Molecular insight of specific cholesterol interactions: A molecular dynamics simulation study

Insight into the Molecular Mechanism of Surface Interactions of Phosphatidylcholines─Langmuir Monolayer Study Complemented with Molecular Dynamics Simulations

Mutual interactions between components of biological membranes are pivotal for maintaining their proper biophysical properties, such as stability, fluidity, or permeability. The main building blocks of biomembranes are lipids, among which the most important are phospholipids (mainly phosphatidylcholines (PCs)) and sterols (mainly cholesterol). Although there is a plethora of reports on interactions between PCs, as well as between PCs and cholesterol, their molecular mechanism has not yet been fully explained. Therefore, to resolve this issue, we carried out systematic investigations based on the classical Langmuir monolayer technique complemented with molecular dynamics simulations. The studies involved systems containing 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) analogues possessing in the structure one or two polar functional groups similar to those of DPPC. The interactions and rheological properties of binary mixtures of DPPC analogues with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and cholesterol were compared with reference systems (DPPC/POPC and DPPC/cholesterol). This pointed to the importance of the ternary amine group in PC/cholesterol interactions, while in PC mixtures, the phosphate group played a key role. In both cases, the esterified glycerol group had an effect on the magnitude of interactions. The obtained results are crucial for establishing structure-property relationships as well as for designing substitutes for natural lipids.

Molecular Dynamics Simulations of Water-Mediated Cholesterol Capture within an Open-Ended Single-Walled Carbon Nanotube

The excess concentration of cholesterol in the bloodstream can be brought down to a safer level by utilizing a potential cholesterol-binding agent such as a carbon nanotube (CNT). Here, we have probed solvent-mediated interactions between cholesterol and CNT by performing molecular dynamics simulations and potential-of-mean force (PMF) calculations. Simulations predict favorable interactions between water-mediated cholesterol and CNT owing to strong mutual interactions between them, whereas water plays an opposing role in the association. The breakdown of PMF into its enthalpic and entropic contributions indicates that contrary to traditional entropy-driven hydrophobic association, the cholesterol encapsulation within a CNT is primarily driven by enthalpy.

Computer modelling studies of the bilayer/water interface

This review summarises high resolution studies on the interface of lamellar lipid bilayers composed of the most typical lipid molecules which constitute the lipid matrix of biomembranes. The presented results were obtained predominantly by computer modelling methods. Whenever possible, the results were compared with experimental results obtained for similar systems. The first and main section of the review is concerned with the bilayer-water interface and is divided into four subsections. The first describes the simplest case, where the interface consists only of lipid head groups and water molecules and focuses on interactions between the lipid heads and water molecules; the second describes the interface containing also mono- and divalent ions and concentrates on lipid-ion interactions; the third describes direct inter-lipid interactions. These three subsections are followed by a discussion on the network of direct and indirect inter-lipid interactions at the bilayer interface. The second section summarises recent computer simulation studies on the interactions of antibacterial membrane active compounds with various models of the bacterial outer membrane. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Effects of cholesterol on membrane molecular dynamics studied by fast field cycling NMR relaxometry

Biological membranes are complex structures composed of various lipids and proteins. Different membrane compositions affect viscoelastic and hydrodynamic properties of membranes, which are critical to their functions. Lipid bilayer vesicles inserted by cholesterol not only enhance membrane surface motional behavior but also strengthen vesicle stability. Cholesterol-rich vesicles are similar to cell membranes in structure and composition. Therefore, cholesterol-rich vesicles can represent a typical model for studying membrane dynamics and functions. In this study, nuclear magnetic relaxation dispersion was used to investigate the detailed molecular dynamics of membrane differences between vesicles and cholesterol vesicles in the temperature range of 278-298 K. Vesicles of two different sizes were prepared. The effect of cholesterol mainly affected the order fluctuation of membranes and the diffusional motion of lipid molecules. In addition, phase variations were also observed in liposomes that contained cholesterol from analyses of the distances between lipid molecules.

Cholesterol and POPC segmental order parameters in lipid membranes: solid state 1H-13C NMR and MD simulation studies

The concentration of cholesterol in cell membranes affects membrane fluidity and thickness, and might regulate different processes such as the formation of lipid rafts. Since interpreting experimental data from biological membranes is rather intricate, investigations on simple models with biological relevance are necessary to understand the natural systems. We study the effect of cholesterol on the molecular structure of multi-lamellar vesicles (MLVs) composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), a phospholipid ubiquitous in cell membranes, with compositions in the range 0-60 mol% cholesterol. Order parameters, |S(CH)|, are experimentally determined by using (1)H-(13)C solid-state nuclear magnetic resonance (NMR) spectroscopy with segmental detail for all parts of both the cholesterol and POPC molecules, namely the ring system and alkyl chain of the sterol, as well as the glycerol backbone, choline headgroup and the sn-1 and sn-2 acyl chains of POPC. With increasing cholesterol concentration the acyl chains gradually adopt a more extended conformation while the orientation and dynamics of the polar groups are rather unaffected. Additionally, we perform classical molecular dynamics simulations on virtual bilayers mimicking the POPC-cholesterol MLVs investigated by NMR. Good agreement between experiments and simulations is found for the cholesterol alignment in the bilayer and for the |S(CH)| profiles of acyl chains below 15 mol% cholesterol. Deviations occur for the choline headgroup and glycerol backbone parts of POPC, as well as for the phospholipid and cholesterol alkyl chains at higher cholesterol concentrations. The unprecedented detail of the NMR data enables a more complete comparison between simulations and experiments on POPC-cholesterol bilayers and may aid in developing more realistic model descriptions of biological membranes.

LIPID11: a modular framework for lipid simulations using amber

Accurate simulation of complex lipid bilayers has long been a goal in condensed phase molecular dynamics (MD). Structure and function of membrane-bound proteins are highly dependent on the lipid bilayer environment and are challenging to study through experimental methods. Within Amber, there has been limited focus on lipid simulations, although some success has been seen with the use of the General Amber Force Field (GAFF). However, to date there are no dedicated Amber lipid force fields. In this paper we describe a new charge derivation strategy for lipids consistent with the Amber RESP approach and a new atom and residue naming and type convention. In the first instance, we have combined this approach with GAFF parameters. The result is LIPID11, a flexible, modular framework for the simulation of lipids that is fully compatible with the existing Amber force fields. The charge derivation procedure, capping strategy, and nomenclature for LIPID11, along with preliminary simulation results and a discussion of the planned long-term parameter development are presented here. Our findings suggest that LIPID11 is a modular framework feasible for phospholipids and a flexible starting point for the development of a comprehensive, Amber-compatible lipid force field.

Molecular dynamics simulations of the interactions of kinin peptides with an anionic POPG bilayer

We have performed molecular dynamics simulations of peptide hormone bradykinin (BK) and its fragment des-Arg9-BK in the presence of an anionic lipid bilayer, with an aim toward delineating the mechanism of action related to their bioactivity. Starting from the initial aqueous environment, both of the peptides are quickly adsorbed and stabilized on the cell surface. Whereas BK exhibits a stronger interaction with the membrane and prefers to stay on the interface, des-Arg9-BK, with the loss of C-terminal Arg, penetrates further. The heterogeneous lipid-water interface induces β-turn-like structure in the otherwise inherently flexible peptides. In the membrane-bound state, we observed C-terminal β-turn formation in BK, whereas for des-Arg9-BK, with the deletion of Arg9, turn formation occurred in the middle of the peptide. The basic Arg residues anchor the peptide to the bilayer by strong electrostatic interactions with charged lipid headgroups. Simulations with different starting orientations of the peptides with respect to the bilayer surface lead to the same observations, namely, the relative positioning of the peptides on the membrane surface, deeper penetration of the des-Arg9-BK, and the formation of turn structures. The lipid headgroups adjacent to the bound peptides become substantially tilted, causing bilayer thinning near the peptide contact region and increase the degree of disorder in nearby lipids. Again, because of hydrogen bonding with the peptide, the neighboring lipid's polar heads exhibit considerably reduced flexibility. Corroborating findings from earlier experiments, our results provide important information about how the lipid environment promotes peptide orientation/conformation and how the peptide adapts to the environment.

Intramolecular hydrogen bonding in articaine can be related to superior bone tissue penetration: a molecular dynamics study

Local anesthetics (LAs) are drugs that cause reversible loss of nociception during surgical procedures. Articaine is a commonly used LA in dentistry that has proven to be exceptionally effective in penetrating bone tissue and induce anesthesia on posterior teeth in maxilla and mandibula. In the present study, our aim was to gain a deeper understanding of the penetration of articaine through biological membranes by studying the interactions of articaine with a phospholipid membrane. Our approach involves Langmuir monolayer experiments combined with molecular dynamics simulations. Membrane permeability of LAs can be modulated by pH due to a titratable amine group with a pKa value close to physiological pH. A change in protonation state is thus known to act as a lipophilicity switch in LAs. Our study shows that articaine has an additional unique lipophilicity switch in its ability to form an intramolecular hydrogen bond. We suggest this intramolecular hydrogen bond as a novel and additional solvent-dependent mechanism for modulation of lipophilicity of articaine which may enhance its diffusion through membranes and connective tissue.

Cause and effect of melittin-induced pore formation: a computational approach

Melittin embedded in a palmitoyl oleyl phosphatidylcholine bilayer at a high peptide/lipid ratio (1:30) was simulated in the presence of explicit water and ions. The simulation results indicate the incipience of an ion-permeable water pore through collective membrane perturbation by bound peptides. The positively charged residues of melittin not only act as "anchors" but also disrupt the membrane, leading to cell lysis. A detailed analysis of the lipid tail order parameter profile depicts localized membrane perturbation. The lipids in the vicinity of the aqueous cavity adopt a tilted conformation, which allows local bilayer thinning. The prepore thus formed can be considered as the melittin-induced structural defects in the bilayer membrane. Because of the strong cationic nature, the melittin-induced prepore exhibits selectivity toward anions over cations. As Cl(-) ions entered into the prepore, they are electrostatically entrapped by positively charged residues located at its wall. The confined motion of the Cl(-) ions in the membrane interior is obvious from calculated diffusion coefficients. Moreover, reorientation of the local lipids occurs in such a way that few lipid heads along with peptide helices can line the surface of the penetrating aqueous phase. The flipping of lipids argued in favor of melittin-induced toroidal pore over a barrel-stave mechanism. Thus, our result provides atomistic level details of the mechanism of membrane disruption by antimicrobial peptide melittin.

Molecular level investigation of organization in ternary lipid bilayer: a computational approach

The differential organization of lipid components in a multicomponent membrane leads to formation of domains having diverse composition and size. Cholesterol and glycosphingolipids are known to be important components of such lateral assembly. We report here the ordering of cholesterol around ganglioside GM1 and the nature of the cluster from an all-atom simulation of a ternary lipid system. The results are compared with a binary bilayer and a pure phospholipid bilayer. The difference in molecular rearrangements in ternary and binary lipid mixture shows the role of GM1 in the rearrangement of cholesterol. Calculation of the radial distribution function, rotational reorientation, and residence time analysis of cholesterol shows that cholesterol is preferentially accumulating near gangliosides, while the lateral translational motion, rotational diffusion, and order parameter of phospholipids characterize the amount of rigidity imparted on the phospholipid bilayer.

Enantiospecific interactions between cholesterol and phospholipids

The effects of cholesterol on various membrane proteins have received considerable attention. An important question regarding each of these effects is whether the cholesterol exerts its influence by binding directly to membrane proteins or by changing the properties of lipid bilayers. Recently it was suggested that a difference in the effects of natural cholesterol and its enantiomer, ent-cholesterol, would originate from direct binding of cholesterol to a target protein. This strategy rests on the fact that ent-cholesterol has appeared to have effects on lipid films similar to those of cholesterol, yet fluorescence microscopy studies of phospholipid monolayers have provided striking demonstrations of the enantiomer effects, showing opposite chirality of domain shapes for phospholipid enantiomer pairs. We observed the shapes of ordered domains in phospholipid monolayers containing either cholesterol or ent-cholesterol and found that the phospholipid chirality had a great effect on the domain chirality, whereas a minor (quantitative) effect of cholesterol chirality could be observed only in monolayers with racemic dipalmitoylphosphatidylcholine. The latter is likely to derive from cholesterol-cholesterol interactions. Accordingly, cholesterol chirality has only a modest effect that is highly likely to require the presence of solidlike domains and, accordingly, is unlikely to play a role in biological membranes.