We describe how membrane proteins diffuse laterally in the membrane plane together with the lipids surrounding them. We find a number of intriguing phenomena. The lateral displacements of the protein and the lipids are strongly correlated, as the protein and the neighboring lipids form a dynamical protein−lipid complex, consisting of ∼50−100 lipids. The diffusion of the lipids in the complex is much slower compared to the rest of the lipids. We also find a strong directional correlation between the movements of the protein and the lipids in its vicinity. The results imply that in crowded membrane environments there are no “free” lipids, as they are all influenced by the protein structure and dynamics. Our results indicate that, in studies of cell membranes, protein and lipid dynamics have to be considered together.

Atomistic molecular dynamics (MD) simulations are used extensively to elucidate membrane protein properties. These simulations are based on three-dimensional protein structures that in turn are often based on crystallography. The protein structures resolved in crystallographic studies typically do not correspond to pristine proteins, however. Instead the crystallized proteins are commonly engineered, including structural modifications (mutations, replacement of protein sequences by antibodies, bound ligands, etc.) whose impact on protein structure and dynamics is largely unknown. Here we explore this issue through atomistic MD simulations (∼5 μs in total), focusing on the β2-adrenergic receptor (β2AR) that is one of the most studied members of the G-protein coupled receptor superfamily. Starting from an inactive-state crystal structure of β2AR, we remove the many modifications in β2AR systematically one at a time, in six consecutive steps. After each step, we equilibrate the system and simulate it quite extensively. The results of this step-by-step approach highlight that the structural modifications used in crystallization can affect ligand and G-protein binding sites, packing at the transmembrane-helix interface region, and the dynamics of connecting loops in β2AR. When the results of the systematic step-by-step approach are compared to an all-at-once technique where all modifications done on β2AR are removed instantaneously at the same time, it turns out that the step-by-step method provides results that are superior in terms of maintaining protein structural stability. The results provide compelling evidence that for membrane proteins whose 3D structure is based on structural engineering, the preparation of protein structure for atomistic MD simulations is a delicate and sensitive process. The results show that most valid results are found when the structural modifications are reverted slowly, one at a time.

The epidermal growth factor receptor (EGFR) regulates several critical cellular processes and is an important target for cancer therapy. In lieu of a crystallographic structure of the complete receptor, atomistic molecular dynamics (MD) simulations have recently shown that they can excel in studies of the full-length receptor. Here we present atomistic MD simulations of the monomeric N-glycosylated human EGFR in biomimetic lipid bilayers that are, in parallel, also used for the reconstitution of full-length receptors. This combination enabled us to experimentally validate our simulations, using ligand binding assays and antibodies to monitor the conformational properties of the receptor reconstituted into membranes. We find that N-glycosylation is a critical determinant of EGFR conformation, and specifically the orientation of the EGFR ectodomain relative to the membrane. In the absence of a structure for full-length, posttranslationally modified membrane receptors, our approach offers new means to structurally define and experimentally validate functional properties of cell surface receptors in biomimetic membrane environments.

Transformation of cellulose into monosaccharides can be achieved in a chemical process performed by a special group of enzymes known as cellulases. We have used atomistic molecular dynamics simulations to study endoglucanase II (Cel5A) that is one of the proteins in this group. Based on the atomistic simulation results, we discuss how the Cel5A enzyme interacts with cellulose fibrils comprised of both crystalline and amorphous regions. We show that the enzyme’s carbohydrate-binding domain prefers to interact with crystalline regions of cellulose, while the catalytic domain has a high affinity to the amorphous regions of fibrils. In particular, through electrostatic interactions the catalytic domain attracts loose glucose chains to its catalytic cleft. The atomistic details of the enzyme–cellulose interaction are presented and the implications for practical applications are briefly discussed.

Using replica exchange umbrella sampling we calculated free energy profiles for uptake of cholesterol and one of its oxysterols (7-ketocholesterol) from an aqueous solution into a high-density lipoprotein particle. These atomistic molecular dynamics simulations show that both sterols are readily taken up from the aqueous solution with comparable free energy minima at the surface of the particle of −17 kcal/mol for cholesterol and −14 kcal/mol for 7-ketocholesterol. Moreover, given its preferred position at the particle surface, 7-ketocholesterol is expected to be able to participate directly in biological signaling processes.

We compare the behavior of unlabeled and BODIPY-labeled cholesteryl ester (CE) in high density lipoprotein by atomistic molecular dynamics simulations. We find through replica exchange umbrella sampling and unbiased molecular dynamics simulations that BODIPY labeling has no significant effect on the partitioning of CE between HDL and the water phase. However, BODIPY-CE was observed to diffuse more slowly and locate itself closer to the HDL-water interface than CE due to the BODIPY probe that is constrained to the surface region, and because the CE body in BODIPY-CE prefers to align itself away from the HDL surface. The implications as to the suitability of BODIPY to explore lipoprotein properties are discussed.

•Cholesterol is unique in terms of its quite superior ordering properties.•Understanding of the functions of glycolipids is still vague.•Cholesterol is able to modulate membrane receptor function.•There is still a great amount of work to be done in force field development.Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.

Highlights•We simulate interactions of pyrene-linked lipids in a lipid membrane.•We study the effects of where pyrenes are attached to the chains of their host lipids.•Pyrene-induced perturbations are largely similar in all cases in a DOPC environment.•Transition to membrane-spanning pyrene dimers is very abrupt.We study how lipid probes based on pyrene-labeling could be designed to minimize perturbations in lipid bilayers, and how the same design principles could be exploited to develop probes which gauge lipid dynamics primarily within a single lipid monolayer or between them. To this end, we use atomistic molecular dynamics simulations to consider membranes where pyrene moieties are attached to lipid acyl chains in varying positions. We find that in a DOPC bilayer the conformational ordering of lipids around di-pyrenyl-PC probes is altered to a largely similar extent regardless of where the pyrene moiety is attached to the hydrocarbon chain. This is in contrast to saturated membranes, where pyrene-induced perturbations have been observed to be more prominent. Meanwhile, the formation of pyrene dimers depends on the linkage point between pyrene and its host lipid. Membrane-spanning dimers between lipids in different membrane leaflets are observed only if the pyrene moiety is attached to the latter half of the acyl chain. A seemingly minor change to link pyrene to an acyl chain that is two carbons shorter leads to a situation where membrane-spanning dimers are no longer observed. Further, simulations suggest that formation of dimers is a slow process, where the rate is limited by both lateral diffusion and the dimerization process once the two probes are neighbors to one another. Typical lifetimes of pyrene dimers turn out be of the order of nanoseconds. The results are expected to pave the way for designing ways to consider experimentally topics such as intraleaflet lateral diffusion, motion of lipids within and between membrane domains, and membrane domain registration across bilayers.Graphical abstract

One of the great challenges in membrane biophysics is to find a means to foster the transport of drugs across complex membrane structures. In this spirit, we elucidate methodological challenges associated with free energy computations of complex chainlike molecules across lipid membranes. As an appropriate standard molecule to this end, we consider 7-nitrobenz-2-oxa-1,3-diazol-4-yl-labeled fatty amine, NBD-Cn, which is here dealt with as a homologous series with varying chain lengths. We found the membrane–water interface region to be highly sensitive to details in free energy computations. Despite considerable simulation times, we observed substantial hysteresis, the cause being the small frequency of insertion/desorption events of the amphiphile’s alkyl chain in the membrane interface. The hysteresis was most pronounced when the amphiphile was pulled from water to the membrane and compromised the data that were not in line with experiments. The subtleties in umbrella sampling for computing distance along the transition path were also observed to be potential causes of artifacts. With the PGD (pull geometry distance) scheme, in which the distance from the molecule was computed to a reference plane determined by an average over all lipids in the membrane, we found marked deformations in membrane structure when the amphiphile was close to the membrane. The deformations were weaker with the PGC (pull geometry cylinder) method, where the reference plane is chosen based on lipids that are within a cylinder of radius 1.7 nm from the amphiphile. Importantly, the free energy results given by PGC were found to be qualitatively consistent with experimental data, while the PGD results were not. We conclude that with long amphiphiles there is reason for concern with regard to computations of their free energy profiles. The membrane–water interface is the region where the greatest care is warranted.

The structure and function of high density lipoprotein (HDL) particles have intrigued the scientific community for decades because of their crucial preventive role in coronary heart disease. However, it has been a taunting task to reveal the precise molecular structure and dynamics of HDL. Further, because of the complex composition of HDL, understanding the impact of its structure and dynamics on the function of HDL in reverse cholesterol transport has also been a major issue. Recent progress in molecular simulation methodology and computing power has made a difference, as it has enabled essentially atomistic considerations of HDL particles over microsecond time scales, thereby proving substantial added value to experimental research. In this article, we discuss recent highlights concerning the structure and dynamics of HDL particles as revealed by atomistic and coarse-grained molecular dynamics simulations. We present examples which demonstrate how simulations and experiments can be carried out in unison, showing the added value that emerges from this interplay. We also discuss the possibilities that simulations could offer to better understand the complex phenomena associated with HDL, the goal being to understand its function.

Fullerene C70 is known to partition into lipid membranes and change their physical properties. Together with gallic acid (GA), C70 induces cell contraction and cell death. How C70 and GA-induced perturbations of lipid membranes affect cellular function and membrane protein activity is not understood, though. Meanwhile, fullerene is also known to interfere with the activity of potassium channel proteins, but the mechanisms of protein inhibition are not known. Here we consider the possibility that membrane protein function would be inhibited by C70 and/or GA through direct contact or through lipid-mediated interactions. To this end, we use microsecond time scale atomistic simulations to explore (a) modifications of membrane properties in the presence of C70 and/or GA, and (b) the possible conformational changes in Kv1.2, a voltage-gated potassium channel, upon exposure to C70, or GA, or both. C70 is found to have an observable effect on structural and elastic properties of protein-free membranes, while the effects of GA on the membrane are less evident. Fullerene–GA interaction is strong and affects significantly the partitioning of C70 in the membrane, stabilizing C70 in the aqueous phase. When Kv1.2 is exposed to the solutes, only small conformational changes are observed on the microsecond time scale – comparable to the fluctuations observed in the absence of any solute. Blocking of the channel entrance is not observed, as fullerene binds mainly to hydrophobic residues, both in the water-exposed loops and in the transmembrane helices. The tilt angle of transmembrane helices in the voltage-sensing domain appears to be affected by direct contact with fullerene, but a generic effect due to the small increase in membrane thickness might also play a role. A small rotation of the S3 and S4 helices in the voltage-sensing domain is noticed when C70 is embedded in the membrane. The interpretation of the observed conformational changes is not straightforward due to the associated time scales, which are difficult to sample with state-of-the-art computing resources. We cannot exclude that both membrane-mediated interactions and specific protein–solute interactions affect the conformation of the protein.

Tear fluid lipid layer (TFLL) residing at the air–water interface of tears has been recognized to play an important role in the development of dry eye syndrome. Yet, the composition, structure, and mechanical properties of TFLL are only partly known. Here, we report results of coarse-grained simulations of a lipid layer comprising phospholipids, free fatty acids, cholesteryl esters, and triglycerides at the air–water interface to shed light on the properties of TFLL. We consider structural as well as dynamical properties of the lipid layer as a function of surface pressure. Simulations revealed that neutral lipids reside heterogeneously between phospholipids at relatively low pressures but form a separate hydrophobic phase with increasing surface pressure, transforming the initial lipid monolayer to a two-layered structure. When the model of TFLL was compared to a one-component phospholipid monolayer system, we found drastic differences in both structural and dynamical properties that explain the prominent role of neutral lipids as stabilizers of the TFLL. Based on our results, we suggest that neutral lipids are able to increase the stability of the TFLL by modulating its dynamical and structural behavior, which is important for the proper function of tear film.

Low-density lipoprotein (LDL) transports cholesterol in the bloodstream and plays an important role in the development of cardiovascular diseases, in particular atherosclerosis. Despite its importance to health, the structure of LDL is not known in detail. This is worrying since the lack of LDL's structural information makes it more difficult to understand its function. In this work, we have combined experimental and theoretical data to construct LDL models comprised of the apoB-100 protein wrapped around a lipid droplet of about 20 nm in size. The models are considered by near-atomistic multi-microsecond simulations to unravel structural as well as dynamical properties of LDL, with particular attention paid to lipids and their interactions with the protein. We find that the distribution and the ordering of the lipids in the LDL particle are rather complex. The previously proposed 2- and 3-layer models turn out to be inadequate to describe the properties of the lipid droplet. At the surface of LDL, apoB-100 is found to interact favorably with cholesterol and its esters. The interactions of apoB-100 with core molecules, in particular cholesteryl esters, are rather frequent and arise from hydrophobic amino acids interacting with the ring of cholesteryl esters, and also in part from the rather loose packing of lipids at the surface of the lipoparticle. The loose packing may foster the function of transfer proteins, which transport lipids between lipoproteins. Finally, the comparison of the several apoB-100 models in our study suggests that the properties of lipids in LDL are rather insensitive to the conformation of apoB-100. Altogether, the findings pave the way for further studies of LDL to better understand the central steps in the emergence of atherosclerosis.

We use atom-scale molecular dynamics simulations to clarify the role of glycosphingolipids in the dynamics of cholesterol-rich lipid rafts. To this end, we consider lipid membranes that contain varying amounts of galactosylceramide (GalCer), sphingomyelin, cholesterol, and phosphatidylcholine. The results indicate that increasing the portion of GalCer molecules greatly slows down the lateral diffusion. Only 5–10 mol % of GalCer causes a decrease of almost an order of magnitude compared to corresponding membranes without GalCer. The slowing down is not related to interdigitation, which becomes weaker with increasing GalCer concentration. Instead, the decrease in diffusion is found to correlate with the increasing number of hydrogen bonds formed between GalCer and the phospholipid molecules, which is also observed to have other effects, such as to increase the friction between the membrane leaflets.

We hereby present a study on lateral diffusion of lipids in Langmuir monolayers. We apply atomistic molecular dynamics simulations to a model system whose composition is consistent with protein-free lung surfactant. Our main focus is on the assessment of the validity of the free volume theory for lateral diffusion and on the interpretation of the cross-sectional area and activation energy parameters appearing in the theory. We find that the diffusion results can be fitted to the description given by the free volume theory, but the interpretation of its parameters is not straightforward. While the cross-sectional area appears to be related to the hard-core cross-sectional area of a lipid, its role in the lateral diffusion process is unclear. Also, the activation energy derived using the free volume theory is different from the activation energy found through Arrhenius analysis, and its physical interpretation remains elusive. Finally, we find that lipid diffusion does not occur via rapid single-particle “jumps”. Instead, lipids move in a concerted manner as loosely defined transient clusters, as observed earlier for lipid bilayers.

We have used atomistic molecular dynamics simulations to consider 1,6-diphenyl-1,3,5-hexatriene (DPH) fluorescent probes in a fluid dipalmitoylphosphatidylcholine bilayer with 5 and 20 mol % cholesterol (CHOL). We show that while DPH affects a number of membrane properties, the perturbations induced by DPH depend on the concentration of cholesterol in a membrane. For example, we find DPH to influence the mass density distribution of lipids across the membrane and to promote the ordering of acyl chains around the probe. Yet, these perturbations get relatively weaker for increasing cholesterol concentration. Meanwhile, we also find that the commonly used analysis in terms of the Brownian rotational diffusion (BRD) model with Legendre polynomials to interpret fluorescence anisotropy (FA) experiments is sensitive to the amount of cholesterol. For small concentrations of cholesterol, the analysis of FA turns out to yield a relatively good approximation of the correct orientational distribution of DPH. However, for a CHOL concentration of 20 mol %, we find that the FA analysis fails to yield the true orientational distribution of DPH, the disagreement being substantial. The results suggest that in highly ordered membrane domains, the view given by FA analysis using the BRD model is likely reliable in a qualitative sense, but the quantitative description deviates substantially from the correct one. The present results imply that FA studies for the orientational distribution of DPH should be interpreted with great care.

Even in small amounts, glycolipids are an integral part of lipid rafts and their cellular functions. Here we employ atomistic molecular dynamics simulations to consider galactosylceramide (GalCer), one of the common glycosphingolipids, and investigate its interactions with other raft components (cholesterol, POPC, sphingomyelin) as well as the role and the effects of GalCer on the physical properties of raft-like membranes. Our results for 5 mol % GalCer indicate that whereas the thickness of raft membranes is clearly increased by the addition of GalCer, the average area per lipid and lipid conformational order remain virtually unchanged. Notable changes are observed in lateral diffusion of the raft lipids. This is found to be associated with the interdigitation of GalCer. With cholesterol, GalCer is observed to interact specifically by shielding it from the water phase.

Free volume pockets inside a cell membrane play a prominent role in a variety of dynamic processes such as the permeability of small molecules across membranes and the diffusion of, e.g., lipids, drugs, and electron carriers in the plane of the membrane. Nonetheless, by now the chances for characterizing free volume voids in a nonperturbative manner through experiments have been very limited. Here we use lipid membranes as an example to show how positron annihilation spectroscopy (PALS) together with atomistic simulations can be employed to gauge changes in free volume pockets in biological macromolecular complexes. The measurements show that PALS is a viable technique to probe free volume in biomolecular systems. As examples, we consider the gel-to-fluid transition and the role of increasing cholesterol concentration in a lipid membrane. Further applications proposed in this work for PALS are likely to provide a great deal of insight into the understanding of the role of free volume in the dynamics of biomolecular complexes.

Using atomic-scale molecular dynamics simulations, we consider the intrinsic cell membrane potential that is found to originate from a subtle interplay between lipid transmembrane asymmetry and the asymmetric distribution of monovalent salt ions on the two sides of the cell membrane. It turns out that both the asymmetric distribution of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipids across a membrane and the asymmetric distribution of NaCl and KCl induce nonzero drops in the transmembrane potential. However, these potential drops are opposite in sign. As the PC leaflet faces a NaCl saline solution and the PE leaflet is exposed to KCl, the outcome is that the effects of asymmetric lipid and salt ion distributions essentially cancel one another almost completely. Overall, our study highlights the complex nature of the intrinsic potential of cell membranes under physiological conditions.

We employ atomistic simulations to consider how mono- (NaCl) and divalent (CaCl2) salt affects properties of inner and outer membranes of mitochondria. We find that the influence of salt on structural properties is rather minute, only weakly affecting lipid packing, conformational ordering, and membrane electrostatic potential. The changes induced by salt are more prominent in dynamical properties related to ion binding and formation of ion-lipid complexes and lipid aggregates, as rotational diffusion of lipids is slowed down by ions, especially in the case of CaCl2. In the same spirit, lateral diffusion of lipids is slowed down rather considerably for increasing concentration of CaCl2. Both findings for dynamic properties can be traced to the binding of ions with lipid head groups and the related changes in interaction patterns in the headgroup region, where the binding of Na+ and Ca2+ ions is clearly different. The role of cardiolipins in these phenomena turns out to be important.

Mitochondrial membranes are unique in many ways. Unlike other cellular membranes, they are comprised of two membranes instead of just one, and cardiolipins, one of the abundant lipid species in mitochondrial membranes, are not found in significant amounts elsewhere in the cell. Among other aspects, the exceptional nature of cardiolipins is characterized by their small charged head group connected to typically four hydrocarbon chains. In this work, we present atomic-scale molecular dynamics simulations of the inner mitochondrial membrane modeled as a mixture of cardiolipins (CLs), phosphatidylcholines (PCs), and phosphatidylethanolamines (PEs). For comparison, we also consider pure one-component bilayers and mixed PC−PE, PC−CL, and PE−CL membranes. We find that the influence of CLs on membrane properties depends strongly on membrane composition. This is highlighted by studies of the stability of CL-containing membranes, which indicate that the interactions of CL in ternary lipid bilayers cannot be deduced from the corresponding ones in binary membranes. Moreover, while the membrane properties in the hydrocarbon region are only weakly affected by CLs, the changes at the membrane−water interface turn out to be prominent. The effects at the interface are most evident in membrane properties related to hydrogen bonding and the binding phenomena associated with electrostatic interactions.

Triglycerides are a major component of many important biological entities such as lipoproteins and lipid droplets. This work focuses on two common triglycerides, tripalmitin and triolein, which have been simulated through atomistic molecular dynamics at temperatures of 310 and 350 K for 300−700 ns. In these systems, both structural and dynamical properties have been characterized, paying particular attention to understanding the packing of triglyceride molecules and their molecular conformations. Additionally, we study the liquid-to-crystalline phase transition of tripalmitin through a temperature quench from the high-temperature isotropic liquid phase to 310 K, corresponding to a polymorphic, crystalline-like phase. The transition is characterized in detail through density, average molecular shape, and, in particular, the relevant order parameter describing the transition.

•Charged lipids play an important role in numerous membrane functions.•Simulations provide detailed information on how charged lipids interact.•For better insight, systematic simulation studies would be welcome.Lipids and proteins are the main components of cell membranes. It is becoming increasingly clear that lipids, in addition to providing an environment for proteins to work in, are in many cases also able to modulate the structure and function of those proteins. Particularly charged lipids such as phosphatidylinositols and phosphatidylserines are involved in several examples of such effects. Molecular dynamics simulations have proved an invaluable tool in exploring these aspects. This so-called computational microscope can provide both complementing explanations for the experimental results and guide experiments to fruitful directions. In this paper, we review studies that have utilized molecular dynamics simulations to unravel the roles of charged lipids in membrane structures. We focus on lipids as active constituents of the membranes, affecting both general membrane properties as well as non-lipid membrane components, mainly proteins. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

We review the relationship between molecular interactions and the properties of lipid environments. A specific focus is given on bilayers which contain sphingomyelin (SM) and sterols due to their essential role for the formation of lipid rafts. The discussion is based on recent atom-scale molecular dynamics simulations, complemented by extensive comparison to experimental data. The discussion is divided into four sections. The first part investigates the properties of one-component SM bilayers and compares them to bilayers with phosphatidylcholine (PC), the focus being on a detailed analysis of the hydrogen bonding network in the two bilayers. The second part deals with binary mixtures of sterols with either SM or PC. The results show how the membrane properties may vary substantially depending on the sterol and SM type available, the membrane order and interdigitation being just two of the many examples of this issue. The third part concentrates on the specificity of intermolecular interactions in three-component mixtures of SM, PC and cholesterol (CHOL) under conditions where the concentrations of SM and CHOL are dilute with respect to that of PC. The results show how SM and CHOL favor one another, thus acting as nucleation sites for the formation of highly ordered nanosized domains. Finally, the fourth part discusses the large-scale properties of raft-like membrane environments and compares them to the properties of non-raft membranes. The differences turn out to be substantial. As a particularly intriguing example of this, the lateral pressure profiles of raft-like and non-raft systems indicate that the lipid composition of membrane domains may have a major impact on membrane protein activation.

•Long-chain sphingomyelins interdigitate substantially across a lipid membrane.•The interdigitation takes places in a cholesterol dependent fashion.•Asymmetrical lipid distribution plays a key role in interdigitation.•Results suggest that membrane domain coupling may take place through the process.It has been a long-standing question how the two leaflets in a lipid bilayer modulate each others' physical properties. In this paper, we discuss how this interaction may take place through interdigitation. We use atomistic molecular dynamics simulations to consider asymmetric lipid membrane models whose compositions are based on the lipidomics data determined for exosomes released by PC-3 prostate cancer cells. The simulations show interdigitation to be exceptionally strong for long-chain sphingomyelin (SM) molecules. In asymmetric membranes the amide-linked chain of SM is observed to extend deep into the opposing membrane leaflet. Interestingly, we find that the conformational order of the amide-linked SM chain increases the deeper it penetrates to the opposing leaflet. Analysis of this finding reveals that the amide-linked SM chain interacts favorably with the lipid chains in the opposite leaflet, and that cholesterol modulates the effect of SM interdigitation by influencing the conformational order of lipid hydrocarbon chains in the opposing (cytosolic) leaflet.Figure optionsDownload full-size imageDownload high-quality image (444 K)Download as PowerPoint slide

•We discuss how molecular simulations can be used to study biomolecular systems.•We focus on glycolipids and discuss their complex behavior.•Importance of understanding the role of glycolipids in numerous diseases is discussed.•Challenges in simulating complex biosystems are identified and discussed.Glycolipids are the most complex lipid type in cell membranes, characterized by a great diversity of different structures and functions. The underlying atomistic/molecular interactions and mechanisms associated with these functions are not well understood. Here we discuss how atomistic and molecular simulations can be used to shed light on the role of glycolipids in membrane structure and dynamics, receptor function, and other phenomena related to emergence of diseases such as Parkinson's. The cases we discuss highlight the challenge to understand how glycolipids function in cell membranes, and the significant added value that one would gain by bridging molecular simulations with experiments. This article is part of a Special Issue entitled Tools to study lipid functions.

In this issue of Structure, Segrest et al. (2015) present a novel picture for the ABCA1-mediated lipid loading of lipid-poor apoA-I.

We describe how membrane proteins diffuse laterally in the membrane plane together with the lipids surrounding them. We find a number of intriguing phenomena. The lateral displacements of the protein and the lipids are strongly correlated, as the protein and the neighboring lipids form a dynamical protein−lipid complex, consisting of ∼50−100 lipids. The diffusion of the lipids in the complex is much slower compared to the rest of the lipids. We also find a strong directional correlation between the movements of the protein and the lipids in its vicinity. The results imply that in crowded membrane environments there are no “free” lipids, as they are all influenced by the protein structure and dynamics. Our results indicate that, in studies of cell membranes, protein and lipid dynamics have to be considered together.

Fullerene C70 is known to partition into lipid membranes and change their physical properties. Together with gallic acid (GA), C70 induces cell contraction and cell death. How C70 and GA-induced perturbations of lipid membranes affect cellular function and membrane protein activity is not understood, though. Meanwhile, fullerene is also known to interfere with the activity of potassium channel proteins, but the mechanisms of protein inhibition are not known. Here we consider the possibility that membrane protein function would be inhibited by C70 and/or GA through direct contact or through lipid-mediated interactions. To this end, we use microsecond time scale atomistic simulations to explore (a) modifications of membrane properties in the presence of C70 and/or GA, and (b) the possible conformational changes in Kv1.2, a voltage-gated potassium channel, upon exposure to C70, or GA, or both. C70 is found to have an observable effect on structural and elastic properties of protein-free membranes, while the effects of GA on the membrane are less evident. Fullerene–GA interaction is strong and affects significantly the partitioning of C70 in the membrane, stabilizing C70 in the aqueous phase. When Kv1.2 is exposed to the solutes, only small conformational changes are observed on the microsecond time scale – comparable to the fluctuations observed in the absence of any solute. Blocking of the channel entrance is not observed, as fullerene binds mainly to hydrophobic residues, both in the water-exposed loops and in the transmembrane helices. The tilt angle of transmembrane helices in the voltage-sensing domain appears to be affected by direct contact with fullerene, but a generic effect due to the small increase in membrane thickness might also play a role. A small rotation of the S3 and S4 helices in the voltage-sensing domain is noticed when C70 is embedded in the membrane. The interpretation of the observed conformational changes is not straightforward due to the associated time scales, which are difficult to sample with state-of-the-art computing resources. We cannot exclude that both membrane-mediated interactions and specific protein–solute interactions affect the conformation of the protein.