Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “MD simulation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9Linked to original sources
PubMed2005

A statistical approach to the interpretation of molecular dynamics simulations of calmodulin equilibrium dynamics.

A sample of 35 independent molecular dynamics (MD) simulations of calmodulin (CaM) equilibrium dynamics was prepared from different but equally plausible initial conditions (20 simulations of the wild-type protein and 15 simulations of the D129N mutant). CaM's radius of gyration and backbone mean-square fluctuations were analyzed for the effect of the D129N mutation, and simulations were compared with experiments. Statistical tests were employed for quantitative comparisons at the desired error level. The computational model predicted statistically significant compaction of CaM relative to the crystal structure, consistent with the results of small-angle X-ray scattering (SAXS) experiments. This effect was not observed in several previously reported studies of (Ca2+)(4)-CaM, which relied on a single MD run. In contrast to radius of gyration, backbone mean-square fluctuations showed a distinctly non-normal and positively skewed distribution for nearly all residues. Furthermore, the D129N mutation affected the backbone dynamics in a complex manner and reduced the mobility of Glu123, Met124, Ile125, Arg126, and Glu127 located in the adjacent alpha-helix G. The implications of these observations for the comparisons of MD simulations with experiments are discussed. The proposed approach may be useful in studies of protein equilibrium dynamics where MD simulations fall short of properly sampling the conformational space, and when the comparison with experiments is affected by the reproducibility of the computational model.

Calmodulin↗
PubMed1996

The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules.

A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with different force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints.

Computer Simulation↗
PubMed2006

Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations.

Two independent replica-exchange molecular dynamics (REMD) simulations with an explicit water model were performed of the Trp-cage mini-protein. In the first REMD simulation, the replicas started from the native conformation, while in the second they started from a nonnative conformation. Initially, the first simulation yielded results qualitatively similar to those of two previously published REMD simulations: the protein appeared to be over-stabilized, with the predicted melting temperature 50-150K higher than the experimental value of 315K. However, as the first REMD simulation progressed, the protein unfolded at all temperatures. In our second REMD simulation, which starts from a nonnative conformation, there was no evidence of significant folding. Transitions from the unfolded to the folded state did not occur on the timescale of these simulations, despite the expected improvement in sampling of REMD over conventional molecular dynamics (MD) simulations. The combined 1.42 micros of simulation time was insufficient for REMD simulations with different starting structures to converge. Conventional MD simulations at a range of temperatures were also performed. In contrast to REMD, the conventional MD simulations provide an estimate of Tm in good agreement with experiment. Furthermore, the conventional MD is a fraction of the cost of REMD and continuous, realistic pathways of the unfolding process at atomic resolution are obtained.

Protein Folding↗
PubMed2005

Tests of the homogeneous nucleation theory with molecular-dynamics simulations. I. Lennard-Jones molecules.

Two kinds of the homogeneous nucleation theory exist at the present: the classical nucleation theory and the semiphenomenological model. To test them, we performed molecular-dynamics (MD) simulations of nucleation from vapor to liquid with 5000-20,000 Lennard-Jones-type molecules. Simulations were done for various values of supersaturation ratios (from 2 to 10) and temperatures (from 80 to 120 K). We compared the size distribution of clusters in MD simulations with those in the theoretical models because the number density of critical clusters governs the nucleation rate. We found that the semiphenomenological model achieves excellent agreements in size distributions of the clusters with all MD simulations we done. The classical theory underestimates the number density of the clusters in the temperature range of 80-100 K, but overestimates in 100-120 K. The semiphenomenological model also predicts well the nucleation rate in MD simulations, while the classical nucleation theory does not. Our results confirmed the validity of the semiphenomenological model for Lennard-Jones-type molecules.

Journal Article↗
PubMed2005

Diffusion coefficients of small gas molecules in amorphous cis-1,4-polybutadiene estimated by molecular dynamics simulations.

Molecular dynamics (MD) simulations were employed to estimate the diffusion coefficients of small gas molecules (Ar, O2, N2, CO2, and CH4) in amorphous cis-1,4-polybutadiene in the temperature range of 250-400 K. The VT diagram and solubility parameter of the amorphous polymer have been successfully reproduced using a full atomistic potential. Diffusion coefficients were calculated from long NPT MD runs (up to 3 ns) at temperature ranging from 250 up to 400 K. Calculated diffusion coefficients compare well with experimental data as well as previous published work, though a systematic overestimation is found due to the finite-size effect of the model. The influence of various physical and computational parameters on the results is discussed. The diffusion mechanism is examined at the different temperatures of study.

Journal Article↗
PubMed1996

Combining Laue diffraction and molecular dynamics to study enzyme intermediates.

Two separate techniques, Laue diffraction and computational molecular dynamics (MD) simulations, have been independently developed to allow the visualization and assessment of transient structural states. Recent studies on isocitrate dehydrogenase show that computational MD simulations of an enzymatic Michaelis complex are consistent with difference Fourier electron density maps of the same structure from a Laue experiment. The use of independent MD studies during crystallographic refinement has allowed us to assign with confidence a number of additional contacts and features important for hydride transfer. We find that unrestrained independent MD simulations provides a very useful method of cross-validation for highly mobile atoms in regions of experimental density that are poorly defined. Likewise, information from Laue difference maps provides information about substrate conformation and interactions that greatly facilitate MD simulations.

Computer Simulation↗
PubMed2004

Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching.

A novel least-squares fitting approach is presented to obtain classical force fields from trajectory and force databases produced by ab initio (e.g., Car-Parrinello) molecular dynamics (MD) simulations. The method was applied to derive effective nonpolarizable three-site force fields for liquid water at ambient conditions from Car-Parrinello MD simulations in the Becke-Lee-Yang-Parr approximation to the electronic density functional theory. The force-matching procedure includes a fit of short-ranged nonbonded forces, bonded forces, and atomic partial charges. The various parameterizations of the water force field differ by an enforced smooth cut-off applied to the short-ranged interaction term. These were obtained by fitting to the trajectory and force data produced by Car-Parrinello MD simulations of systems of 32 and 64 H(2)O molecules. The new water force fields were developed assuming both flexible or rigid molecular geometry. The simulated structural and self-diffusion properties of liquid water using the fitted force fields are in close agreement with those observed in the underlying Car-Parrinello MD simulations. The resulting empirical models compare to experiment much better than many conventional simple point charge (SPC) models. The fitted potential is also shown to combine well with more sophisticated intramolecular potentials. Importantly, the computational cost of the new models is comparable to that for SPC-like potentials.

Journal Article↗
PubMed2005

Characterization of the denaturation of human alpha-lactalbumin in urea by molecular dynamics simulations.

Molecular dynamics (MD) simulations were used to characterize the non-cooperative denaturation of the molten globule A-state of human alpha-lactalbumin by urea. A solvent of explicit urea and water molecules was used, corresponding to a urea concentration of approximately 6M. Three simulations were performed at temperatures of 293K, 360K and 400K, with lengths of 2 ns, 8 ns and 8 ns respectively. The results of the simulations were compared with experimental data from NMR studies of human alpha-lactalbumin and related peptides. During the simulations, hydrogen bonds were formed from the protein to both urea and water molecules as intra-protein hydrogen bonds were lost. Urea was shown to compete efficiently with water as both a hydrogen bond donor and acceptor. Radial distribution functions of water and urea around hydrophobic side chain atoms showed a significant increase in urea molecules in the solvation shell as the side chains became exposed during denaturation. A considerable portion of the native-like secondary structure persisted throughout the simulations. However, in the simulations at 360K and 400K, there were substantial changes in the packing of aromatic and other hydrophobic side chains in the protein, and many native contacts were lost. The results suggest that during the non-cooperative denaturation of the molten globule, secondary structure elements are stabilized by non-specific, non-native interactions.

Circular Dichroism↗
PubMed2003

Effects of a carane derivative local anesthetic on a phospholipid bilayer studied by molecular dynamics simulation.

Molecular dynamics (MD) simulations of two hydrated palmitoyloleoylphosphatidylcholine (POPC) bilayers each containing eight carane derivative (KP-23) local anesthetic (LA) molecules in neutral (POPC-LA) or protonated (POPC-LAH) forms were carried out to investigate the effect of KP-23 and its protonation on the bilayer. 3-ns trajectories were used for analyses. A pure POPC bilayer was employed as a reference system. In both POPC-LA and POPC-LAH systems a few KP-23 molecules intercalated into the bilayer and moved near the bilayer/water interface. They were located on the hydrophobic core side of the interface in the POPC-LA bilayer, but on the water phase side in the POPC-LAH bilayer. The order of the POPC chains was higher in the POPC-LA bilayer than in the pure POPC bilayer and was lower in the POPC-LAH bilayer. Interactions between polar groups of KP-23 and POPC or water were responsible for a lower hydration of POPC headgroups in POPC bilayers containing KP-23 than in the pure POPC bilayer. KP-23 molecules were found to form aggregates both in POPC-LA and POPC-LAH bilayers. Due to higher amphiphilicity of LAH, the LAH aggregate was more micelle-like and larger than the LA one. The results demonstrate the rapid timescales of the initial processes that take place at and near the bilayer interface as well as details of the atomic level interactions between local anesthetic and the lipid matrix of a cell membrane.

Anesthetics, Local↗
PubMed2006

Transport behavior of oxygen and nitrogen through organasilicon-containing polystyrenes by molecular simulation.

Molecular dynamics (MD) simulations have been used to study the transport properties of oxygen and nitrogen in the para-substituted polystyrenes which possess one to four Si atoms in each substituent. The Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies (COMPASS) force field was used to construct the polymers. Diffusion coefficients were obtained from molecular dynamics (NVT ensemble) with up to 3 ns simulation times. After molecular dynamic simulation, the trajectories of the small molecules in the polymer matrix were obtained. Then diffusion coefficients have been calculated from the Einstein relationship revealing a considerable agreement between the simulated and the experimental data. And solubility coefficients have been calculated by the Grand Canonical Monte Carlo (GCMC) method. The solubility of oxygen increased with increasing Si content in the polymer membrane. The para-substituted polystyrenes with a branched substituent at the alpha-position showed higher permeability than those of the nonbranched ones. The higher the glass transition temperature (T(g)) of the membrane, the larger the diffusion coefficients of oxygen and nitrogen obtained.

Journal Article↗
PubMed1993

Protein hydration elucidated by molecular dynamics simulation.

Molecular dynamics (MD) simulation covering a wide range of hydration indicate that myoglobin is fully hydrated by 350 water molecules, in agreement with experiment. These waters, originally placed uniformly about the protein, form clusters that hydrate every charged group throughout the entire simulation. Some atoms in charged groups are hydrated by two water layers while 37% of the protein surface remains uncovered. The locations of the 350 waters are consistent with those of crystallographic waters resolved by x-ray and neutron diffraction. Hydration by 350 waters at 300 K stabilizes the conformation of carboxymyoglobin measured by x-ray diffraction throughout the entire protein, halves the rate of torsional transitions, and promotes alternative conformations for surface atoms. The glass transition observed experimentally in hydrated myoglobin near 220 K is also seen in the simulations and correlates with an increase in the number of dihedral angles undergoing transitions. The anharmonic protein motion above 220 K is enhanced by protein hydration.

Computer Simulation↗
PubMed2006

Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design.

To test the anticorrelated relationship that was recently displayed in conventional molecular dynamics (MD) simulations, several different restrained MD simulations on a wild type and on the V82F/I84V drug-resistant mutant of HIV-1 protease were performed. This anticorrelated relationship refers to the observation that compression of the peripheral ear-to-cheek region of HIV protease (i.e., the elbow of the flap to the fulcrum and the cantilever) occurred as the active site flaps were opening, and, conversely, expansion of that ear-to-cheek region occurred as both flaps were closing. An additional examination of this anticorrelated relationship was necessary to determine whether it can be harnessed in a useful manner. Consequently, six different MD experiments were performed that incorporated pairwise distance restraints in that ear-to-cheek region (i.e., the distance between the alpha-carbons of Gly40 and Gln61 was restrained to either 7.7 or 10.5 A, in both monomers). Pushing the backbones of the ear and the cheek regions away from each other slightly did force the flaps that guard the active site to remain closed in both the wild type and the mutant systems-even though there were no ligands in the active sites. Thus, these restrained MD simulations provided evidence that the anticorrelated relationship can be exploited to affect the dynamic behavior of the flaps that guard the active site of HIV-1 protease. These simulations supported our hypothesis of the mechanism governing flap motion, and they are the first step towards validating that peripheral surface as a new target for drug design.

Binding Sites↗
PubMed2002

Exploring nucleoside hydrolase catalysis in silico: molecular dynamics study of enzyme-bound substrate and transition state.

The mechanism of action of inosine-uridine nucleoside hydrolase has been investigated by long-term molecular dynamics (MD) simulation in TIP3P water using stochastic boundary conditions. Five MD studies have been performed with enzyme substrate complex (E.S), enzyme substrate complex with protonated His241 (EH.S), enzyme transition state complex (E.TS), enzyme transition state complex with protonated His241 (EH.TS), and His241Ala transition state complex E(H241A).TS. Special attention has been given to the role of His241, which has been considered as the general acid catalyst to assist departure of the leaving nucleobase on the basis of its location in the active site in the X-ray crystal structure (). Yet on the basis of the location in the active site, Tyr229 is closer to the aniline ring of pAPIR as compared to His241. On initiation of MD simulations, His241 does not approach the nucleobase in the structures of EH.S, E.S, EH.TS, and E.TS. In the solvated enzyme, Tyr229, which is a member of the hydrogen bonding network inosine O2'.Asp14.His241.Tyr229.inosine N7, serves as a proton source to the leaving nucleobase. The loss of significant activity of His241Ala mutant is shown to be related to the disruption of the above hydrogen bonded network and the distancing of Tyr229 from inosine N7. The structures of the enzyme complexes with substrate or TS are not visibly altered on protonation of His241, a most unusual outcome. The bell-shaped pH dependence upon pK(app)'s of 7.1 and 9.1 may be attributed to the necessity of the dissociation of Asp10 or Asp15 and the acid form of Tyr229, respectively. In TS, the residue Ile81 migrated closer, whereas Arg233 moved away from the nucleobase. The probability of ribooxocarbenium ion stabilization by Asn168 and Asp14 is discussed. The Asp14-CO(2)(-) is hydrogen bonded to the ribose 2'-OH for 96% of the MD simulation time. Nucleophilic addition of water138 to ribooxocarbenium ion is suggested to be assisted by the proton shuttle from water138 --> Asp10 --> Asp15 --> water pool. An anticorrelation motion between Tyr229-OH and Asn168-OD1 in EH.S and E.S is observed. The relationship of this anticorrelated motion to mechanism, if any, deserves further exploration, perhaps the formation of a near attack conformation.

Animals↗
PubMed2005

Role of ions on structure and stability of a synthetic gramicidin ion channel in solution. A molecular dynamics study.

We performed a molecular dynamics (MD) simulation to the investigate structure and stability of a synthetic gramicidin-like peptide in solution with and without ions. The starting structures of the MD simulations were taken from two recently solved NMR structures of this peptide in isotropic solution, which forms stable monomers or dimers in the presence or absence of ions, respectively. The monomeric structure is channel-like and is assumed to be stabilized by the presence of two Cs(+) ions bound in the channel, each one close to one channel entrance. In our MD simulations, we observed how the Cs(+) ions bind in the channel formed by the monomeric gramicidin-like peptide using implicit solvent and explicit ions with a concentration of 2 M. MD simulations were performed with and without explicit ions but with an implicit solvent model defined by the generalized Born approximation, which was used to mimic the dielectric properties of the solvent and to speed up the computations.

Gramicidin↗
PubMed2006

Drag on a nanotube in uniform liquid argon flow.

In this work, nonequilibrium molecular dynamics (MD) simulations were performed to investigate uniform liquid argon flow past a carbon nanotube. In the simulation, nanotubes were modeled as rigid cylinders of carbon atoms. Both argon-argon and argon-carbon interactions were calculated based on Lennard-Jones potential. Simulated drag coefficients were compared with (i) published empirical equation which was based on experiments conducted with macroscale cylinders and (ii) finite element (FE) analyses based on Navier-Stokes equation for flow past a circular cylinder using the same dimensionless parameters used in MD simulations. Results show that classical continuum mechanics cannot be used to calculate drag on a nanotube. In slow flows, the drag coefficients on a single-walled nanotube calculated from MD simulations were larger than those from the empirical equation or FE analysis. The difference increased as the flow velocity decreased. For higher velocity flows, slippage on the surface of the nanotube was identified which resulted in lower drag coefficient from MD simulation. This explains why the drag coefficient from MD dropped faster than those from the empirical equation or FE simulation as the flow velocity increased. It was also found that the drag forces are almost equal for single- and double-walled nanotubes with the same outer diameter, implying that inner tubes do not interact with fluid molecules.

Journal Article↗
PubMed2003

In silico mutations and molecular dynamics studies on a winged bean chymotrypsin inhibitor protein.

Winged bean chymotrypsin inhibitor (WCI) has an intruding residue Asn14 that plays a crucial role in stabilizing the reactive site loop conformation. This residue is found to be conserved in the Kunitz (STI) family of serine protease inhibitors. To understand the contribution of this scaffolding residue on the stability of the reactive site loop, it was mutated in silico to Gly, Ala, Ser, Thr, Leu and Val and molecular dynamics (MD) simulations were carried out on the mutants. The results of MD simulations reveal the conformational variability and range of motions possible for the reactive site loop of different mutants. The N-terminus side of the scissile bond, which is close to a beta-barrel, is conformationally less variable, while the C-terminus side, which is relatively far from any such secondary structural element, is more variable and needs stability through hydrogen-bonding interactions. The simulated structures of WCI and the mutants were docked in the peptide-binding groove of the cognate enzyme chymotrypsin and the ability to form standard hydrogen-bonding interactions at P3, P1 and P2' residues were compared. The results of the MD simulations coupled with docking studies indicate that hydrophobic residues like Leu and Val at the 14th position are disruptive for the integrity of the reactive site loop, whereas a residue like Thr, which can stabilize the C-terminus side of the scissile bond, can be predicted at this position. However, the size and charge of the Asn residue made it most suitable for the best maintenance of the integrity of the reactive site loop, explaining its conserved nature in the family.

Binding Sites↗
PubMed2003

Molecular dynamics simulations of the unfolding of beta(2)-microglobulin and its variants.

In this study, we examined the unfolding processes of native beta(2)-microglobulin and two related variants, one with an N-terminal hexapeptide deletion DeltaN6 and another with Lys57-Asp58 cleavage, by high-temperature molecular dynamics simulations. Three simulation models were used, molecular dynamics (MD) simulations with explicit water solvation, MD simulations with the CHARMM EEF1 force field and Langevin dynamics with the CHARMM EEF1 force field. Our simulations reproduce many of the experimentally observed structural changes. The most striking agreement is in the beta-strands to alpha-helix transition. In our simulations, strands beta(3), beta(4) and beta(5) consistently change to alpha-helix, whereas beta(8) changes to an alpha-helix only briefly. Through comparisons of the conformational behavior of the native, the DeltaN6 and the Lys-cut beta(2)-m, using the three simulation methods, we identified the consensus conformational changes that differentiate between the native beta(2)-m and its two variants. We found that the main effect of the removal of the N-terminal hexapeptide is to increase the separation between strands beta(2) and beta(6) and to facilitate the beta to alpha transition. On the other hand, the lysine cleavage only increases the flexibility of strand beta(5) and does not affect the interactions between strands beta(2) and beta(6). These conformational changes may relate to polymerization tendencies of these variants.

Amyloidosis↗
PubMed2007

Insight into the activity of SARS main protease: Molecular dynamics study of dimeric and monomeric form of enzyme.

The phenomenon that SARS coronavirus main protease (SARS M(pro)) dimer is the main functional form has been confirmed by experiment. However, because of the absence of structural information of the monomer, the reasons for this remain unknown. To investigate it, two molecular dynamics (MD) simulations in water for dimer and monomer models have been carried out, using the crystal structure of protomer A of the dimer as the starting structure for the monomer. During the MD simulation of dimer, three interest phenomena of protomer A have been observed: (i) the distance between NE2 of His41 and SG of Cys145 averages 3.72 A, which agrees well with the experimental observations made by X-ray crystallography; (ii) His163 and Glu166 form the "tooth" conformational properties, resulting in the specificity for glutamine at substrate P1 site; and (iii) the substrate-binding pocket formed by loop 140-146 and loop 184-197 is large enough to accommodate the substrate analog. However, during the MD simulation of the monomer complex, the three structural characteristics are all absent, which results directly in the inactivation of the monomer. Throughout the MD simulation of the dimer, the N-terminus of protomer B forms stable hydrogen bonds with Phe140 and Glu166, through which His163, Glu166, and loop 140-146 are kept active form. Furthermore, a water-bridge has been found between the N-terminus of protomer B and Gly170, which stabilizes His172 and avoids it moving toward Tyr161 to disrupt the H-bond between Tyr161 and His163, stabilizing the conformation of His163. The interactions between the N-terminus and another monomer maintain the activity of dimer.

Catalytic Domain↗