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PubMed2006

Computational study of coagulation factor VIIa's affinity for phospholipid membranes.

The interaction between the gamma-carboxyglutamic acid-rich domain of coagulation factor VIIa (FVIIa), a vitamin-K-dependent enzyme, and phospholipid membranes plays a major role in initiation of blood coagulation. However, despite a high sequence and structural similarity to the Gla domain of other vitamin-K-dependent enzymes with a high membrane affinity, its affinity for negatively charged phospholipids is poor. A few amino acid differences are responsible for this observation. Based on the X-ray structure of lysophosphatidylserine (lysoPS) bound to the Gla domain of bovine prothrombin (Prth), models of the Gla domain of wildtype FVIIa and mutated FVIIa Gla domains in complex with lysoPS were built. Molecular dynamics (MD) and steered molecular dynamics (SMD) simulations on the complexes were applied to investigate the significant difference in the binding affinity. The MD simulation approach provides a structural and dynamic support to the role of P10Q and K32E mutations in the improvement of the membrane contact. Hence, rotation of the Gly11 main chain generated during the MD simulation results in a hydrogen bond with Q10 side chain as well as the appearance of a hydrogen bond between E32 and Q10 forcing the loop harbouring Arg9 and Arg15 to shrink and thereby enhances the accessibility of the phospholipids to the calcium ions. Furthermore, the application of the SMD simulation method to dissociate C6-lysoPS from a series of Gla domain models exhibits a ranking of the rupture force that can be useful in the interpretation of the PS interaction with Gla domains. Finally, adiabatic mapping of Gla6 residue in FVIIa with or without insertion of Tyr4 confirms the critical role of the insertion on the conformation of the side chain Gla6 in FVIIa and the corresponding Gla7 in Prth.

Binding Sites↗
PubMed2006

Nonreactive molecular dynamics force field for crystalline hexahydro-1,3,5-trinitro-1,3,5 triazine.

An empirical nonreactive force field has been developed for molecular dynamics (MD)/Monte Carlo simulation of the formation, diffusion, and agglomeration of point defects in the crystal lattice of the alpha modification of hexahydro-1,3,5-trinitro-1,3,5 triazine (RDX) using flexible molecules. Bond stretching and angle bending are represented by Morse and harmonic functions, and torsion by a truncated cosine series. Nonbonded interactions, both inter- and intramolecular, are described by Buckingham potentials separately parametrized. Intermolecular electrostatic interactions are treated via a Coulomb term coupled with a smooth 15.0 A cutoff radius. Parameters were taken in part from earlier published works and were determined partly by fitting to known molecular and crystal properties of RDX. In MD simulations at constant pressure and temperature, the model was able to stabilize and maintain the correct crystal structure, symmetry, and molecular conformation of alpha-RDX. Vibrational frequencies, lattice binding energy and dimensions, coefficients of thermal expansion, and several unusually short intermolecular distances are all reproduced in satisfactory agreement with experimental data.

Journal Article↗
PubMed2001

Coupling length scales for multiscale atomistics-continuum simulations: atomistically induced stress distributions in Si/Si3N4 nanopixels.

A hybrid molecular-dynamics (MD) and finite-element simulation approach is used to study stress distributions in silicon/silicon-nitride nanopixels. The hybrid approach provides atomistic description near the interface and continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are in good agreement with full multimillion-atom MD simulations: atomic structures at the lattice-mismatched interface between amorphous silicon nitride and silicon induce inhomogeneous stress patterns in the substrate that cannot be reproduced by a continuum approach alone.

Journal Article↗
PubMed1995

Conformational analysis of the disaccharide alpha-L-Rhap-(1-->2)-alpha-L-Rhap-OMe: comparison of dynamics simulations with NMR experiments.

The conformational behaviour of the disaccharide alpha-L-Rhap-(1-->2)-alpha-L-Rhap-(1-->OMe) has been examined using molecular dynamics (MD) and Langevin dynamics simulations and nuclear magnetic resonance (NMR) spectroscopy; an 800 ps MD trajectory with the explicit inclusion of water was also determined. The results of the MD simulations were found to be sensitive to the choice of dielectric constant and force-field parameters. NOE build-up curves were constructed from the water and vacuum dynamics trajectories and compared with experimental values. Calculation of NOE data sets from the simulations was problematic for several reasons, including the similarity in time scales for the internal and overall motions.

Carbohydrate Conformation↗
PubMed2004

Molecular dynamics simulation study of oriented polyamine- and Na-DNA: sequence specific interactions and effects on DNA structure.

Molecular dynamics (MD) computer simulations have been carried out on four systems that correspond to an infinite array of parallel ordered B-DNA, mimicking the state in oriented DNA fibers and also being relevant for crystals of B-DNA oligonucleotides. The systems were all comprised of a periodical hexagonal cell with three identical DNA decamers, 15 water molecules per nucleotide, and counterions balancing the DNA charges. The sequence of the double helical DNA decamer was d(5'-ATGCAGTCAG)xd(5'-TGACTGCATC). The counterions were the two natural polyamines spermidine(3+) (Spd(3+)) and putrescine(2+) (Put(2+)), the synthetic polyamine diaminopropane(2+) (DAP(2+)), and the simple monovalent cation Na(+). This work compares the specific structures of the polyamine- and Na-DNA systems and how they are affected by counterion interactions. It also describes sequence-specific hydration and interaction of the cations with DNA. The local DNA structure is dependent on the nature of the counterion. Even the very similar polyamines, Put(2+) and DAP(2+), show clear differences in binding to DNA and in effect on hydration and local structure. Generally, the polyamines disorder the hydration of the DNA around their binding sites whereas Na(+) being bound to DNA attracts and organizes water in its vicinity. Cation binding at the selected sites in the minor and in the major groove is compared for the different polyamines and Na(+). We conclude that the synthetic polyamine (DAP(2+)) binds specifically to several structural and sequence-specific motifs on B-DNA, unlike the natural polyamines, Spd(3+) and Put(2+). This specificity of DAP(2+) compared to the more dynamic behavior of Spd(3+) and Put(2+) may explain why the latter polyamines are naturally occurring in cells.

Base Sequence↗
PubMed2001

Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins.

The effects of internal motions on residual dipolar NMR couplings of proteins partially aligned in a liquid-crystalline environment are analyzed using a 10 ns molecular dynamics (MD) computer simulation of ubiquitin. For a set of alignment tensors with different orientations and rhombicities, MD-averaged dipolar couplings are determined and subsequently interpreted for different scenarios in terms of effective alignment tensors, average orientations of dipolar vectors, and intramolecular reorientational vector distributions. Analytical relationships are derived that reflect similarities and differences between motional scaling of dipolar couplings and scaling of dipolar relaxation data (NMR order parameters). Application of the self-consistent procedure presented here to dipolar coupling measurements of biomolecules aligned in different liquid-crystalline media should allow one to extract in a "model-free" way average orientations of dipolar vectors and specific aspects of their motions.

Computer Simulation↗
PubMed2004

Monte Carlo versus molecular dynamics simulations in heterogeneous systems: an application to the n-pentane liquid-vapor interface.

The Monte Carlo (MC) and molecular dynamics (MD) methodologies are now well established for computing equilibrium properties in homogeneous fluids. This is not yet the case for the direct simulation of two-phase systems, which exhibit nonuniformity of the density distribution across the interface. We have performed direct MC and MD simulations of the liquid-gas interface of n-pentane using a standard force-field model. We obtained density and pressure components profiles along the direction normal to the interface that can be very different, depending on the truncation and long range correction strategies. We discuss the influence on predicted properties of different potential truncation schemes implemented in both MC and MD simulations. We show that the MD and MC profiles can be made in agreement by using a Lennard-Jones potential truncated via a polynomial function that makes the first and second derivatives of the potential continuous at the cutoff distance. In this case however, the predicted thermodynamic properties (phase envelope, surface tension) deviate from experiments, because of the changes made in the potential. A further readjustment of the potential parameters is needed if one wants to use this method. We conclude that a straightforward use of bulk phase force fields in MD simulations may lead to some physical inconsistencies when computing interfacial properties.

Journal Article↗
PubMed1994

Hydration of cytidine, 2'-deoxycytidine and their phosphate salts in the aqueous solutions. A molecular dynamics computer simulation study.

To compare the hydration pattern of the cytidine (Cyd) and 2'-deoxycytidine (dCyd) in the aqueous solutions at the level of microscopic interactions. Molecular Dynamics (MD) computer simulations have been undertaken. The results indicate that the hydration of the heterocyclic base moiety in cytidine and 2'-deoxycytidine has a hydrophobic character. None of the three potential Watson-Crick base pair centres hydrogen bonds with the water molecules and the formation of something akin to a clathrate cage structure of water around base moieties of nucleosides in the aqueous solution is suggested. In contrast, the hydration of Cyd and dCyd sugar moieties shows a hydrophilic character and the three-dimensional networks of H-bonds involving all hydrophilic centres are formed differently around the ribose and 2'-deoxyribose. The sugar hydroxyl groups participate in the hydrogen bonding with water both as H-donor and as H-acceptor. Their donor-acceptor abilities have been evaluated and compared. The coordination numbers, the geometrical data of the first hydration shell, and the number of hydrogen bonds have been calculated. The changes in the pattern of hydration with the increased concentration of nucleosides and upon nucleoside protonation are discussed. The analysis of the pairwise interaction energies are also presented.

Computer Simulation↗
PubMed2006

Microscopic and thermodynamic properties of the HFA134a-water interface: atomistic computer simulations and tensiometry under pressure.

A combined computational and experimental approach is used to determine the interfacial thermodynamic and structural properties of the liquid 1,1,1,2-tetrafluoroethane (HFA134a)-vapor and liquid HFA134a-water (HFA134a|W) interfaces at 298 K and saturation pressure. Molecular dynamics (MD) computer simulations reveal a stable interface between HFA134a and water. The "10-90" interfacial thickness is comparable with those typically reported for organic-water systems. The interfacial tension of the HFA134a|W interface obtained from the pressure tensor analysis of the MD trajectory is in good agreement with the experimental value determined using in situ high-pressure tensiometry. These results indicate that the potential models utilized are capable of describing the intermolecular interactions between these two fluids. The tension of the HFA134a|W interface is significantly lower than those typically observed for conventional oil-water interfaces and similar to that of the compressed CO(2)-water interface, observed at moderate CO(2) pressures. The MD and tensiometric results are also compared and contrasted with the HFA134a|W and chlorofluorocarbon-water tension values estimated from a parametric relationship. This represents the first report of the interfacial and microscopic properties of the (propellant) hydrofluoroalkanes (HFA)|W interface. The results presented here are of relevance in the design of surfactants capable of forming and stabilizing water-in-HFA microemulsions. Reverse aqueous microemulsions in HFA-based pressurized metered-dose inhalers are candidate formulations for the systemic delivery of biomolecules to and through the lungs.

Computer Simulation↗
PubMed2005

The microscopic switching mechanism of a [2]catenane.

We apply numerical simulations at an all-atom level to investigate the switching mechanism of a [2]catenane, a prototype of a molecular machine. This system is able to switch reversibly between two different stable states, upon external stimuli, with a time scale ranging from microseconds up to milliseconds, well over the typical domain of molecular dynamics (MD) computer simulations. However, combining a strategy recently developed for investigating rare events with ordinary MD, we are able to unravel the microscopic mechanism of the conformational rearrangements involved in the switching process, including dynamical effects. Along the path that connects the product and reactant state, we find several intermediate states characterized by pi-pi stacking interactions and hydrogen bonds. Moreover, counterions interact strongly with the system in a correlated way, in agreement with recent static calculations performed on [2]rotaxanes.

Journal Article↗
PubMed2005

Application of accelerated molecular dynamics schemes to the production of amorphous silicon.

The evolving nature of a Stillinger-Weber modeled silicon glass is studied using two accelerated molecular dynamics scheme, specifically, hyperdynamics and self-guided algorithms due to Voter and due to Wu and Wang, respectively. We obtain an acceleration of the dynamics, a "boost," on the order of 20 without incurring any significant computational overhead. The validity of the results using accelerated methods is provided by comparison to a conventional molecular dynamics (MD) algorithm simulated under constant temperature conditions for more than 100 ns. We found that performing a sensitivity analysis of the effect of the parameters lambda and t1 before applying the self-guided MD scheme was important. Values of lambda greater than 0.1 and t1 equal to 1 ps were found to give improved structural evolution as compared to a conventional MD scheme. The hyperdynamics approximation scheme was found to be effective in obtaining boosts in the range of 4-12 for a small system without changing the dynamics of the evolution. However, for a large system size such an approach introduces significant perturbations to the pertinent equations of motion.

Algorithms↗
PubMed2005

Hybrid method coupling molecular dynamics and Monte Carlo simulations to study the properties of gases in microchannels and nanochannels.

We combine molecular dynamics (MD) and Monte Carlo (MC) simulations to study the properties of gas molecules confined between two hard walls of a microchannel or nanochannel. The coupling between MD and MC simulations is introduced by performing MD near the boundaries for accuracy and MC in the bulk because of the low computational cost. We characterize the influence of different densities and molecule sizes on the equilibrium properties of the gas in the microchannel. The effect of the particle size on the simulation results is very small in the case of a dilute gas and increases with the density. The hybrid MD-MC simulation method is validated by comparing the results for density and temperature profiles with those of pure MD and pure MC simulations. These results compare well for pure MD and pure MC, as well as hybrid MD-MC, both in the bulk and near the boundaries, when hard-sphere interactions are used. When Lennard-Jones potentials are used to accurately model the interactions between the gas and wall molecules instead, the results of pure MD simulations differ significantly from the pure MC simulations near the boundaries, but the results of the hybrid method compare well with the pure MD results near the wall, and with the pure MC and pure MD results in the middle of the channel. The hybrid method also very accurately simulates the interface between the MD and MC simulation domains. Comparisons between MD, MC, and hybrid MD-MC computational costs are outlined. The speedup when using 50% of the domain for MD simulations and 50% for MC simulations is very small compared to pure MD simulations times, but this speedup increases drastically for more realistic situations where the region near the wall is small compared to the bulk region.

Journal Article↗
PubMed1998

A molecular dynamics computer simulation study of nucleotide analogues. Comparison of the hydration pattern of dithymidine phosphate with those of the dithymidine methylphosphonate diastereomers.

The hydration pattern of thymidyl(3'->5') thymidine 1 and those of Rp and Sp diastereomers of the corresponding methylphosphonate analogue 2, have been studied using Molecular Dynamics (MD) computer simulation. It was found that the methylphosphonate modification leads to significant changes in the coordination of water molecules around the internucleotidic linkage and these, in turn, affect the hydration pattern of other parts of the molecule. The most notable differences between Rp and Sp diastereomers 2a and 2b were found to occur at the deoxyribose moieties of the nucleosid-5'-yl units.

Computer Simulation↗
PubMed1998

[Clinical-virologic course after superinfection of persistently infected cattle with cytopathogenic bovine viral diarrhea virus strains].

Vaccination with live cytopathogenic (cp) bovine viral diarrhoea virus (BVDV) is often used for control of this disease. In animals which are persistently infected with noncytopathogenic (ncp) BVDV this can lead to the outbreak of mucosal disease (MD). To simulate vaccination of such animals and to monitor the clinical-virological course after superinfection, nine clinically healthy calves which were persistently viremic were superinfected with different cp BVDV strains. One animal succumbed to early onset MD within three weeks after superinfection. During the observation period of 18 months four animals developed severe clinical signs. While two animals developed late onset MD, the other two had to be euthanized due to clinical signs which could not be related to the superinfecting BVDV. These results indicated that after superinfection or vaccination of persistently infected calves with cp BVDV the probability of developing early and/or late onset MD is significantly increased. The risks arising from uncritical vaccination of herds with unknown virological status in relation with the control of BVDV conforming to the actual official guidelines are discussed.

Animals↗
PubMed2006

A molecular dynamics simulation of SNase and its hydration shell at high temperature and high pressure.

Temperature- and pressure-induced unfolding of staphylococcal nuclease (SNase) was studied by Royer, Winter et al. using a variety of experimental techniques (SAXS, FT-IR and fluorescence spectroscopy, DSC, PPC, densimetry). For a more detailed understanding of the underlying mechanistic processes of the different unfolding scenarios, we have carried out a series of molecular dynamics (MD) computer simulations on SNase. We investigated the initial changes of the structure of the protein upon application of pressure (up to 5 kbar) and discuss volumetric and structural differences between the native and pressure pre-denatured state. Additionally, we have obtained the compressibility of the protein and hydration water and compare these data with experimental results. As water plays a crucial role in determining the structure, dynamics and function of proteins, we undertook a detailed analysis of the structure of the interfacial water and the protein-solvent H-bond network as well. Moreover, we report here also MD results on the temperature-induced unfolding of SNase. The time evolution of the protein volume and solvent accessible surface area during thermal unfolding have been investigated, and we present a detailed discussion of the temperature-induced unfolding pathway of SNase in terms of secondary and tertiary structural changes.

Computer Simulation↗
PubMedDate not supplied

NMR T2 distributions and two phase flow simulations from x-ray micro-tomography images of sandstones.

The distribution of fluids in the pore space of a series of sandstones is calculated as a function of capillary pressure using a two phase flow simulation model. The pore space is represented by a system of channels and nodes which are derived from x-ray micro-tomography images of sandstones. The sandstones studied varied in permeability from approximately 40 to 3,000 mD. The simulation results illustrate the significance of the pore level by-pass phenomena in controlling the location of fluids within the pore structure. The implications of these results on the interpretation of NMR T(2) distributions to determine the irreducible water saturation are discussed.

Computer Simulation↗
PubMed1999

Experiment and theory highlight role of native state topology in SH3 folding.

We use a combination of experiments, computer simulations and simple model calculations to characterize, first, the folding transition state ensemble of the src SH3 domain, and second, the features of the protein that determine its folding mechanism. Kinetic analysis of mutations at 52 of the 57 residues in the src SH3 domain revealed that the transition state ensemble is even more polarized than suspected earlier: no single alanine substitution in the N-terminal 15 residues or the C-terminal 9 residues has more than a two-fold effect on the folding rate, while such substitutions at 15 sites in the central three-stranded beta-sheet cause significant decreases in the folding rate. Molecular dynamics (MD) unfolding simulations and ab initio folding simulations on the src SH3 domain exhibit a hierarchy of folding similar to that observed in the experiments. The similarity in folding mechanism of different SH3 domains and the similar hierarchy of structure formation observed in the experiments and the simulations can be largely accounted for by a simple native state topology-based model of protein folding energy landscapes.

Amino Acid Sequence↗
PubMed2003

Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm.

The influence of various factors on the accuracy of protein-ligand docking is examined. The factors investigated include the role of a grid representation of protein-ligand interactions, the initial ligand conformation and orientation, the sampling rate of the energy hyper-surface, and the final minimization. A representative docking method is used to study these factors, namely, CDOCKER, a molecular dynamics (MD) simulated-annealing-based algorithm. A major emphasis in these studies is to compare the relative performance and accuracy of various grid-based approximations to explicit all-atom force field calculations. In these docking studies, the protein is kept rigid while the ligands are treated as fully flexible and a final minimization step is used to refine the docked poses. A docking success rate of 74% is observed when an explicit all-atom representation of the protein (full force field) is used, while a lower accuracy of 66-76% is observed for grid-based methods. All docking experiments considered a 41-member protein-ligand validation set. A significant improvement in accuracy (76 vs. 66%) for the grid-based docking is achieved if the explicit all-atom force field is used in a final minimization step to refine the docking poses. Statistical analysis shows that even lower-accuracy grid-based energy representations can be effectively used when followed with full force field minimization. The results of these grid-based protocols are statistically indistinguishable from the detailed atomic dockings and provide up to a sixfold reduction in computation time. For the test case examined here, improving the docking accuracy did not necessarily enhance the ability to estimate binding affinities using the docked structures.

Algorithms↗