Studies on viral fusion peptides: the distribution of lipophilic and electrostatic potential over the peptide determines the angle of insertion into a membrane.

The oblique insertion of type 1 viral fusion peptides into the cell membrane of the host cell has been shown previously to be an essential element of viral fusion. The actual physical explanation of the cause of the oblique insertion has been the subject of speculation. In this study the physical properties of the fusion peptide surface have been determined computationally and compared to the tilt angles determined both experimentally and by the use of molecular dynamics. It has been shown that the relationship between the distribution of lipophilic potential over the peptide surface and the peptide geometry control the tilt angle of the peptide in a biomimetic DMPC bilayer whereas the depth of penetration into the bilayer appears to be determined by the electrostatic potential and hydrogen bonding at the C-terminus.

Chemical reactions in 2D: self-assembly and self-esterification of 9(10),16-dihydroxypalmitic acid on mica surface.

9(10),16-Dihydroxypalmitic acid (diHPA) is a particularly interesting polyhydroxylated fatty acid (1) because it is the main monomer of cutin, the most abundant biopolyester in nature, and (2) because the presence of a terminal and a secondary hydroxyl group in midchain positions provides an excellent model to study their intermolecular interactions in a confined phase such as self-assembled layers. In this study we have combined atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), attenuated total reflection Fourier transform infrared (ATR-FT-IR) spectroscopy, as well as molecular dynamics (MD) simulations to conclude that the self-assembling of diHPA molecules on mica is a layer by layer process following a Brunauer-Emmett-Teller (BET) type isotherm and with the first layer growing much faster than the rest. Interactions between secondary hydroxyls reinforce the cohesive energy of the monolayer, while the presence of the terminal hydroxyl group is necessary to trigger the multilayered growth. Besides, XPS and ATR-FT-IR spectroscopies clearly indicate that spontaneous self-esterification occurs upon self-assembling. The esterification reaction is a prerequisite to propose a self-assembly route for the biosynthesis of cutin in nature. Molecular dynamics simulations have shown that internal molecular reorganization within the self-assembled layers provides the appropriate intermolecular orientation to facilitate the nucleophilic attack and the release of a water molecule required by the esterification reaction.

On a novel rate theory for transport in narrow ion channels and its application to the study of flux optimization via geometric effects.

We present a novel rate theory based on the notions of splitting probability and mean first passage time to describe single-ion conduction in narrow, effectively one-dimensional membrane channels. In contrast to traditional approaches such as transition state theory or Kramers theory, transitions between different conduction states in our model are governed by rates which depend on the full geometry of the potential of mean force (PMF) resulting from the superposition of an equilibrium free energy profile and a transmembrane potential induced by a nonequilibrium constraint. If a detailed theoretical PMF is available (e.g., from atomistic molecular dynamics simulations), it can be used to compute characteristic conductance curves in the framework of our model, thereby bridging the gap between the atomistic and the mesoscopic level of description. Explicit analytic solutions for the rates, the ion flux, and the associated electric current can be obtained by approximating the actual PMF by a piecewise linear potential. As illustrative examples, we consider both a theoretical and an experimental application of the model. The theoretical example is based on a hypothetical channel with a fully symmetric sawtooth equilibrium PMF. For this system, we explore how changes in the spatial extent of the binding sites affect the rate of transport when a linear voltage ramp is applied. Already for the case of a single binding site, we find that there is an optimum size of the site which maximizes the current through the channel provided that the applied voltage exceeds a threshold value given by the binding energy of the site. The above optimization effect is shown to arise from the complex interplay between the channel structure and the applied electric field, expressed by a nonlinear dependence of the rates with respect to the linear size of the binding site. In studying the properties of current-voltage curves, we find a double crossover between sublinear and superlinear behaviors as the size of the binding site is varied. The ratio of unidirectional fluxes clearly deviates from the Ussing limit and can be characterized by a flux ratio exponent which decreases below unity as the binding site becomes wider. We also explore effects arising from changes in the ion bulk concentration under symmetric ionic conditions and the presence of additional binding sites in the hypothetical channel. As for the experimental application, we show that our rate theory is able to provide good fits to conductance data for sodium permeation through the gramicidin A channel. Possible extensions of the theory to treat the case of an asymmetric equilibrium PMF, fluctuations in the mean number of translocating ions, the case of fluctuating energy barriers, and multi-ion conductance are briefly discussed.

Simulation studies of the interactions between membrane proteins and detergents.

Interactions between membrane proteins and detergents are important in biophysical and structural studies and are also biologically relevant in the context of folding and transport. Despite a paucity of high-resolution data on protein-detergent interactions, novel methods and increased computational power enable simulations to provide a means of understanding such interactions in detail. Simulations have been used to compare the effect of lipid or detergent on the structure and dynamics of membrane proteins. Moreover, some of the longest and most complex simulations to date have been used to observe the spontaneous formation of membrane protein-detergent micelles. Common mechanistic steps in the micelle self-assembly process were identified for both alpha-helical and beta-barrel membrane proteins, and a simple kinetic mechanism was proposed. Recently, simplified (i.e. coarse-grained) models have been utilized to follow long timescale transitions in membrane protein-detergent assemblies.

Molecular simulations and lipid-protein interactions: potassium channels and other membrane proteins.

Molecular dynamics simulations may be used to probe the interactions of membrane proteins with lipids and with detergents at atomic resolution. Examples of such simulations for ion channels and for bacterial outer membrane proteins are described. Comparison of simulations of KcsA (an alpha-helical bundle) and OmpA (a beta-barrel) reveals the importance of two classes of side chains in stabilizing interactions with the head groups of lipid molecules: (i) tryptophan and tyrosine; and (ii) arginine and lysine. Arginine residues interacting with lipid phosphate groups play an important role in stabilizing the voltage-sensor domain of the KvAP channel within a bilayer. Simulations of the bacterial potassium channel KcsA reveal specific interactions of phosphatidylglycerol with an acidic lipid-binding site at the interface between adjacent protein monomers. A combination of molecular modelling and simulation reveals a potential phosphatidylinositol 4,5-bisphosphate-binding site on the surface of Kir6.2.

Kv channel S6 helix as a molecular switch: simulation studies.

Ion channels form pores of nanoscopic dimensions in biological membranes and play a key role in the physiology of cells. The majority of ion channels are gated, i.e. they contain a molecular switch that allows a transition between a closed (functionally 'off') and open (functionally 'on') state. Comparison of crystal structures of potassium channels suggest that the gating mechanism of voltage-gated potassium (Kv) channels involves a key role for the pore-lining S6 helix. There is a conserved PVP sequence motif in the S6 helix. Molecular dynamics simulations are used here to explore the conformational dynamics of the S6 helix hinge in models of fragments of a Kv channel, namely an S5-P-S6 monomer and an (S5-P-S6)4 tetramer. The latter is a model of the complete pore-forming domain of a Kv channel. All models were simulated embedded in an octane slab (a simple membrane mimetic). The results of these simulations indicate that the PVP motif may form a molecular hinge, even when the S6 helix forms part of a more complex model. The conformational dynamics of S6 are modulated by the remainder of protein, but it remains flexible. These simulation results are compatible with a channel gating model in which S6 bends in the vicinity of the PVP motif in addition to the region around the conserved glycine (G466) that is N-terminal to the PVP motif. This model is supported by comparison of the Kv S6 models with the S6 helix of the bacterial KvAP channel crystal structure. Thus, K channel gating may depend on a complex nanoswitch with three rigid helical sections linked by two molecular hinges.

Pores formed by the nicotinic receptor m2delta Peptide: a molecular dynamics simulation study.

The M2delta peptide self-assembles to form a pentameric bundle of transmembrane alpha-helices that is a model of the pore-lining region of the nicotinic acetylcholine receptor. Long (>15 ns) molecular dynamics simulations of a model of the M2delta(5) bundle in a POPC bilayer have been used to explore the conformational dynamics of the channel assembly. On the timescale of the simulation, the bundle remains relatively stable, with the polar pore-lining side chains remaining exposed to the lumen of the channel. Fluctuations at the helix termini, and in the helix curvature, result in closing/opening transitions at both mouths of the channel, on a timescale of approximately 10 ns. On average, water within the pore lumen diffuses approximately 4x more slowly than water outside the channel. Examination of pore water trajectories reveals both single-file and path-crossing regimes to occur at different times within the simulation.

Bundles consisting of extended transmembrane segments of Vpu from HIV-1: computer simulations and conductance measurements.

Part of the genome of the human immunodeficiency virus type 1 (HIV-1) encodes for a short membrane protein Vpu, which has a length of 81 amino acids. It has two functional roles: (i) to downregulate CD4 and (ii) to support particle release. These roles are attributed to two distinct domains of the peptide, the cytoplasmic and transmembrane (TM) domains, respectively. It has been suggested that the enhanced particle release function is linked to the ion channel activity of Vpu, with a slight preference for cations over anions. To allow ion flux across the membrane Vpu would be required to assemble in homooligomers to form functional water-filled pores. In this study molecular dynamics simulations are used to address the role of particular amino acids in 4, 5, and 6 TM helix bundle structures. The helices (Vpu(6-33)) are extended to include hydrophilic residues such as Glu, Tyr, and Arg (EYR motif). Our simulations indicate that this motif destabilizes the bundles at their C-terminal ends. The arginines point into the pore to form a positive charged ring that could act as a putative selectivity filter. The helices of the bundles adopt slightly higher average tilt angles with decreasing number of helices. We also suggest that the helices are kinked. Conductance measurements on a peptide (Vpu(1-32)) reconstituted into lipid membranes show that the peptide forms ion channels with several conductance levels.