Volker Knecht

Solvent-Exposed Tails as Prestalk Transition States for Membrane Fusion at Low Hydration

Membrane fusion is a key step in intracellular trafficking and viral infection. The underlying molecular mechanism is poorly understood. We have used molecular dynamics simulations in conjunction with a coarse grained model to study early metastable and transition states during the fusion of two planar palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayers separated by five waters per lipid in the cis leaflets at zero tension. This system mimics the contact area between two vesicles with large diameters compared to the membrane thickness at conditions where fusion may start in the core of the contact area. At elevated temperatures, the two proximal leaflets become connected via multiple lipid molecules and form a stalklike structure. At room temperature, this structure has a free energy of 3k(B)T and is separated from the unconnected state by a significant free energy barrier of 20k(B)T. Stalk formation is initiated by the establishment of a localized hydrophobic contact between the bilayers. This contact is either formed by two partially splayed lipids or a single fully splayed one leading to the formation of a (metastable) splayed lipid bond intermediate. These findings indicate that, for low hydration, early membrane fusion kinetics is not determined by the stalk energy but by the energy of prestalk transition states involving solvent-exposed lipid tails.

Interactions of Alkali Metal Chlorides with Phosphatidylcholine Vesicles

We study the interaction of alkali metal chlorides with lipid vesicles made of palmitoyloleoylphosphatidylcholine (POPC). An elaborate set of techniques is used to investigate the binding process at physiological conditions. The alkali cation binding to POPC is characterized thermodynamically using isothermal titration calorimetry. The isotherms show that for all ions in the alkali group the binding process is endothermic, counterintuitively to what is expected for Coulomb interactions between the slightly negatively charged POPC liposomes and the cations. The process is entropy driven and presumably related to the liberation of water molecules from the hydration shells of the ions and the lipid headgroups. The measured molar enthalpies of the binding of the ions follows the Hofmeister series. The binding constants were also estimated, whereby lithium shows the strongest affinity to POPC membranes, followed by the rest of the ions according to the Hofmeister series. Cation adsorption increases the net surface potential of the vesicles as observed from electrophoretic mobility and zeta potential measurements. While lithium adsorption leads to slightly positive zeta potentials above a concentration of 100 mM, the adsorption of the rest of the ions mainly causes neutralization of the membrane. This is the first study characterizing the binding equilibrium of alkali metal chlorides to phosphatidylcholine membranes at physiological salt concentrations.

Mechanical Coupling via the Membrane Fusion SNARE Protein Syntaxin 1A: A Molecular Dynamics Study

SNARE trans complexes between membranes likely promote membrane fusion. For the t-SNARE syntaxin 1A involved in synaptic transmission, the secondary structure and bending stiffness of the five-residue juxtamembrane linker is assumed to determine the required mechanical energy transfer from the cytosolic core complex to the membrane. These properties have here been studied by molecular dynamics and annealing simulations for the wild-type and a C-terminal-prolongated mutant within a neutral and an acidic bilayer, suggesting linker stiffnesses above 1.7 but below 50 x 10(-3) kcal mol(-1) deg(-2). The transmembrane helix was found to be tilted by 15 degrees and tightly anchored within the membrane with a stiffness of 4-5 kcal mol(-1) A(-2). The linker turned out to be marginally helical and strongly influenced by its lipid environment. Charged lipids increased the helicity and H3 helix tilt stiffness. For the wild type, the linker was seen embedded deeply within the polar region of the bilayer, whereas the prolongation shifted the linker outward. This reduced its helicity and increased its average tilt, thereby presumably reducing fusion efficiency. Our results suggest that partially unstructured linkers provide considerable mechanical coupling; the energy transduced cooperatively by the linkers in a native fusion event is thus estimated to be 3-8 kcal/mol, implying a two-to-five orders of magnitude fusion rate increase.

Simulation studies of pore and domain formation in a phospholipid monolayer

Despite extensive study the phase behavior of phospholipid monolayers at an air-water interface is still not fully understood. In particular recent vibrational sum-frequency generation (VSFG) spectra of DPPC monolayers as a function of area density show a sharp transition in the order of the lipid chains at 1.10 nm2/molecule. This is in a region where the lateral pressure as a function of area is effectively constant. We have investigated the nature of this transition by studying the phase behavior of DPPC monolayers as a function of area density using molecular-dynamics simulations. The changes in order within the monolayer as a function of area density correlate well with the experimental signal. At 0.58 nm2/molecule we observe the onset of lateral separation of highly ordered and disordered lipids, indicating the coexistence of a gel-like liquid condensed and a fluidlike liquid expanded phase. At 0.97 nm2/molecule the monolayer ruptures, marking the onset of the liquid-gas (G) coexistence region. This is much earlier than suggested by fluorescence microscopy results and implies that at the point of rupture, the initial pores have an equilibrium size smaller than approximately 500 nm in diameter. The rupture of the monolayer leads to a sharp increase in the overall lipid order that explains the sharp transition observed in the VSFG measurements. VSFG measurements thus may represent a sensitive means to determine the onset of the liquid-gas (G) coexistence region for such systems.

Electrical Forces Determine Glomerular Permeability

There is ongoing controversy about the mechanisms that determine the characteristics of the glomerular filter. Here, we tested whether flow across the glomerular filter generates extracellular electrical potential differences, which could be an important determinant of glomerular filtration. In micropuncture experiments in Necturus maculosus, we measured a potential difference across the glomerular filtration barrier that was proportional to filtration pressure (-0.045 mV/10 cm H₂O). The filtration-dependent potential was generated without temporal delay and was negative within Bowmans space. Perfusion with the cationic polymer protamine abolished the potential difference. We propose a mathematical model that considers the relative contributions of diffusion, convection, and electrophoretic effects on the total flux of albumin across the filter. According to this model, potential differences of -0.02 to -0.05 mV can induce electrophoretic effects that significantly influence the glomerular sieving coefficient of albumin. This model of glomerular filtration has the potential to provide a mechanistic theory, based on experimental data, about the filtration characteristics of the glomerular filtration barrier. It provides a unique approach to the microanatomy of the glomerulus, renal autoregulation, and the pathogenesis of proteinuria.

A Single Bicontinuous Cubic Phase Induced by Fusion Peptides

We report a bicontinuous cubic phase forming in the presence of the Influenza HA fusion peptide in coarse grained molecular dynamics simulations. Starting from a random mixture of DOPE, water, and fusion peptides, we observe spontaneous formation of a stable bicontinuous phase. Unlike all previously reported bicontinuous cubic phases the one formed in our simulations is a single phase in the sense that there are no multiple isolated compartments of water or lipid.

Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detail

Molecular dynamics simulations have been used to study the phase behavior of a dipalmitoylphosphatidylcholine (DPPC)/palmitic acid (PA)/water 1:2:20 mixture in atomic detail. Starting from a random solution of DPPC and PA in water, the system adopts either a gel phase at temperatures below approximately 330 K or an inverted hexagonal phase above approximately 330 K in good agreement with experiment. It has also been possible to observe the direct transformation from a gel to an inverted hexagonal phase at elevated temperature (approximately 390 K). During this transformation, a metastable fluid lamellar intermediate is observed. Interlamellar connections or stalks form spontaneously on a nanosecond time scale and subsequently elongate, leading to the formation of an inverted hexagonal phase. This work opens the possibility of studying in detail how the formation of nonlamellar phases is affected by lipid composition and (fusion) peptides and, thus, is an important step toward understanding related biological processes, such as membrane fusion.

Kirkwood–Buff derived force field for alkali chlorides in simple point charge water

Solvated ions are a fundamental constituent of many biological systems. An important class consists of the alkali cations. In particular, potassium (K(+)) is the most abundant ion in the cytoplasm, whereas lithium (Li(+)), rubidium (Rb(+)), and cesium (Cs(+)) are of fundamental physicochemical and medical relevance. A powerful tool to understand ion specificity and cellular systems on a microscopic level is provided by molecular dynamics simulations. Previously, reliable force field parameters for Li(+), K(+), Rb(+), and Cs(+) in aqueous solution have not been available for the simple point charge (SPC) water model widely used in conjunction with the GROMOS force field. We used the Kirkwood-Buff theory to develop force fields for Li(+), K(+), Rb(+), and Cs(+) in SPC water to reproduce experimental data on respective aqueous alkali chloride solutions (LiCl, KCl, RbCl, CsCl). The force field developed reproduces many of the known properties of alkali metal chlorides solutions including densities and partial molar volumes. Our force field is shown to be superior to other common alkali chloride force fields in terms of reproducing the activity derivative, as a prerequisite for a realistic measure of ion-solute association underlying ion-specific phenomena (Hofmeister effects). For lithium and potassium, the ionic radii from cation-water oxygen pair correlation functions and hydration numbers are well reproduced. The force field developed will be useful for modeling physiological conditions and ion-specific phenomena for biomolecular systems.

Specific Binding of Chloride Ions to Lipid Vesicles and Implications at Molecular Scale

Biological membranes composed of lipids and proteins are in contact with electrolytes like aqueous NaCl solutions. Based on molecular dynamics studies it is widely believed that Na(+) ions specifically bind to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes, whereas Cl(-) ions stay in solution. Here, we present a careful comparison of recent data from electrophoresis and isothermal titration calorimetry experiments as well as molecular dynamics simulations suggesting that in fact both ions show very similar affinities. The corresponding binding constants are 0.44(±0.05) M(-1) for Na(+) and 0.40(±0.04) M(-1) for Cl(-) ions. This is highlighted by our observation that a widely used simulation setup showing asymmetric affinities of Na(+) and Cl(-) for POPC bilayers overestimates the effect of NaCl on the electrophoretic mobility of a POPC membrane by an order of magnitude. Implications for previous simulation results on the effect of NaCl on polarization of interfacial water, transmembrane potentials, and mechanisms for ion transport through bilayers are discussed. Our findings suggest that a range of published simulations results on the interaction of NaCl with phosphocholine bilayers have to be reconsidered and revised and that force field refinements are necessary for reliable simulation studies of membranes at physiological conditions on a molecular level.

Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir

Amprenavir (APV) is a high affinity (0.15 nM) HIV-1 protease (PR) inhibitor. However, the affinities of the drug resistant protease variants V32I, I50V, I54V, I54M, I84V and L90M to amprenavir are decreased 3 to 30-fold compared to the wild-type. In this work, the popular molecular mechanics Poisson-Boltzmann surface area method has been used to investigate the effectiveness of amprenavir against the wild-type and these mutated protease variants. Our results reveal that the protonation state of Asp25/Asp25′ strongly affects the dynamics, the overall affinity and the interactions of the inhibitor with individual residues. We emphasize that, in contrast to what is often assumed, the protonation state may not be inferred from the affinities but requires pKa calculations. At neutral pH, Asp25 and Asp25′ are ionized or protonated, respectively, as suggested from pKa calculations. This protonation state was thus mainly considered in our study. Mutation induced changes in binding affinities are in agreement with the experimental findings. The decomposition of the binding free energy reveals the mechanisms underlying binding and drug resistance. Drug resistance arises from an increase in the energetic contribution from the van der Waals interactions between APV and PR (V32I, I50V, and I84V mutant) or a rise in the energetic contribution from the electrostatic interactions between the inhibitor and its target (I54M and I54V mutant). For the V32I mutant, also an increased free energy for the polar solvation contributes to the drug resistance. For the L90M mutant, a rise in the van der Waals energy for APV-PR interactions is compensated by a decrease in the polar solvation free energy such that the net binding affinity remains unchanged. Detailed understanding of the molecular forces governing binding and drug resistance might assist in the design of new inhibitors against HIV-1 PR variants that are resistant against current drugs.