Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Molecular Dynamic 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 1,531 records · Page 85Linked to original sources
PubMed2005

How homogeneous are the trehalose, maltose, and sucrose water solutions? An insight from molecular dynamics simulations.

The structural properties resulting from the reciprocal influence between water and three well-known homologous disaccharides, namely, trehalose, maltose, and sucrose, in aqueous solutions have been investigated in the 4-66 wt % concentration range by means of molecular dynamics computer simulations. Hydration numbers clearly show that trehalose binds to a larger number of water molecules than do maltose or sucrose, thus affecting the water structure to a deeper extent. Two-dimensional radial distribution functions of trehalose solutions definitely reveal that water is preferentially localized at the hydration sites found in the trehalose dihydrate crystal, this tendency being enhanced when increasing trehalose concentration. Over a rather wide concentration range (4-49 wt %), the fluctuations of the radius of gyration and of the glycosidic dihedral angles of trehalose indicate a higher flexibility with respect to maltose and sucrose. At sugar concentrations between 33 and 66 wt %, the mean sugar cluster size and the number of sugar-sugar hydrogen bonds formed within sugar clusters reveal that trehalose is able to form larger clusters than sucrose but smaller than maltose. These features suggest that trehalose-water mixtures would be more homogeneous than the two others, thus reducing both desiccation stresses and ice formation.

Biophysics↗
PubMed2005

Phi-value analysis by molecular dynamics simulations of reversible folding.

In Phi-value analysis, the effects of mutations on the folding kinetics are compared with the corresponding effects on thermodynamic stability to investigate the structure of the protein-folding transition state (TS). Here, molecular dynamics (MD) simulations (totaling 0.65 ms) have been performed for a large set of single-point mutants of a 20-residue three-stranded antiparallel beta-sheet peptide. Between 57 and 120 folding events were sampled at near equilibrium for each mutant, allowing for accurate estimates of folding/unfolding rates and stability changes. The Phi values calculated from folding and unfolding rates extracted from the MD trajectories are reliable if the stability loss upon mutation is larger than approximately 0.6 kcal/mol, which is observed for 8 of the 32 single-point mutants. The same heterogeneity of the TS of the wild type was found in the mutated peptides, showing two possible pathways for folding. Single-point mutations can induce significant TS shifts not always detected by Phi-value analysis. Specific nonnative interactions at the TS were observed in most of the peptides studied here. The interpretation of Phi values based on the ratio of atomic contacts at the TS over the native state, which has been used in the past in MD and Monte Carlo simulations, is in agreement with the TS structures of wild-type peptide. However, Phi values tend to overestimate the nativeness of the TS ensemble, when interpreted neglecting the nonnative interactions.

Computer Simulation↗
PubMed1998

Time resolved fluorescence properties of phenylalanine in different environments. Comparison with molecular dynamics simulation.

Time resolved fluorescence of the phenylalanine residue (Phe) alone and included in the transmembrane domain (TMD) sequences of the epidermal growth factor receptor (EGFR) and ErbB-2 was studied using the synchrotron radiation source of light, and compared to molecular dynamics (MD) simulations. The fluorescence intensity decay is strongly sensitive to the environment. A mono-exponential decay was obtained for Phe amino acid alone in two different solvents and for Phe included in EGFR transmembrane sequence, with fluorescence lifetime values varying from 1.7 ns (EGFR) to 7.4 ns (Phe dissolved in water). In ErbB-2 transmembrane sequence three lifetimes were detected. The relative amplitude of the shortest one (0.14 ns) is smaller than 10%, whereas the others (0.6 and 2.2 ns) are almost equally represented. They have been attributed to different rotamers exchanging slowly. This interpretation is supported by MD simulations which evidence transitions in time series of the chi 1 dihedral angle of Phe observed in the case of ErbB-2. The anisotropy decays are similar for both peptides and indicate the presence of a correlation time in the nanosecond range (1-4 ns) and the probable existence of a very fast one (< 0.05 ns). Autocorrelation functions computed from MD simulations corroborate these results.

Amino Acid Sequence↗
PubMed2005

Nucleophilic substitution reactions at liquid/liquid interfaces: molecular dynamics simulation of a model S(N)1 dissociation reaction at the water/carbon tetrachloride interface.

The ionic dissociation step of the nucleophilic substitution reaction t-BuCl --> t-Bu(+) + Cl(-) is studied at the water/carbon tetrachloride interface using molecular dynamics computer simulations. The empirical valence bond approach is used to couple two diabatic states, covalent and ionic, in the electronically adiabatic limit. The umbrella sampling technique is used to calculate the potential of mean force along the reaction coordinate (defined as the t-Bu to Cl distance) at several interface regions of varying distances from the Gibbs dividing surface. We find a significant increase of the ionic dissociation barrier height and of the reaction free energy at the interface relative to bulk water. This is shown to be due to the reduced polarity of the interface which causes a destabilization of the pure ionic state. However, deformation to the neat interface structure in the form of water protrusions into the organic phase may provide partial stabilization of the ionic species. The importance of these structural effects is examined by repeating the calculations with an artificially smooth interface. The destabilization of the ionic state at the interface also manifests itself with a rapid (picosecond time scale) recombination dynamics of the ions to form the parent molecule followed by a slow vibrational relaxation.

Journal Article↗
PubMed2004

Water motion in reverse micelles studied by quasielastic neutron scattering and molecular dynamics simulations.

Motion of water molecules in Aerosol OT [sodium bis(2-ethylhexyl) sulfosuccinate, AOT] reverse micelles with water content w(0) ranging from 1 to 5 has been explored both experimentally through quasielastic neutron scattering (QENS) and with molecular dynamics (MD) simulations. The experiments were performed at the energy resolution of 85 microeV over the momentum transfer (Q) range of 0.36-2.53 A(-1) on samples in which the nonpolar phase (isooctane) and the AOT alkyl chains were deuterated, thereby suppressing their contribution to the QENS signal. QENS results were analyzed via a jump-diffusion/isotropic rotation model, which fits the results reasonably well despite the fact that confinement effects are not explicitly taken into account. This analysis indicates that in reverse micelles with low-water content (w(0)=1 and 2.5) translational diffusion rate is too slow to be detected, while for w(0)=5 the diffusion coefficient is much smaller than for bulk water. Rotational diffusion coefficients obtained from this analysis increase with w(0) and are smaller than for bulk water, but rotational mobility is less drastically reduced than translational mobility. Using the Faeder/Ladanyi model [J. Phys. Chem. B 104, 1033 (2000)] of reverse micelle interior, MD simulations were performed to calculate the self-intermediate scattering function F(S)(Q,t) for water hydrogens. Comparison of the time Fourier transform of this F(S)(Q,t) with the QENS dynamic structure factor S(Q,omega), shows good agreement between the model and experiment. Separate intermediate scattering functions F(S) (R)(Q,t) and F(S) (CM)(Q,t) were determined for rotational and translational motion. Consistent with the decoupling approximation used in the analysis of QENS data, the product of F(S) (R)(Q,t) and F(S) (CM)(Q,t) is a good approximation to the total F(S)(Q,t). We find that the decay of F(S) (CM)(Q,t) is nonexponential and our analysis of the MD data indicates that this behavior is due to lower water mobility close to the interface and to confinement-induced restrictions on the range of translational displacements. Rotational relaxation also exhibits nonexponential decay. However, rotational mobility of O-H bond vectors in the interfacial region remains fairly high due to the lower density of water-water hydrogen bonds in the vicinity of the interface.

Journal Article↗
PubMed1994

Molecular dynamics simulation of oligosaccharides containing N-acetyl neuraminic acid.

alpha D-N-acetyl neuraminic acid (Neu5Ac, sialic acid) is a commonly occurring carbohydrate residue in various cell surface glycolipids and glycoproteins. This residue is linked terminally or internally to Gal residues via an alpha(2-->3) or alpha(2-->6) linkage. In the cell surface receptor, sialyl-LewisX, a terminal alpha(2-->3) linkage is present. Previous studies from our laboratory have shown that in solution LewisX adopts a relatively rigid structure. In order to model the Neu5Ac residue, vacuum molecular dynamics of this monosaccharide were compared with simulations that explicitly include solvent water. The dynamical average of the monosaccharide conformation obtained from the two simulations was similar. Vacuum calculations for the disaccharide Neu5Ac alpha(2-->3) Gal beta-O-methyl show that a number of low energy minima are accessible to this disaccharide. Molecular dynamics simulations starting from the low energy minima show conformational transitions with a time scale of 10-50 ps among several of the minima while large barriers between other minima prevent transitions on the time scale studied. Simulations of this disaccharide in the presence of solvent show fewer conformational transitions, illustrating a dampening effect of the solvent that has been observed in some other studies. Our results are most consistent with an equilibrium among multiple conformations for the Neu5Ac alpha(2-->3) Gal beta linkage.

Carbohydrate Conformation↗
PubMed2006

Molecular dynamics simulations of lithium alkyl carbonates.

A quantum chemistry-based many-body polarizable force field has been developed for two model solid-electrolyte interphase (SEI) components: dilithium ethylene dicarbonate (Li(2)EDC) and lithium methyl carbonate (LiMC). Molecular dynamics (MD) simulations of amorphous Li(2)EDC and LiMC were performed at temperatures from 393 to 600 K. Simulations reveal that Li(+) is coordinated by approximately 4.6 oxygen atoms from -COO(-) groups coming from different alkyl carbonate molecules. Charge transport in Li(2)EDC was found to be almost entirely due to Li(+). The temperature dependence of the ionic conductivity of the SEI model compounds Li(2)EDC and LiMC was found to be significantly stronger than that of liquid electrolytes (e.g., ethylene carbonate + LiTFSI), yielding extrapolated conductivities of the Li(2)EDC on order of 10(-10) S/cm at -30 degrees C.

Journal Article↗
PubMed2006

Structure of poly(propyl ether imine) dendrimer from fully atomistic molecular dynamics simulation and by small angle x-ray scattering.

We study the structure of carboxylic acid terminated neutral poly(propyl ether imine) (PETIM) dendrimer from generations 1-6 (G1-G6) in a good solvent (water) by fully atomistic molecular dynamics (MD) simulations. We determine as a function of generation the structural properties such as radius of gyration, shape tensor, asphericity, fractal dimension, monomer density distribution, and end-group distribution functions. The sizes obtained from the MD simulations have been validated by small angle x-ray scattering experiment on dendrimer of generations 2-4 (G2-G4). A good agreement between the experimental and theoretical value of radius of gyration has been observed. We find a linear increase in radius of gyration with the generation. In contrast, Rg scales as approximately Nx with the number of monomers. We find two distinct exponents depending on the generations, x=0.47 for G1-G3 and x=0.28 for G3-G6, which reveal their nonspace filling nature. In comparison with the amine terminated poly(amidoamine) (PAMAM) dendrimer, we find that Rg of Gth generation PETIM dendrimer is nearly equal to that of (G+1)th generation of PAMAM dendrimer as observed by Maiti et al. [Macromolecules 38, 979 (2005)]. We find substantial back folding of the outer subgenerations into the interior of the dendrimer. Due to their highly flexible nature of the repeating branch units, the shape of the PETIM dendrimer deviates significantly from the spherical shape and the molecules become more and more spherical as the generation increases. The interior of the dendrimer is quite open with internal cavities available for accommodating guest molecules, suggesting the use of PETIM dendrimer for guest-host applications. We also give a quantitative measure of the number of water molecules present inside the dendrimer.

Journal Article↗
PubMed1995

Conformations and internal mobility of a glycopeptide derived from bromelain using molecular dynamics simulations and NOESY analysis.

The conformation and internal flexibility of a glycopeptide Manalpha1-6 (Xylbeta1-2)Manbeta1-4GlcNAcbeta1-4(Fucalpha1-3) GlcNAcbeta1-N(Asn-Glu-Ser-Ser), prepared from pineapple stem bromelain, have been analyzed using a combination of molecular dynamics (MD) simulations in water with NOESY 1H NMR spectroscopy. Theoretical NOESY cross-peak intensities were calculated by the CROSREL program on the basis of models, obtained from MD simulations, using a full relaxation matrix approach. Special attention was paid to the description of internal flexibility of the hexasaccharide moiety by the use of generalized order parameters, in combination with the application of an individual rotation correlation tme for each monosaccharide residue. The tetrapeptide moiety appeared to be very mobile during the MD simulations, which was confirmed by the absence of NOE cross peaks. For the oligosaccharide part a model was developed to estimate characteristic times for large reorientational motions around the glycosidic linkages, associated with conformational transitions. For the Manalpha1-6Man and the Fucalpha1-3GlcNAc linkages such a flexibility was found with a characteristic time of 2 ns. In contrast, the Xylbeta1-2Manbeta1-4GlcNAcbeta1-4GlcNAc part of the glycan appears to be relatively rigid.

Amino Acid Sequence↗
PubMed1998

Molecular dynamics simulations of the structure of aldose reductase complexed with the inhibitor tolrestat.

This study reports a molecular dynamics (MD) investigation on the structure of aldose reductase (ALR2) complexed with the potent inhibitor tolrestat. The simulations predict four different orientations of tolrestat into the ALR2 binding site; these orientations have in common a strong interaction of the anionic carboxylate with Tyr48, His110, Trp111 and NADP+, but completely differ for the orientation of the aromatic portion of the inhibitor. Interestingly, the orientation in which tolrestat gives the most attractive interaction energy with the enzyme is in full accord with the x-ray crystal structure of the complex that has been reported in the literature after this work was completed. In addition, the suggestion of more than one orientation of tolrestat during MD is in agreement with recent electrospray mass spectrometry experiments on the ALR2-tolrestat complex.

Aldehyde Reductase↗
PubMed2002

Molecular dynamics simulations of adrenocorticotropin (1-24) peptide in a solvated dodecylphosphocholine (DPC) micelle and in a dimyistoylphosphatidylcholine (DMPC) bilayer.

The structure and interactions of the 1-24 fragment of the adrenocorticotropin hormone, ACTH (1-24), with membrane have been studied by molecular dynamics (MD) simulation in an NPT ensembles in two explicit membrane mimics, a dodecylphosphocholine (DPC) micelle and a dimyristoylphosphatidylcholine (DMPC) bilayer. The starting configuration of the peptide/lipid systems had the 1-10 segment of the peptide lying on the surface of the model membrane, the same as the equilibrated structure (by MD) of ACTH (1-10) in a DPC micelle. The simulations showed that the peptide adopts the surface-binding mode and essentially the same structure in both systems. Thus the results of this work lend support to the assumption that micelles are reasonable mimics for biological membranes for the study of peptide binding. The 1-10 segment is slightly tilted from the parallel orientation to the interface and interacts strongly with the membrane surface while the more polar 11-24 segment shows little tendency to interact with the membrane surface, preferring to reside primarily in the aqueous phase. Furthermore, the 1-10 segment of the peptide binds to the DPC micelle in essentially the same way as ACTH (1-10). Thus the MD results are in excellent agreement with the model of interaction of ACTH (1-24) with membrane derived from NMR experiments. The secondary structure and the hydration of the peptide and the interactions of specific residues with the lipid head groups have also been analyzed.

Adrenocorticotropic Hormone↗
PubMed2003

Conformational interconversion in compstatin probed with molecular dynamics simulations.

Compstatin is a 13-residue cyclic peptide that has the potential to become a therapeutic agent against unregulated complement activation. In our effort to understand the structural and dynamic characteristics of compstatin that form the basis for rational and combinatorial optimization of structure and activity, we performed 1-ns molecular dynamics (MD) simulations. We used as input in the MD simulations the ensemble of 21 lowest energy NMR structures, the average minimized structure, and a global optimization structure. At the end of the MD simulations we identified five conformations, with populations ranging between 9% and 44%. These conformations are as follows: 1) coil with alphaR-alphaR beta-turn, as was the conformation of the initial ensemble of NMR structures; 2) beta-hairpin with epsilon-alphaR beta-turn; 3) beta-hairpin with alphaR-alphaR beta-turn; 4) beta-hairpin with alphaR-beta beta-turn; and 5) alpha-helical. Conformational switch was possible with small amplitude backbone motions of the order of 0.1-0.4 A and free energy barrier crossing of 2-11 kcal/mol. All of the 21 MD structures corresponding to the NMR ensemble possessed a beta-turn, with 14 structures retaining the alphaR-alphaR beta-turn type, but the average minimized structure and the global optimization structures were converted to alpha-helical conformations. Overall, the MD simulations have aided to gain insight into the conformational space sampled by compstatin and have provided a measure of conformational interconversion. The calculated conformers will be useful as structural and possibly dynamic templates for optimization in the design of compstatin using structure-activity relations (SAR) or dynamics-activity relations (DAR).

Computer Simulation↗
PubMed2006

Molecular dynamics simulation of structure, thermodynamic, and dynamic properties of poly(dimethylsilamethylene), poly(dimethylsilatrimethylene) and their alternating copolymer.

Molecular dynamics is used for the simulation of silicon-containing polymers with promising membrane material properties. An atomistic force field is developed for the description of bond bending, torsional angle variation, and nonbonded intra- and intermolecular interactions. Detailed ab initio quantum mechanics calculations on corresponding monomers that appeared recently in the literature are used for the parametrization of the bonded and nonbonded local intramolecular force field. For the intermolecular and nonbonded nonlocal intramolecular interactions, parameters are obtained from accurate force fields proposed in the literature for similar compounds. The force field is used subsequently for the calculation of thermodynamic, structure, and dynamic properties of two homopolymers, namely, poly(dimethylsilamethylene) and poly(dimethylsilatrimethylene), and their alternating copolymer. A wide range of temperatures and pressures is examined. Polymer systems of different molecular weights are simulated. Experimental data available for these polymers are very limited. In all cases, simulation results are in good agreement with these data. Furthermore, simulation results agree very well with empirical macroscopic correlations used widely for rubbery polymers for the properties under consideration.

Journal Article↗
PubMed1994

200 picosecond molecular dynamics simulation of interaction of nifedipine with 1-2 dimyristoyl phosphatidylcholine membrane.

Interaction of calcium channel antagonist nifedipine (Nif) with 1-2 dimyristoyl phosphatidylcholine (DMPC) membrane has been studied using molecular dynamics approach. The simulations for one molecule of nifedipine with four DMPC molecules were carried out for 200 pico seconds (ps) using AMBER (Assisted Model Building with Energy Refinement) 3.0 adopted to CYBER 180/930 computer and changes in the structural parameters of DMPC were compared with those for DMPC monolayer (a matrix of nine molecules) optimized separately. Dynamics simulations for the latter had been carried for 40 ps. Our results show that the drug molecule (Nif) penetrates a discrete depth within the phospholipid matrix causing hydrocarbon chains of lipid molecules to swing that makes enough room for the receptor adjacent to the drug molecule.

Computer Simulation↗
PubMed2005

Molecular dynamics simulations of retinal in rhodopsin: from the dark-adapted state towards lumirhodopsin.

The formation of photointermediates and conformational changes observed in the retinal chromophore of bilayer-embedded rhodopsin during the early steps of the protein activation have been studied by molecular dynamics (MD) simulation. In particular, the lysine-bound retinal has been examined, focusing on its conformation in the dark-adapted state (10 ns) and on the early steps after the isomerization of the 11-cis bond to trans (up to 10 ns). The parametrization for the chromophore is based on a recent quantum study [Sugihara, M., Buss, V., Entel, P., Elstner, M., and Frauenheim, T. (2002) Biochemistry 41, 15259-15266] and shows good conformational agreement with recent experimental results. The isomerization, induced by switching the function governing the dihedral angle for the C11=C12 bond, was repeated with several different starting conformations. From the repeated simulations, it is shown that the retinal model exhibits a conserved activation pattern. The conformational changes are sequential and propagate outward from the C11=C12 bond, starting with isomerization of the C11=C12 bond, then a rotation of methyl group C20, and followed by increased fluctuations at the beta-ionone ring. The dynamics of these changes suggest that they are linked with photointermediates observed by spectroscopy. The exact moment when these events occur after the isomerization is modulated by the starting conformation, suggesting that retinal isomerizes through multiple pathways that are slightly different. The amplitudes of the structural fluctuations observed for the protein in the dark-adapted state and after isomerization of the retinal are similar, suggesting a subtle mechanism for the transmission of information from the chromophore to the protein.

Adaptation, Physiological↗
PubMed2004

Ab initio molecular dynamics simulations and g-tensor calculations of aqueous benzosemiquinone radical anion: effects of regular and "T-stacked" hydrogen bonds.

Car-Parrinello molecular dynamics (CP-MD) simulations of the benzosemiquinone radical anion in aqueous solution have been performed at ambient conditions. Analysis of the trajectory shows not only extensive hydrogen bonding to the carbonyl oxygen atoms (ca. 4-5.6 water molecules depending on distance criteria), but also relatively long-lived "T-stacked" hydrogen bonds to the semiquinone pi-system. These results are discussed in the context of recent findings on semiquinone-protein interactions in photosynthetic reaction centers, and of EPR and vibration spectroscopical data for the aqueous system. Snapshots from the CP-MD trajectory are used for the first quantum chemical analyses of dynamical effects on electronic g-tensors, using cluster models and a recently developed density functional method. In particular, the effects of intermolecular hydrogen-bond dynamics on the g-tensor components are examined, in comparison with recent EPR and ENDOR studies.

Benzoquinones↗
PubMed2003

Molecular dynamics simulations of a mixed DOPC/DOPG bilayer.

We have constructed a mixed dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylglycerol bilayer (DOPG) bilayer utilizing MD simulations. The aim was to develop an explicit molecular model of biological membranes as a complementary technique to neutron diffraction studies that are well established within the group. A monolayer was constructed by taking a previously customized PDB file of each molecule and arranging them in a seven rows of ten molecules and duplicated and rotated to form a bilayer. The 140-molecule bilayer contained 98 DOPC molecules and 42 DOPG molecules, in a 7:3 ratio in favour of DOPC. Sodium counter ions were placed near the phosphate moiety of DOPG to counteract the negative charge of DOPG. This was representative of the lipid ratio in a sample used for neutron diffraction. The MD package GROMACS was used for confining the bilayer in a triclinic box, adding Simple Polar Charge water molecules, energy minimization (EM). The bilayer/solvent system was subjected to EM using the steepest descent method to nullify bad contacts and reduce the potential energy of the system. Subsequent MD simulation using an initial NVT (constant number of particles, volume and temperature) for a 20 ps MD run followed by a NPT (constant number of particles, pressure and temperature) was performed. Structural parameters including volume of lipid, area of lipid, order parameter of the fatty acyl carbons and electron density profiles generated by the MD simulation were verified with values obtained from experimental data of DOPC, as there are no comparable experimental data available for the mixed bilayer.

Electrons↗
PubMed2005

Molecular dynamics simulation study on a monolayer of half [2]rotaxane self-assembled on Au(111).

The self-assembled monolayer (SAM) structure of the tetrathiafulvalene-side half of the Stoddart-Heath type [2]rotaxane on Au(111) surface was investigated using molecular dynamics (MD) simulations. We find that the orientation of the cyclobis(paraquat-p-phenylene) (CBPQT) ring depends dramatically on the coverage, changing in order to obtain highly packed SAMs. The ring lies with its large hollow parallel to the surface at lower coverage (up to one CBPQT per 27 surface Au atoms with a footprint of 1.9 nm(2); 1/27) when free space is available around it, but as the coverage increases (up to one CBPQT per 12 surface Au atoms with a footprint of 0.9 nm(2); 1/12), it tilts completely around its axis and lies with its smaller side (paraquat or phenyl ring) parallel to the surface to accommodate the reduced area available. We find that the best packing densities correspond to one CBPQT per 12-18 surface Au atoms (1/18-1/12) with footprints in the range between 0.9 nm(2) and 1.3 nm(2).

Journal Article↗