Proton dissociation dynamics in the aqueous layer of multilamellar phospholipid vesicles

Summary The water layers interspacing between the phospholipid membranes of a multilamellar vesicle are 3–10 water layers across and their width is adjusted by osmotic pressure (Parsegian, V.A., et al., 1986.Methods Enzymol. 127:400–416).In these thin water layers we dissolved pyranine (8 hydroxypyrene 1,3,6 trisulfonate), a compound which, upon photo excitation, ejects it hydroxy proton with time constant of 100 psec. (Gutman, M. 1986.Methods Enzymol. 127:522–538).In the present study we investigated how the width of the aqueous layer, the density of phosphomoieties on the membrane's surface and the activity of water in the layer affect the capacity of protons to diffuse out from the electrostatic cage of the excited anion before it decays to the ground state.Using a combination of steady-state and subnanosecond time-resolved fluorescence measurements we determined the average number of proton excited-anion recombinations before the proton escapes from the Coulomb cage.The probability of recombination in thin water layer is significantly higher than in bulk. The factor contributing most to enhancement of recombination is the diminished water activity of the thin aqueous layer.The time frame for proton escape from an electrostatic trap as big as a membrane-bound protein is 3 orders of magnitude shorter than turnover time of membrane-bound enzymes. Thus the effects of local forces on proton diffusion, at the time scale of physiological processes, is negligible.     

Molecular dynamics study on the conformational flexibility and energetics in aqueous solution of methylated beta-cyclodextrins

All possible methylated beta-cyclodextrins (CDs) with C7-symmetry have been studied by molecular dynamics simulations, in gas phase and in water solution. Energetic and structural information were obtained from the trajectory analysis. CD flexibility increases with degree of methylation, very likely due to the concomitant reduction of the intramolecular hydrogen bonds. Solvation-free energy was computed for each of the studied CDs using the MM/GBSA method. An analysis of radial distribution functions was used to determine distribution of solvent molecules around the O2, O3, and O6. The number of solvent molecules around these oxygens decreases with an increase in the degree of methylation. The DeltaS contribution from solvent thus becomes more positive when the degree of methylation increases and, consequently, the overall DeltaG in water diminishes.     

A steered molecular dynamics method with direction optimization and its applications on ligand molecule dissociation

In this paper, a steered molecular dynamics method with pulling direction optimization is proposed to dissociate ligand molecule from receptor. A multi-population genetic algorithm based on the information entropy is developed to search the optimal pulling direction. By imposing an optimization phase in the conventional steered molecular dynamics simulation, a better substrate-exit channel for the buried active site can be found. The novel simulation method has been used to dissociate the substrate-bound complex structure of cytochrome P450 3A4-metyrapone. The results show that the new pathway obtained by the proposed method has advantages such as lower energy barrier, less dissociation time and shorter motion trajectory than that by the conventional steered molecular dynamics.     

Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments

Filamentous amyloid aggregates are central to the pathology of Alzheimer's disease. We use all-atom molecular dynamics (MD) simulations with explicit solvent and multiple force fields to probe the structural stability and the conformational dynamics of several models of Alzheimer's beta-amyloid fibril structures, for both wild-type and mutated amino acid sequences. The structural models are based on recent solid state NMR data. In these models, the peptides form in-register parallel beta-sheets along the fibril axis, with dimers of two U-shaped peptides located in layers normal to the fibril axis. Four different topologies are explored for stacking the beta-strand regions against each other to form a hydrophobic core. Our MD results suggest that all four NMR-based models are structurally stable, and we find good agreement with dihedral angles estimated from solid-state NMR experiments. Asp23 and Lys28 form buried salt-bridges, resulting in an alternating arrangement of the negatively and positively charged residues along the fibril axis that is reminiscent of a one-dimensional ionic crystal. Interior water molecules are solvating the buried salt-bridges. Based on data from NMR measurements and MD simulations of short amyloid fibrils, we constructed structural models of long fibrils. Calculated X-ray fiber diffraction patterns show the characteristics of packed beta-sheets seen in experiments, and suggest new experiments that could discriminate between various fibril topologies.     

Analysis of dissociation process for gas hydrates by molecular dynamics simulation

The dissociation processes of methane and carbon dioxide hydrates were investigated by molecular dynamics simulation. The simulations were performed with 368 water molecules and 64 gas molecules using NPT ensembles. The TraPPE (single-site) and 5-site models were adopted for methane molecules. The EPM2 (3-site) and SPC/E models were used for carbon dioxide and water molecules, respectively. The simulations were carried out at 270 K and 5.0 MPa for hydrate stabilisation. Then, temperature was increased up to 370 K. The temperature increasing rates were 0.1–20 TK/s. The gas hydrates dissociated during increasing temperature or at 370 K. The potential models of methane molecule did not much influence the dissociation process of methane hydrate. The mechanisms of dissociation process were analysed with the coordination numbers and mean square displacements. It was found that the water cages break down first, then the gas molecules escape from the water cages. The methane hydrate was more stable than the carbon dioxide hydrate at the calculated conditions.     

Molecular dynamics simulation of methane hydrate dissociation by depressurisation

Methane (CH₄) hydrate dissociation and the mechanism by depressurisation are investigated by molecular dynamics (MD) simulation. The hydrate decomposition processes are studied by the ‘vacuum removal method’ and the normal method. It is found that the hydrate decomposition is promoted by depressurisation. The quasi-liquid layer is formed in the hydrate surface layer. The driving force of dissociation is found to be controlled by the concentration gradient between the H₂O molecules of the hydrate surface layer and the H₂O molecules of the hydrate inner layer. The clathrates collapse gradually, and the hydrate decomposes layer by layer. Relative to our previous MD simulation results, this study shows that the rate of the hydrate dissociation by depressurisation is slower than that by the thermal stimulation and the inhibitor injection. This study illustrated that MD simulation can play a significant role in investigating the hydrate decomposition mechanisms.     

Molecular dynamics simulations of membrane proteins

Membrane proteins control the traffic across cell membranes and thereby play an essential role in cell function from transport of various solutes to immune response via molecular recognition. Because it is very difficult to determine the structures of membrane proteins experimentally, computational methods have been increasingly used to study their structure and function. Here we focus on two classes of membrane proteins—ion channels and transporters—which are responsible for the generation of action potentials in nerves, muscles, and other excitable cells. We describe how computational methods have been used to construct models for these proteins and to study the transport mechanism. The main computational tool is the molecular dynamics (MD) simulation, which can be used for everything from refinement of protein structures to free energy calculations of transport processes. We illustrate with specific examples from gramicidin and potassium channels and aspartate transporters how the function of these membrane proteins can be investigated using MD simulations.     

Change of the unbinding mechanism upon a mutation: a molecular dynamics study of an antibody-hapten complex

We study forced unbinding of fluorescein from the wild type (WT) and a mutant [H(H58)A] of the single-chain variable-fragment (scFv) anti-fluorescein antibody FITC-E2 by molecular dynamics simulations using various pulling techniques. A large number of long simulations were needed to obtain statistically meaningful results as both the wild type and the H(H58)A mutant unbinding occurs through multiple pathways, often with metastable intermediates. For the wild type, the rate-limiting step in the unbinding process corresponds to the breaking of the non-native interactions characteristic of a specific intermediate. The H(H58)A mutation disfavors the occurrence of this intermediate. Two events where the hapten partially unbinds in the absence of pulling force are observed in extensive equilibrium simulations of the wild type, and their analysis indicates that forced unbinding and spontaneous unbinding proceed along similar pathways. The different unbinding mechanisms observed in the simulations suggest a possible reason for the difference in the experimental off-rate between the two antibodies. We predict mutations that are expected to modulate the occurrence of the unbinding intermediate. For two such new mutants [H(H58)A and S(H52)A], our predictions are validated in silico by additional simulations. The accompanying paper in this issue by Honegger et al. reports the X-ray structure of FITC-E2 with a derivative of fluorescein, which was used as the starting conformation for the work presented here.     

Ca(2+) dissociation from the C-terminal EF-hand pair in calmodulin: a steered molecular dynamics study

We used steered molecular dynamics (SMD) to simulate the process of Ca²⁺ dissociation from the EF-hand motifs of the C-terminal lobe of calmodulin. Based on an analysis of the pulling forces, the dissociation sequences and the structural changes, we show that the Ca²⁺-coordinating residues lose their binding to Ca²⁺ in a stepwise fashion. The two Ca²⁺ ions dissociate from the two EF-hands simultaneously, with two distinct groups among the five Ca²⁺-coordinating residues affecting the EF-hand conformational changes differently. These results provide new insights into the effects of Ca²⁺ on calmodulin conformation, from which a novel sequential mechanism of Ca²⁺-calmodulin dissociation is proposed.     

Molecular modeling of an antigenic complex between a viral peptide and a class I major histocompatibility glycoprotein.

Computer simulation of the conformations of short antigenic peptides (5-10 residues) either free or bound to their receptor, the major histocompatibility complex (MHC)-encoded glycoprotein H-2 Ld, was employed to explain experimentally determined differences in the antigenic activities within a set of related peptides. Starting for each sequence from the most probable conformations disclosed by a pattern-recognition technique, several energy-minimized structures were subjected to molecular dynamics simulations (MD) either in vacuo or solvated by water molecules. Notably, antigenic potencies were found to correlate to the peptides propensity to form and maintain an overall alpha-helical conformation through regular i,i + 4 hydrogen bonds. Accordingly, less active or inactive peptides showed a strong tendency to form i,i + 3 hydrogen bonds at their N-terminal end. Experimental data documented that the C-terminal residue is critical for interaction of the peptide with H-2 Ld. This finding could be satisfactorily explained by a 3-D Q.S.A.R. analysis postulating interactions between ligand and receptor by hydrophobic forces. A 3-D model is proposed for the complex between a high-affinity nonapeptide and the H-2 Ld receptor. First, the H-2 Ld molecule was built from X-ray coordinates of two homologous proteins: HLA-A2 and HLA-Aw68, energy-minimized and studied by MD simulations. With HLA-A2 as template, the only realistic simulation was achieved for a solvated model with minor deviations of the MD mean structure from the X-ray conformation. Water simulation of the H-2 Ld protein in complex with the antigenic nonapeptide was then achieved with the template-derived optimal parameters. The bound peptide retains mainly its alpha-helical conformation and binds to hydrophobic residues of H-2 Ld that correspond to highly polymorphic positions of MHC proteins. The orientation of the nonapeptide in the binding cleft is in accordance with the experimentally determined distribution of its MHC receptor-binding residues (agretope residues). Thus, computer simulation was successfully employed to explain functional data and predicts alpha-helical conformation for the bound peptide.     

Ab initio molecular dynamics study of the hydration of the formohydroxamate anion

We apply ab initio molecular dynamics (AIMD) to study the hydration structures and electronic properties of the formohydroxamate anion in liquid water. We consider the cis- nitrogen-deprotonated, cis- oxygen-deprotonated, and trans- oxygen-deprotonated formohydroxamate tautomers. They form an average of 6.3, 6.9, and 6.0 hydrogen bonds with water molecules, respectively. The predicted pair correlation functions and time dependence of the hydration numbers suggest that water is highly structured around the nominally negatively charged oxime oxygen in O-deprotonated tautomers but significantly less so around the nitrogen atom in the N-deprotonated species. Wannier function analysis suggests that, in the O-deprotonated anions, the negative charge is concentrated on the oxime oxygen, while in the N-deprotonated case, it is partially delocalized between the nitrogen and the adjoining oxime oxygen atom.     

Molecular dynamics of the P450cam–Pdx complex reveals complex stability and novel interface contacts

Cytochrome P450cam catalyzes the stereo and regiospecific hydroxylation of camphor to 5‐exo‐hydroxylcamphor. The two electrons for the oxidation of camphor are provided by putidaredoxin (Pdx), a Fe₂S₂ containing protein. Two recent crystal structures of the P450cam–Pdx complex, one solved with the aid of covalent cross‐linking and one without, have provided a structural picture of the redox partner interaction. To study the stability of the complex structure and the minor differences between the recent crystal structures, a 100 nanosecond molecular dynamics (MD) simulation of the cross‐linked structure, mutated in silico to wild type and the linker molecule removed, was performed. The complex was stable over the course of the simulation though conformational changes including the movement of the C helix of P450cam further toward Pdx allowed for the formation of a number of new contacts at the complex interface that remained stable throughout the simulation. While several minor crystal contacts were lost in the simulation, all major contacts that had been experimentally studied previously were maintained. The equilibrated MD structure contained a mixture of contacts resembling both the cross‐linked and noncovalent structures and the newly identified interactions. Finally, the reformation of the P450cam Asp251–Arg186 ion pair in the MD simulation mirrors the ion pair observed in the more promiscuous CYP101D1 and suggests that the Asp251–Arg186 ion pair may be important.     

Molecular dynamics simulation of spherical-to -threadlike micelle transition in a cationic surfactant solution

The effect of sodium salicylate (NaSal) on the spherical-to-threadlike micelle shape transition in 3-hexadecyloxy-2-hydroxy-propyl trimethyl ammonium bromide (R₁₆HTAB) solution was studied using molecular dynamics simulation. The simulations were started from a preassembled infinitely long threadlike micelle of R₁₆HTAB. By analyzing the aggregation morphologies and structural details, we find that the preassembled threadlike micelle in the absence of NaSal was unstable and assembled into a spherical micelle. While in the presence of NaSal, the threadlike micelle exhibited fluctuations but remained the threadlike shape during the long simulation run. The Sal^? ions were found to penetrate inside the micelle, which promoted the junction between the surfactant and salicylate counterion. The aromatic Sal^? ions located in the surfactant headgroup region with their phenyl groups pointing toward the interior core region of the micelle. From another simulation started with two individual spherical micelles, we found that the Sal^? ions can link the two spherical micelles into a long threadlike micelle, in accordance with a mode proposed by experimental studies. Our studies showed that the H-bonds and electrostatic interactions between the Sal^? ions and the surfactants played an important role in micellar growth and stabilising the threadlike micelle.     

On the stability of different experimental dimeric structures of the SL1 sequence from the genomic RNA of HIV-1 in solution: a molecular dynamics simulation and electrophoresis study

SL1 is a stem-loop RNA sequence from the genome of HIV-1 thought to be the initiation site for the dimerization of the retroviral genomic RNA. The aim of this study is to check the stability in solution of different experimental dimeric structures available in the literature. Two kinds of dimer have been evidenced: an extended duplex looking like a double helix with two internal bulges and a kissing complex in which the monomers with a stem/loop conformation are linked by intermolecular loop-loop interactions. Two divergent experimental structures of the kissing complex from the Lai isolate are reported in the literature, one obtained from NMR (Mujeeb et al., Nature Structural Biology, 1998, Vol. 5, pp. 432-436) and the other one from x-ray crystallography (Ennifar et al., Nature Structural Biology, 2001, Vol. 8, pp. 1064-1068). A crystallographic structure of the Mal isolate was also reported (Ennifar et al., Nature Structure Biology, 2001, Vol. 8, pp. 1064-1068). Concerning the extended duplex, a NMR structure is available for Lai (Girard et al., Journal of Biomolecular Structure and Dynamics, 1999, Vol. 16, pp. 1145-1157) and a crystallographic structure for Mal (Ennifar et al., Structure, 1999, Vol. 7, pp. 1439-1449). Using a molecular dynamics technique, all these experimental structures have been simulated in solution with explicit water and counterions. We show that both extended duplex structures are stable. On the contrary, the crystallographic structures of the Lai and Mal kissing complexes are rapidly destabilized in aqueous environment. Finally, the NMR structure of the Lai loop-loop kissing complex remains globally stable over a 20 ns MD simulation, although large rearrangements occur at the level of the stem/loop junctions that are flexible, as shown from free energy calculations. These results are compared to electrophoresis experiments on dimer formation.     

Molecular dynamics simulation of interleukin-2 and its complex and determination of the binding free energy

Interleukin-2 (IL-2) protein belongs to the signal modulator cytokine's family and therefore it is prevalent for immunological responses. It has been identified as a centrally important potential drug target for the inhibition of protein-protein interactions; so as to suppress the immunological responses associated with autoimmune, inflammatory and immunological diseases, and cancer. In the present work, we have performed two independent 100?ns of molecular dynamics (MD) simulations on the apo IL-2 protein and its ligand-bound complex (with a potent inhibitor FRG), to study the effect of inhibitor binding on the dynamics and stability of the protein. The calculation of binding free energy via post-processing end state method of Molecular Mechanics Poisson Boltzmann Surface Area (MM-PBSA) and Molecular Mechanics Generalised Born Surface Area (MM-GBSA) has inferred a good correlation in accordance with the already reported experimental data, demonstrating that the free energy of binding calculated by the two methods has no significant difference. The investigation of individual components of free energy revealed that the association of IL-2 protein with FRG ligand is primarily driven by the van der Waals energy contribution that represents the non-polar/hydrophobic energy contribution as dominant in this case of ligand binding.     

Molecular dynamics simulation of truncated bovine adrenodoxin

The 128 amino acid long soluble protein adrenodoxin (Adx) is a typical member of the ferredoxin protein family that are electron carrier proteins with an iron-sulfur cofactor. Adx carries electrons from adrenodoxin reductase (AdR) to cytochrome P450s. Its binding modes to these proteins were previously characterized by site-directed mutagenesis, by X-ray crystallography for the complex Adx:AdR, and by NMR. However, no clear evidence has been provided for the driving force that promotes Adx detachment from AdR upon reduction. Here, we characterized the conformational dynamics of unbound Adx in the oxidized and reduced forms using 2-20 ns long molecular dynamics simulations. The most noticeable difference between both forms is the enhanced flexibility of the loop (47-51) surrounding the iron-sulfur cluster in the reduced form. Together with several structural displacements at the binding interface, this increased flexibility may be the key factor promoting unbinding of reduced Adx from AdR. This points to an intrinsic property of reduced Adx that drives dissociation.     

A molecular dynamics study of the stoichiometric complex formed by poly (alpha, L-glutamate) and octyltrimethylammonium ions in chloroform solution.

We present a molecular dynamics simulation at 300 K in explicit solvent environment of chloroform of the stoichiometric complex formed by poly(alpha,L-glutamate) and octyltrimethylammonium ions. We observed that the alpha-helix conformation of the polypeptide chain remains stable during a 2-ns run. The surfactant ions predominantly adopted an extended conformation that is stabilized by favorable interactions with the organic solvent. Analysis of the organization of the surfactant with respect to the polypeptide chain indicated that each octyltrimethylammonium cation was preferentially bound to more than one carboxylate group. It was found that the most populated arrangement was that with the surfactant cations interacting with two carboxylate groups simultaneously.     

Molecular dynamics study of a calmodulin-like protein with an IQ peptide: spontaneous refolding of the protein around the peptide

The Calmodulin (CaM) is a small (16.7 kDa), highly acidic protein that is crucial to all eukaryotes by serving as a prototypical calcium sensor. In the present study, we investigated, through molecular dynamics simulations, the dynamics of a complex between the Mlc1p protein, which is a CaM-like protein, and the IQ4 peptide. This protein-peptide interaction is of high importance because IQ motifs are widely distributed among different kinds of CaM-binding proteins. The Mlc1p-IQ4 complex, which had been resolved by crystallography to 2.1 A, confers to a Ca(+2)-independent stable structure. During the simulations, the complex undergoes a complicated modulation process, which involves bending of the angles between the alpha-helices of the protein, breaking of the alpha-helical structure of the IQ4 peptide into two sections, and formation of new contact points between the protein and the peptide. The dynamics of the process consist of fast sub picosecond events and much slower ones that take a few nanoseconds to completion. Our study expands the information embedded in the crystal structure of the Mlc1p-IQ4 complex by describing its dynamic behavior as it evolves from the crystal structure to a form stable in solution. The article shows that careful application of molecular dynamics simulations can be used for extending the structural information presented by the crystal structure, thereby revealing the dynamic configuration of the protein in its physiological environment.     

The Influence of Charge Calculation on Molecular Dynamics Simulation of Adenine in Water

Abstract

Molecular dynamics simulations of an aqueous solution of adenine have been performed using different methods of charge calculation to evaluate the influence of the values of the atomic charges on the dynamical results and to incorporate new information about the interaction between adenine and water. Four sets of partial charges where computed using ab-initio methods. In all cases the hydration properties of adenine were similar. These results support the view that the simulations by molecular dynamics, at least for the regime of infinite dilution, are not sensitive with respect to the different sets of partial charges used. A net hydrophobic behavior of the adenine molecule, on the water was observed.     

Molecular dynamics modelling of an electrical-driven linear nanopump

The dynamics of an electrical-driven linear nanopump, consisting of a carbon nanotube, a C60⁺ molecule and a graphene sheet, has been simulated via the application of the molecular dynamics method. In this nanopump, the nanotube and the graphene sheet are used as the sleeve of the pump and the boundary between the two sides of the nanopump, respectively. By exposing the nanopump to an external alternative electric field, the C60⁺ molecule will be oscillating linearly in the nanotube. We found that the linear oscillating motion of the C60⁺ molecule causes the gas atoms to flow through the nanotube, and a density gradient is generated between the two sides of the nanopump. Also, it was observed that the frequency of the external alternative electric field affected the pump performance in the generation of the density gradient amount. The maximum performance occurred at a specific frequency of the electric field. This specific frequency can be computed by an analytical formula for given materials and temperatures. Moreover, the results indicate that the length of the nanotube can affect the gas pumping.