron, Thomas Vosegaard, Ayyalusamy Ramamoorthy
Journal of Magnetic Resonance 2015 250() pp: 37-44
Publication Date(Web):1 January 2015
DOI:10.1016/j.jmr.2014.10.013
•A 1H-evolved, 1H-detected rotating-frame SLF is demonstrated under ultrafast MAS.•CP-based SLF sequence is quite sensitive to Hartmann–Hahn mismatch.•CP-based SLF sequence is insensitive to offset when high RF fields are used.•A constant-amplitude-CP SLF renders a better performance than a ramped-CP SLF.•1H-detection greatly enhances the sensitivity of CP-based rotating-frame SLF.Rotating-frame separated-local-field solid-state NMR experiments measure highly resolved heteronuclear dipolar couplings which, in turn, provide valuable interatomic distances for structural and dynamic studies of molecules in the solid-state. Though many different rotating-frame SLF sequences have been put forth, recent advances in ultrafast MAS technology have considerably simplified pulse sequence requirements due to the suppression of proton–proton dipolar interactions. In this study we revisit a simple two-dimensional 1H–13C dipolar coupling/chemical shift correlation experiment using 13C detected cross-polarization with a variable contact time (CPVC) and systematically study the conditions for its optimal performance at 60 kHz MAS. In addition, we demonstrate the feasibility of a proton-detected version of the CPVC experiment. The theoretical analysis of the CPVC pulse sequence under different Hartmann–Hahn matching conditions confirms that it performs optimally under the ZQ (w1H − w1C = ±wr) condition for polarization transfer. The limits of the cross polarization process are explored and precisely defined as a function of offset and Hartmann–Hahn mismatch via spin dynamics simulation and experiments on a powder sample of uniformly 13C-labeled L-isoleucine. Our results show that the performance of the CPVC sequence and subsequent determination of 1H–13C dipolar couplings are insensitive to 1H/13C frequency offset frequency when high RF fields are used on both RF channels. Conversely, the CPVC sequence is quite sensitive to the Hartmann–Hahn mismatch, particularly for systems with weak heteronuclear dipolar couplings. We demonstrate the use of the CPVC based SLF experiment as a tool to identify different carbon groups, and hope to motivate the exploration of more sophisticated 1H detected avenues for ultrafast MAS.Download high-res image (128KB)Download full-size image
Co-reporter:Rongchun Zhang, Yusuke Nishiyama, Pingchuan Sun, Ayyalusamy Ramamoorthy
Journal of Magnetic Resonance 2015 252() pp: 55-66
Publication Date(Web):
DOI:10.1016/j.jmr.2014.12.010
Co-reporter:Jeffrey R. Brender, Janarthanan Krishnamoorthy, Michele F. M. Sciacca, Subramanian Vivekanandan, Luisa D’Urso, Jennifer Chen, Carmelo La Rosa, and Ayyalusamy Ramamoorthy
The Journal of Physical Chemistry B 2015 Volume 119(Issue 7) pp:2886-2896
Publication Date(Web):January 19, 2015
DOI:10.1021/jp511758w
The aggregation of amyloidogenic proteins is infamous for being highly chaotic, with small variations in conditions sometimes leading to large changes in aggregation rates. Using the amyloidogenic protein IAPP (islet amyloid polypeptide protein, also known as amylin) as an example, we show that a part of this phenomenon may be related to the formation of micellelike oligomers at specific critical concentrations and temperatures. We show that pyrene fluorescence can sensitively detect micellelike oligomer formation by IAPP and discriminate between micellelike oligomers from fibers and monomers, making pyrene one of the few chemical probes specific to a prefibrillar oligomer. We further show that oligomers of this type reversibly form at critical concentrations in the low micromolar range and at specific critical temperatures. Micellelike oligomer formation has several consequences for amyloid formation by IAPP. First, the kinetics of fiber formation increase substantially as the critical concentration is approached but are nearly independent of concentration below it, suggesting a direct role for the oligomers in fiber formation. Second, the critical concentration is strongly correlated with the propensity to form amyloid: higher critical concentrations are observed for both IAPP variants with lower amyloidogenicity and for native IAPP at acidic pH in which aggregation is greatly slowed. Furthermore, using the DEST NMR technique, we show that the pathway of amyloid formation switches as the critical point is approached, with self-interactions primarily near the N-terminus below the critical temperature and near the central region above the critical temperature, reconciling two apparently conflicting views of the initiation of IAPP aggregation.
Co-reporter:Samuel A. Kotler, Patrick Walsh, Jeffrey R. Brender and Ayyalusamy Ramamoorthy
Chemical Society Reviews 2014 vol. 43(Issue 19) pp:6692-6700
Publication Date(Web):24 Jan 2014
DOI:10.1039/C3CS60431D
The association of the amyloid-β (Aβ) peptide with cellular membranes is hypothesized to be the underlying phenomenon of neurotoxicity in Alzheimer's disease. Misfolding of proteins and peptides, as is the case with Aβ, follows a progression from a monomeric state, through intermediates, ending at long, unbranched amyloid fibers. This tutorial review offers a perspective on the association of toxic Aβ structures with membranes as well as details of membrane-associated mechanisms of toxicity.
Co-reporter:Alaina S. DeToma, Janarthanan Krishnamoorthy, Younwoo Nam, Hyuck Jin Lee, Jeffrey R. Brender, Akiko Kochi, Dongkuk Lee, Valentina Onnis, Cenzo Congiu, Stefano Manfredini, Silvia Vertuani, Gianfranco Balboni, Ayyalusamy Ramamoorthy and Mi Hee Lim
Chemical Science 2014 vol. 5(Issue 12) pp:4851-4862
Publication Date(Web):03 Sep 2014
DOI:10.1039/C4SC01531B
Metal ion homeostasis in conjunction with amyloid-β (Aβ) aggregation in the brain has been implicated in Alzheimer's disease (AD) pathogenesis. To uncover the interplay between metal ions and Aβ peptides, synthetic, multifunctional small molecules have been employed to modulate Aβ aggregation in vitro. Naturally occurring flavonoids have emerged as a valuable class of compounds for this purpose due to their ability to control both metal-free and metal-induced Aβ aggregation. Although flavonoids have shown anti-amyloidogenic effects, the structural moieties of flavonoids responsible for such reactivity have not been fully identified. In order to understand the structure–interaction–reactivity relationship within the flavonoid family for metal-free and metal-associated Aβ, we designed, synthesized, and characterized a set of isoflavone derivatives, aminoisoflavones (1–4), that displayed reactivity (i.e., modulation of Aβ aggregation) in vitro. NMR studies revealed a potential binding site for aminoisoflavones between the N-terminal loop and central helix of prefibrillar Aβ, which is different from the non-specific binding observed for other flavonoids. The absence or presence of the catechol group, responsible for metal binding, differentiated the binding affinities of aminoisoflavones with Aβ and enthalpy/entropy balance for their Aβ interaction. Furthermore, having a catechol group influenced the binding mode with fibrillar Aβ. Inclusion of additional substituents moderately tuned the impact of aminoisoflavones on Aβ aggregation. Overall, through these studies, we obtained valuable insights into the requirements for parity among metal chelation, intermolecular interactions, and substituent variation for Aβ interaction.
Co-reporter:Masha G. Savelieff, Yuzhong Liu, Russell R. P. Senthamarai, Kyle J. Korshavn, Hyuck Jin Lee, Ayyalusamy Ramamoorthy and Mi Hee Lim
Chemical Communications 2014 vol. 50(Issue 40) pp:5301-5303
Publication Date(Web):10 Dec 2013
DOI:10.1039/C3CC48473D
Alzheimer's disease (AD) is a complex, multifactorial, neurodegenerative disease that poses tremendous difficulties in pinpointing its precise etiology. A toolkit, which specifically targets and modulates suggested key players, may elucidate their roles in disease onset and progression. We report high-resolution insights on the activity of a small molecule (L2-NO) which exhibits reactivity toward Cu(II)–amyloid-β (Aβ) over Zn(II)–Aβ.
Co-reporter:Manami Tsukamoto, Kenichi Kuroda, Ayyalusamy Ramamoorthy and Kazuma Yasuhara
Chemical Communications 2014 vol. 50(Issue 26) pp:3427-3430
Publication Date(Web):16 Dec 2013
DOI:10.1039/C3CC47738J
The function and mode of action of curcumin in modulating the formation of lipid raft domains were investigated by microscopic observation using model membranes. Curcumin induces fusion of lipid raft domains at extremely low concentrations through the alteration of the boundary between the ordered and disordered phases.
Co-reporter:Jun Zhao, Rundong Hu, Michele F. M. Sciacca, Jeffrey R. Brender, Hong Chen, Ayyalusamy Ramamoorthy and Jie Zheng
Physical Chemistry Chemical Physics 2014 vol. 16(Issue 6) pp:2368-2377
Publication Date(Web):26 Nov 2013
DOI:10.1039/C3CP53345J
Fundamental understanding of ion channel formation by amyloid peptides, which is strongly linked to cell toxicity, is very critical for (pre)clinical treatment of neurodegenerative diseases. Here, we combine atomistic simulations and experiments to demonstrate a broad range of conformational states of hIAPP double channels in lipid membranes. All individual channels display high selectivity for Cl− ions over cations, but the co-existence of polymorphic double channels of different conformations and orientations with different populations determines the non-ionic selectivity nature of the channels, which is different from the typical amyloid-β channels that exhibit Ca2+ selective ion-permeable characteristics. This work provides a more complete physicochemical mechanism of amyloid-channel-induced toxicity.
Co-reporter:Kenjirou Higashi, Kazutoshi Yamamoto, Manoj Kumar Pandey, Kamal H. Mroue, Kunikazu Moribe, Keiji Yamamoto, and Ayyalusamy Ramamoorthy
Molecular Pharmaceutics 2014 Volume 11(Issue 1) pp:351-357
Publication Date(Web):November 27, 2013
DOI:10.1021/mp4005723
The intermolecular interaction between mefenamic acid (MFA), a poorly water-soluble nonsteroidal anti-inflammatory drug, and Eudragit EPO (EPO), a water-soluble polymer, is investigated in their supersaturated solution using high-resolution magic-angle spinning (HRMAS) nuclear magnetic resonance (NMR) spectroscopy. The stable supersaturated solution with a high MFA concentration of 3.0 mg/mL is prepared by dispersing the amorphous solid dispersion into a d-acetate buffer at pH 5.5 and 37 °C. By virtue of MAS at 2.7 kHz, the extremely broad and unresolved 1H resonances of MFA in one-dimensional 1H NMR spectrum of the supersaturated solution are well-resolved, thus enabling the complete assignment of MFA 1H resonances in the aqueous solution. Two-dimensional (2D) 1H/1H nuclear Overhauser effect spectroscopy (NOESY) and radio frequency-driven recoupling (RFDR) under MAS conditions reveal the interaction of MFA with EPO in the supersaturated solution at an atomic level. The strong cross-correlations observed in the 2D 1H/1H NMR spectra indicate a hydrophobic interaction between the aromatic group of MFA and the backbone of EPO. Furthermore, the aminoalkyl group in the side chain of EPO forms a hydrophilic interaction, which can be either electrostatic or hydrogen bonding, with the carboxyl group of MFA. We believe these hydrophobic and hydrophilic interactions between MFA and EPO molecules play a key role in the formation of this extremely stable supersaturated solution. In addition, 2D 1H/1H RFDR demonstrates that the molecular MFA–EPO interaction is quite flexible and dynamic.Keywords: 1H NMR; Eudragit EPO; intermolecular interaction; NOESY; RFDR; supersaturated solution;
Co-reporter:Hiren R. Patel, Amit S. Pithadia, Jeffrey R. Brender, Carol A. Fierke, and Ayyalusamy Ramamoorthy
The Journal of Physical Chemistry Letters 2014 Volume 5(Issue 11) pp:1864-1870
Publication Date(Web):May 9, 2014
DOI:10.1021/jz5001775
The deposition of aggregates of human islet amyloid peptide (hIAPP) has been correlated with the death of insulin-producing beta (β) cells in type II diabetes mellitus. The actual molecular mechanism of cell death remains unknown; however, it has been postulated that the process of aggregation and amyloid fibril growth from monomeric hIAPP is closely involved. Intermediate IAPP aggregates are highly toxic to islet cells, but lack of structural knowledge of these oligomers and complications in applying biophysical techniques to their study have been the main obstacles in designing structure-based therapeutics. Furthermore, the involvement of metal ions (Cu2+ and Zn2+) associated with hIAPP has demonstrated an effect on the aggregation pathway. In the absence of well-defined targets, research attempting to attenuate amyloid-linked toxicity has been substantially slowed. Therefore, obtaining high-resolution structural insights on these intermediates through NMR techniques can provide information on preventing IAPP aggregation. In this Perspective, a review of avenues to obtain fundamental new insights into the aggregation pathway of IAPP and other amyloidogenic proteins through NMR and other techniques is presented.
Co-reporter:Manoj Kumar Pandey, Subramanian Vivekanandan, Kazutoshi Yamamoto, Sangchoul Im, Lucy Waskell, Ayyalusamy Ramamoorthy
Journal of Magnetic Resonance 2014 242() pp: 169-179
Publication Date(Web):1 May 2014
DOI:10.1016/j.jmr.2014.02.016
•2D 1H/1H RFDR MAS spectra of an unlabeled cytochrome-b5 are presented.•Dipolar couplings are recoupled by RFDR-MAS for aromatic and side chain protons.•Residues interacting with membrane are revealed.•Dipolar couplings with amide-protons are suppressed due to exchange with water.•T1 values of 1H resonances observed in RFDR are shorter than that in NOESY.Solid-state NMR spectroscopy is increasingly used in the high-resolution structural studies of membrane-associated proteins and peptides. Most such studies necessitate isotopically labeled (13C, 15N and 2H) proteins/peptides, which is a limiting factor for some of the exciting membrane-bound proteins and aggregating peptides. In this study, we report the use of a proton-based slow magic angle spinning (MAS) solid-state NMR experiment that exploits the unaveraged 1H–1H dipolar couplings from a membrane-bound protein. We have shown that the difference in the buildup rates of cross-peak intensities against the mixing time – obtained from 2D 1H–1H radio frequency-driven recoupling (RFDR) and nuclear Overhauser effect spectroscopy (NOESY) experiments on a 16.7-kDa micelle-associated full-length rabbit cytochrome-b5 (cytb5) – can provide insights into protein dynamics and could be useful to measure 1H–1H dipolar couplings. The experimental buildup curves compare well with theoretical simulations and are used to extract relaxation parameters. Our results show that due to fast exchange of amide protons with water in the soluble heme-containing domain of cyb5, coherent 1H–1H dipolar interactions are averaged out for these protons while alpha and side chain protons show residual dipolar couplings that can be obtained from 1H–1H RFDR experiments. The appearance of resonances with distinct chemical shift values in 1H–1H RFDR spectra enabled the identification of residues (mostly from the transmembrane region) of cytb5 that interact with micelles.Download high-res image (178KB)Download full-size image
Co-reporter:Yusuke Nishiyama, Rongchun Zhang, Ayyalusamy Ramamoorthy
Journal of Magnetic Resonance 2014 243() pp: 25-32
Publication Date(Web):1 June 2014
DOI:10.1016/j.jmr.2014.03.004
•2D 1H/1H RFDR experiments are demonstrated under ultrafast MAS conditions.•Performances of various XY-based phase cycling schemes are compared.•Results show that XY4 and its super-cycle XY414 render excellent performances.•The use of RFDR-XY414 shortens the recycle delay for faster data acquisition.The first-order recoupling sequence radio frequency driven dipolar recoupling (RFDR) is commonly used in single-quantum/single-quantum homonuclear correlation 2D experiments under magic angle spinning (MAS) to determine homonuclear proximities. From previously reported analysis of the use of XY-based super-cycling schemes to enhance the efficiency of the finite-pulse-RFDR (fp-RFDR) pulse sequence, XY814 phase cycling was found to provide the optimum performance for 2D correlation experiments on low-γ nuclei. In this study, we analyze the efficiency of different phase cycling schemes for proton-based fp-RFDR experiments. We demonstrate the advantages of using a short phase cycle, XY4, and its super-cycle XY414 that only recouples the zero-quantum homonuclear dipolar coupling, for the fp-RFDR sequence in 2D 1H/1H correlation experiments at ultrafast MAS frequencies. The dipolar recoupling efficiencies of XY4, XY414 and XY814 phase cycling schemes are compared based on results obtained from 2D 1H/1H correlation experiments, utilizing the fp-RFDR pulse sequence, on powder samples of U–13C,15N-l-alanine, N-acetyl–15N-l-valyl–15N-l-leucine, and glycine. Experimental results and spin dynamics simulations show that XY414 performs the best when a high RF power is used for the 180° pulse, whereas XY4 renders the best performance when a low RF power is used. The effects of RF field inhomogeneity and chemical shift offsets are also examined. Overall, our results suggest that a combination of fp-RFDR-XY414 employed in the recycle delay with a large RF-field to decrease the recycle delay, and fp-RFDR-XY4 in the mixing period with a moderate RF-field, is a robust and efficient method for 2D single-quantum/single-quantum 1H/1H correlation experiments at ultrafast MAS frequencies.Graphical abstractDownload high-res image (206KB)Download full-size image
Co-reporter:Rongchun Zhang, Ayyalusamy Ramamoorthy
Journal of Magnetic Resonance 2014 243() pp: 85-92
Publication Date(Web):1 June 2014
DOI:10.1016/j.jmr.2014.03.012
•RINEPT’s efficiency depends on the MAS frequency.•Polarization transfer by 1H-undecoupled RINEPT depends on the dipolar couplings.•Scalar coupling plays an insignificant role under ultrafast MAS.The refocused insensitive nuclei enhanced by polarization transfer (RINEPT) technique is commonly used for heteronuclear polarization transfer in solution and solid-state NMR spectroscopy. Suppression of dipolar couplings, either by fast molecular motions in solution or by a combination of MAS and multiple pulse sequences in solids, enables the polarization transfer via scalar couplings. However, the presence of unsuppressed dipolar couplings could alter the functioning of RINEPT, particularly under fast/ultrafast MAS conditions. In this study, we demonstrate, through experiments on rigid solids complemented by numerical simulations, that the polarization transfer efficiency of RINEPT is dependent on the MAS frequency. In addition, we show that heteronuclear dipolar coupling is the dominant factor in the polarization transfer, which is strengthened by the presence of 1H–1H dipolar couplings. In fact, the simultaneous presence of homonuclear and heteronuclear dipolar couplings is the premise for the polarization transfer by RINEPT, whereas the scalar coupling plays an insignificant role under ultrafast MAS conditions on rigid solids. Our results additionally reveal that the polarization transfer efficiency decreases with the increasing duration of RF pulses used in the RINEPT sequence.Graphical abstractDownload high-res image (64KB)Download full-size image
Co-reporter:Yusuke Nishiyama, Michal Malon, Yuji Ishii, Ayyalusamy Ramamoorthy
Journal of Magnetic Resonance 2014 244() pp: 1-5
Publication Date(Web):1 July 2014
DOI:10.1016/j.jmr.2014.04.008
•A new 3D 15N/15N/1H chemical shift correlation MAS technique is demonstrated.•1H-mixing via the recoupled 1H–1H dipolar couplings enable faster 15N/15N correlation.•1H-detection under ultrafast MAS renders fast acquisition of the 3D spectrum.Homonuclear correlation NMR experiments are commonly used in the high-resolution structural studies of proteins. While 13C/13C chemical shift correlation experiments utilizing dipolar recoupling techniques are fully utilized under MAS, correlation of the chemical shifts of 15N nuclei in proteins has been a challenge. Previous studies have shown that the negligible 15N–15N dipolar coupling in peptides or proteins necessitates the use of a very long mixing time (typically several seconds) for effective spin diffusion to occur and considerably slows down a 15N/15N correlation experiment. In this study, we show that the use of mixing proton magnetization, instead of 15N, via the recoupled 1H–1H dipolar couplings enable faster 15N/15N correlation. In addition, the use of proton-detection under ultrafast MAS overcomes the sensitivity loss due to multiple magnetization transfer (between 1H and 15N nuclei) steps. In fact, less than 300 nL (∼1.1 micromole quantity) sample is sufficient to acquire the 3D spectrum within 5 h. Our results also demonstrate that a 3D 15N/15N/1H experiment can render higher resolution spectra that will be useful in the structural studies of proteins at ultrafast MAS frequencies. 3D 15N/15N/1H and 2D radio frequency-driven dipolar recoupling (RFDR)-based 1H/1H experimental results obtained from a powder sample of N-acetyla-l-15N-valyl-l-15N-leucine at 70 and 100 kHz MAS frequencies are presented.Download high-res image (48KB)Download full-size image
Co-reporter:Kamal H. Mroue, Rongchun Zhang, Peizhi Zhu, Erin McNerny, David H. Kohn, Michael D. Morris, Ayyalusamy Ramamoorthy
Journal of Magnetic Resonance 2014 244() pp: 90-97
Publication Date(Web):1 July 2014
DOI:10.1016/j.jmr.2014.04.020
•Gd-DTPA was successfully used to speed up solid-state NMR measurements on bone.•1H-detected ultrafast and 13C CPMAS were used to evaluate longitudinal PREs.•A 3.5-fold reduction in NMR time was obtained using as low as 10 mM Gd-DTPA.•No line-broadening or peak shift was observed on bone in the presence of Gd-DTPA.Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin–lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA = Diethylene triamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the 1H T1 values were calculated from data collected by 1H spin-inversion recovery method detected in natural-abundance 13C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the 1H T1 values can be successfully reduced by a factor of 3.5 using as low as 10 mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the 13C CPMAS spectra. These results obtained from 13C-detected CPMAS experiments were further confirmed using 1H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans.Download high-res image (96KB)Download full-size image
Co-reporter:Kazutoshi Yamamoto, Marc A. Caporini, Sangchoul Im, Lucy Waskell, Ayyalusamy Ramamoorthy
Journal of Magnetic Resonance 2014 245() pp: 177
Publication Date(Web):1 August 2014
DOI:10.1016/j.jmr.2014.07.009
Co-reporter:Manoj Kumar Pandey, Subramanian Vivekanandan, Kazutoshi Yamamoto, Sangchoul Im, Lucy Waskell, Ayyalusamy Ramamoorthy
Journal of Magnetic Resonance 2014 245() pp: 178
Publication Date(Web):1 August 2014
DOI:10.1016/j.jmr.2014.07.008
Co-reporter:Kazutoshi Yamamoto, Paige Pearcy, and Ayyalusamy Ramamoorthy
Langmuir 2014 Volume 30(Issue 6) pp:1622-1629
Publication Date(Web):2017-2-22
DOI:10.1021/la404331t
Bicelles are increasingly used as model membranes to suitably mimic the biological cell membrane for biophysical and biochemical studies by a variety of techniques including NMR and X-ray crystallography. Recent NMR studies have successfully utilized bicelles for atomic-resolution structural and dynamic studies of antimicrobial peptides, amyloid peptides, and membrane-bound proteins. Though bicelles composed with several different types of lipids and detergents have been reported, the NMR requirement of magnetic alignment of bicelles limits the temperature range in which they can be used and subsequently their composition. Because of this restriction, low-temperature experiments desirable for heat-sensitive membrane proteins have not been conducted because bicelles could not be aligned. In this study, we characterize the magnetic alignment of bicelles with various compositions for a broad range of temperatures using 31P static NMR spectroscopy in search of temperature-resistant bicelles. Our systematic investigation identified a temperature range of magnetic alignment for bicelles composed of 4:1 DLPC:DHexPC, 4:1:0.2 DLPC:DHexPC:cholesterol, 4:1:0.13 DLPC:DHexPC:CTAB, 4:1:0.13:0.2 DLPC:DHexPC:CTAB:cholesterol, and 4:1:0.4 DLPC:DHexPC:cholesterol-3-sulfate. The amount of cholesterol-3-sulfate used was based on mole percent and was varied in order to determine the optimal amount. Our results indicate that the presence of 75 wt % or more water is essential to achieve maximum magnetic alignment, while the presence of cholesterol and cholesterol-3-sulfate stabilizes the alignment at extreme temperatures and the positively charged CTAB avoids the mixing of bicelles. We believe that the use of magnetically aligned 4:1:0.4 DLPC:DHexPC:cholesterol-3-sulfate bicelles at as low as −15 °C would pave avenues to study the structure, dynamics, and membrane orientation of heat-sensitive proteins such as cytochrome P450 and could also be useful to investigate protein–protein interactions in a membrane environment.
Co-reporter:Sanghyun Lee ; Xueyun Zheng ; Janarthanan Krishnamoorthy ; Masha G. Savelieff ; Hyun Min Park ; Jeffrey R. Brender ; Jin Hoon Kim ; Jeffrey S. Derrick ; Akiko Kochi ; Hyuck Jin Lee ; Cheal Kim ; Ayyalusamy Ramamoorthy ; Michael T. Bowers ;Mi Hee Lim
Journal of the American Chemical Society 2013 Volume 136(Issue 1) pp:299-310
Publication Date(Web):December 27, 2013
DOI:10.1021/ja409801p
Alzheimer’s disease (AD) is characterized by multiple, intertwined pathological features, including amyloid-β (Aβ) aggregation, metal ion dyshomeostasis, and oxidative stress. We report a novel compound (ML) prototype of a rationally designed molecule obtained by integrating structural elements for Aβ aggregation control, metal chelation, reactive oxygen species (ROS) regulation, and antioxidant activity within a single molecule. Chemical, biochemical, ion mobility mass spectrometric, and NMR studies indicate that the compound ML targets metal-free and metal-bound Aβ (metal–Aβ) species, suppresses Aβ aggregation in vitro, and diminishes toxicity induced by Aβ and metal-treated Aβ in living cells. Comparison of ML to its structural moieties (i.e., 4-(dimethylamino)phenol (DAP) and (8-aminoquinolin-2-yl)methanol (1)) for reactivity with Aβ and metal–Aβ suggests the synergy of incorporating structural components for both metal chelation and Aβ interaction. Moreover, ML is water-soluble and potentially brain permeable, as well as regulates the formation and presence of free radicals. Overall, we demonstrate that a rational structure-based design strategy can generate a small molecule that can target and modulate multiple factors, providing a new tool to uncover and address AD complexity.
Co-reporter:Jeffrey R. Brender, Janarthanan Krishnamoorthy, Grazia M. L. Messina, Aniruddha Deb, Subramanian Vivekanandan, Carmelo La Rosa, James E. Penner-Hahn and Ayyalusamy Ramamoorthy
Chemical Communications 2013 vol. 49(Issue 32) pp:3339-3341
Publication Date(Web):06 Mar 2013
DOI:10.1039/C3CC40383A
The aggregation of human islet amyloid polypeptide (hIAPP) has been linked to beta-cell death in type II diabetes. Zinc present in secretory granules has been shown to affect this aggregation. A combination of EXAFS, NMR, and AFM experiments shows that the influence of zinc is most likely due to the stabilization of prefibrillar aggregates of hIAPP.
Co-reporter:Ulrich H.N. Dürr, Ronald Soong, Ayyalusamy Ramamoorthy
Progress in Nuclear Magnetic Resonance Spectroscopy 2013 Volume 69() pp:1-22
Publication Date(Web):February 2013
DOI:10.1016/j.pnmrs.2013.01.001
Graphical abstractFigure optionsDownload full-size imageDownload high-quality image (93 K)Download as PowerPoint slideHighlights► Lipid bicelles have matured to full membership in the club of lipid phases. ► Numerous techniques have elucidated the character traits of bicelles. ► Bicelles are exemplary citizens in the realm of model membranes. ► They contribute particularly in studies of membrane protein structure.
Co-reporter:Jeffrey R. Brender, Deborah L. Heyl, Shyamprasad Samisetti, Samuel A. Kotler, Joshua M. Osborne, Ranadheer R. Pesaru and Ayyalusamy Ramamoorthy
Physical Chemistry Chemical Physics 2013 vol. 15(Issue 23) pp:8908-8915
Publication Date(Web):01 Mar 2013
DOI:10.1039/C3CP44696D
A key factor in the development of type II diabetes is the loss of insulin-producing beta-cells. Human islet amyloid polypeptide protein (human-IAPP) is believed to play a crucial role in this process by forming small aggregates that exhibit toxicity by disrupting the cell membrane. The actual mechanism of membrane disruption is complex and appears to involve an early component before fiber formation and a later component associated with fiber formation on the membrane. By comparing the peptide–lipid interactions derived from solid-state NMR experiments of two IAPP fragments that cause membrane disordering to IAPP derived peptides known to cause significant early membrane permeabilization, we show here that membrane disordering is not likely to be sufficient by itself to cause the early membrane permeabilization observed by IAPP, and may play a lesser role in IAPP membrane disruption than expected.
Co-reporter:Pratima Tripathi, Bagganahalli S. Somashekar, M. Ponnusamy, Amy Gursky, Stephen Dailey, Priya Kunju, Cheryl T. Lee, Arul M. Chinnaiyan, Thekkelnaycke M. Rajendiran, and Ayyalusamy Ramamoorthy
Journal of Proteome Research 2013 Volume 12(Issue 7) pp:3519-3528
Publication Date(Web):2017-2-22
DOI:10.1021/pr4004135
Effective diagnosis and surveillance of bladder cancer (BCa) is currently challenged by detection methods that are of poor sensitivity, particularly for low-grade tumors, resulting in unnecessary invasive procedures and economic burden. We performed HR-MAS NMR-based global metabolomic profiling and applied unsupervised principal component analysis (PCA) and hierarchical clustering performed on NMR data set of bladder-derived tissues and identified metabolic signatures that differentiate BCa from benign disease. A partial least-squares discriminant analysis (PLS-DA) model (leave-one-out cross-validation) was used as a diagnostic model to distinguish benign and BCa tissues. Receiver operating characteristic curve generated either from PC1 loadings of PCA or from predicted Y-values resulted in an area under curve of 0.97. Relative quantification of more than 15 tissue metabolites derived from HR-MAS NMR showed significant differences (P < 0.001) between benign and BCa samples. Noticeably, striking metabolic signatures were observed even for early stage BCa tissues (Ta-T1), demonstrating the sensitivity in detecting BCa. With the goal of cross-validating metabolic signatures derived from HR-MAS NMR, we utilized the same tissue samples to analyze 8 metabolites through gas chromatography–mass spectrometry (GC–MS)-targeted analysis, which undoubtedly complements HR-MAS NMR-derived metabolomic information. Cross-validation through GC–MS clearly demonstrates the utility of a straightforward, nondestructive, and rapid HR-MAS NMR technique for clinical diagnosis of BCa with even greater sensitivity. In addition to its utility as a diagnostic tool, these studies will lead to a better understanding of aberrant metabolic pathways in cancer as well as the design and implementation of personalized cancer therapy through metabolic modulation.
Co-reporter:Yuta Suzuki, Jeffrey R. Brender, Molly T. Soper, Janarthanan Krishnamoorthy, Yunlong Zhou, Brandon T. Ruotolo, Nicholas A. Kotov, Ayyalusamy Ramamoorthy, and E. Neil G. Marsh
Biochemistry 2013 Volume 52(Issue 11) pp:
Publication Date(Web):February 27, 2013
DOI:10.1021/bi400027y
In the commonly used nucleation-dependent model of protein aggregation, aggregation proceeds only after a lag phase in which the concentration of energetically unfavorable nuclei reaches a critical value. The formation of oligomeric species prior to aggregation can be difficult to detect by current spectroscopic techniques. By using real-time 19F NMR along with other techniques, we are able to show that multiple oligomeric species can be detected during the lag phase of Aβ1–40 fiber formation, consistent with a complex mechanism of aggregation. At least six types of oligomers can be detected by 19F NMR. These include the reversible formation of large β-sheet oligomer immediately after solubilization at high peptide concentration, a small oligomer that forms transiently during the early stages of the lag phase, and four spectroscopically distinct forms of oligomers with molecular weights between ∼30 and 100 kDa that appear during the later stages of aggregation. The ability to resolve individual oligomers and track their formation in real-time should prove fruitful in understanding the aggregation of amyloidogenic proteins and in isolating potentially toxic nonamyloid oligomers.
Co-reporter:Dong-Kuk Lee, Jeffrey R. Brender, Michele F. M. Sciacca, Janarthanan Krishnamoorthy, Changsu Yu, and Ayyalusamy Ramamoorthy
Biochemistry 2013 Volume 52(Issue 19) pp:3254-3263
Publication Date(Web):April 16, 2013
DOI:10.1021/bi400087n
The potency and selectivity of many antimicrobial peptides (AMPs) are correlated with their ability to interact with and disrupt the bacterial cell membrane. In vitro experiments using model membranes have been used to determine the mechanism of membrane disruption of AMPs. Because the mechanism of action of an AMP depends on the ability of the model membrane to accurately mimic the cell membrane, it is important to understand the effect of membrane composition. Anionic lipids that are present in the outer membrane of prokaryotes but are less common in eukaryotic membranes are usually thought to be key for the bacterial selectivity of AMPs. We show by fluorescence measurements of peptide-induced membrane permeabilization that the presence of anionic lipids at high concentrations can actually inhibit membrane disruption by the AMP MSI-78 (pexiganan), a representative of a large class of highly cationic AMPs. Paramagnetic quenching studies suggest MSI-78 is in a surface-associated inactive mode in anionic sodium dodecyl sulfate micelles but is in a deeply buried and presumably more active mode in zwitterionic dodecylphosphocholine micelles. Furthermore, a switch in mechanism occurs with lipid composition. Membrane fragmentation with MSI-78 can be observed in mixed vesicles containing both anionic and zwitterionic lipids but not in vesicles composed of a single lipid of either type. These findings suggest membrane affinity and membrane permeabilization are not always correlated, and additional effects that may be more reflective of the actual cellular environment can be seen as the complexity of the model membranes is increased.
Co-reporter:Ayyalusamy Ramamoorthy and Jiadi Xu
The Journal of Physical Chemistry B 2013 Volume 117(Issue 22) pp:6693-6700
Publication Date(Web):May 14, 2013
DOI:10.1021/jp4034003
There is significant interest in solving high-resolution dynamic structures of membrane-associated peptides using solid-state NMR spectroscopy. Previous solid-state NMR studies have provided valuable insights into the functional properties of an exciting class of biomacromolecules such as antimicrobial peptides and amyloid peptides. However, it has been a major challenge to apply solid-state NMR techniques to study peptides or proteins that are not labeled with specific isotopes such as 13C, 15N, and/or 2H. This study utilizes 2D 1H/1H radio frequency-driven recoupling (RFDR) and nuclear Overhauser effect spectroscopy (NOESY) pulse sequences under magic angle spinning to study a membrane-bound antimicrobial peptide MSI-78 (or also known as pexiganan). We demonstrate that proton resonances can be assigned and structural constraints, NOE and 1H–1H dipolar couplings, can be measured without the need for any isotopic enrichment. The buildup curves, showing the dependence of the cross peak intensity against the mixing time, obtained from 2D 1H/1H NOESY and RFDR experiments are compared. Our results reveal that the RFDR-recovered 1H–1H dipolar couplings associated with alpha and side chain protons are larger than that with the amide-protons. This study provides a means to measure residual 1H–1H dipolar couplings for the investigation of structure, dynamics, and aggregation of peptides using a suitable model membrane like micelles or bicelles.
Co-reporter:Manoj Kumar Pandey, Subramanian Vivekanandan, Shivani Ahuja, Rui Huang, Sang-Choul Im, Lucy Waskell, and Ayyalusamy Ramamoorthy
The Journal of Physical Chemistry B 2013 Volume 117(Issue 44) pp:13851-13860
Publication Date(Web):October 9, 2013
DOI:10.1021/jp4086206
It has been well realized that the dependence of chemical shift anisotropy (CSA) tensors on the amino acid sequence, secondary structure, dynamics, and electrostatic interactions can be utilized in the structural and dynamic studies of proteins by NMR spectroscopy. In addition, CSA tensors could also be utilized to measure the structural interactions between proteins in a protein–protein complex. To this end, we report the experimentally measured backbone amide-15N CSA tensors for a membrane-bound 16.7 kDa full-length rabbit cytochrome-b5 (cytb5), in complexation with a 55.8 kDa microsomal rabbit cytochrome P450 2B4 (cytP4502B4). The 15N-CSAs, determined using the 15N CSA/15N–1H dipolar coupling transverse cross-correlated rates, for free cytb5 are compared with those for the cytb5 bound to cytP4502B4. An overall increase in backbone amide-15N transverse cross-correlated rates for the cytb5 residues in the cytb5–cytP450 complex is observed as compared to the free cytb5 residues. Due to fast spin–spin relaxation (T2) and subsequent broadening of the signals in the complex, we could measure amide-15N CSAs only for 48 residues of cytb5 as compared to 84 residues of free cytb5. We observed a change in 15N CSA for most residues of cytb5 in the complex, as compared to free cytb5, suggesting a dynamic interaction between the oppositely charged surfaces of anionic cytb5 and cationic cytP450. The mean values of 15N CSA determined for residues in helical, sheet, and turn regions of cytb5 in the complex are −184.5, −146.8, and −146.2 ppm, respectively, with an overall average value of −165.5 ppm (excluding the values from residues in more flexible termini). The measured CSA value for residues in helical conformation is slightly larger as compared to previously reported values. This may be attributed to the paramagnetic effect from Fe(III) of the heme in cytb5, which is similar to our previously reported values for the free cytb5.
Co-reporter:Neil MacKinnon, Bagganahalli S. Somashekar, Pratima Tripathi, Wencheng Ge, Thekkelnaycke M. Rajendiran, Arul M. Chinnaiyan, Ayyalusamy Ramamoorthy
Journal of Magnetic Resonance 2013 226() pp: 93-99
Publication Date(Web):
DOI:10.1016/j.jmr.2012.11.008
Co-reporter:Kazutoshi Yamamoto, Marc A. Caporini, Sangchoul Im, Lucy Waskell, Ayyalusamy Ramamoorthy
Journal of Magnetic Resonance 2013 237() pp: 175-181
Publication Date(Web):
DOI:10.1016/j.jmr.2013.10.017
Co-reporter:Manoj Kumar Pandey and Ayyalusamy Ramamoorthy
The Journal of Physical Chemistry B 2013 Volume 117(Issue 3) pp:859-867
Publication Date(Web):December 26, 2012
DOI:10.1021/jp311116p
There is considerable interest in determining amide-15N chemical shift anisotropy (CSA) tensors from biomolecules and understanding their variation for structural and dynamics studies using solution and solid-state NMR spectroscopy and also by quantum chemical calculations. Due to the difficulties associated with the measurement of CSA tensors from membrane proteins, NMR-based structural studies heavily relied on the CSA tensors determined from model systems, typically single crystals of model peptides. In the present study, the principal components of backbone amide-15N CSA tensors have been determined using density functional theory for a 16.7 kDa membrane-bound paramagnetic heme containing protein, cytochrome-b5 (cytb5). All the calculations were performed by taking residues within 5 Å distance from the backbone amide-15N nucleus of interest. The calculated amide-15N CSA spans agree less well with our solution NMR data determined for an effective internuclear distance rN–H = 1.023 Å and a constant angle β = 18° that the least shielded component (δ11) makes with the N–H bond. The variation of amide-15N CSA span obtained using quantum chemical calculations is found to be smaller than that obtained from solution NMR measurements, whereas the trends of the variations are found to be in close agreement. We believe that the results reported in this study will be useful in studying the structure and dynamics of membrane proteins and heme-containing proteins, and also membrane-bound protein–protein complexes such as cytochromes-b5-P450.
Co-reporter:Suk-Joon Hyung;Alaina S. DeToma;Sanghyun Lee;Jeffrey R. Brender;Akiko Kochi;Jung-Suk Choi;Mi Hee Lim;Subramanian Vivekanandan;Brandon T. Ruotolo
PNAS 2013 Volume 110 (Issue 10 ) pp:3743-3748
Publication Date(Web):2013-03-05
DOI:10.1073/pnas.1220326110
Despite the significance of Alzheimer’s disease, the link between metal-associated amyloid-β (metal–Aβ) and disease etiology
remains unclear. To elucidate this relationship, chemical tools capable of specifically targeting and modulating metal–Aβ
species are necessary, along with a fundamental understanding of their mechanism at the molecular level. Herein, we investigated
and compared the interactions and reactivities of the green tea extract, (−)-epigallocatechin-3-gallate [(2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate; EGCG], with metal [Cu(II) and Zn(II)]–Aβ and metal-free Aβ species. We found
that EGCG interacted with metal–Aβ species and formed small, unstructured Aβ aggregates more noticeably than in metal-free
conditions in vitro. In addition, upon incubation with EGCG, the toxicity presented by metal-free Aβ and metal–Aβ was mitigated
in living cells. To understand this reactivity at the molecular level, structural insights were obtained by ion mobility-mass
spectrometry (IM-MS), 2D NMR spectroscopy, and computational methods. These studies indicated that (i) EGCG was bound to Aβ monomers and dimers, generating more compact peptide conformations than those from EGCG-untreated Aβ
species; and (ii) ternary EGCG–metal–Aβ complexes were produced. Thus, we demonstrate the distinct antiamyloidogenic reactivity of EGCG toward
metal–Aβ species with a structure-based mechanism.
Co-reporter:Ulrich H. N. Dürr, Melissa Gildenberg, and Ayyalusamy Ramamoorthy
Chemical Reviews 2012 Volume 112(Issue 11) pp:6054
Publication Date(Web):August 24, 2012
DOI:10.1021/cr300061w
Co-reporter:Alaina S. DeToma, Samer Salamekh, Ayyalusamy Ramamoorthy and Mi Hee Lim
Chemical Society Reviews 2012 vol. 41(Issue 2) pp:608-621
Publication Date(Web):04 Aug 2011
DOI:10.1039/C1CS15112F
This tutorial review presents descriptions of two amyloidogenic proteins, amyloid-β (Aβ) peptides and islet amyloid polypeptide (IAPP), whose misfolding propensities are implicated in Alzheimer's disease (AD) and type II diabetes, respectively. Protein misfolding diseases share similarities, as well as some unique protein-specific traits, that could contribute to the initiation and/or development of their associated conditions. Aβ and IAPP are representative amyloidoses and are used to highlight some of the primary considerations for studying misfolded proteins associated with human diseases in this review. Among these factors, their physiological formation, aggregation, interactions with metal ions and other protein partners, and toxicity are presented. Small molecules that target and modulate the metal–Aβ interaction and neurotoxicity are included to illustrate one of the current approaches for uncovering the complexities of protein misfolding at the molecular level.
Co-reporter:Jeffrey R. Brender, Samer Salamekh, and Ayyalusamy Ramamoorthy
Accounts of Chemical Research 2012 45(3) pp: 454-462
Publication Date(Web):September 25, 2011
DOI:10.1021/ar200189b
The aggregation of proteins is tightly controlled in living systems, and misfolded proteins are normally removed before aggregation of the misfolded protein can occur. But for reasons not clearly understood, in some individuals this degradation process breaks down, and misfolded proteins accumulate in insoluble protein aggregates (amyloid deposits) over time. Of the many proteins expressed in humans, a small but growing number have been found to form the long, highly ordered β-sheet protein fibers that comprise amyloid deposits. Despite a lack of obvious sequence similarity, the amyloid forms of diverse proteins are strikingly similar, consisting of long, highly ordered insoluble fibers with a characteristic crossed β-sheet pattern. Amyloidogenesis has been the focus of intense basic and clinical research, because a high proportion of amyloidogenic proteins have been linked to common degenerative diseases, including Alzheimer’s disease, type II diabetes, and Parkinson’s disease.The apparent link between amyloidogenic proteins and disease was initially attributed to the amyloid form of the protein; however, increasing evidence suggests that the toxicity is due to intermediates generated during the assembly of amyloid fibers. These intermediates have been proposed to attack cells in a variety of ways, such as by generating inflammation, creating reactive oxygen species, and overloading the misfolded protein response pathway. One common, well-studied mechanism is the disruption of the plasma and organelle membranes.In this Account, we examine the early molecular-level events in the aggregation of the islet amyloid polypeptide (IAPP, also called amylin) and its ensuing disruption of membranes. IAPP is a 37-residue peptide secreted in conjunction with insulin; it is highly amyloidogenic and often found in amyloid deposits in type II diabetics. IAPP aggregates are highly toxic to the β-cells that produce insulin, and thus IAPP is believed to be one of the factors involved in the transition from early to later stages of type II diabetes. Using variants of IAPP that are combinations of toxic or non-toxic and amyloidogenic or nonamyloidogenic forms, we have shown that formation of amyloid fibers is a sufficient but not necessary condition for the disruption of β-cells. Instead, the ability to induce membrane disruption in model membranes appears to be related to the peptide’s ability to stabilize curvature in the membrane, which in turn is related to the depth of penetration in the membrane.Although many similarities exist between IAPP and other amyloidogenic proteins, one important difference appears to be the role of small oligomers in the assembly process of amyloid fibers. In many amyloidogenic proteins, small oligomers form a distinct metastable intermediate that is frequently the most toxic species; however, in IAPP, small oligomers appear to be transient and are rapidly converted to amyloid fibers. Moreover, the aggregation and toxicity of IAPP is controlled by other cofactors present in the secretory granule from which it is released, such as zinc and insulin, in a control mechanism that is somehow unbalanced in type II diabetics. Investigations into this process are likely to give clues to the mysterious origins of type II diabetes at the molecular level.
Co-reporter:Neil MacKinnon, Wencheng Ge, Amjad P. Khan, Bagganahalli S. Somashekar, Pratima Tripathi, Javed Siddiqui, John T. Wei, Arul M. Chinnaiyan, Thekkelnaycke M. Rajendiran, and Ayyalusamy Ramamoorthy
Analytical Chemistry 2012 Volume 84(Issue 12) pp:5372
Publication Date(Web):May 20, 2012
DOI:10.1021/ac301327k
In an effort to address the variable correspondence problem across large sample cohorts common in metabolomic/metabonomic studies, we have developed a prealignment protocol that aims to generate spectral segments sharing a common target spectrum. Under the assumption that a single reference spectrum will not correctly represent all spectra of a data set, the goal of this approach is to perform local alignment corrections on spectral regions which share a common “most similar” spectrum. A natural beneficial outcome of this procedure is the automatic definition of spectral segments, a feature that is not common to all alignment methods. This protocol is shown to specifically improve the quality of alignment in 1H NMR data sets exhibiting large intersample compositional variation (e.g., pH, ionic strength). As a proof-of-principle demonstration, we have utilized two recently developed alignment algorithms specific to NMR data, recursive segment-wise peak alignment and interval correlated shifting, and applied them to two data sets composed of 15 aqueous cell line extract and 20 human urine 1H NMR profiles. Application of this protocol represents a fundamental shift from current alignment methodologies that seek to correct misalignments utilizing a single representative spectrum, with the added benefit that it can be appended to any alignment algorithm.
Co-reporter:Bagganahalli S. Somashekar, Anita G. Amin, Pratima Tripathi, Neil MacKinnon, Christopher D. Rithner, Crystal A Shanley, Randall Basaraba, Marcela Henao-Tamayo, Midori Kato-Maeda, Ayyalusamy Ramamoorthy, Ian M. Orme, Diane J. Ordway, and Delphi Chatterjee
Journal of Proteome Research 2012 Volume 11(Issue 10) pp:4873-4884
Publication Date(Web):2017-2-22
DOI:10.1021/pr300345x
With the understanding that the laboratory propagated strain of Mycobacterium tuberculosis H37Rv is of modest virulence and is drug susceptible, in the present study, we performed a nuclear magnetic resonance-based metabolomic analysis of lung tissues and serum obtained from guinea pigs infected by low dose aerosol exposure to clinical isolates of Mycobacterium tuberculosis. High Resolution Magic Angle Spinning NMR coupled with multivariate statistical analysis of 159 lung tissues obtained from multiple locations of age-matched naïve and 30 and 60 days of infected guinea pig lungs revealed a wide dispersal of metabolic patterns, but within these, distinct clusters of signatures could be seen that differentiated between naive control and infected animals. Several metabolites were identified that changed in concert with the progression of each infection. Major metabolites that could be interpreted as indicating host glutaminolysis were consistent with activated host immune cells encountering increasingly hypoxic conditions in the necrotic lung lesions. Moreover, glutathione levels were constantly elevated, probably in response to oxygen radical production in these lesions. Additional distinct signatures were also seen in infected serum, with altered levels of several metabolites. Multivariate statistical analysis clearly differentiated the infected from the uninfected sera; in addition, Receiver Operator Characteristic curve generated with principal component 1 scores showed an area under the curve of 0.908. These data raise optimism that discrete metabolomic signatures can be defined that can predict the progression of the tuberculosis disease process, and form the basis of an innovative and rapid diagnostic process.
Co-reporter:Michele F. M. Sciacca, Jeffrey R. Brender, Dong-Kuk Lee, and Ayyalusamy Ramamoorthy
Biochemistry 2012 Volume 51(Issue 39) pp:
Publication Date(Web):September 12, 2012
DOI:10.1021/bi3009888
The toxicity of amyloid-forming peptides has been hypothesized to reside in the ability of protein oligomers to interact with and disrupt the cell membrane. Much of the evidence for this hypothesis comes from in vitro experiments using model membranes. However, the accuracy of this approach depends on the ability of the model membrane to accurately mimic the cell membrane. The effect of membrane composition has been overlooked in many studies of amyloid toxicity in model systems. By combining measurements of membrane binding, membrane permeabilization, and fiber formation, we show that lipids with the phosphatidylethanolamine (PE) headgroup strongly modulate the membrane disruption induced by IAPP (islet amyloid polypeptide protein), an amyloidogenic protein involved in type II diabetes. Our results suggest that PE lipids hamper the interaction of prefibrillar IAPP with membranes but enhance the membrane disruption correlated with the growth of fibers on the membrane surface via a detergent-like mechanism. These findings provide insights into the mechanism of membrane disruption induced by IAPP, suggesting a possible role of PE and other amyloids involved in other pathologies.
Co-reporter:Yuta Suzuki, Jeffrey R. Brender, Kevin Hartman, Ayyalusamy Ramamoorthy, and E. Neil G. Marsh
Biochemistry 2012 Volume 51(Issue 41) pp:
Publication Date(Web):September 21, 2012
DOI:10.1021/bi3012548
Amyloid formation, a complex process involving many intermediate states, is proposed to be the driving force for amyloid-related toxicity in common degenerative diseases. Unfortunately, the details of this process have been obscured by the limitations in the methods that can follow this reaction in real time. We show that alternative pathways of aggregation can be distinguished by using 19F nuclear magnetic resonance (NMR) to monitor monomer consumption along with complementary measurements of fibrillogenesis. The utility of this technique is demonstrated by tracking amyloid formation in the diabetes-related islet amyloid polypeptide (IAPP). Using this technique, we show IAPP fibrillizes without an appreciable buildup of nonfibrillar intermediates, in contrast to the well-studied Aβ and α-synuclein proteins. To further develop the usage of 19F NMR, we have tracked the influence of the polyphenolic amyloid inhibitor epigallocatechin gallate (EGCG) on the aggregation pathway. Polyphenols have been shown to strongly inhibit amyloid formation in many systems. However, spectroscopic measurements of amyloid inhibition by these compounds can be severely compromised by background signals and competitive binding with extrinsic probes. Using 19F NMR, we show that thioflavin T strongly competes with EGCG for binding sites on IAPP fibers. By comparing the rates of monomer consumption and fiber formation, we are able to show that EGCG stabilizes nonfibrillar large aggregates during fibrillogenesis.
Co-reporter:Nataliya Popovych, Jeffrey R. Brender, Ronald Soong, Subramanian Vivekanandan, Kevin Hartman, Venkatesha Basrur, Peter M. Macdonald, and Ayyalusamy Ramamoorthy
The Journal of Physical Chemistry B 2012 Volume 116(Issue 11) pp:3650-3658
Publication Date(Web):February 23, 2012
DOI:10.1021/jp2121577
Recently, a 39 amino acid peptide fragment from prostatic acid phosphatase has been isolated from seminal fluid that can enhance infectivity of the HIV virus by up to 4–5 orders of magnitude. PAP(248–286) is effective in enhancing HIV infectivity only when it is aggregated into amyloid fibers termed SEVI. The polyphenol EGCG (epigallocatechin-3-gallate) has been shown to disrupt both SEVI formation and HIV promotion by SEVI, but the mechanism by which it accomplishes this task is unknown. Here, we show that EGCG interacts specifically with the side chains of monomeric PAP(248–286) in two regions (K251–R257 and N269–I277) of primarily charged residues, particularly lysine. The specificity of interaction to these two sites is contrary to previous studies on the interaction of EGCG with other amyloidogenic proteins, which showed the nonspecific interaction of EGCG with exposed backbone sites of unfolded amyloidogenic proteins. This interaction is specific to EGCG as the related gallocatechin (GC) molecule, which shows greatly decreased antiamyloid activity, exhibits minimal interaction with monomeric PAP(248–286). The EGCG binding was shown to occur in two steps, with the initial formation of a weakly bound complex followed by a pH dependent formation of a tightly bound complex. Experiments in which the lysine residues of PAP(248–286) have been chemically modified suggest the tightly bound complex is created by Schiff-base formation with lysine residues. The results of this study could aid in the development of small molecule inhibitors of SEVI and other amyloid proteins.
Co-reporter:Manoj Kumar Pandey, Subramanian Vivekanandan, Shivani Ahuja, Kumar Pichumani, Sang-Choul Im, Lucy Waskell, and Ayyalusamy Ramamoorthy
The Journal of Physical Chemistry B 2012 Volume 116(Issue 24) pp:7181-7189
Publication Date(Web):May 23, 2012
DOI:10.1021/jp3049229
Chemical shift anisotropy (CSA) tensors are essential in the structural and dynamic studies of proteins using NMR spectroscopy. Results from relaxation studies in biomolecular solution and solid-state NMR experiments on aligned samples are routinely interpreted using well-characterized CSA tensors determined from model compounds. Since CSA tensors, particularly the 15N CSA, highly depend on a number of parameters including secondary structure, electrostatic interaction, and the amino acid sequence, there is a need for accurately determined CSA tensors from proteins. In this study, we report the backbone amide-15N CSA tensors for a 16.7-kDa membrane-bound and paramagnetic-heme containing protein, rabbit Cytochrome b5 (cytb5), determined using the 15N CSA/15N–1H dipolar transverse cross-correlation rates. The mean values of 15N CSA determined for residues in helical, sheet, and turn regions are −187.9, −166.0, and −161.1 ppm, respectively, with an overall average value of −171.7 ppm. While the average CSA value determined from this study is in good agreement with previous solution NMR experiments on small globular proteins, the CSA value determined for residues in helical conformation is slightly larger, which may be attributed to the paramagnetic effect from Fe(III) of the heme unit in cytb5. However, like in previous solution NMR studies, the CSA values reported in this study are larger than the values measured from solid-state NMR experiments. We believe that the CSA parameters reported in this study will be useful in determining the structure, dynamics, and orientation of proteins, including membrane proteins, using NMR spectroscopy.
Co-reporter:Kamal H. Mroue, Neil MacKinnon, Jiadi Xu, Peizhi Zhu, Erin McNerny, David H. Kohn, Michael D. Morris, and Ayyalusamy Ramamoorthy
The Journal of Physical Chemistry B 2012 Volume 116(Issue 38) pp:11656-11661
Publication Date(Web):September 6, 2012
DOI:10.1021/jp307935g
The hierarchical heterogeneous architecture of bone imposes significant challenges to structural and dynamic studies conducted by traditional biophysical techniques. High-resolution solid-state nuclear magnetic resonance (SSNMR) spectroscopy is capable of providing detailed atomic-level structural insights into such traditionally challenging materials. However, the relatively long data-collection time necessary to achieve a reliable signal-to-noise ratio (S/N) remains a major limitation for the widespread application of SSNMR on bone and related biomaterials. In this study, we attempt to overcome this limitation by employing the paramagnetic relaxation properties of copper(II) ions to shorten the 1H intrinsic spin–lattice (T1) relaxation times measured in natural-abundance 13C cross-polarization (CP) magic-angle-spinning (MAS) NMR experiments on bone tissues for the purpose of accelerating the data acquisition time in SSNMR. To this end, high-resolution solid-state 13C CPMAS experiments were conducted on type I collagen (bovine tendon), bovine cortical bone, and demineralized bovine cortical bone, each in powdered form, to measure the 1H T1 values in the absence and in the presence of 30 mM Cu(II)(NH4)2EDTA. Our results show that the 1H T1 values were successfully reduced by a factor of 2.2, 2.9, and 3.2 for bovine cortical bone, type I collagen, and demineralized bone, respectively, without reducing the spectral resolution and thus enabling faster data acquisition. In addition, paramagnetic quenching of particular 13C NMR resonances on exposure to Cu2+ ions in the absence of mineral was also observed, potentially suggesting the relative proximity of three main amino acids in the protein backbone (glycine, proline, and alanine) to the bone mineral surface.
Co-reporter:Janarthanan Krishnamoorthy, Jeffrey R. Brender, Subramanian Vivekanandan, Nicole Jahr, and Ayyalusamy Ramamoorthy
The Journal of Physical Chemistry B 2012 Volume 116(Issue 46) pp:13618-13623
Publication Date(Web):November 1, 2012
DOI:10.1021/jp305279w
Low-lying excited states that correspond to rare conformations or transiently bound species have been hypothesized to play an important role for amyloid nucleation. Despite their hypothesized importance in amyloid formation, transiently occupied states have proved difficult to detect directly. To experimentally characterize these invisible states, we performed a series of Carr–Purcell–Meiboom–Gill (CPMG)-based relaxation dispersion NMR experiments for the amyloidogenic Aβ1–40 peptide implicated in Alzheimer’s disease. Significant relaxation dispersion of the resonances corresponding to the side-chain amides of Q15 and N27 was detected before the onset of aggregation. The resonances corresponding to the peptide backbone did not show detectable relaxation dispersion, suggesting an exchange rate that is not within the practical limit of detection. This finding is consistent with the proposed “dock and lock” mechanism based on molecular dynamics simulations in which the Aβ1–40 monomer transiently binds to the Aβ1–40 oligomer by non-native contacts with the side chains before being incorporated into the fiber through native contacts with the peptide backbone.
Co-reporter:Neil MacKinnon;Amjad P. Khan;Arul M. Chinnaiyan
Metabolomics 2012 Volume 8( Issue 6) pp:1026-1036
Publication Date(Web):2012 December
DOI:10.1007/s11306-012-0398-4
Metabolomic studies have proven to provide a unique perspective of the cellular dysfunction developing as a result of prostate cancer (PCa) onset and progression, facilitated primarily by mass spectrometry (MS) and nuclear magnetic resonance (NMR) techniques. PCa develops as an androgen-dependent disease with the expression of the androgen receptor (AR), where patient treatment typically involves androgen ablation therapy. In response, it is theorized that PCa transforms to an androgen-hypersensitive or androgen-independent state, where treatment options are severely reduced. Under the hypothesis that AR stimulation increases the aggressivity of pre-existing PCa, NMR spectroscopy was utilized in the delineation of the metabonomic response of an androgen-dependent PCa cell line (LnCAP) as a result of AR activation. Metabolite profiles were determined after 12, 24, and 48 h of exposure to methyltrienolone (R1881), an AR agonist. Principal components analysis revealed the relative myo-inositol and phosphocholine levels were severely altered after androgen treatment. Furthermore, univariate analysis revealed multiple metabolic perturbations in response to R1881 exposure, including amino acid, choline, the phosphocholine/glycerophosphocholine ratio, and UDP-coupled sugar metabolism, which are consistent with reported measurements between normal and PCa samples. These results suggest that androgen-sensitive PCa may transform to an aggressive phenotype upon AR activation.
Co-reporter:Bagganahalli S. Somashekar, Pachiyappan Kamarajan, Theodora Danciu, Yvonne L. Kapila, Arul M. Chinnaiyan, Thekkelnaycke M. Rajendiran, and Ayyalusamy Ramamoorthy
Journal of Proteome Research 2011 Volume 10(Issue 11) pp:5232-5241
Publication Date(Web):2017-2-22
DOI:10.1021/pr200800w
High-resolution magic-angle spinning (HR-MAS) proton NMR spectroscopy is used to explore the metabolic signatures of head and neck squamous cell carcinoma (HNSCC) which included matched normal adjacent tissue (NAT) and tumor originating from tongue, lip, larynx and oral cavity, and associated lymph-node metastatic (LN-Met) tissues. A total of 43 tissues (18 NAT, 18 Tumor and 7 LN-Met) from 22 HNSCC patients were analyzed. Principal Component Analysis of NMR data showed a clear classification between NAT and tumor tissues, however, LN-Met tissues were classified among tumor. A partial least-squares discriminant analysis model generated from NMR metabolic profiles was used to differentiate normal from tumor samples (Q2 > 0.80, Receiver Operator Characteristic area under the curve >0.86, using 7-fold cross validation). HNSCC and LN-Met tissues showed elevated levels of lactate, amino acids including leucine, isoleucine, valine, alanine, glutamine, glutamate, aspartate, glycine, phenylalanine and tyrosine, choline containing compounds, creatine, taurine, glutathione, and decreased levels of triglycerides. These elevated metabolites were associated with highly active glycolysis, increased amino acids influx (anaplerosis) into the TCA cycle, altered energy metabolism, membrane choline phospholipid metabolism, and oxidative and osmotic defense mechanisms. Moreover, decreased levels of triglycerides may indicate lipolysis followed by β-oxidation of fatty acids that may exist to deliver bioenergy for rapid tumor cell proliferation and growth.
Co-reporter:Kazutoshi Yamamoto, Subramanian Vivekanandan, and Ayyalusamy Ramamoorthy
The Journal of Physical Chemistry B 2011 Volume 115(Issue 43) pp:12448-12455
Publication Date(Web):September 22, 2011
DOI:10.1021/jp2076098
In spite of recent technological advances in NMR spectroscopy, its low sensitivity continues to be a major limitation particularly for the structural studies of membrane proteins. The need for a large quantity of a membrane protein and acquisition of NMR data for a long duration are not desirable. Therefore, there is considerable interest in the development of methods to speed up the NMR data acquisition from model membrane samples. In this study, we demonstrate the feasibility of acquiring two-dimensional spectra of an antimicrobial peptide (MSI-78; also known as pexiganan) embedded in isotropic bicelles using natural-abundance 15N nuclei. A copper-chelated lipid embedded in bicelles is used to speed-up the spin–lattice relaxation of protons without affecting the spectral resolution and thus enabling fast data acquisition. Our results suggest that even a 2D SOFAST-HMQC spectrum can be obtained four times faster using a very small amount (∼3 mM) of a copper-chelated lipid. These results demonstrate that this approach will be useful in the structural studies of membrane-associated peptides and proteins without the need for isotopic enrichment for solution NMR studies.
Co-reporter:Jiadi Xu, Pieter E. S. Smith, Ronald Soong, and Ayyalusamy Ramamoorthy
The Journal of Physical Chemistry B 2011 Volume 115(Issue 16) pp:4863-4871
Publication Date(Web):April 5, 2011
DOI:10.1021/jp201501q
Rapidly expanding research on nonsoluble and noncrystalline chemical and biological materials necessitates sophisticated techniques to image these materials at atomic-level resolution. Although their study poses a formidable challenge, solid-state NMR is a powerful tool that has demonstrated application to the investigation of their molecular architecture and functioning. In particular, 2D separated-local-field (SLF) spectroscopy is increasingly applied to obtain high-resolution molecular images of these materials. However, despite the common use of SLF experiments in the structural studies of a variety of aligned molecules, the lack of a resonance assignment approach has been a major disadvantage. As a result, solid-state NMR studies have mostly been limited to aligned systems that are labeled with an isotope at a single site. Here, we demonstrate an approach for resonance assignment through a controlled reintroduction of proton spin diffusion in the 2D proton-evolved-local-field (PELF) pulse sequence. Experimental results and simulations suggest that the use of spin diffusion also enables the measurement of long-range heteronuclear dipolar couplings that can be used as additional constraints in the structural and dynamical studies of aligned molecules. The new method is used to determine the de novo atomic-level resolution structure of a liquid crystalline material, N-(4-methoxybenzylidene)-4-butylaniline, and its use on magnetically aligned bicelles is also demonstrated. We expect this technique to also be valuable in the structural studies of functional molecules like columnar liquid crystals and other biomaterials.
Co-reporter:Jiadi Xu, Peizhi Zhu, Michael D. Morris, and Ayyalusamy Ramamoorthy
The Journal of Physical Chemistry B 2011 Volume 115(Issue 33) pp:9948-9954
Publication Date(Web):July 25, 2011
DOI:10.1021/jp205663z
An atomic-level insight into the functioning of articular cartilage would be useful to develop prevention strategies and therapies for joint diseases such as osteoarthritis. However, the composition and structure of cartilage and their relationship to its unique mechanical properties are quite complex and pose tremendous challenges to most biophysical techniques. In this study, we present an investigation of the structure and dynamics of polymeric molecules of articular cartilage using time-resolved solid-state NMR spectroscopy during dehydration. Full-thickness cartilage explants were used in magic-angle spinning experiments to monitor the structural changes of rigid and mobile carbons. Our results reveal that the dehydration reduced the mobility of collagen amino acid residues and carbon sugar ring structures in glycosaminoglycans but had no effect on the trans-Xaa-Pro conformation. Equally interestingly, our results demonstrate that the dehydration effects are reversible, and the molecular structure and mobility are restored upon rehydration.
Co-reporter:Aanatoly K. Khitrin, Jiadi Xu, Ayyalusamy Ramamoorthy
Journal of Magnetic Resonance 2011 212(1) pp: 95-101
Publication Date(Web):
DOI:10.1016/j.jmr.2011.06.015
Co-reporter:Prerna N Domadia ; Anirban Bhunia ; Ayyalusamy Ramamoorthy ;Surajit Bhattacharjya
Journal of the American Chemical Society 2010 Volume 132(Issue 51) pp:18417-18428
Publication Date(Web):December 3, 2010
DOI:10.1021/ja1083255
Lipopolysaccharide (LPS) provides a well-organized permeability barrier at the outer membrane of Gram-negative bacteria. Host defense cationic antimicrobial peptides (AMPs) need to disrupt the outer membrane before gaining access to the inner cytoplasmic membrane or intracellular targets. Several AMPs are largely inactive against Gram-negative pathogens due to the restricted permeation through the LPS layer of the outer membrane. MSI-594 (GIGKFLKKAKKGIGAVLKVLTTG) is a highly active AMP with a broad-spectrum of activities against bacteria, fungi, and virus. In the context of LPS, MSI-594 assumes a hairpin helical structure dictated by packing interactions between two helical segments. Residue Phe5 of MSI-594 has been found to be engaged in important interhelical interactions. In order to understand plausible structural and functional inter-relationship of the helical hairpin structure of MSI-594 with outer membrane permeabilization, a mutant peptide, termed MSI-594F5A, containing a replacement of Phe5 with Ala has been prepared. We have compared antibacterial activities, outer and inner membrane permeabilizations, LPS binding affinity, perturbation of LPS micelles structures by MSI-594 and MSI-594F5A peptides. Our results demonstrated that the MSI-594F5A has lower activities against Gram-negative bacteria, due to limited permeabilization through the LPS layer, however, retains Gram-positive activity, akin to MSI-594. The atomic-resolution structure of MSI-594F5A has been determined in LPS micelles by NMR spectroscopy showing an amphipathic curved helix without any packing interactions. The 3D structures, interactions, and activities of MSI-594 and its mutant MSI-594F5A in LPS provide important mechanistic insights toward the requirements of LPS specific conformations and outer membrane permeabilization by broad-spectrum antimicrobial peptides.
Co-reporter:Pieter E. S. Smith ; Jeffrey R. Brender ; Ulrich H. N. Dürr ; Jiadi Xu ; Douglas G. Mullen ; Mark M. Banaszak Holl
Journal of the American Chemical Society 2010 Volume 132(Issue 23) pp:8087-8097
Publication Date(Web):May 20, 2010
DOI:10.1021/ja101524z
Poly(amidoamine) (PAMAM) dendrimer nanobiotechnology shows great promise in targeted drug delivery and gene therapy. Because of the involvement of cell membrane lipids with the pharmacological activity of dendrimer nanomedicines, the interactions between dendrimers and lipids are of particular relevance to the pharmaceutical applications of dendrimers. In this study, solid-state NMR was used to obtain a molecular image of the complex of generation-5 (G5) PAMAM dendrimer with the lipid bilayer. Using 1H radio frequency driven dipolar recoupling (RFDR) and 1H magic angle spinning (MAS) nuclear Overhauser effect spectroscopy (NOESY) techniques, we show that dendrimers are thermodynamically stable when inserted into zwitterionic lipid bilayers. 14N and 31P NMR experiments on static samples and measurements of the mobility of C−H bonds using a 2D proton detected local field protocol under MAS corroborate these results. The localization of dendrimers in the hydrophobic core of lipid bilayers restricts the motion of bilayer lipid tails, with the smaller G5 dendrimer having more of an effect than the larger G7 dendrimer. Fragmentation of the membrane does not occur at low dendrimer concentrations in zwitterionic membranes. Because these results show that the amphipathic dendrimer molecule can be stably incorporated in the interior of the bilayer (as opposed to electrostatic binding at the surface), they are expected to be useful in the design of dendrimer-based nanobiotechnologies.
Co-reporter:Khoi Tan Nguyen ; Ronald Soong ; Sang-Choul lm ; Lucy Waskell ; Ayyalusamy Ramamoorthy ;Zhan Chen
Journal of the American Chemical Society 2010 Volume 132(Issue 43) pp:15112-15115
Publication Date(Web):October 8, 2010
DOI:10.1021/ja106508f
In addition to providing a semipermeable barrier that protects a cell from harmful stimuli, lipid membranes occupy a central role in hosting a variety of biological processes, including cellular communications and membrane protein functions. Most importantly, protein−membrane interactions are implicated in a variety of diseases and therefore many analytical techniques were developed to study the basis of these interactions and their influence on the molecular architecture of the cell membrane. In this study, sum frequency generation (SFG) vibrational spectroscopy is used to investigate the spontaneous membrane insertion process of cytochrome b5 and its mutants. Experimental results show a significant difference in the membrane insertion and orientation properties of these proteins, which can be correlated with their functional differences. In particular, our results correlate the nonfunctional property of a mutant cytochrome b5 with its inability to insert into the lipid bilayer. The approach reported in this study could be used as a potential rapid screening tool in measuring the topology of membrane proteins as well as interactions of biomolecules with lipid bilayers in situ.
Co-reporter:Ronald Soong ; Pieter E. S. Smith ; Jiadi Xu ; Kazutoshi Yamamoto ; Sang-Choul Im ; Lucy Waskell
Journal of the American Chemical Society 2010 Volume 132(Issue 16) pp:5779-5788
Publication Date(Web):March 24, 2010
DOI:10.1021/ja910807e
Structural biology of membrane proteins has rapidly evolved into a new frontier of science. Although solving the structure of a membrane protein with atomic-level resolution is still a major challenge, separated local field (SLF) NMR spectroscopy has become an invaluable tool in obtaining structural images of membrane proteins under physiological conditions. Recent studies have demonstrated the use of rotating-frame SLF techniques to accurately measure strong heteronuclear dipolar couplings between directly bonded nuclei. However, in these experiments, all weak dipolar couplings are suppressed. On the other hand, weak heteronuclear dipolar couplings can be measured using laboratory-frame SLF experiments, but only at the expense of spectral resolution for strongly dipolar coupled spins. In the present study, we implemented two-dimensional proton-evolved local-field (2D PELF) pulse sequences using either composite zero cross-polarization (COMPOZER-CP) or windowless isotropic mixing (WIM) for magnetization transfer. These PELF sequences can be used for the measurement of a broad range of heteronuclear dipolar couplings, allowing for a complete mapping of protein dynamics in a lipid bilayer environment. Experimental results from magnetically aligned bicelles containing uniformly 15N-labeled cytochrome b5 are presented and theoretical analyses of the new PELF sequences are reported. Our results suggest that the PELF-based experimental approaches will have a profound impact on solid-state NMR spectroscopy of membrane proteins and other membrane-associated molecules in magnetically aligned bicelles.
Co-reporter:Kazutoshi Yamamoto ; Jiadi Xu ; Karen E. Kawulka ; John C. Vederas
Journal of the American Chemical Society 2010 Volume 132(Issue 20) pp:6929-6931
Publication Date(Web):April 30, 2010
DOI:10.1021/ja102103n
Recent studies have demonstrated the abilities of solid-state NMR techniques to solve atomic-level-resolution structures and dynamics of membrane-associated proteins and peptides. However, high-throughput applications of solid-state NMR spectroscopy are hampered by long acquisition times due to the low sensitivity of the technique. In this study, we demonstrate the use of a paramagnetic copper-chelated lipid to enhance the spin−lattice relaxation and thereby speed up solid-state NMR measurements. Fluid lamellar-phase bicelles composed of a lipid, detergent, and the copper-chelated lipid and containing a uniformly 15N-labeled antimicrobial peptide, subtilosin A, were used at room temperature. The use of a chelating lipid reduces the concentration of free copper and limits RF-induced heating, a major problem for fluid samples. Our results demonstrate a 6.2-fold speed increase and a 2.7-fold improvement in signal-to-noise ratio for solid-state NMR experiments under magic-angle spinning and static conditions, respectively. Furthermore, solid-state NMR measurements are shown to be feasible even for nanomole concentrations of a membrane-associated peptide.
Co-reporter:Jeffrey R. Brender ; Kevin Hartman ; Ravi Prakash Reddy Nanga ; Nataliya Popovych ; Roberto de la Salud Bea ; Subramanian Vivekanandan ; E. Neil G. Marsh
Journal of the American Chemical Society 2010 Volume 132(Issue 26) pp:8973-8983
Publication Date(Web):June 10, 2010
DOI:10.1021/ja1007867
Human Islet Amyloid Polypeptide (hIAPP) is a highly amyloidogenic protein found in islet cells of patients with type II diabetes. Because hIAPP is highly toxic to β-cells under certain conditions, it has been proposed that hIAPP is linked to the loss of β-cells and insulin secretion in type II diabetics. One of the interesting questions surrounding this peptide is how the toxic and aggregation prone hIAPP peptide can be maintained in a safe state at the high concentrations that are found in the secretory granule where it is stored. We show here zinc, which is found at millimolar concentrations in the secretory granule, significantly inhibits hIAPP amyloid fibrillogenesis at concentrations similar to those found in the extracellular environment. Zinc has a dual effect on hIAPP fibrillogenesis: it increases the lag-time for fiber formation and decreases the rate of addition of hIAPP to existing fibers at lower concentrations, while having the opposite effect at higher concentrations. Experiments at an acidic pH which partially neutralizes the change in charge upon zinc binding show inhibition is largely due to an electrostatic effect at His18. High-resolution structures of hIAPP determined from NMR experiments confirm zinc binding to His18 and indicate zinc induces localized disruption of the secondary structure of IAPP in the vicinity of His18 of a putative helical intermediate of IAPP. The inhibition of the formation of aggregated and toxic forms of hIAPP by zinc provides a possible mechanism between the recent discovery of linkage between deleterious mutations in the SLC30A8 zinc transporter, which transports zinc into the secretory granule, and type II diabetes.
Co-reporter:Jiadi Xu ; Ronald Soong ; Sang-Choul Im ; Lucy Waskell
Journal of the American Chemical Society 2010 Volume 132(Issue 29) pp:9944-9947
Publication Date(Web):July 2, 2010
DOI:10.1021/ja103983f
Despite recent advances in NMR approaches for structural biology, determination of membrane protein dynamics in its native environment continues to be a monumental challenge, as most NMR structural studies of membrane proteins are commonly carried out either in micelles or in vesicle systems under frozen conditions. To overcome this difficulty, we propose a solid-state NMR technique that allows for the determination of side-chain dynamics from membrane proteins in lipid bilayers. This new technique, namely dipolar enhanced polarization transfer (DREPT), allows for a wide range of dipolar couplings to be encoded, providing high resolution and sensitivity for systems that undergo motional averaging such as that of amino acid side chains. NMR observables such as dipolar couplings and chemical shift anisotropy, which are highly sensitive to molecular motions, provide a direct way of probing protein dynamics over a wide range of time scales. Therefore, using an appropriate model, it is possible to determine side-chain dynamics and provide additional information on the topology and function of a membrane protein in its native environment.
Co-reporter:Jiadi Xu ; Peizhi Zhu ; Zhehong Gan ; Nadder Sahar ; Mary Tecklenburg ; Michael D. Morris ; David H. Kohn
Journal of the American Chemical Society 2010 Volume 132(Issue 33) pp:11504-11509
Publication Date(Web):August 3, 2010
DOI:10.1021/ja101961x
Structural information about the coordination environment of calcium present in bone is highly valuable in understanding the role of calcium in bone formation, biomineralization, and bone diseases like osteoporosis. While a high-resolution structural study on bone has been considered to be extremely challenging, NMR studies on model compounds and bone minerals have provided valuable insight into the structure of bone. Particularly, the recent demonstration of 43Ca solid-state NMR experiments on model compounds is an important advance in this field. However, application of 43Ca NMR is hampered due to the low natural-abundance and poor sensitivity of 43Ca. In this study, we report the first demonstration of natural-abundance 43Ca magic angle spinning (MAS) NMR experiments on bone, using powdered bovine cortical bone samples. 43Ca NMR spectra of bovine cortical bone are analyzed by comparing to the natural-abundance 43Ca NMR spectra of model compounds including hydroxyapatite and carbonated apatite. While 43Ca NMR spectra of hydroxyapatite and carbonated apatite are very similar, they significantly differ from those of cortical bone. Raman spectroscopy shows that the calcium environment in bone is more similar to carbonated apatite than hydroxyapatite. A close analysis of 43Ca NMR spectra reveals that the chemical shift frequencies of cortical bone and 10% carbonated apatite are similar but the quadrupole coupling constant of cortical bone is larger than that measured for model compounds. In addition, our results suggest that an increase in the carbonate concentration decreases the observed 43Ca chemical shift frequency. A comparison of experimentally obtained 43Ca MAS spectra with simulations reveal a 3:4 mol ratio of Ca-I/Ca-II sites in carbonated apatite and a 2.3:3 mol ratio for hydroxyapatite. 2D triple-quantum 43Ca MAS experiments performed on a mixture of carbonated apatite and the bone protein osteocalcin reveal the presence of protein-bound and free calcium sites, which is in agreement with a model developed from X-ray crystal structure of the protein.
Co-reporter:Hazime Saitô, Isao Ando, Ayyalusamy Ramamoorthy
Progress in Nuclear Magnetic Resonance Spectroscopy 2010 Volume 57(Issue 2) pp:181-228
Publication Date(Web):August 2010
DOI:10.1016/j.pnmrs.2010.04.005
Co-reporter:Sathiah Thennarasu, Rui Huang, Dong-Kuk Lee, Pei Yang, Lee Maloy, Zhan Chen, and Ayyalusamy Ramamoorthy
Biochemistry 2010 Volume 49(Issue 50) pp:
Publication Date(Web):November 9, 2010
DOI:10.1021/bi101394r
In a minimalist design approach, a synthetic peptide MSI-367 [(KFAKKFA)3-NH2] was designed and synthesized with the objective of generating cell-selective nonlytic peptides, which have a significant bearing on cell targeting. The peptide exhibited potent activity against both bacteria and fungi, but no toxicity to human cells at micromolar concentrations. Bacterial versus human cell membrane selectivity of the peptide was determined via membrane permeabilization assays. Circular dichroism investigations revealed the intrinsic helix propensity of the peptide, β-turn structure in aqueous buffer and extended and turn conformations upon binding to lipid vesicles. Differential scanning calorimetry experiments with 1,2-dipalmitoleoyl-sn-glycero-3-phosphatidylethanolamine bilayers indicated the induction of positive curvature strain and repression of the fluid lamellar to inverted hexagonal phase transition by MSI-367. Results of isothermal titration calorimetry (ITC) experiments suggested the possibility of formation of specific lipid−peptide complexes leading to aggregation. 2H nuclear magnetic resonance (NMR) of deuterated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) multilamellar vesicles confirmed the limited effect of the membrane-embedded peptide at the lipid−water interface. 31P NMR data indicated changes in the lipid headgroup orientation of POPC, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol, and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylethanolamine lipid bilayers upon peptide binding. Membrane-embedded and membrane-inserted states of the peptide were observed via sum frequency generation vibrational spectroscopy. Circular dichroism, ITC, and 31P NMR data for Escherichia coli lipids agree with the hypothesis that strong electrostatic lipid−peptide interactions embrace the peptide at the lipid−water interface and provide the basis for bacterial cell selectivity.
Co-reporter:Pieter E. S. Smith ; Jeffrey R. Brender
Journal of the American Chemical Society 2009 Volume 131(Issue 12) pp:4470-4478
Publication Date(Web):March 11, 2009
DOI:10.1021/ja809002a
The death of insulin-producing β-cells is a key step in the pathogenesis of type 2 diabetes. The amyloidogenic peptide Islet Amyloid Polypeptide (IAPP, also known as amylin) has been shown to disrupt β-cell membranes leading to β-cell death. Despite the strong evidence linking IAPP to the destruction of β-cell membrane integrity and cell death, the mechanism of IAPP toxicity is poorly understood. In particular, the effect of IAPP on the bilayer structure has largely been uncharacterized. In this study, we have determined the effect of the amyloidogenic and toxic hIAPP1−37 peptide and the nontoxic and nonamyloidogenic rIAPP1−37 peptide on membranes by a combination of DSC and solid-state NMR spectroscopy. We also characterized the toxic but largely nonamyloidogenic rIAPP1−19 and hIAPP1−19 fragments. DSC shows that both amyloidogenic (hIAPP1−37) and largely nonamyloidogenic (hIAPP1−19 and rIAPP1−19) toxic versions of the peptide strongly favor the formation of negative curvature in lipid bilayers, while the nontoxic full-length rat IAPP1−37 peptide does not. This result was confirmed by solid-state NMR spectroscopy which shows that in bicelles composed of regions of high curvature and low curvature, nontoxic rIAPP1−37 binds to the regions of low curvature while toxic rIAPP1−19 binds to regions of high curvature. Similarly, solid-state NMR spectroscopy shows that the toxic rIAPP1−19 peptide significantly disrupts the lipid bilayer structure, whereas the nontoxic rIAPP1−37 does not have a significant effect. These results indicate IAPP may induce the formation of pores by the induction of excess membrane curvature and can be used to guide the design of compounds that can prevent the cell-toxicity of IAPP. This mechanism may be important to understand the toxicity of other amyloidogenic proteins. Our solid-state NMR results also demonstrate the possibility of using bicelles to measure the affinity of biomolecules for negatively or positively curved regions of the membrane, which we believe will be useful in a variety of biochemical and biophysical investigations related to the cell membrane.
Co-reporter:Ronald Soong ; Jeffrey R. Brender ; Peter M. Macdonald
Journal of the American Chemical Society 2009 Volume 131(Issue 20) pp:7079-7085
Publication Date(Web):April 30, 2009
DOI:10.1021/ja900285z
Self-association of human islet amyloid polypeptide (hIAPP) is correlated with the development of type II diabetes by the disruption of cellular homeostasis in islet cells through the formation of membrane-active oligomers. The toxic species of hIAPP responsible for membrane damage has not been identified. In this study, we show by pulsed field gradient NMR spectroscopy that the monomeric form of the toxic, amyloidogenic human variant of IAPP (hIAPP) adopts a temperature dependent compact folded conformation that is absent in both the nontoxic and nonamyloidogenic rat variant of IAPP and absent in hIAPP at low temperatures, suggesting this compact form of monomeric hIAPP may be linked to its later aggregation and cytotoxicity. In addition to the monomeric form of hIAPP, a large oligomeric species greater than 100 nm in diameter is also present but does not trigger the nucleation-dependent aggregation of IAPP at 4 °C, indicating the large oligomeric species may be an off-pathway intermediate that has been predicted by kinetic models of IAPP fiber formation. Furthermore, analysis of the polydispersity of the calculated diffusion values indicates small oligomeric species of hIAPP are absent in agreement with a recent ultracentrifugation study. The absence of small oligomeric species in solution suggests the formation of small, well-defined ion channels by hIAPP may proceed by aggregation of monomeric IAPP on the membrane, rather than by the insertion of preformed structured oligomers from the solution state as has been proposed for other amyloidogenic proteins.
Co-reporter:E. Neil G. Marsh, Benjamin C. Buer and Ayyalusamy Ramamoorthy
Molecular BioSystems 2009 vol. 5(Issue 10) pp:1143-1147
Publication Date(Web):28 Jul 2009
DOI:10.1039/B909864J
Antimicrobial peptides (also known as genetically encoded peptide antibiotics) are a diverse class of short cationic amphipathic polypeptides that exhibit a broad-spectrum of antimicrobial activities by selectively disrupting the bacterial cell membrane. In this review article, we present the use of fluorinated amino acids in the design of antimicrobial peptides and other membrane-active peptides.
Co-reporter:Ayyalusamy Ramamoorthy
Solid State Nuclear Magnetic Resonance 2009 Volume 35(Issue 4) pp:201-207
Publication Date(Web):July 2009
DOI:10.1016/j.ssnmr.2009.03.003
There is a considerable current interest in understanding the function of antimicrobial peptides for the development of potent novel antibiotic compounds with a very high selectivity. Since their interaction with the cell membrane is the major driving force for their function, solid-state NMR spectroscopy is the unique method of choice to study these insoluble, non-crystalline, membrane-peptide complexes. Here I discuss solid-state NMR studies of antimicrobial peptides that have reported high-resolution structure, dynamics, orientation, and oligomeric states of antimicrobial peptides in a membrane environment, and also address important questions about the mechanism of action at atomic-level resolution. Increasing number of solid-state NMR applications to antimicrobial peptides are expected in the near future, as these compounds are promising candidates to overcome ever-increasing antibiotic resistance problem and are well suited for the development and applications of solid-state NMR techniques.
Co-reporter:Kazutoshi Yamamoto, Ronald Soong and Ayyalusamy Ramamoorthy
Langmuir 2009 Volume 25(Issue 12) pp:7010-7018
Publication Date(Web):April 27, 2009
DOI:10.1021/la900200s
Bicelles of various lipid/detergent ratios are commonly used in nuclear magnetic resonance (NMR) studies of membrane-associated molecules without the need to freeze the sample. While a decrease in the size (defined at a low temperature or by the q value) of a bicelle decreases its overall order parameter, the variation of lipid dynamics with a change in the lipid/detergent ratio is unknown. In this study, we report a thorough atomistic level analysis on the variation of lipid dynamics with the size and hydration level of bicelles composed of a phospholipid, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and a detergent, 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC). Two-dimensional (2D) separated-local-field NMR experiments were performed on magnetically aligned bicelles to measure 1H−13C dipolar couplings, which were used to determine order parameters at various (head-group, glycerol, and acyl chain) regions of lipids in the bilayer. From our analysis, we uncover the extreme sensitivity of the glycerol region to the motion of the bicelle, which can be attributed to the effect of viscosity because of an extensive network of hydrogen bonds. As such, the water−membrane interface region exhibits the highest order parameter values among all three regions of a lipid molecule. Our experimental results demonstrate that the laboratory-frame 2D proton-detected-local-field pulse sequence is well-suited for the accurate measurement of motionally averaged (or long-range) weak and multiple 1H−13C dipolar couplings associated with a single carbon site at the natural abundance of 13C nuclei.
Co-reporter:Anirban Bhunia Dr. Dr.;Surajit Bhattacharjya Dr.
Chemistry - A European Journal 2009 Volume 15( Issue 9) pp:2036-2040
Publication Date(Web):
DOI:10.1002/chem.200802635
Co-reporter:Lindsey M. Gottler, Roberto de la Salud Bea, Charles E. Shelburne, Ayyalusamy Ramamoorthy and E. Neil G. Marsh
Biochemistry 2008 Volume 47(Issue 35) pp:
Publication Date(Web):August 12, 2008
DOI:10.1021/bi801045n
Protegrins are potent members of the β-hairpin-forming class of antimicrobial peptides. Key to their antimicrobial activity is their assembly into oligomeric structures upon binding to the bacterial membrane. To examine the relationship between the physicochemical properties of the peptide and its biological activity, we have synthesized variants of protegrin-1 in which key residues in the hydrophobic core, valine-14 and -16, are changed to leucine and to the extensively fluorinated analogue hexafluoroleucine. These substitutions have the effect of making the peptide progressively more hydrophobic while minimally perturbing the secondary structure. The leucine-containing peptide was significantly more active than wild-type protegrin against several common pathogenic bacterial strains, whereas the hexafluoroleucine-substituted peptide, in contrast, showed significantly diminished activity against several bacterial strains. Isothermal titration calorimetry measurements revealed significant changes in the interaction of the peptides binding to small unilamelar vesicles that mimic the lipid composition of the bacterial membrane. The binding isotherms for wild-type and leucine-substituted protegrins indicate that electrostatic interactions dominate the membrane−peptide interaction, whereas the isotherm for the hexafluoroleucine-substituted protegrin suggests a diminished electrostatic component to binding. Notably both of these substitutions appear to alter the stoichiometry of the lipid−peptide interaction, suggesting that these substitutions may stabilize oligomerized forms of protegrin that are postulated to be intermediates in the assembly of the β-barrel membrane pore structure.
Co-reporter:Fernando Porcelli, Raffaello Verardi, Lei Shi, Katherine A. Henzler-Wildman, Ayyalusamy Ramamoorthy and Gianluigi Veglia
Biochemistry 2008 Volume 47(Issue 20) pp:
Publication Date(Web):April 26, 2008
DOI:10.1021/bi702036s
LL-37 is the only cathelicidin-derived polypeptide found in humans. Its eclectic function makes this peptide one of the most intriguing chemical defense agents, with crucial roles in moderating inflammation, promoting wound healing, and boosting the human immune system. LL-37 kills both prokaryotic and eukaryotic cells through physical interaction with cell membranes. In order to study its active conformation in membranes, we have reconstituted LL-37 into dodecylphosphocholine (DPC) micelles and determined its three-dimensional structure. We found that, under our experimental conditions, this peptide adopts a helix−break−helix conformation. Both the N- and C-termini are unstructured and solvent exposed. The N-terminal helical domain is more dynamic, while the C-terminal helix is more solvent protected and structured (high density of NOEs, slow H/D exchange). When it interacts with DPC, LL-37 is adsorbed on the surface of the micelle with the hydrophilic face exposed to the water phase and the hydrophobic face buried in the micelle hydrocarbon region. The break between the helices is positioned at K12 and is probably stabilized by a hydrophobic cluster formed by I13, F17, and I20 in addition to a salt bridge between K12 and E16. These results support the proposed nonpore carpet-like mechanism of action, in agreement with the solid-state NMR studies, and pave the way for understanding the function of the mature LL-37 at the atomic level.
Co-reporter:Ravi Prakash Reddy Nanga, Jeffrey R. Brender, Jiadi Xu, Gianluigi Veglia and Ayyalusamy Ramamoorthy
Biochemistry 2008 Volume 47(Issue 48) pp:12689-12697
Publication Date(Web):November 6, 2008
DOI:10.1021/bi8014357
Disruption of the cellular membrane by the amyloidogenic peptide IAPP (or amylin) has been implicated in β-cell death during type 2 diabetes. While the structure of the mostly inert fibrillar form of IAPP has been investigated, the structural details of the highly toxic prefibrillar membrane-bound states of IAPP have been elusive. A recent study showed that a fragment of IAPP (residues 1−19) induces membrane disruption to a similar extent as the full-length peptide. However, unlike the full-length IAPP peptide, IAPP1−19 is conformationally stable in an α-helical conformation when bound to the membrane. In vivo and in vitro measurements of membrane disruption indicate the rat version of IAPP1−19, despite differing from hIAPP1−19 by the single substitution of Arg18 for His18, is significantly less toxic than hIAPP1−19, in agreement with the low toxicity of the full-length rat IAPP peptide. To investigate the origin of this difference at the atomic level, we have solved the structures of the human and rat IAPP1−19 peptides in DPC micelles. While both rat and human IAPP1−19 fold into similar mostly α-helical structures in micelles, paramagnetic quenching NMR experiments indicate a significant difference in the membrane orientation of hIAPP1−19 and rIAPP1−19. At pH 7.3, the more toxic hIAPP1−19 peptide is buried deeper within the micelle, while the less toxic rIAPP1−19 peptide is located at the surface of the micelle. Deprotonating H18 in hIAPP1−19 reorients the peptide to the surface of the micelle. This change in orientation is in agreement with the significantly reduced ability of hIAPP1−19 to cause membrane disruption at pH 6.0. This difference in peptide topology in the membrane may correspond to similar topology differences for the full-length human and rat IAPP peptides, with the toxic human IAPP peptide adopting a transmembrane orientation and the nontoxic rat IAPP peptide bound to the surface of the membrane.
Co-reporter:Jeffrey R. Brender, Kevin Hartman, Kendra R. Reid, Robert T. Kennedy and Ayyalusamy Ramamoorthy
Biochemistry 2008 Volume 47(Issue 48) pp:12680-12688
Publication Date(Web):November 6, 2008
DOI:10.1021/bi801427c
Islet amyloid polypeptide (IAPP or amylin) is a 37-residue peptide secreted with insulin by β-cells in the islets of Langerhans. The aggregation of the peptide into either amyloid fibers or small soluble oligomers has been implicated in the death of β-cells during type 2 diabetes through disruption of the cellular membrane. The actual form of the peptide responsible for β-cell death has been a subject of controversy. Previous research has indicated that the N-terminal region of the peptide (residues 1−19) is primarily responsible for the membrane-disrupting effect of the hIAPP peptide and induces membrane disruption to a similar extent as the full-length peptide without forming amyloid fibers when bound to the membrane. The rat version of the peptide, which is both noncytotoxic and nonamyloidogenic, differs from the human peptide by only one amino acid residue: Arg18 in the rat version while His18 in the human version. To elucidate the effect of this difference, we have measured in this study the effects of the rat and human versions of IAPP1−19 on islet cells and model membranes. Fluorescence microscopy shows a rapid increase in intracellular calcium levels of islet cells after the addition of hIAPP1−19, indicating disruption of the cellular membrane, while the rat version of the IAPP1−19 peptide is significantly less effective. Circular dichroism experiments and dye leakage assays on model liposomes show that rIAPP1−19 is deficient in binding to and disrupting lipid membranes at low but not at high peptide to lipid ratios, indicating that the ability of rIAPP1−19 to form small aggregates necessary for membrane binding and disruption is significantly less than hIAPP1−19. At pH 6.0, where H18 is likely to be protonated, hIAPP1−19 resembles rIAPP1−19 in its ability to cause membrane disruption. Differential scanning calorimetry suggests a different mode of binding to the membrane for rIAPP1−19 compared to hIAPP1−19. Human IAPP1−19 has a minimal effect on the phase transition of lipid vesicles, suggesting a membrane orientation of the peptide in which the mobility of the acyl chains of the membrane is relatively unaffected. Rat IAPP1−19, however, has a strong effect on the phase transition of lipid vesicles at low concentrations, suggesting that the peptide does not easily insert into the membrane after binding to the surface. Our results indicate that the modulation of the peptide orientation in the membrane by His18 plays a key role in the toxicity of nonamyloidogenic forms of hIAPP.
Co-reporter:Jiadi Xu Dr.;UlrichH.N. Dürr Dr.;Sang-Choul Im Dr.;Zhehong Gan Dr.;Lucy Waskell Dr.
Angewandte Chemie 2008 Volume 120( Issue 41) pp:7982-7985
Publication Date(Web):
DOI:10.1002/ange.200801338
Co-reporter:Sergey V. Dvinskikh, Kazutoshi Yamamoto, David Scanu, Robert Deschenaux and Ayyalusamy Ramamoorthy
The Journal of Physical Chemistry B 2008 Volume 112(Issue 39) pp:12347-12353
Publication Date(Web):September 9, 2008
DOI:10.1021/jp803265z
Liquid-crystalline materials containing fullerenes are valuable in the development of supramolecular switches and in solar cell technology. In this study, we characterize the liquid-crystalline and dynamic properties of fullerene-containing thermotropic compounds using solid-state natural abundance 13C NMR experiments under stationary and magic angle spinning sample conditions. Chemical shifts spectra were measured in isotropic, liquid-crystalline nematic and smectic A and crystalline phases using one-dimensional 13C experiments, while two-dimensional separated local-field experiments were used to measure the 1H−13C dipolar couplings in mesophases. Chemical shift and dipolar coupling parameters were used to characterize the structure and dynamics of the liquid-crystalline dyads. NMR data of fullerene-containing thermotropic liquid crystals are compared to that of basic mesogenic unit and mesomorphic promoter compounds. Our NMR results suggest that the fullerene−ferrocene dyads form highly dynamic liquid-crystalline phases in which molecules rotate fast around the symmetry axis on the characteristic NMR time scale of ∼10−4 s.
Co-reporter:Dong-Kuk Lee, Byung Soo Kwon and Ayyalusamy Ramamoorthy
Langmuir 2008 Volume 24(Issue 23) pp:13598-13604
Publication Date(Web):November 7, 2008
DOI:10.1021/la8023698
Lipid−water interaction plays an important role in the properties of lipid bilayers, cryoprotectants, and membrane-associated peptides and proteins. The temperature at which water bound to lipid bilayers freezes is lower than that of free water. Here, we report a solid-state NMR investigation on the freezing point depression of water in phospholipid bilayers in the presence and absence of cholesterol. Deuterium NMR spectra at different temperatures ranging from −75 to +10 °C were obtained from fully 2H2O-hydrated POPC (1-palmitoyl-2-oleoylphosphatidylcholine) multilamellar vesicles (MLVs), prepared with and without cholesterol, to determine the freezing temperature of water and the effect of cholesterol on the freezing temperature of water in POPC bilayers. Our 2H NMR experiments reveal the motional behavior of unfrozen water molecules in POPC bilayers even at temperatures significantly below 0 °C and show that the presence of cholesterol further lowered the freezing temperature of water in POPC bilayers. These results suggest that in the presence of cholesterol the fluidity and dynamics of lipid bilayers can be retained even at very low temperatures as exist in the liquid crystalline phase of the lipid. Therefore, bilayer samples prepared with a cryoprotectant like cholesterol should enable the performance of multidimensional solid-state NMR experiments to investigate the structure, dynamics, and topology of membrane proteins at a very low temperature with enhanced sample stability and possibly a better sensitivity. Phosphorus-31 NMR data suggest that lipid bilayers can be aligned at low temperatures, while 15N NMR experiments demonstrate that such aligned samples can be used to enhance the signal-to-noise ratio of 15N chemical shift spectra of a 37-residue human antimicrobial peptide, LL-37.
Co-reporter:Jiadi Xu Dr.;UlrichH.N. Dürr Dr.;Sang-Choul Im Dr.;Zhehong Gan Dr.;Lucy Waskell Dr.
Angewandte Chemie International Edition 2008 Volume 47( Issue 41) pp:7864-7867
Publication Date(Web):
DOI:10.1002/anie.200801338
Co-reporter:Sergey V. Dvinskikh, Kazutoshi Yamamoto, Ulrich H.N. Dürr, Ayyalusamy Ramamoorthy
Journal of Magnetic Resonance 2007 Volume 184(Issue 2) pp:228-235
Publication Date(Web):February 2007
DOI:10.1016/j.jmr.2006.10.004
Magnetically aligned bicelles are becoming attractive model membranes to investigate the structure, dynamics, geometry, and interaction of membrane-associated peptides and proteins using solution- and solid-state NMR experiments. Recent studies have shown that bicelles are more suitable than mechanically aligned bilayers for multidimensional solid-state NMR experiments. In this work, we describe experimental aspects of the natural abundance 13C and 14N NMR spectroscopy of DMPC/DHPC bicelles. In particular, approaches to enhance the sensitivity and resolution and to quantify radio-frequency heating effects are presented. Sensitivity of 13C detection using single pulse excitation, conventional cross-polarization (CP), ramp-CP, and NOE techniques are compared. Our results suggest that the proton decoupling efficiency of the FLOPSY pulse sequence is better than that of continuous wave decoupling, TPPM, SPINAL, and WALTZ sequences. A simple method of monitoring the water proton chemical shift is demonstrated for the measurement of sample temperature and calibration of the radio-frequency-induced heating in the sample. The possibility of using 14N experiments on bicelles is also discussed.
Co-reporter:Sathiah Thennarasu, Dong-Kuk Lee, Alan Poon, Karen E. Kawulka, John C. Vederas, Ayyalusamy Ramamoorthy
Chemistry and Physics of Lipids 2005 Volume 137(1–2) pp:38-51
Publication Date(Web):October 2005
DOI:10.1016/j.chemphyslip.2005.06.003
Subtilosin A is an antimicrobial peptide produced by the soil bacterium Bacillus subtilis that possesses bactericidal activity against a diverse range of bacteria, including Listeria monocytogenes. Recent structural studies have found that subtilosin A is posttranslationally modified in a unique way, placing it in a new class of bacteriocins. In this study, in order to understand the mechanism of membrane-disruption by subtilosin A, the interaction of the peptide with model phospholipid bilayers is characterized using fluorescence, solid-state NMR and differential scanning calorimetry (DSC) experiments. Our results in this study show that subtilosin A interacts with the lipid head group region of bilayer membranes in a concentration dependent manner. Fluorescence experiments reveal the interaction of subtilosin A with small unilamellar vesicles (SUVs) composed of POPC, POPG and E. coli total lipids, and that at least one edge of the molecule is buried in membrane bilayers. At high concentrations, it induces leakage from SUVs of POPC and POPE/POPG (7:3) mixture. 15N solid-state NMR data suggests that the cyclic peptide is partially inserted into bilayers, which is in agreement with the fluorescence data. 31P and 2H NMR experiments and DSC data support the hypothesis that subtilosin A adopts a partially buried orientation in lipid bilayers, by showing that it induces a conformational change in the lipid headgroup and disordering in the hydrophobic region of bilayers. These results suggest that the lipid perturbation observed in this study may be one of the consequences of subtilosin A binding to lipid bilayers, which results in membrane permeabilization at high peptide concentrations.
Co-reporter:Caroline D. Pointer-Keenan, Dong-Kuk Lee, Kevin Hallok, Anmin Tan, Robert Zand, Ayyalusamy Ramamoorthy
Chemistry and Physics of Lipids 2004 Volume 132(Issue 1) pp:47-54
Publication Date(Web):November 2004
DOI:10.1016/j.chemphyslip.2004.09.004
Interaction of bovine myelin basic protein and its constituent charge isomers (C1–C3) with phospholipid bilayers was studied using solid-state NMR experiments on model membranes. 31P NMR experiments on multilamellar vesicles and mechanically aligned bilayers were used to measure the degree of protein-induced disorder in the lipid headgroup region while 2H NMR data provided the disorder caused by the protein in the hydrophobic core of the bilayers. Our results suggest that MBP and its charge isomers neither fragment nor significantly disrupt DMPC, POPC, POPC:POPG, and POPE bilayers. These results demonstrate that the MBP-induced fragmentation of POPC bilayers is due to the freeze-thaw cycles used in the preparation of multilamellar vesicles and not due to intrinsic protein–lipid interactions.
Co-reporter:Jose S. Santos;Dong-Kuk Lee
Magnetic Resonance in Chemistry 2004 Volume 42(Issue 2) pp:105-114
Publication Date(Web):14 JAN 2004
DOI:10.1002/mrc.1327
The effect of tricyclic antidepressants (TCA) on phospholipid bilayer structure and dynamics was studied to provide insight into the mechanism of TCA-induced intracellular accumulation of lipids (known as lipidosis). Specifically we asked if the lipid–TCA interaction was TCA or lipid specific and if such physical interactions could contribute to lipidosis. These interactions were probed in multilamellar vesicles and mechanically oriented bilayers of mixed phosphatidylcholine–phosphatidylglycerol (PC–PG) phospholipids using 31P and 14N solid-state NMR techniques. Changes in bilayer architecture in the presence of TCAs were observed to be dependent on the TCA's effective charge and steric constraints. The results further show that desipramine and imipramine evoke distinguishable changes on the membrane surface, particularly on the headgroup order, conformation and dynamics of phospholipids. Desipramine increases the disorder of the choline site at the phosphatidylcholine headgroup while leaving the conformation and dynamics of the phosphate region largely unchanged. Incorporation of imipramine changes both lipid headgroup conformation and dynamics. Our results suggest that a correlation between TCA-induced changes in bilayer architecture and the ability of these compounds to induce lipidosis is, however, not straightforward as imipramine was shown to induce more dramatic changes in bilayer conformation and dynamics than desipramine. The use of 14N as a probe was instrumental in arriving at the presented conclusions. Copyright © 2004 John Wiley & Sons, Ltd.
Co-reporter:Katherine A.Henzler Wildman, Erin E. Wilson, Dong-Kuk Lee, A. Ramamoorthy
Solid State Nuclear Magnetic Resonance 2003 Volume 24(2–3) pp:94-109
Publication Date(Web):September–November 2003
DOI:10.1016/S0926-2040(03)00048-1
15N CPMAS, 13C CPMAS and 1H CRAMPS spectra of several polypeptide samples were compared to determine the useful features of each technique. 13C CPMAS is the most well-established technique and is useful for quick determination of secondary structure. The 15N nucleus is more sensitive to exact hydrogen-bonding parameters, which complicates interpretation of the spectra. However, it is better for resolving end effects and structural types in short oligomers. 1H CRAMPS spectra are similar to 13C CPMAS in the information obtained, but the resolution is not as good. Using 13C CPMAS, the conformation of polyglycine was investigated in detail. Precipitation from solvents such as DCA or TFA resulted in the rippled β-sheet structure (PG I), while 31-helix (PG II) was formed by precipitation from aqueous solutions of LiBr. Grinding the sample resulted in an increase in the amount of PG I, indicating that this form is more stable in the solid state. These results agree with previous work on poly(l-alanine) showing that the β-sheet form is more stable in the solid state. Homopolypeptides with larger side chains did not change conformation upon grinding due to the greater difficulty in disrupting van der Waals interactions and inertia of the large side chains.
Co-reporter:Alessro Mascioni;Ferno Porcelli;Udayar Ilangovan;Gianluigi Veglia
Biopolymers 2003 Volume 69(Issue 1) pp:
Publication Date(Web):13 MAR 2003
DOI:10.1002/bip.10305
Human islet amyloid polypeptide (hIAPP), or amylin, is a 37 amino acid hormone secreted by pancreatic β-cells. hIAPP constitutes ∼90% of the amyloid deposits found in type II diabetic patients. It has been shown that the central region of the peptide (hIAPP20–29) constitutes the nucleation site for the amyloidogenic process with F23 playing a key role in the formation of the β-pleated structures. In addition, it has been proposed that an important stage in the cytotoxicity of hIAPP is its interaction with the β-cell membranes. As a first step toward the characterization of the interaction of hIAPP with cell membranes, we determined conformational preferences of hIAPP20–29 in membrane-mimicking environments. We found that upon interacting with negatively charged micelles, the dominant conformation of hIAPP20–29 is a distorted type I β-turn centered on residues F23 and G24, with F23, A25, and I26 forming a small hydrophobic cluster that may facilitate the interaction of this peptide with the membrane bilayer. Moreover, we were able to elucidate the topological orientation of the peptide that is absorbed on the micelle surface, with the hydrophobic cluster oriented toward the hydrocarbon region of the micelles and both N- and C-termini exposed to the solvent. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 29–41, 2003
Co-reporter:D.M. Taylor, A. Ramamoorthy
Journal of Molecular Structure 2002 Volumes 602–603() pp:115-124
Publication Date(Web):9 January 2002
DOI:10.1016/S0022-2860(01)00737-2
Dipolar coupling is a valuable NMR parameter to study the structure and dynamics of solids and partially aligned biological molecules in solution. The transfer of magnetization via the homonuclear dipolar coupling, known as dipolar coherence transfer (DCT), has been used to obtain the internuclear distances between two specific sites of interest in a biological solid. In this study, DCT for a pair of dipolar coupled spin-1/2 nuclei in a powder sample under static experimental condition is analyzed in detail by the numerical calculation of the analytical solutions for the time development of the density matrix. The density matrix evolution under the effect of the homonuclear dipolar interaction is evaluated using the product operator formalism. The effect of scalar coupling on DCT is also discussed.
Co-reporter:Katherine A. Henzler Wildman;Dong-Kuk Lee;A. Ramamoorthy
Biopolymers 2002 Volume 64(Issue 5) pp:
Publication Date(Web):30 MAY 2002
DOI:10.1002/bip.10180
The relative stability of α-helix and β-sheet secondary structure in the solid state was investigated using poly(L-alanine) (PLA) as a model system. Protein folding and stability has been well studied in solution, but little is known about solid-state environments, such as the core of a folded protein, where peptide packing interactions are the dominant factor in determining structural stability. 13C cross-polarization with magic angle spinning (CPMAS) NMR spectroscopy was used to determine the backbone conformation of solid powder samples of 15-kDa and 21.4-kDa PLA before and after various sample treatments. Reprecipitation from helix-inducing solvents traps the α-helical conformation of PLA, although the method of reprecipitation also affects the conformational distribution. Grinding converts the secondary structure of PLA to a final steady-state mixture of 55% β-sheet and 45% α-helix at room temperature regardless of the initial secondary structure. Grinding PLA at liquid nitrogen temperatures leads to a similar steady-state mixture with 60% β-sheet and 40% α-helix, indicating that mechanical shear force is sufficient to induce secondary structure interconversion. Cooling the sample in liquid nitrogen or subjecting it to high pressure has no effect on secondary structure. Heating the sample without grinding results in equilibration of secondary structure to 50% α-helix/50% β-sheet at 100°C when starting from a mostly α-helical state. No change was observed upon heating a β-sheet sample, perhaps due to kinetic effects and the different heating rate used in the experiments. These results are consistent with β-sheet approximately 260 J/mol more stable than α-helix in solid-state PLA. © 2002 Wiley Periodicals, Inc. Biopolymers 64: 246–254, 2002
Co-reporter:Jeffrey R. Brender, Ulrich H.N. Dürr, Deborah Heyl, Mahender B. Budarapu, Ayyalusamy Ramamoorthy
Biochimica et Biophysica Acta (BBA) - Biomembranes (September 2007) Volume 1768(Issue 9) pp:2026-2029
Publication Date(Web):September 2007
DOI:10.1016/j.bbamem.2007.07.001
Co-reporter:Ravi Prakash Reddy Nanga, Jeffrey R. Brender, Subramanian Vivekanandan, Ayyalusamy Ramamoorthy
Biochimica et Biophysica Acta (BBA) - Biomembranes (October 2011) Volume 1808(Issue 10) pp:
Publication Date(Web):1 October 2011
DOI:10.1016/j.bbamem.2011.06.012
Human islet amyloid polypeptide is a hormone coexpressed with insulin by pancreatic beta-cells. For reasons not clearly understood, hIAPP aggregates in type II diabetics to form oligomers that interfere with beta-cell function, eventually leading to the loss of insulin production. The cellular membrane catalyzes the formation of amyloid deposits and is a target of amyloid toxicity through disruption of the membrane's structural integrity. Therefore, there is considerable current interest in solving the 3D structure of this peptide in a membrane environment. NMR experiments could not be directly utilized in lipid bilayers due to the rapid aggregation of the peptide. To overcome this difficulty, we have solved the structure of the naturally occurring peptide in detergent micelles at a neutral pH. The structure has an overall kinked helix motif, with residues 7–17 and 21–28 in a helical conformation, and with a 310 helix from Gly 33–Asn 35. In addition, the angle between the N- and C-terminal helices is constrained to 85°. The greater helical content of human IAPP in the amidated versus free acid form is likely to play a role in its aggregation and membrane disruptive activity.Download high-res image (51KB)Download full-size imageHighlights► NMR structure of amidated IAPP at pH 7.3 was solved in SDS (PDB 2L86). ► C-terminus is more structured compared to the free acid form at low pH in SDS. ► The angle between the N- and C-terminal helices is constrained to 85°.
Co-reporter:Senthil K. Kandasamy, Dong-Kuk Lee, Ravi P.R. Nanga, Jiadi Xu, Jose S. Santos, Ronald G. Larson, Ayyalusamy Ramamoorthy
Biochimica et Biophysica Acta (BBA) - Biomembranes (March 2009) Volume 1788(Issue 3) pp:
Publication Date(Web):March 2009
DOI:10.1016/j.bbamem.2008.11.009
The second transmembrane (TM2) domain of GABAA receptor forms the inner-lining surface of chloride ion-channel and plays important roles in the function of the receptor protein. In this study, we report the first structure of TM2 in lipid bilayers determined using solid-state NMR and MD simulations. The interatomic 13C–15N distances measured from REDOR magic angle spinning experiments on multilamellar vesicles, containing a TM2 peptide site specifically labeled with 13C′ and 15N isotopes, were used to determine the secondary structure of the peptide. The 15N chemical shift and 1H–15N dipolar coupling parameters measured from PISEMA experiments on mechanically aligned phospholipid bilayers, containing a TM2 peptide site specifically labeled with 15N isotopes, under static conditions were used to determine the membrane orientation of the peptide. Our results reveal that the TM2 peptide forms an alpha helical conformation with a tilted transmembrane orientation, which is unstable as a monomer but stable as pentameric oligomers as indicated by MD simulations. Even though the peptide consists of a number of hydrophilic residues, the transmembrane folding of the peptide is stabilized by intermolecular hydrogen bondings between the side chains of Ser and Thr residues as revealed by MD simulations. The results also suggest that peptide–peptide interactions in the tilted transmembrane orientation overcome the hydrophobic mismatch between the peptide and bilayer thickness.
Co-reporter:David W. Hoskin, Ayyalusamy Ramamoorthy
Biochimica et Biophysica Acta (BBA) - Biomembranes (February 2008) Volume 1778(Issue 2) pp:
Publication Date(Web):February 2008
DOI:10.1016/j.bbamem.2007.11.008
In spite of great advances in cancer therapy, there is considerable current interest in developing anticancer agents with a new mode of action because of the development of resistance by cancer cells towards current anticancer drugs. A growing number of studies have shown that some of the cationic antimicrobial peptides (AMPs), which are toxic to bacteria but not to normal mammalian cells, exhibit a broad spectrum of cytotoxic activity against cancer cells. Such studies have considerably enhanced the significance of AMPs, both synthetic and from natural sources, which have been of importance both for an increased understanding of the immune system and for their potential as clinical antibiotics. The electrostatic attraction between the negatively charged components of bacterial and cancer cells and the positively charged AMPs is believed to play a major role in the strong binding and selective disruption of bacterial and cancer cell membranes, respectively. However, it is unclear why some host defense peptides are able to kill cancer cells when others do not. In addition, it is not clear whether the molecular mechanism(s) underlying the antibacterial and anticancer activities of AMPs are the same or different. In this article, we review various studies on different AMPs that exhibit cytotoxic activity against cancer cells. The suitability of cancer cell-targeting AMPs as cancer therapeutics is also discussed.
Co-reporter:Ayyalusamy Ramamoorthy
Biochimica et Biophysica Acta (BBA) - Biomembranes (December 2007) Volume 1768(Issue 12) pp:2947-2948
Publication Date(Web):December 2007
DOI:10.1016/j.bbamem.2007.12.001
Co-reporter:Ulrich H.N. Dürr, Lucy Waskell, Ayyalusamy Ramamoorthy
Biochimica et Biophysica Acta (BBA) - Biomembranes (December 2007) Volume 1768(Issue 12) pp:3235-3259
Publication Date(Web):December 2007
DOI:10.1016/j.bbamem.2007.08.007
Co-reporter:Lindsey M. Gottler, Ayyalusamy Ramamoorthy
Biochimica et Biophysica Acta (BBA) - Biomembranes (August 2009) Volume 1788(Issue 8) pp:
Publication Date(Web):August 2009
DOI:10.1016/j.bbamem.2008.10.009
The growing problem of bacterial resistance to conventional antibiotic compounds and the need for new antibiotics have stimulated interest in the development of antimicrobial peptides (AMPs) as human therapeutics. Development of topically applied agents, such as pexiganan (also known as MSI-78, an analog of the naturally occurring magainin2, extracted from the skin of the African frog Xenopus laevis) has been the focus of pharmaceutical development largely because of the relative safety of topical therapy and the uncertainty surrounding the long-term toxicology of any new class of drug administered systemically. The main hurdle that has hindered the development of antimicrobial peptides is that many of the naturally occurring peptides (such as magainin), although active in vitro, are effective in animal models of infection only at very high doses, often close to the toxic doses of the peptide, reflecting an unacceptable margin of safety. Though MSI-78 did not pass the FDA approval, it is still the best-studied AMP to date for therapeutic purposes. Biophysical studies have shown that this peptide is unstructured in solution, forms an antiparallel dimer of amphipathic helices upon binding to the membrane, and disrupts membrane via toroidal-type pore formation. This article covers functional, biophysical, biochemical and structural studies on pexiganan.
Co-reporter:Jeffrey R. Brender, Ravi Prakash Reddy Nanga, Nataliya Popovych, Ronald Soong, Peter M. Macdonald, Ayyalusamy Ramamoorthy
Biochimica et Biophysica Acta (BBA) - Biomembranes (April 2011) Volume 1808(Issue 4) pp:
Publication Date(Web):April 2011
DOI:10.1016/j.bbamem.2011.01.010
Amyloid fibers in human semen known as SEVI (semen-derived enhancer of viral infection) dramatically increase the infectivity of HIV and other enveloped viruses, which appears to be linked to the promotion of bridging interactions and the neutralization of electrostatic repulsion between the host and the viral cell membranes. The SEVI precursor PAP248–286 is mostly disordered when bound to detergent micelles, in contrast to the highly α-helical structures found for most amyloid proteins. To determine the origin of this difference, the structures of PAP248–286 were solved in aqueous solution and with 30% and 50% trifluoroethanol. In solution, pulsed field gradient (PFG)-NMR and 1H-1H NOESY experiments indicate that PAP248–286 is unfolded to an unusual degree for an amyloidogenic peptide but adopts significantly helical structures in TFE solutions. The clear differences between the structures of PAP248–286 in TFE and SDS indicate electrostatic interactions play a large role in the folding of the peptide, consistent with the slight degree of penetration of PAP248–286 into the hydrophobic core of the micelle. This is another noticeable difference between PAP248–286 and other amyloid peptides, which generally show penetration into at least the headgroup region of the bilayer, and may explain some of the unusual properties of SEVI.Figure optionsDownload full-size imageDownload high-quality image (61 K)Download as PowerPoint slideResearch Highlights► PAP248–286 folds into a disordered structure upon binding to SDS micelles. ► PAP248–286 is significantly unfolded in solution. ► PAP248–286 adopts helical structures in TFE solutions. ► Disordered structure of PAP248–286 in SDS results from electrostatic interactions. ► Unusual degree of disorder of PAP248–286 may account for its unusual properties.
Co-reporter:Samer Salamekh, Jeffrey R. Brender, Suk-Joon Hyung, Ravi Prakash Reddy Nanga, ... Ayyalusamy Ramamoorthy
Journal of Molecular Biology (8 July 2011) Volume 410(Issue 2) pp:294-306
Publication Date(Web):8 July 2011
DOI:10.1016/j.jmb.2011.05.015
Human islet amyloid polypeptide (hIAPP) is a highly amyloidogenic protein co-secreted with insulin in response to glucose levels. The formation of hIAPP amyloid plaques near islet cells has been linked to the death of insulin-secreting β-cells in humans and the progression of type II diabetes. Since both healthy individuals and those with type II diabetes produce and secrete hIAPP, it is reasonable to look for factors involved in storing hIAPP and preventing amyloidosis. We have previously shown that zinc inhibits the formation of insoluble amyloid plaques of hIAPP; however, there remains significant ambiguity in the underlying mechanisms. In this study, we show that zinc binds unaggregated hIAPP at micromolar concentrations similar to those found in the extracellular environment. By contrast, the fibrillar amyloid form of hIAPP has low affinity for zinc. The binding stoichiometry obtained from isothermal titration calorimetry experiments indicates that zinc favors the formation of hIAPP hexamers. High-resolution NMR structures of hIAPP bound to zinc reveal changes in the electron environment along residues that would be located along one face of the amphipathic hIAPP α-helix proposed as an intermediate for amyloid formation. Results from electrospray ionization mass spectroscopy investigations showed that a single zinc atom is predominantly bound to hIAPP and revealed that zinc inhibits the formation of the dimer. At higher concentrations of zinc, a second zinc atom binds to hIAPP, suggesting the presence of a low-affinity secondary binding site. Combined, these results suggest that zinc promotes the formation of oligomers while creating an energetic barrier for the formation of amyloid fibers.Download high-res image (95KB)Download full-size imageResearch Highlights► IAPP has micro- and millimolar-affinity binding sites for zinc. hIAPP fibers display a decreased affinity for zinc compared to the monomeric form. ► hIAPP binds to zinc as a hexamer by minimizing unfavorable steric interactions. ► The displacement of zinc precedes the formation of mature fiber. ► Zinc inhibits the formation of the hIAPP dimer and mature fiber while promoting oligomers.
Co-reporter:Michele F.M. Sciacca, Danilo Milardi, Grazia M.L. Messina, Giovanni Marletta, Jeffrey R. Brender, Ayyalusamy Ramamoorthy, Carmelo La Rosa
Biophysical Journal (8 January 2013) Volume 104(Issue 1) pp:
Publication Date(Web):8 January 2013
DOI:10.1016/j.bpj.2012.11.3811
Disruption of the integrity of the plasma membrane by amyloidogenic proteins is linked to the pathogenesis of a number of common age-related diseases. Although accumulating evidence suggests that adverse environmental stressors such as unbalanced levels of metal ions may trigger amyloid-mediated membrane damage, many features of the molecular mechanisms underlying these events are unknown. Using human islet amyloid polypeptide (hIAPP, aka amylin), an amyloidogenic peptide associated with β-cell death in type 2 diabetes, we demonstrate that the presence of Ca2+ ions inhibits membrane damage occurring immediately after the interaction of freshly dissolved hIAPP with the membrane, but significantly enhances fiber-dependent membrane disruption. In particular, dye leakage, quartz crystal microbalance, atomic force microscopy, and NMR experiments show that Ca2+ ions promote a shallow membrane insertion of hIAPP, which leads to the removal of lipids from the bilayer through a detergent-like mechanism triggered by fiber growth. Because both types of membrane-damage mechanisms are common to amyloid toxicity by most amyloidogenic proteins, it is likely that unregulated ion homeostasis, amyloid aggregation, and membrane disruption are all parts of a self-perpetuating cycle that fuels amyloid cytotoxicity.
Co-reporter:Jeffrey R. Brender, Kevin Hartman, Lindsey M. Gottler, Marchello E. Cavitt, Daniel W. Youngstrom, Ayyalusamy Ramamoorthy
Biophysical Journal (4 November 2009) Volume 97(Issue 9) pp:
Publication Date(Web):4 November 2009
DOI:10.1016/j.bpj.2009.08.034
In previous in vivo studies, amyloid fibers formed from a peptide ubiquitous in human seminal fluid (semen-derived enhancer of viral infection (SEVI)) were found to dramatically enhance the infectivity of the HIV virus (3–5 orders of magnitude by some measures). To complement those studies, we performed in vitro assays of PAP248-286, the most active precursor to SEVI, and other polycationic polymers to investigate the physical mechanisms by which the PAP248-286 promotes the interaction with lipid bilayers. At acidic (but not at neutral) pH, freshly dissolved PAP248-286 catalyzes the formation of large lipid flocculates in a variety of membrane compositions, which may be linked to the promotion of convective transport in the vaginal environment rather than transport by a random Brownian motion. Furthermore, PAP248-286 is itself fusiogenic and weakens the integrity of the membrane in such a way that may promote fusion by the HIV gp41 protein. An α-helical conformation of PAP248-286, lying parallel to the membrane surface, is implicated in promoting bridging interactions between membranes by the screening of the electrostatic repulsion that occurs when two membranes are brought into close contact. This suggests that nonspecific binding of monomeric or small oligomeric forms of SEVI in a helical conformation to lipid membranes may be an additional mechanism by which SEVI enhances the infectivity of the HIV virus.
Co-reporter:Michele F.M. Sciacca, Samuel A. Kotler, Jeffrey R. Brender, Jennifer Chen, Dong-kuk Lee, Ayyalusamy Ramamoorthy
Biophysical Journal (22 August 2012) Volume 103(Issue 4) pp:
Publication Date(Web):22 August 2012
DOI:10.1016/j.bpj.2012.06.045
Disruption of cell membranes by Aβ is believed to be one of the key components of Aβ toxicity. However, the mechanism by which this occurs is not fully understood. Here, we demonstrate that membrane disruption by Aβ occurs by a two-step process, with the initial formation of ion-selective pores followed by nonspecific fragmentation of the lipid membrane during amyloid fiber formation. Immediately after the addition of freshly dissolved Aβ1–40, defects form on the membrane that share many of the properties of Aβ channels originally reported from single-channel electrical recording, such as cation selectivity and the ability to be blockaded by zinc. By contrast, subsequent amyloid fiber formation on the surface of the membrane fragments the membrane in a way that is not cation selective and cannot be stopped by zinc ions. Moreover, we observed that the presence of ganglioside enhances both the initial pore formation and the fiber-dependent membrane fragmentation process. Whereas pore formation by freshly dissolved Aβ1–40 is weakly observed in the absence of gangliosides, fiber-dependent membrane fragmentation can only be observed in their presence. These results provide insights into the toxicity of Aβ and may aid in the design of specific compounds to alleviate the neurodegeneration of Alzheimer’s disease.
Co-reporter:Rui Huang, Kazutoshi Yamamoto, Meng Zhang, Nataliya Popovych, Ivan Hung, Sang-Choul Im, Zhehong Gan, Lucy Waskell, Ayyalusamy Ramamoorthy
Biophysical Journal (20 May 2014) Volume 106(Issue 10) pp:
Publication Date(Web):20 May 2014
DOI:10.1016/j.bpj.2014.03.051
NADPH-cytochrome P450 oxidoreductase (CYPOR) is an essential redox partner of the cytochrome P450 (cyt P450) superfamily of metabolic enzymes. In the endoplasmic reticulum of liver cells, such enzymes metabolize ∼75% of the pharmaceuticals in use today. It is known that the transmembrane domain of CYPOR plays a crucial role in aiding the formation of a complex between CYPOR and cyt P450. Here we present the transmembrane structure, topology, and dynamics of the FMN binding domain of CYPOR in a native membrane-like environment. Our solid-state NMR results reveal that the N-terminal transmembrane domain of CYPOR adopts an α-helical conformation in the lipid membrane environment. Most notably, we also show that the transmembrane helix is tilted ∼13° from the lipid bilayer normal, and exhibits motions on a submillisecond timescale including rotational diffusion of the whole helix and fluctuation of the helical director axis. The approaches and the information reported in this study would enable further investigations on the structure and dynamics of the full-length NADPH-cytochrome P450 oxidoreductase and its interaction with other membrane proteins in a membrane environment.
Co-reporter:Sathiah Thennarasu, Anmin Tan, Rajesh Penumatchu, Charles E. Shelburne, Deborah L. Heyl, Ayyalusamy Ramamoorthy
Biophysical Journal (20 January 2010) Volume 98(Issue 2) pp:248-257
Publication Date(Web):20 January 2010
DOI:10.1016/j.bpj.2009.09.060
Co-reporter:Ayyalusamy Ramamoorthy, Mi Hee Lim
Biophysical Journal (16 July 2013) Volume 105(Issue 2) pp:
Publication Date(Web):16 July 2013
DOI:10.1016/j.bpj.2013.05.004
Co-reporter:Michele F.M. Sciacca, Fabio Lolicato, Giacomo Di Mauro, Danilo Milardi, Luisa D’Urso, Cristina Satriano, Ayyalusamy Ramamoorthy, Carmelo La Rosa
Biophysical Journal (12 July 2016) Volume 111(Issue 1) pp:
Publication Date(Web):12 July 2016
DOI:10.1016/j.bpj.2016.05.050
Our knowledge of the molecular events underlying type 2 diabetes mellitus—a protein conformational disease characterized by the aggregation of islet amyloid polypeptide (IAPP) in pancreatic β cells—is limited. However, amyloid-mediated membrane damage is known to play a key role in IAPP cytotoxicity, and therefore the effects of lipid composition on modulating IAPP-membrane interactions have been the focus of intense research. In particular, membrane cholesterol content varies with aging and consequently with adverse environmental factors such as diet and lifestyle, but its role in the development of the disease is controversial. In this study, we employ a combination of experimental techniques and in silico molecular simulations to shed light on the role of cholesterol in IAPP aggregation and the related membrane disruption. We show that if anionic POPC/POPS vesicles are used as model membranes, cholesterol has a negligible effect on the kinetics of IAPP fibril growth on the surface of the bilayer. In addition, cholesterol inhibits membrane damage by amyloid-induced poration on membranes, but enhances leakage through fiber growth on the membrane surface. Conversely, if 1:2 DOPC/DPPC raft-like model membranes are used, cholesterol accelerates fiber growth. Next, it enhances pore formation and suppresses fiber growth on the membrane surface, leading to leakage. Our results highlight a twofold effect of cholesterol on the amyloidogenicity of IAPP and help explain its debated role in type 2 diabetes mellitus.
Co-reporter:Rui Huang, Subramanian Vivekanandan, Jeffrey R. Brender, Yuki Abe, ... Ayyalusamy Ramamoorthy
Journal of Molecular Biology (10 February 2012) Volume 416(Issue 1) pp:108-120
Publication Date(Web):10 February 2012
DOI:10.1016/j.jmb.2011.12.023
Calcitonin is a 32-residue peptide hormone known for its hypocalcemic effect and its inhibition of bone resorption. While calcitonin has been used in therapy for osteoporosis and Paget's disease for decades, human calcitonin (hCT) forms fibrils in aqueous solution that limit its therapeutic application. The molecular mechanism of fiber formation by calcitonin is not well understood. Here, high-resolution structures of hCT at concentrations of 0.3 mM and 1 mM have been investigated using NMR spectroscopy. Comparing the structures of hCT at different concentrations, we discovered that the peptide undergoes a conformational transition from an extended to a β-hairpin structure in the process of molecular association. This conformational transition locates the aromatic side chains of Tyr12 and Phe16 in a favorable way for intermolecular π–π stacking, which is proposed to be a crucial interaction for peptide association and fibrillation. One-dimensional 1H NMR experiments confirm that oligomerization of hCT accompanies the conformational transition at 1 mM concentration. The effect of the polyphenol epigallocatechin 3-gallate (EGCG) on hCT fibrillation was also investigated by NMR and electron microscopy, which show that EGCG efficiently inhibits fibril formation of hCT by preventing the initial association of hCT before fiber formation. The NMR experiments also indicate that the interaction between aromatic rings of EGCG and the aromatic side chains of the peptide may play an important role in inhibiting fibril formation of hCT.Download high-res image (90KB)Download full-size imageResearch Highlights► hCT is exclusively monomeric at 0.3 mM and a mixture of monomer and large oligomers at hairpin at 1 mM in acidic solution. ► hCT is unfolded at 0.3 mM and forms β-hairpin at 1 mM in acidic solution. ► Aromatic side chains are important for the formation of the oligomer. ► EGCG disrupts the initial oligomerization of hCT before fibrillization.
Co-reporter:Peizhi Zhu ; Jiadi Xu ; Nadder Sahar ; Michael D. Morris ; David H. Kohn
Journal of the American Chemical Society () pp:
Publication Date(Web):November 6, 2009
DOI:10.1021/ja9081028
Understanding the structure and structural changes of bone, a highly heterogeneous material with a complex hierarchical architecture, continues to be a significant challenge even for high-resolution solid-state NMR spectroscopy. While it is known that dehydration affects mechanical properties of bone by decreasing its strength and toughness, the underlying structural mechanism at the atomic level is unknown. Solid-state NMR spectroscopy, controlled dehydration, and H/D exchange were used for the first time to reveal the structural changes of an intact piece of bovine cortical bone. 1H spectra were used to monitor the dehydration of the bone inside the rotor, and high-resolution 13C chemical shift spectra obtained under magic-angle spinning were used evaluate the dehydration-induced conformational changes in the bone. The experiments revealed the slow denaturation of collagen due to dehydration while the trans-Xaa-Pro conformation in collagen remained unchanged. Our results suggest that glycosaminoglycans in the collagen fiber and mineral interface may chelate with a Ca2+ ion present on the surface of the mineral through sulfate or carboxylate groups. These results provide insights into the role of water molecules in the bone structure and shed light on the relationship between the structure and mechanics of bone.
Co-reporter:Jeffrey R. Brender, Deborah L. Heyl, Shyamprasad Samisetti, Samuel A. Kotler, Joshua M. Osborne, Ranadheer R. Pesaru and Ayyalusamy Ramamoorthy
Physical Chemistry Chemical Physics 2013 - vol. 15(Issue 23) pp:NaN8915-8915
Publication Date(Web):2013/03/01
DOI:10.1039/C3CP44696D
A key factor in the development of type II diabetes is the loss of insulin-producing beta-cells. Human islet amyloid polypeptide protein (human-IAPP) is believed to play a crucial role in this process by forming small aggregates that exhibit toxicity by disrupting the cell membrane. The actual mechanism of membrane disruption is complex and appears to involve an early component before fiber formation and a later component associated with fiber formation on the membrane. By comparing the peptide–lipid interactions derived from solid-state NMR experiments of two IAPP fragments that cause membrane disordering to IAPP derived peptides known to cause significant early membrane permeabilization, we show here that membrane disordering is not likely to be sufficient by itself to cause the early membrane permeabilization observed by IAPP, and may play a lesser role in IAPP membrane disruption than expected.
Co-reporter:Kamal H. Mroue, Jiadi Xu, Peizhi Zhu, Michael D. Morris and Ayyalusamy Ramamoorthy
Physical Chemistry Chemical Physics 2016 - vol. 18(Issue 28) pp:NaN18691-18691
Publication Date(Web):2016/06/29
DOI:10.1039/C6CP03506J
Using 1H-based magic angle spinning solid-state NMR spectroscopy, we report an atomistic-level characterization of triglycerides in compact cortical bone. By suppressing contributions from immobile molecules present in bone, we show that a 1H-based constant-time uniform-sign cross-peak (CTUC) two-dimensional COSY-type experiment that correlates the chemical shifts of protons can selectively detect a mobile triglyceride layer as the main component of small lipid droplets embedded on the surface of collagen fibrils. High sensitivity and resolution afforded by this NMR approach could be potentially utilized to investigate the origin of triglycerides and their pathological roles associated with bone fractures, diseases, and aging.
Co-reporter:Alaina S. DeToma, Samer Salamekh, Ayyalusamy Ramamoorthy and Mi Hee Lim
Chemical Society Reviews 2012 - vol. 41(Issue 2) pp:NaN621-621
Publication Date(Web):2011/08/04
DOI:10.1039/C1CS15112F
This tutorial review presents descriptions of two amyloidogenic proteins, amyloid-β (Aβ) peptides and islet amyloid polypeptide (IAPP), whose misfolding propensities are implicated in Alzheimer's disease (AD) and type II diabetes, respectively. Protein misfolding diseases share similarities, as well as some unique protein-specific traits, that could contribute to the initiation and/or development of their associated conditions. Aβ and IAPP are representative amyloidoses and are used to highlight some of the primary considerations for studying misfolded proteins associated with human diseases in this review. Among these factors, their physiological formation, aggregation, interactions with metal ions and other protein partners, and toxicity are presented. Small molecules that target and modulate the metal–Aβ interaction and neurotoxicity are included to illustrate one of the current approaches for uncovering the complexities of protein misfolding at the molecular level.
Co-reporter:Samuel A. Kotler, Patrick Walsh, Jeffrey R. Brender and Ayyalusamy Ramamoorthy
Chemical Society Reviews 2014 - vol. 43(Issue 19) pp:NaN6700-6700
Publication Date(Web):2014/01/24
DOI:10.1039/C3CS60431D
The association of the amyloid-β (Aβ) peptide with cellular membranes is hypothesized to be the underlying phenomenon of neurotoxicity in Alzheimer's disease. Misfolding of proteins and peptides, as is the case with Aβ, follows a progression from a monomeric state, through intermediates, ending at long, unbranched amyloid fibers. This tutorial review offers a perspective on the association of toxic Aβ structures with membranes as well as details of membrane-associated mechanisms of toxicity.
Co-reporter:Alaina S. DeToma, Janarthanan Krishnamoorthy, Younwoo Nam, Hyuck Jin Lee, Jeffrey R. Brender, Akiko Kochi, Dongkuk Lee, Valentina Onnis, Cenzo Congiu, Stefano Manfredini, Silvia Vertuani, Gianfranco Balboni, Ayyalusamy Ramamoorthy and Mi Hee Lim
Chemical Science (2010-Present) 2014 - vol. 5(Issue 12) pp:NaN4862-4862
Publication Date(Web):2014/09/03
DOI:10.1039/C4SC01531B
Metal ion homeostasis in conjunction with amyloid-β (Aβ) aggregation in the brain has been implicated in Alzheimer's disease (AD) pathogenesis. To uncover the interplay between metal ions and Aβ peptides, synthetic, multifunctional small molecules have been employed to modulate Aβ aggregation in vitro. Naturally occurring flavonoids have emerged as a valuable class of compounds for this purpose due to their ability to control both metal-free and metal-induced Aβ aggregation. Although flavonoids have shown anti-amyloidogenic effects, the structural moieties of flavonoids responsible for such reactivity have not been fully identified. In order to understand the structure–interaction–reactivity relationship within the flavonoid family for metal-free and metal-associated Aβ, we designed, synthesized, and characterized a set of isoflavone derivatives, aminoisoflavones (1–4), that displayed reactivity (i.e., modulation of Aβ aggregation) in vitro. NMR studies revealed a potential binding site for aminoisoflavones between the N-terminal loop and central helix of prefibrillar Aβ, which is different from the non-specific binding observed for other flavonoids. The absence or presence of the catechol group, responsible for metal binding, differentiated the binding affinities of aminoisoflavones with Aβ and enthalpy/entropy balance for their Aβ interaction. Furthermore, having a catechol group influenced the binding mode with fibrillar Aβ. Inclusion of additional substituents moderately tuned the impact of aminoisoflavones on Aβ aggregation. Overall, through these studies, we obtained valuable insights into the requirements for parity among metal chelation, intermolecular interactions, and substituent variation for Aβ interaction.
Co-reporter:Masha G. Savelieff, Yuzhong Liu, Russell R. P. Senthamarai, Kyle J. Korshavn, Hyuck Jin Lee, Ayyalusamy Ramamoorthy and Mi Hee Lim
Chemical Communications 2014 - vol. 50(Issue 40) pp:NaN5303-5303
Publication Date(Web):2013/12/10
DOI:10.1039/C3CC48473D
Alzheimer's disease (AD) is a complex, multifactorial, neurodegenerative disease that poses tremendous difficulties in pinpointing its precise etiology. A toolkit, which specifically targets and modulates suggested key players, may elucidate their roles in disease onset and progression. We report high-resolution insights on the activity of a small molecule (L2-NO) which exhibits reactivity toward Cu(II)–amyloid-β (Aβ) over Zn(II)–Aβ.
Co-reporter:Kyle J. Korshavn, Anirban Bhunia, Mi Hee Lim and Ayyalusamy Ramamoorthy
Chemical Communications 2016 - vol. 52(Issue 5) pp:NaN885-885
Publication Date(Web):2015/11/06
DOI:10.1039/C5CC08634E
Aggregation at the neuronal cell membrane's lipid bilayer surface is implicated in amyloid-β (Aβ) toxicity associated with Alzheimer's disease; however, structural and mechanistic insights into the process remain scarce. We have identified a conserved binding mode of Aβ40 on lipid bilayer surfaces with a conserved helix containing the self-recognition site (K16-E22).
Co-reporter:Amit S. Pithadia, Anirban Bhunia, Rajendran Sribalan, Vediappen Padmini, Carol A. Fierke and Ayyalusamy Ramamoorthy
Chemical Communications 2016 - vol. 52(Issue 5) pp:NaN945-945
Publication Date(Web):2015/11/13
DOI:10.1039/C5CC07792C
The deposition of aggregates of human islet amyloid polypeptide (hIAPP) has been correlated with the death of β-cells in type II diabetes mellitus. The actual molecular mechanism of cell death remains largely unknown; however, it has been postulated that the process of aggregation from monomeric hIAPP is closely involved. A possible cause of cellular toxicity may be through the disruption of structural integrity of the cell membrane by IAPP. Herein, a water-soluble curcumin derivative, CurDAc, is used to investigate the mitigation of hIAPP aggregation in the absence and presence of lipid membrane.
Co-reporter:Jeffrey R. Brender, Janarthanan Krishnamoorthy, Grazia M. L. Messina, Aniruddha Deb, Subramanian Vivekanandan, Carmelo La Rosa, James E. Penner-Hahn and Ayyalusamy Ramamoorthy
Chemical Communications 2013 - vol. 49(Issue 32) pp:NaN3341-3341
Publication Date(Web):2013/03/06
DOI:10.1039/C3CC40383A
The aggregation of human islet amyloid polypeptide (hIAPP) has been linked to beta-cell death in type II diabetes. Zinc present in secretory granules has been shown to affect this aggregation. A combination of EXAFS, NMR, and AFM experiments shows that the influence of zinc is most likely due to the stabilization of prefibrillar aggregates of hIAPP.
Co-reporter:Manami Tsukamoto, Kenichi Kuroda, Ayyalusamy Ramamoorthy and Kazuma Yasuhara
Chemical Communications 2014 - vol. 50(Issue 26) pp:NaN3430-3430
Publication Date(Web):2013/12/16
DOI:10.1039/C3CC47738J
The function and mode of action of curcumin in modulating the formation of lipid raft domains were investigated by microscopic observation using model membranes. Curcumin induces fusion of lipid raft domains at extremely low concentrations through the alteration of the boundary between the ordered and disordered phases.
Co-reporter:Jun Zhao, Rundong Hu, Michele F. M. Sciacca, Jeffrey R. Brender, Hong Chen, Ayyalusamy Ramamoorthy and Jie Zheng
Physical Chemistry Chemical Physics 2014 - vol. 16(Issue 6) pp:NaN2377-2377
Publication Date(Web):2013/11/26
DOI:10.1039/C3CP53345J
Fundamental understanding of ion channel formation by amyloid peptides, which is strongly linked to cell toxicity, is very critical for (pre)clinical treatment of neurodegenerative diseases. Here, we combine atomistic simulations and experiments to demonstrate a broad range of conformational states of hIAPP double channels in lipid membranes. All individual channels display high selectivity for Cl− ions over cations, but the co-existence of polymorphic double channels of different conformations and orientations with different populations determines the non-ionic selectivity nature of the channels, which is different from the typical amyloid-β channels that exhibit Ca2+ selective ion-permeable characteristics. This work provides a more complete physicochemical mechanism of amyloid-channel-induced toxicity.
Co-reporter:Shruti Mukherjee, Rajiv K. Kar, Ravi Prakash Reddy Nanga, Kamal H. Mroue, Ayyalusamy Ramamoorthy and Anirban Bhunia
Physical Chemistry Chemical Physics 2017 - vol. 19(Issue 29) pp:NaN19299-19299
Publication Date(Web):2017/06/29
DOI:10.1039/C7CP01941F
Multidrug resistance against the existing antibiotics is one of the most challenging threats across the globe. Antimicrobial peptides (AMPs), in this regard, are considered to be one of the effective alternatives that can overcome bacterial resistance. MSI-594, a 24-residue linear alpha-helical cationic AMP, has been shown to function via the carpet mechanism to disrupt bacterial membrane systems. To better understand the role of lipid composition in the function of MSI-594, in the present study, eight different model membrane systems have been studied using accelerated molecular dynamics (aMD) simulations. The simulated results are helpful in discriminating the particular effects of cationic MSI-594 against zwitterionic POPC, anionic POPG and POPS, and neutral POPE lipid moieties. Additionally, the effects of various heterogeneous POPC/POPG (7:3), POPC/POPS (7:3), and POPG/POPE (1:3 and 3:1) bilayer systems on the dynamic interaction of MSI-594 have also been investigated. The effect on the lipid bilayer due to the interaction with the peptide is characterized by lipid acyl-chain order, membrane thickness, and acyl-chain dynamics. Our simulation results show that the lipid composition affects the membrane interaction of MSI-594, suggesting that membrane selectivity is crucial to its mechanism of action. The results reported in this study are helpful to obtain accurate atomistic-level information governing MSI-594 and its membrane disruptive antimicrobial mechanism of action, and to design next generation potent antimicrobial peptides.