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Results for “Molecular Dynamics Simulation”

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PubMed1996

Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation.

Molecular dynamics (MD) simulations of 100 ps have been carried out to study the active-site behaviour of the Cu,Zn superoxide dismutase dimer (SOD) in water. The active site of each subunit was monitored during the whole simulation by calculating the distances between functional residues and the catalytic copper. The results indicate that charge orientation is maintained at each active site but the solvent accessibility varies. Analysis of the MD simulation, carried out by using the atomic displacement covariance matrix, has shown a different intra-subunit correlation pattern for the two monomers and the presence of inter-subunit correlations. The MD simulation presented here indicates an asymmetry in the two active sites and different dynamic behaviour of the two SOD subunits.

Animals↗

PubMed2004

Characterization of the conformational space of a triple-stranded beta-sheet forming peptide with molecular dynamics simulations.

Molecular dynamics (MD) simulations have been performed on a series of mutants of the 20 amino acid peptide Betanova in order to critically assess the ability of MD simulations to reproduce the folding and stability of small beta-sheet-forming peptides on currently accessible timescales. Simulations were performed in both water and in 40% methanol solution, using an explicit solvent model. The simulations suggest that all mutants adopt a wide range of conformations in solution, that the structures are highly flexible, and that stabilization of compact structures is due to a delicate balance of hydrophobic and polar side-chain interactions. Simulations longer than 100 ns, although not sufficient for a complete thermodynamic and kinetic description of the system, sample an ensemble of compact conformations characterized by the loss of ordered beta-sheet secondary structure. This suggests that no significant free energy barrier separates the different conformations available.

Algorithms↗

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↗

PubMed1993

A model for the dynemicin-A cleavage of DNA using molecular dynamics simulation.

Molecular dynamics (MD) simulations to model possible reaction pathways of the dynemicin-A-DNA cleavage mechanism were performed. Two base-pairs sequences, ApCpTpApCpTp-3'/TpGpApTpGpAp-5' and CpApCpGpGpGp-3'/GpTpGpCpCpCp-5', were considered in the calculations. A model based on a prior study of intercalation of dynemicin-A and posterior activation of the drug was assumed in this study. The minimum energy minor groove intercalation complexes for dynemicin-A were used as starting structures in the MD simulations for the reactive intermediate species involved in the postulated action mechanism. The dynemicin-A diol derivative product of the opening of the epoxy ring was used as a "steric mimic" ligand for the DNA-reactive diaryl intermediate. The calculated changes in the geometry of the intercalation complex, due to the opening of the epoxy ring, correspond to the approach of the postulated intermolecular reaction centers in the intercalation states that are responsible for the highest observed DNA cleavage frequency observed. Conversely, unfavorable reaction geometries were found for the intercalation modes corresponding to the lowest observed DNA cutting frequencies.

Anthraquinones↗

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

LiTFSI structure and transport in ethylene carbonate from molecular dynamics simulations.

Molecular dynamics (MD) simulations using a many-body polarizable force field were performed on ethylene carbonate (EC) doped with lithium bistrifluoromethanesulfonamide (LiTFSI) salt as a function of temperature and salt concentration. At 313 K Li+ was coordinated by 2.7-3.2 EC carbonyl oxygen atoms and 0.67-1.05 TFSI- oxygen atoms at EC:Li = 10 and 20 salt concentrations. In completely dissociated electrolytes, however, Li+ was solvated by approximately 3.8 carbonyl oxygen atoms from EC on average. The probability of ions to participate ion aggregates decreased exponentially with an increase in the size of the aggregate. Ion and solvent self-diffusion coefficients and conductivity predicted by MD simulations were in good agreement with experiments. Approximately half of the charge was transported by charged ion aggregates with the other half carried by free (uncomplexed by counterion) ions. Investigation of the Li+ transport mechanism revealed that contribution from the Li+ diffusion together with its coordination shell to the total Li+ transport is similar to the contribution arising from Li+ exchanging solvent molecules in its first coordination shell with solvents from the outer shells.

Journal Article↗

PubMed2006

Structure and dynamics of N-methyl-N-propylpyrrolidinium bis(trifluoromethanesulfonyl)imide ionic liquid from molecular dynamics simulations.

Molecular dynamics (MD) simulations were performed on N-methyl-N-propylpyrrolidinium bis(trifluoromethanesulfonyl)imide (mppy+TFSI-) from 303 to 393 K to improve understanding of the structure and ion transport of this ionic liquid. The density, ion self-diffusion coefficients, conductivity, and viscosity of mppy+TFSI- predicted from MD simulations are in good agreement with experimental measurements. The time-dependent shear modulus of the ionic liquids was calculated and compared with that for nonionic liquids. On average each mppy+ cation was found to be coordinated by four TFSI- anions. The angular distributions of N(TFSI-)-N(mppy+)-N(TFSI-) and N(mppy+)-N(TFSI-)-N(mppy+) exhibit a maximum at 80-90 degrees and a second maximum at 180 degrees . Correlation of ion motion was found to lower ionic conductivity by approximately one-third from the expected value based upon ion self-diffusion coefficients. Rotational motion of the cation and anion are anisotropic with the degree of anisotropy increasing with decreasing temperature. Electrostatic interactions are responsible for slowing down the dynamics of the ionic liquid by more than an order of magnitude and a dramatic decrease of the time-dependent shear modulus.

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↗

PubMed2002

Bridge function and other structural properties of core-softened model fluids from molecular dynamics simulations.

Molecular dynamics (MD) simulations in three dimensions have been performed for a fluid with particles interacting with a continuous version of the Stell-Hemmer core-softened potential that in two dimensions has been known to reproduce most of the static and dynamic anomalies of liquid water. The pair distribution function obtained from the MD simulation is extrapolated with the help of integral equation theory with a suitable closure relation and the bridge function is extracted. A strong dependence of the bridge function on the system size, i.e., the total number of particles (N) used in the simulation box is observed, which leads to spurious values of the structure factor at long wavelengths. A simple self-consistent correction scheme for the finite size effect has been adopted to correct the bridge function and this scheme produces the correct bridge function even for a small system size. The effects of temperature, number density, and potential parameters on the pair distribution functions and extracted bridge functions are extensively studied.

Journal Article↗

PubMed2005

Structure, energetics, and dynamics of water adsorbed on the muscovite (001) surface: a molecular dynamics simulation.

Molecular dynamics (MD) computer simulations of liquid water adsorbed on the muscovite (001) surface provide a greatly increased, atomistically detailed understanding of surface-related effects on the spatial variation in the structural and orientational ordering, hydrogen bond (H-bond) organization, and local density of H2O molecules at this important model phyllosilicate surface. MD simulations at constant temperature and volume (statistical NVT ensemble) were performed for a series of model systems consisting of a two-layer muscovite slab (representing 8 crystallographic surface unit cells of the substrate) and 0 to 319 adsorbed H2O molecules, probing the atomistic structure and dynamics of surface aqueous films up to 3 nm in thickness. The results do not demonstrate a completely liquid-like behavior, as otherwise suggested from the interpretation of X-ray reflectivity measurements and earlier Monte Carlo simulations. Instead, a more structurally and orientationally restricted behavior of surface H2O molecules is observed, and this structural ordering extends to larger distances from the surface than previously expected. Even at the largest surface water coverage studied, over 20% of H2O molecules are associated with specific adsorption sites, and another 50% maintain strongly preferred orientations relative to the surface. This partially ordered structure is also different from the well-ordered 2-dimensional ice-like structure predicted by ab initio MD simulations for a system with a complete monolayer water coverage. However, consistent with these ab initio results, our simulations do predict that a full molecular monolayer surface water coverage represents a relatively stable surface structure in terms of the lowest diffusional mobility of H2O molecules along the surface. Calculated energies of water adsorption are in good agreement with available experimental data.

Journal Article↗

PubMed1995

Dramatic differences in the motions of the mouth of open and closed cytochrome P450BM-3 by molecular dynamics simulations.

Molecular dynamics trajectories were calculated separately for each of the two molecules in the asymmetric unit of the crystal structure of the hemoprotein domain of cytochrome P450BM-3. Each simulation was 200 ps in length and included a 10 A layer of explicit solvent. The simulated time-average structure of each P450BM-3 molecule is closer to its crystal structure than the two molecular dynamics time-averaged structures are to each other. In the crystal structure, molecule 2 has a more accessible substrate binding pocket than molecule 1, and this difference is maintained throughout the simulations presented here. In particular, the substrate docking regions of molecule 1 and molecule 2 diverge in the solution state simulations. The mouth of the substrate binding pocket is significantly more mobile in the simulation of molecule 2 than in the simulation of molecule 1. For molecule 1, the width of the mouth is only slightly larger than its X-ray value of 8.7 A and undergoes fluctuations of about 1 A. However, in molecule 2, the mouth of the substrate binding pocket is dramatically more open in the time-average molecular dynamics structure (14.7 A) than in the X-ray structure (10.9 A). Furthermore, this region of the protein undergoes large amplitude motions during the trajectory that are not seen in the trajectory of molecule 1, repeatedly opening and closing up to 7 A. Presumably, the binding of different substrates will induce the mouth region to adopt different conformations from within the wide range of structures that are accessible.

Binding Sites↗

PubMed2004

Characterization of polyethylene crystallization from an oriented melt by molecular dynamics simulation.

Molecular dynamics is used to characterize the process of crystallization for a united atom model of polyethylene. An oriented melt is produced by uniaxial deformation under constant load, followed by quenching below the melting temperature at zero load. The development of crystallinity is monitored simultaneously using molecular-based order parameters for density, energy, and orientation. For crystallization temperatures ranging from 325 to 375 K, these simulations clearly show the hallmarks of crystal nucleation and growth. We can identify multiple nucleation events, lamellar growth up to the limit imposed by periodic boundaries of the simulation cell, and lamellar thickening. We observe a competition between the rate of nucleation, which results in multiple crystallites, the rate of chain extension, which results in thicker lamellae, and the rate of chain conformational relaxation, which is manifested in lower degrees of residual order in the noncrystalline portion of the simulation. The temperature dependence of lamellar thickness is in accord with experimental data. At the higher temperatures, tilted chain lamellae are observed to form with lamellar interfaces corresponding approximately to the [201] facet, indicative of the influence of interfacial energy.

Journal Article↗

PubMed2006

An investigation of the ionic and solvation patterns of dsDNG versus dsDNA by use of molecular dynamics simulations.

Molecular dynamics has been employed to analyze the counterion and water atmospheres around the deoxynucleic guanidine (DNG) duplex G(12)-C(12). These features are compared to those of DNA G(12)-C(12). The chloride counterions of cationic DNG demonstrate fewer penetrations and only fleeting residence times in the minor groove, as opposed to the multi-nanosecond visits seen by sodium ions in DNA minor grooves. The 10 ns simulations also show the differences in hydration patterns between the DNG and DNA duplexes.

Cations, Monovalent↗

PubMed1993

Mechanism for the rotamase activity of FK506 binding protein from molecular dynamics simulations.

Molecular dynamics (MD) and free energy perturbation (FEP) methods are used to study the binding and mechanism of isomerization of a tetrapeptide (AcAAPFNMe) by FK506 binding protein (FKBP). Detailed structures are predicted for the complexes of FKBP with the peptide in both ground-state and transition-state forms. The results support a mechanism of catalysis by distortion, where a large number of nonbonded interactions act together to stabilize preferentially the twisted transition state. The two most important groups for the catalysis are suggested to be Trp59 and Asp37, but several other groups are identified as directly or indirectly involved in the binding and catalysis. However, the structural results do not support the notion that the keto oxygen of the immunosuppressive agents FK506 and rapamycin mimics the oxygen for the twisted peptide bond in the FKBP-transition-state complex.

Amino Acid Sequence↗

PubMed1994

Computer simulations of cyclic and acyclic cholinergic agonists: conformational search and molecular dynamics simulations.

Molecular dynamics simulations have been performed on aqueous solutions of two chemically similar nicotinic cholinergic agonists in order to compare their structural and dynamical differences. The cyclic 1,1-dimethyl-4-acetylpiperazinium iodide (HPIP) molecule was previously shown to be a strong agonist for nicotinic acetylcholine receptors (McGroddy et al., 1993), while the acyclic N,N,N,N'-tetramethyl-N'-acetylethylenediamine iodide (HTED) derivative is much less potent. These differences were expected to arise from differences in the solution structures and internal dynamics of the two molecules. HPIP was originally thought to be relatively rigid; however, molecular dynamics simulations suggest that the acetyl portion of the molecule undergoes significant ring dynamics on a psec timescale. The less constrained HTED molecule is relatively rigid, with only one transition observed about any of the major dihedrals in four 100 psec simulations, each started from a different conformation. The average structures obtained from the simulations are very similar to the starting minimized structure in each case, except for the HTED simulation where a single rotation about the N-C-C-N(+) backbone occurred. In each case, HTED had three to five more water molecules in its primary solvation shell than HPIP, indicating that differences in the energetics of desolvation before binding may partially explain the increased potency of HPIP as compared to HTED.

Biophysical Phenomena↗

PubMed2005

Simulation of screw dislocation motion in iron by molecular dynamics simulations.

Molecular dynamics (MD) simulations are used to investigate the response of a/2<111> screw dislocation in iron submitted to pure shear strain. The dislocation glides and remains in a (110) plane; the motion occurs exclusively through the nucleation and propagation of double kinks. The critical stress is calculated as a function of the temperature. A new method is developed and used to determine the activation energy of the double kink mechanism from MD simulations. It is shown that the differences between experimental and simulation conditions lead to a significant difference in activation energy. These differences are explained, and the method developed provides the link between MD and mesoscopic simulations.

Journal Article↗

PubMed2005

Accommodation of a 1S-(-)-benzo[c]phenanthrenyl-N6-dA adduct in the Y-family Dpo4 DNA polymerase active site: structural insights through molecular dynamics simulations.

Molecular modeling and molecular dynamics simulations have been performed to elucidate feasible structures in the Y-family Dpo4 DNA polymerase for the 1S-(-)-trans-anti-B[c]Ph-N6-dA adduct, derived from the fjord region polycyclic aromatic hydrocarbon (PAH) benzo[c]phenanthrene. Three types of models were delineated as follows: an intercalation model, a model with the aromatic ring system in the polymerase major groove open pocket, and a -1 deletion major groove model. All four 2'-deoxyribonucleoside 5'-triphosphates (dNTPs) were considered in the first two cases, and a normal Watson-Crick partner positioned to have skipped the modified template was employed as the incoming dNTP in the -1 deletion case. The trajectories derived from the dynamics simulations were analyzed in detail to evaluate the extents of distortion for each system. Overall, our results suggest that the major groove model is the least distorted, followed by the -1 deletion model, while the intercalation model is perturbed the most. The syn-dGTP and syn-dATP mismatches opposite the lesion are well-accommodated in the major groove model, as is the normal Watson-Crick partner dTTP. The intercalation model appears most likely to impede the polymerase. More broadly, these models look reasonable for other PAH metabolite-derived adducts to adenine with similar 1S stereochemistry. Furthermore, these models suggest how error-prone translesion synthesis by Y-family polymerases might produce mutations that may play a role in the initiation of cancer.

Carcinogens↗