Computer modelling of glycolipids at membrane surfaces

Computational studies of peptide-induced membrane pore formation

A variety of peptides induce pores in biological membranes; the most common ones are naturally produced antimicrobial peptides (AMPs), which are small, usually cationic, and defend diverse organisms against biological threats. Because it is not possible to observe these pores directly on a molecular scale, the structure of AMP-induced pores and the exact sequence of steps leading to their formation remain uncertain. Hence, these questions have been investigated via molecular modelling. In this article, we review computational studies of AMP pore formation using all-atom, coarse-grained, and implicit solvent models; evaluate the results obtained and suggest future research directions to further elucidate the pore formation mechanism of AMPs.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.

Structure-based prediction of drug distribution across the headgroup and core strata of a phospholipid bilayer using surrogate phases

Solvation of drugs in the core (C) and headgroup (H) strata of phospholipid bilayers affects their physiological transport rates and accumulation. These characteristics, especially a complete drug distribution profile across the bilayer strata, are tedious to obtain experimentally, to the point that even simplified preferred locations are only available for a few dozen compounds. Recently, we showed that the partition coefficient (P) values in the system of hydrated diacetyl phosphatidylcholine (DAcPC) and n-hexadecane (C16), as surrogates of the H- and C-strata of the bilayer composed of the most abundant mammalian phospholipid, PC, agree well with the preferred bilayer location of compounds. High P values are typical for lipophiles accumulating in the core, and low P values are characteristic of cephalophiles preferring the headgroups. This simple pattern does not hold for most compounds, which usually have more even distribution and may also accumulate at the H/C interface. To model complete distribution, the correlates of solvation energies are needed for each drug state in the bilayer: (1) for the H-stratum it is the DAcPC/W P value, calculated as the ratio of the C16/W and C16/DAcPC (W for water) P values; (2) for the C-stratum, the C16/W P value; (3) for the H/C interface, the P values for all plausible molecular poses are characterized using the fragment DAcPC/W and C16/W solvation parameters for the parts of the molecule embedded in the H- and C-strata, respectively. The correlates, each scaled by two Collander coefficients, were used in a nonlinear, mass-balance based model of intrabilayer distribution, which was applied to the easily measurable overall P values of compounds in the DMPC (M = myristoyl) bilayers and monolayers as the dependent variables. The calibrated model for 107 neutral compounds explains 94% of experimental variance, achieves similar cross-validation levels, and agrees well with the nontrivial, experimentally determined bilayer locations for 27 compounds. The resulting structure-based prediction system for intrabilayer distribution will facilitate more realistic modeling of passive transport and drug interactions with those integral membrane proteins, which have the binding sites located in the bilayer, such as some enzymes, influx and efflux transporters, and receptors. If only overall bilayer accumulation is of interest, the 1-octanol/W P values suffice to model the studied set.

Implicit solvent simulations of peptide interactions with anionic lipid membranes

A recently developed implicit membrane model (IMM1) is supplemented with a Gouy-Chapman term describing counterion-screened electrostatic interactions of a solute with negatively charged membrane lipids. The new model is tested on peptides that bind to anionic membranes. Pentalysine binds just outside the plane of negative charge, whereas Lys-Phe peptides insert their aromatic rings into the hydrophobic core. Melittin and magainin 2 bind more strongly to anionic than to neutral membranes and in both cases insert their hydrophobic residues into the hydrocarbon core. The third domain of Antennapedia homeodomain (penetratin) binds as an alpha-helix in the headgroup region. Cardiotoxin II binds strongly to anionic membranes but marginally to neutral ones. In all cases, the location and configuration of the peptides are consistent with experimental data, and the effective energy changes upon binding compare favorably with experimental binding free energies. The model opens the way to exploring the effect of membrane charge on the location, conformation, and dynamics of a large variety of biologically active peptides on membranes.

Effective energy function for proteins in lipid membranes

A simple extension of the EEF1 energy function to heterogeneous membrane-aqueous media is proposed. The extension consists of (a) development of solvation parameters for a nonpolar phase using experimental data for the transfer of amino acid side-chains from water to cyclohexane, (b) introduction of a heterogeneous membrane-aqueous system by making the reference solvation free energy of each atom dependent on the vertical coordinate, (c) a modification of the distance-dependent dielectric model to account for reduced screening of electrostatic interactions in the membrane, and (d) an adjustment of the EEF1 aqueous model in light of recent calculations of the potential of mean force between amino acid side-chains in water. The electrostatic model is adjusted to match experimental observations for polyalanine, polyleucine, and the glycophorin A dimer. The resulting energy function (IMM1) reproduces the preference of Trp and Tyr for the membrane interface, gives reasonable energies of insertion into or adsorption onto a membrane, and allows stable 1-ns MD simulations of the glycophorin A dimer. We find that the lowest-energy orientation of melittin in bilayers varies, depending on the thickness of the hydrocarbon layer.

Conformation of sulfoquinovosyldiacylglycerol bound to a magnetically oriented membrane system

The conformation of uniformly 13C-labeled sulfoquinovosyldiacylglycerol (SQDG) is studied in both membrane and solution environments using NMR spectroscopy. Analysis in a membrane-like environment is based on the measurement of dipolar interactions between 13C-13C and 1H-13C spin pairs and on the measurement of 13C chemical shift anisotropy offsets, which appear in magnetically oriented phospholipid-based membrane fragments. Potential energy maps for glycosidic torsions, phi, psi and theta 1, are calculated with a membrane interaction energy and are used in the interpretation of experimental data. The membrane-bound description for SQDG is most consistent with a set of low-energy conformations that extends the headgroup of SQDG away from the membrane surface. Analysis of the conformation of SQDG in CD3OD solution is based on measured 3JCH scalar couplings. The description of the solution conformation is modeled as a mixture of low-energy conformers predicted in the absence of a membrane interaction term and involves more extensive motional averaging than the model for SQDG embedded in the lipid matrix.

7-nitrobenz-2-oxa-1,3-diazole-4-yl-labeled phospholipids in lipid membranes: differences in fluorescence behavior

Steady-state and time-resolved fluorescence properties of the 7-nitrobenz-2-oxa-1, 3-diazole-4-yl (NBD) fluorophore attached either to the sn-2 acyl chain of various phospholipids (phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and phosphatidic acid) or to the polar headgroup of phosphatidylethanolamine were studied after insertion of these NBD-labeled lipid probes into unilamellar vesicles of phosphatidylcholine, phosphatidylglycerol, phosphatidic acid, and phosphatidylserine. The fluorescence response of the NBD group was observed to strongly depend on the chemical structure and physical state of the host phospholipids and on the chemical structure of the lipid probe itself. Among the various fluorescence parameters studied, i.e., Stokes' shifts, lifetimes, and quantum yields, the quantum yields were by far the most affected by these structural and environmental factors, whereas the Stokes' shifts were practically unaffected. Thus, depending on the phospholipid probe and the host phospholipid, the fluorescence emission of the NBD group was found to vary by a factor of up to 5. Careful analysis of the data shows that for the various couples of probe and host lipid molecules studied, deexcitation of the fluorophore was dominated by nonradiative deactivation processes. This great sensitivity of the NBD group to environmental factors originates from its well-known solvatochromic properties, and comparison of these knr values with those obtained for n-propylamino-NBD in a set of organic solvents covering a large scale of polarity indicates that in phospholipids, the NBD fluorophore experiences a dielectric constant of around 27-41, corresponding to a medium of relatively high polarity. From these epsilon values and on the basis of models of the dielectric transition that characterizes any water-phospholipid interface, it can be inferred that for all of the phospholipid probes and host phospholipids tested, the NBD group is located in the region of the polar headgroups, near the phosphoglycerol moiety of the lipids.

13C NMR studies of wheat germ agglutinin interactions with N-acetylglucosamine at a magnetically oriented bilayer surface

The orientation of synthetic 13C-labeled glycolipid receptors and their interaction with the plant lectin wheat germ agglutinin have been studied in an oriented membrane system using NMR spectroscopy. A series of 2-[1,2-13C2]acetamido-2-deoxy-beta-D-glucopyranosides were synthesized with between zero and four hydrophilic ethoxy units between the headgroup and an alkyl chain which anchors the receptors in the bilayers. The chemical shift anisotropy of the 13C carbonyl and a 13C-13C dipolar coupling between the labeled carbons provide information about the orientation and dynamics of the receptor headgroup in oriented membrane systems. It was found that the headgroups of the receptors with two, three, or four ethoxy units appeared isotropic when incorporated in the oriented bilayers, but those of the receptors with zero or one ethoxy units were significantly ordered by the bilayers. The average orientations consistent with measured spectral parameters were determined for the receptors with zero and one ethoxy units and were found to coincide with low-energy conformations from molecular modeling. When the plant lectin wheat germ agglutinin was added to the sample, only the receptors with two, three, or four ethoxy units separating the headgroup from the alkyl chain showed evidence of binding by the lectin. Although the 13C-labeled resonances broadened when the protein bound, no changes in dipolar couplings or chemical shift anisotropies could be detected, suggesting that the motion of the headgroup was slowed by protein binding, but average orientation and overall order changed little. Competition studies demonstrated that none of the lectin/receptor complexes are more stable than the complex of the lectin and N-acetylglucosamine in solution. These results suggest that the membrane does not stabilize the interactions of wheat germ agglutinin with these cell-surface receptors. Furthermore, molecular modeling demonstrates that the zero- and one-spacer receptors may not bind wheat germ agglutinin because the orientations of the N-acetyl groups in these receptors would result in significant steric contacts between the lectin/receptor complex and the membrane.

Electrostatic potentials and electrostatic interaction energies of rat cytochrome b5 and a simulated anion-exchange adsorbent surface

Electrostatic potentials were determined for the soluble tryptic core of rat cytochrome b5 (using a structure derived from homology modeling) and a simulated anion-exchange surface through application of the linearized finite-difference Poisson-Boltzmann equation with the simulation code UHBD. Objectives of this work included determination of the contributions of the various charged groups on the protein surface to electrostatic interactions with a simulated anion-exchange surface as a function of orientation, separation distance, and ionic strength, as well as examining the potential existence of a preferred contact orientation. Electrostatic interaction free energies for the complex of the model protein and the simulated surface were computed using the electrostatics section of UHBD employing a 110(3) grid. An initial coarse grid spacing of 2.0 A was required to obtain correct boundary conditions. The boundary conditions of the coarse grid were used in subsequent focusing steps until the electrostatic interaction free energies were relatively independent of grid spacing (at approximately 0.5 A). Explicit error analyses were performed to determine the effects of grid spacing and other model assumptions on the electrostatic interaction free energies. The computational results reveal the presence of a preferred interaction orientation; the interaction energy between these two entities, of opposite net charge, is repulsive over a range of orientations. The electrostatic interaction free energies appear to be the summation of multiple fractional interactions between the protein and the anion-exchange surface. The simulation results are compared with those of ion-exchange adsorption experiments with site-directed mutants of the recombinant protein. Comparisons of the results from the computational and experimental studies should lead to a better understanding of electrostatic interactions of proteins and charged surfaces.

An approximate model and empirical energy function for solute interactions with a water-phosphatidylcholine interface

An empirical model of a liquid crystalline (L alpha phase) phosphatidylcholine (PC) bilayer interface is presented along with a function which calculates the position-dependent energy of associated solutes. The model approximates the interface as a gradual two-step transition, the first step being from an aqueous phase to a phase of reduced polarity, but which maintains a high enough concentration of water and/or polar head group moieties to satisfy the hydrogen bond-forming potential of the solute. The second transition is from the hydrogen bonding/low polarity region to an effectively anhydrous hydrocarbon phase. The "interfacial energies" of solutes within this variable medium are calculated based upon atomic positions and atomic parameters describing general polarity and hydrogen bond donor/acceptor propensities. This function was tested for its ability to reproduce experimental water-solvent partitioning energies and water-bilayer partitioning data. In both cases, the experimental data was reproduced fairly well. Energy minimizations carried out on beta-hexyl glucopyranoside led to identification of a global minimum for the interface-associated glycolipid which exhibited glycosidic torsion angles in agreement with prior results (Hare, B.J., K.P. Howard, and J.H. Prestegard. 1993. Biophys. J. 64:392-398). Molecular dynamics simulations carried out upon this same molecule within the simulated interface led to results which were consistent with a number of experimentally based conclusions from previous work, but failed to quantitatively reproduce an available NMR quadrupolar/dipolar coupling data set (Sanders, C.R., and J.H. Prestegard. 1991. J. Am. Chem. Soc. 113:1987-1996). The proposed model and functions are readily incorporated into computational energy modeling algorithms and may prove useful in future studies of membrane-associated molecules.