Anna F. A. Peacock

Location dependent coordination chemistry and MRI relaxivity, in de novo designed lanthanide coiled coils

Co-reporter:Matthew R. Berwick, Louise N. Slope, Caitlin F. Smith, Siobhan M. King, Sarah L. Newton, Richard B. Gillis, Gary G. Adams, Arthur J. Rowe, Stephen E. Harding, Melanie M. Britton and Anna F. A. Peacock

Chemical Science 2016 vol. 7(Issue 3) pp:2207-2216

Publication Date(Web):22 Dec 2015

DOI:10.1039/C5SC04101E

Herein, we establish for the first time the design principles for lanthanide coordination within coiled coils, and the important consequences of binding site translation. By interrogating design requirements and by systematically translating binding site residues, one can influence coiled coil stability and more importantly, the lanthanide coordination chemistry. A 10 Å binding site translation along a coiled coil, transforms a coordinatively saturated Tb(Asp)3(Asn)3 site into one in which three exogenous water molecules are coordinated, and in which the Asn layer is no longer essential for binding, Tb(Asp)3(H2O)3. This has a profound impact on the relaxivity of the analogous Gd(III) coiled coil, with more than a four-fold increase in the transverse relaxivity (21 to 89 mM−1 s−1), by bringing into play, in addition to the outer sphere mechanism present for all Gd(III) coiled coils, an inner sphere mechanism. Not only do these findings warrant further investigation for possible exploitation as MRI contrast agents, but understanding the impact of binding site translation on coordination chemistry has important repercussions for metal binding site design, taking us an important step closer to the predictable and truly de novo design of metal binding sites, for new functional applications.

Recent advances in designed coiled coils and helical bundles with inorganic prosthetic groups — from structural to functional applications

Co-reporter:Anna FA Peacock

Current Opinion in Chemical Biology 2016 Volume 31() pp:160-165

Publication Date(Web):April 2016

DOI:10.1016/j.cbpa.2016.03.009

•Recent advances in the design of coiled coils for inorganic cofactor coordination, are described.•Both water and membrane soluble functional designs can be achieved.•Artificial functional proteins can be designed for non-biological applications.Recent contributions to the de novo design of metalloproteins based on coiled coils and helical bundles are described herein, with examples covering mononuclear, multinuclear, and metallo-porphyrin sites, as well as membrane soluble designs. Important progress is being made in the field with a diverse range of functionalities, sometimes beyond those found in biology, being successfully engineered into these simplified scaffolds and represents an exciting prospect for the future.

Coiled coil type neoglycoproteins presenting three lactose residues

Co-reporter:Sinclair M. Sweeney, Gemma A. Bullen, Richard B. Gillis, Gary G. Adams, Arthur J. Rowe, Stephen E. Harding, James H.R. Tucker, Anna F.A. Peacock, Paul V. Murphy

Tetrahedron Letters 2016 Volume 57(Issue 13) pp:1414-1417

Publication Date(Web):30 March 2016

DOI:10.1016/j.tetlet.2016.02.005

Scaffold design, synthesis and application are relevant for biomedical research. For example, multivalent interactions, such as those between cell surface glycoproteins and lectins can influence the potency and duration of signalling. The spacing between carbohydrates on their native protein scaffold could be important. Herein, the coiled coil design principle is used to generate synthetic coiled coil type glycoproteins, where three lactose residues are grafted to the coil via N-linkages to asparagine. Molecular modelling indicates that the distance between the galactose anomeric carbon atoms on the neoglycoproteins is ∼30 Å. The inclusion of lactose was accommodated in both the final heptad towards the N-terminus, or more centrally in the penultimate heptad. In either case, neither the helicity nor the assembly to the trimeric form was unduly altered by the presence of the disaccharide.

De Novo Design of Xeno-Metallo Coiled Coils

Co-reporter:Louise N. Slope ;Dr. Anna F. A. Peacock

Chemistry – An Asian Journal 2016 Volume 11( Issue 5) pp:660-666

Publication Date(Web):

DOI:10.1002/asia.201501173

Abstract

Bioinorganic chemists aspire to achieve the same exquisite and highly controlled inorganic chemistry featured in biology. An exciting mimetic approach involves the use of miniature artificial protein scaffolds designed de novo (often based on the coiled coil (CC) scaffold), for reproducing native metal ion sites and their function. Recently, there is increased interest, instead, in the design of xeno-metal sites within CC assemblies. This involves incorporating either non-biological metal ions, cofactors or non-proteinogenic amino acid ligands for metal ion coordination, whilst retaining a minimal CC protein scaffold. Using this approach, one should be able to create functional designs with unique and unusual properties, which combine the advantages of both biology and ‘traditional’ non-biological inorganic chemistry. It is the recent progress with respect to the design of xeno-metallo CCs which will be discussed in this Focus Review.

Exploiting anthracene photodimerization within peptides: light induced sequence-selective DNA binding

Co-reporter:Gemma A. Bullen, James H. R. Tucker and Anna F. A. Peacock

Chemical Communications 2015 vol. 51(Issue 38) pp:8130-8133

Publication Date(Web):07 Apr 2015

DOI:10.1039/C5CC01618E

The unprecedented use of anthracene photodimerization within a protein or peptide system is explored through its incorporation into a DNA-binding peptide, derived from the GCN4 transcription factor. This study demonstrates an effective and dynamic interplay between a photoreaction and a peptide–DNA assembly, with each process able to exert control over the other.

De Novo Design of Ln(III) Coiled Coils for Imaging Applications

Co-reporter:Matthew R. Berwick ; David J. Lewis ; Andrew W. Jones ; Rosemary A. Parslow ; Timothy R. Dafforn ; Helen J. Cooper ; John Wilkie ; Zoe Pikramenou ; Melanie M. Britton

Journal of the American Chemical Society 2014 Volume 136(Issue 4) pp:1166-1169

Publication Date(Web):January 9, 2014

DOI:10.1021/ja408741h

A new peptide sequence (MB1) has been designed which, in the presence of a trivalent lanthanide ion, has been programmed to self-assemble to form a three stranded metallo-coiled coil, Ln(III)(MB1)3. The binding site has been incorporated into the hydrophobic core using natural amino acids, restricting water access to the lanthanide. The resulting terbium coiled coil displays luminescent properties consistent with a lack of first coordination sphere water molecules. Despite this the gadolinium coiled coil, the first to be reported, displays promising magnetic resonance contrast capabilities.

Metal-Ion-Regulated Miniature DNA-Binding Proteins Based on GCN4 and Non-native Regulation Sites

Co-reporter:Emmanuel Oheix ;Dr. Anna F. A. Peacock

Chemistry - A European Journal 2014 Volume 20( Issue 10) pp:2829-2839

Publication Date(Web):

DOI:10.1002/chem.201303747

Abstract

The design of artificial peptide dimers containing polypyridine switching domains, for which metal-ion coordination is shown to regulate DNA binding, is reported. Short peptides, based on the basic domain of the GCN4 transcription factor (GCN4bd), dimerised with either 2,2′-bipyridine (bipy(GCN4bd)₂) or 2,2′:6′,2′′-terpyridine (terpy(GCN4bd)₂) linker units, undergo a conformational rearrangement on Cu^II and Zn^II coordination. Depending on the linker substitution pattern, this is proposed to alter the relative alignment of the two peptide moieties, and in turn regulate DNA binding. Circular dichroism and UV–visible spectroscopy reveal that Cu^II and Zn^II coordination promotes binding to DNA containing the CRE target site, but to a differing and opposite degree for the two linkers, and that the metal-ion affinity for terpy(GCN4bd)₂ is enhanced in the presence of CRE DNA. Binding to DNA containing the shorter AP1 target site, which lacks a single nucleobase pair compared to CRE, as well as half-CRE, which contains only half of the CRE target site, was also investigated. Cu^II and Zn^II coordination to terpy(GCN4bd)₂ promotes binding to AP1 DNA, and to a lesser extent half-CRE DNA. Whereas, bipy(GCN4bd)₂, for which interpeptide distances are largely independent of metal-ion coordination and less suitable for binding to these shorter sites, displays allosteric ineffective behaviour in these cases. These findings for the first time demonstrate that biomolecular recognition, and specifically sequence-selective DNA binding, can be controlled by metal-ion coordination to designed switching units, non-native regulation sites, in artificial biomolecules. We believe that in the future these could find a wide range of applications in biotechnology.

Computational and Experimental Investigations into the Conformations of Cyclic Tetra-α/β-peptides

Co-reporter:Mark T. Oakley, Emmanuel Oheix, Anna F. A. Peacock, and Roy L. Johnston

The Journal of Physical Chemistry B 2013 Volume 117(Issue 27) pp:8122-8134

Publication Date(Web):June 12, 2013

DOI:10.1021/jp4043039

We present a combined computational and experimental study of the energy landscapes of cyclic tetra-α/β-peptides. We have performed discrete path sampling calculations on a series of cyclic tetra-α/β-peptides to obtain the relative free energies and barriers to interconversion of their conformers. The most stable conformers of cyclo-[(β-Ala-Gly)2] contain all-trans peptide groups. The relative energies of the cis isomers and the cis–trans barriers are lower than in acyclic peptides but not as low as in the highly strained cyclic α-peptides. For cyclic tetra-α/β-peptides containing a single proline residue, of the type cyclo-[β-Ala-Xaa-β-Ala-Pro], the energy landscapes show that the most stable isomers containing cis and trans β-Ala-Pro have similar free energies and are separated by barriers of approximately 15 kcal mol–1. We show that the underlying energy landscapes of cyclo-[β-Ala-Lys-β-Ala-Pro] and cyclo-[β-Ala-Ala-β-Ala-Pro] are similar, allowing the substitution of the flexible side chain of Lys with Ala to reduce the computational demand of our calculations. However, the steric bulk of the Val side chain in cyclo-[β-Ala-Val-β-Ala-Pro] affects the conformations of the ring, leading to significant differences between its energy landscape and that of cyclo-[β-Ala-Ala-β-Ala-Pro]. We have synthesized the cyclic peptide cyclo-[β-Ala-Lys-β-Ala-Pro], and NMR spectroscopy shows the presence of conformers that interconvert slowly on the NMR time scale at temperatures up to 80 °C. Calculated circular dichroism (CD) spectra for the proposed major isomer of cyclo-[β-Ala-Ala-β-Ala-Pro] are in good agreement with the experimental spectra of cyclo-[β-Ala-Lys-β-Ala-Pro], suggesting that the Ala cyclic tetrapeptide is a viable model for the Lys analogue.

Gold-phosphine binding to de novo designed coiled coil peptides

Co-reporter:Anna F.A. Peacock, Gemma A. Bullen, Lee A. Gethings, Jonathan P. Williams, Frederik H. Kriel, Judy Coates

Journal of Inorganic Biochemistry 2012 Volume 117() pp:298-305

Publication Date(Web):December 2012

DOI:10.1016/j.jinorgbio.2012.05.010

The coordination of the therapeutically interesting [AuCl(PEt3)] to the de novo designed peptide, TRIL23C, under aqueous conditions, is reported here. TRIL23C represents an ideal model to investigate the binding of [AuCl(PEt3)] to small proteins in an effort to develop novel gold(I) phosphine peptide adducts capable of mimicking biological recognition and targeting. This is due to the small size of TRIL23C (30 amino acids), yet stable secondary and tertiary fold, symmetric nature and the availability of only one thiol binding site. [AuCl(PEt3)] was found to react readily with the Cys side chain in a 1:1 ratio as confirmed by UV-visible, 31P NMR and mass spectrometry. Circular dichroism confirmed that the coiled coil structure was retained on coordination of the {Au(PEt3)}+ unit. Redesign of the exterior of TRIL23C based on a biologically relevant recognition sequence found in GCN4, did not alter the coordination chemistry of [AuCl(PEt3)]. To the best of our knowledge, this represents the first report on the coordination of gold(I) phosphine compounds to de novo designed peptides, and could lead to the generation of novel gold(I) phosphine peptide therapeutics in the future.Graphical abstractThe coordination of gold triethylphosphine through the cysteine side chain of a de novo designed coiled coil peptide has been investigated under mild aqueous conditions. The secondary structure is retained in the gold–peptide adduct and could ultimately be exploited to develop novel gold–peptide therapeutics capable of biomolecular recognition.

Location dependent coordination chemistry and MRI relaxivity, in de novo designed lanthanide coiled coils

Co-reporter:Matthew R. Berwick, Louise N. Slope, Caitlin F. Smith, Siobhan M. King, Sarah L. Newton, Richard B. Gillis, Gary G. Adams, Arthur J. Rowe, Stephen E. Harding, Melanie M. Britton and Anna F. A. Peacock

Chemical Science (2010-Present) 2016 - vol. 7(Issue 3) pp:NaN2216-2216

Publication Date(Web):2015/12/22

DOI:10.1039/C5SC04101E

Herein, we establish for the first time the design principles for lanthanide coordination within coiled coils, and the important consequences of binding site translation. By interrogating design requirements and by systematically translating binding site residues, one can influence coiled coil stability and more importantly, the lanthanide coordination chemistry. A 10 Å binding site translation along a coiled coil, transforms a coordinatively saturated Tb(Asp)3(Asn)3 site into one in which three exogenous water molecules are coordinated, and in which the Asn layer is no longer essential for binding, Tb(Asp)3(H2O)3. This has a profound impact on the relaxivity of the analogous Gd(III) coiled coil, with more than a four-fold increase in the transverse relaxivity (21 to 89 mM−1 s−1), by bringing into play, in addition to the outer sphere mechanism present for all Gd(III) coiled coils, an inner sphere mechanism. Not only do these findings warrant further investigation for possible exploitation as MRI contrast agents, but understanding the impact of binding site translation on coordination chemistry has important repercussions for metal binding site design, taking us an important step closer to the predictable and truly de novo design of metal binding sites, for new functional applications.

Exploiting anthracene photodimerization within peptides: light induced sequence-selective DNA binding

Co-reporter:Gemma A. Bullen, James H. R. Tucker and Anna F. A. Peacock

Chemical Communications 2015 - vol. 51(Issue 38) pp:NaN8133-8133

Publication Date(Web):2015/04/07

DOI:10.1039/C5CC01618E

The unprecedented use of anthracene photodimerization within a protein or peptide system is explored through its incorporation into a DNA-binding peptide, derived from the GCN4 transcription factor. This study demonstrates an effective and dynamic interplay between a photoreaction and a peptide–DNA assembly, with each process able to exert control over the other.

Anna F. A. Peacock

TOPICS

Abstract

Abstract