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At least 865 records · Page 48Linked to original sources
PubMed2002

Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation.

The aggregation observed in protein conformational diseases is the outcome of significant new beta-sheet structure not present in the native state. Peptide model systems have been useful in studies of fibril aggregate formation. Experimentally, it was found that a short peptide AGAAAAGA is one of the most highly amyloidogenic peptides. This peptide corresponds to the Syrian hamster prion protein (ShPrP) residues 113-120. The peptide was observed to be conserved in all species for which the PrP sequence has been determined. We have simulated the stabilities of oligomeric AGAAAAGA and AAAAAAAA (A8) by molecular dynamic simulations. Oligomers of both AGAAAAGA and AAAAAAAA were found to be stable when the size is 6 to 8 (hexamer to octamer). Subsequent simulation of an additional alpha-helical AAAAAAAA placed on the A8-octamer surface has revealed molecular events related to conformational change and oligomer growth. Our study addresses both the minimal oligomeric size of an aggregate seed and the mechanism of seed growth. Our simulations of the prion-derived 8-residue amyloidogenic peptide and its variant have indicated that an octamer is stable enough to be a seed and that the driving force for stabilization is the hydrophobic effect.

Amyloid↗
PubMed2006

Cholesterol-sphingomyelin interactions: a molecular dynamics simulation study.

Stearoylsphingomyelin (SSM) bilayers containing 0, 22, and 50 mol % cholesterol (Chol) and a pentadecanoyl-stearoylphosphatidylcholine (15SPC) bilayer containing 22 mol % Chol were molecular dynamics simulated at two temperatures (37 degrees C and 60 degrees C). 15SPC is the best PC equivalent of SSM. The Chol effect on the SSM bilayer differs significantly from that on the 15SPC bilayer. At the same temperature and Chol content, H-bonding of Chol with SSM is more extensive than with 15SPC. SSM-Chol H-bonding anchors the OH group of Chol in the lower regions of the SSM-Chol bilayer interface. Such a location strengthens the influence of Chol on the SSM chains. In effect, the phase of the SSM-Chol bilayer containing 22 mol % Chol at 37 degrees C is shifted from the gel to the liquid-ordered phase, and the bilayer displays similar properties below and above the main phase-transition temperature for a pure SSM bilayer of approximately 45 degrees C. In contrast, due to a higher location, Chol is not able to change the phase of the 15SPC-Chol bilayer, which at 37 degrees C remains in the gel phase. Chol affects both the core and interface of the SSM bilayer. With increasing Chol content, the order of SSM chains and hydration of SSM headgroups increase, whereas polar interactions between lipids decrease.

Cholesterol↗
PubMed2004

beta-hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solution.

The structural properties of a 10-residue and a 15-residue peptide in aqueous solution were investigated by molecular dynamics simulation. The two designed peptides, SYINSDGTWT and SESYINSDGTWTVTE, had been studied previously by NMR at 278 K and the resulting model structures were classified as 3:5 beta-hairpins with a type I + G1 beta-bulge turn. In simulations at 278 K, starting from the NMR model structure, the 3:5 beta-hairpin conformers proved to be stable over the time period evaluated (30 ns). Starting from an extended conformation, simulations of the decapeptide at 278 K, 323 K and 353 K were also performed to study folding. Over the relatively short time scales explored (30 ns at 278 K and 323 K, 56 ns at 353 K), folding to the 3:5 beta-hairpin could only be observed at 353 K. At this temperature, the collapse to beta-hairpin-like conformations is very fast. The conformational space accessible to the peptide is entirely dominated by loop structures with different degrees of beta-hairpin character. The transitions between different types of ordered loops and beta-hairpins occur through two unstructured loop conformations stabilized by a single side-chain interaction between Tyr2 and Trp9, which facilitates the changes of the hydrogen-bond register. In agreement with previous experimental results, beta-hairpin formation is initially driven by the bending propensity of the turn segment. Nevertheless, the fine organization of the turn region appears to be a late event in the folding process.

Amino Acid Sequence↗
PubMed1994

Molecular dynamics simulation of the docking of substrates to proteins.

A simple method is described to perform docking of substrates to proteins or probes to receptor molecules by a modification of molecular dynamics simulations. The method consists of a separation of the center-of-mass motion of the substrate from its internal and rotational motions, and a separate coupling to different thermal baths for both types of motion of the substrate and for the motion of the receptor. Thus the temperatures and the time constants of coupling to the baths can be arbitrarily varied for these three types of motion, allowing either a frozen or a flexible receptor and allowing control of search rate without disturbance of internal structure. In addition, an extra repulsive term between substrate and protein was applied to smooth the interaction. The method was applied to a model substrate docking onto a model surface, and to the docking of phosphocholine onto immunoglobulin McPC603, in both cases with a frozen receptor. Using translational temperatures of the substrate in the range of 1300-1700 K and room temperature for the internal degrees of freedom of the substrate, an efficient nontrapping exploratory search ("helicopter view") is obtained which visits the correct binding sites. Low energy conformations can then be further investigated by separate search or by dynamic simulated annealing. In both cases the correct minima were identified. The possibility to work with flexible receptors is discussed.

Antibodies↗
PubMedDate not supplied

Predicted unfolding order of the 13 alpha-helices in the catalytic domain of glucoamylase from Aspergillus awamori var. X100 by molecular dynamics simulations.

The unfolding mechanism of the 13 alpha-helices in the catalytic domain of Aspergillus awamori var. X100 glucoamylase was investigated by 200 ps molecular dynamics simulations in explicit water with temperature jump technique. Rather than a simultaneous event, the unfolding of these 13 alpha-helices followed a random ordered mechanism as alpha8-->alpha1-->alpha11-->alpha7-->alpha10-->alpha3-->alpha12-->alpha13-->alpha4-->alpha5-->alpha9-->alpha6-->alpha2. No significant relationships were found between the unfolding order and the length and the hydrophobicity of the helix. alpha-Helix 8 located in the inner region of the catalytic domain was predicted to be the first helix to unfold, indicating that the destruction of the secondary structure motif was initiated from the inner region of the catalytic domain. The dynamic behavior of these alpha-helices induced by increased kinetic energy during the unfolding process is considered to be similar to the expansion and compression of a series of springs under the influence of mechanical stress.

Amino Acid Sequence↗
PubMed2004

Replica exchange molecular dynamics simulations of amyloid peptide aggregation.

The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant temperature molecular dynamics (CTMD). During the aggregation process the energetic and structural properties are essentially the same in REMD and CTMD. A condensation stage toward disordered aggregates precedes the beta-sheet formation. Two order parameters, borrowed from anisotropic fluid analysis, are used to monitor the aggregation process. The order parameters do not depend on the peptide sequence and length and therefore allow to compare the amyloidogenic propensity of different peptides

Amyloid↗
PubMed2006

A highly strained nuclear conformation of the exportin Cse1p revealed by molecular dynamics simulations.

To investigate the stability of the open nuclear state of the exportin Cse1p and its closing mechanism at the atomic level, we have performed multiple molecular dynamics simulations. The simulations revealed a strikingly fast transition of Cse1p from the open conformation to the closed cytoplasmic form, consistent with the proposal that Cse1p represents a "spring-loaded molecule." The structure of the ring-shaped state obtained in the simulations is remarkably close to the crystal structure of the cytoplasmic state, though the open nuclear structure was used as the only input. The conformational change is initially driven by release of strain due to RanGTP/importin-alpha binding. Subsequently, a stable closed state is formed, driven by attraction of electrostatically complementary interfaces. These results are consistent with and extend previous proposals. Reverse-charge and neutral mutants remained in an open state. The simulations predict a detailed reaction pathway and resolve the role of suggested hinge regions.

Cell Nucleus↗
PubMed2004

A force-field description of short-range repulsions for high density alkane molecular dynamics simulations.

The use of Buckingham (exp-6) van der Waals potentials in molecular dynamics (MD) simulations can quite successfully reproduce experimental thermodynamic data at low densities. However, they are less successful in producing a description of the repulsive regions of the potential energy surface (PES) that is in accord with the results of high-level ab initio computations. We show that Morse potentials can be parameterized to give excellent fits to both the attractive and repulsive regions of the PES. The best set of alkane van der Waals Morse function parameters reported to date for the description of nonbond repulsive interactions is presented, as determined by comparison with both ab initio and experimental results. C...C, H...H and C...H atom-pair potentials employing parameter sets based on the use of the geometric mean in the fitting procedure are found to be portable from methane to n-butane. Fitting to a combination of methane dimer interaction energies and forces from ab initio calculations yields parameter sets whose performance is superior to those determined from the interaction energies alone. Used in MD simulations, our newly developed parameter sets predict thermodynamic functions that show better agreement with experiment than those based on parameter sets in common use.

Journal Article↗
PubMed2003

Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study.

The relative stability of protein structures determined by either X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy has been investigated by using molecular dynamics simulation techniques. Published structures of 34 proteins containing between 50 and 100 residues have been evaluated. The proteins selected represent a mixture of secondary structure types including all alpha, all beta, and alpha/beta. The proteins selected do not contain cysteine-cysteine bridges. In addition, any crystallographic waters, metal ions, cofactors, or bound ligands were removed before the systems were simulated. The stability of the structures was evaluated by simulating, under identical conditions, each of the proteins for at least 5 ns in explicit solvent. It is found that not only do NMR-derived structures have, on average, higher internal strain than structures determined by X-ray crystallography but that a significant proportion of the structures are unstable and rapidly diverge in simulations.

Computer Simulation↗
PubMed2000

Automated docking and molecular dynamics simulations of nimesulide in the cyclooxygenase active site of human prostaglandin-endoperoxide synthase-2 (COX-2).

Molecular models of the complex between the selective COX-2 inhibitor nimesulide and the cyclooxygenase active site of human prostaglandin-endoperoxide synthase-2 have been built using a combination of homology modelling, conformational searching and automated docking techniques. The stability of the resulting complexes has been assessed by molecular dynamics simulations and interaction energy decomposition. It is found that nimesulide exploits the extra space made available by the replacement at position 523 of an isoleucine residue in COX-1 by a valine in COX-2 and establishes electrostatic interactions with both Arg-106 and Arg-499 (Arg-120 and Arg-513 in PGHS-1 numbering). Two alternate binding modes are proposed which are compatible with the pharmacological profile of this agent as a COX-2 selective inhibitor.

Amino Acid Sequence↗
PubMed1996

A high performance system for molecular dynamics simulation of biomolecules using a special-purpose computer.

GRAPE (GRavity PipE) processors are special purpose computers for simulation of classical particles. The performance of MD-GRAPE, one of the GRAPEs developed for molecular dynamics, was investigated. The effective speed of MD-GRAPE was equivalent to approximately 6 Gflops. The precision of MD-GRAPE was good judging from the acceptable fluctuation of the total energy. Then a software named PEACH (Program for Energetic Analysis of bioCHemical molecules) was developed for molecular dynamics of biomolecules in combination with MD-GRAPE. Molecular dynamics simulation was performed for several protein-solvent systems with different sizes. Simulation of the largest system investigated (27,000 atoms) took only 5 sec/step. Thus, the PEACH-GRAPE system is expected to be useful in accurate and reliable simulation of large biomolecules.

Computational Biology↗
PubMed2005

Molecular dynamics simulations of layer-by-layer assembly of polyelectrolytes at charged surfaces: effects of chain degree of polymerization and fraction of charged monomers.

We performed molecular dynamics simulations of the electrostatic assembly of multilayers of flexible polyelectrolytes at a charged surface. The multilayer build-up was achieved through sequential adsorption of oppositely charged polymers in a layer-by-layer fashion from dilute polyelectrolyte solutions. The steady-state multilayer growth proceeds through a charge reversal of the adsorbed polymeric film which leads to a linear increase in the polymer surface coverage after completion of the first few deposition steps. Moreover, substantial intermixing between chains adsorbed during different deposition steps is observed. This intermixing is consistent with the observed requirement for several deposition steps to transpire for completion of a single layer. However, despite chain intermixing, there are almost perfect periodic oscillations of the density difference between monomers belonging to positively and negatively charged macromolecules in the adsorbed film. Weakly charged chains show higher polymer surface coverage than strongly charged ones.

Journal Article↗
PubMed2005

The hydrophobicity of nanostructured alkane and perfluoro alkane surfaces: a comparison by molecular dynamics simulation.

In this contribution we investigate the differences in the hydrophobicity of a perfluoro-n-eicosane crystal and the n-eicosane crystal by molecular dynamics simulation. The results were analysed in terms of density of water at the interface, the chemical potential of water at the interface and the orientational ordering of water at the interface. The perfluoro-n-eicosane crystal-water interface is found to have a less density, higher chemical potential and a weaker orientational ordering at the interface than the corresponding n-eicosane crystal.

Journal Article↗
PubMed2005

Polarizability response in polar solvents: molecular-dynamics simulations of acetonitrile and chloroform.

The relaxation of the many-body polarizability in liquid acetonitrile and chloroform at room temperature was studied by molecular-dynamics simulations. The collective polarizability induced by intermolecular interactions was included using first- and all-orders dipole-induced-dipole models and calculated considering both molecule-centered and distributed site polarizabilities. The anisotropic response was analyzed using a separation scheme that allows a decomposition of the total response in terms of orientational and collision-induced effects. We found the method effective in approximately separating the contributions of these relaxation mechanisms, although the orientational-collision-induced interference makes a non-negligible contribution to the total response. In both liquids the main contribution to the anisotropic response is due to orientational dynamics, but intermolecular collision-induced (or translational) effects are important, especially at short times. We found that higher-order interaction-induced effects were essentially negligible for both liquids. Larger differences were found between the center-center and site-site models, with the latter showing faster polarizability relaxation and better agreement with experiment. Isotropic and anisotropic spectra were computed from the corresponding time correlation functions. The lowest-frequency contributions are largely suppressed in the isotropic spectra and their overall shape is similar to the purely collision-induced contribution to the anisotropic spectra, but with an amplitude which is smaller by a factor of approximately 5 in acetonitrile and approximately 3 in chloroform.

Journal Article↗
PubMed2006

Ab initio based tight-binding molecular dynamics simulation of the sticking and scattering of O2Pt(111).

The sticking and scattering of O(2)Pt(111) has been studied by tight-binding molecular dynamics simulations based on an ab initio potential energy surface. We focus, in particular, on the sticking probability as a function of the angle of incidence and the energy and angular distributions in scattering. Our simulations provide an explanation for the seemingly paradox experimental findings that adsorption experiments suggest that the O(2)Pt(111) interaction potential should be strongly corrugated while scattering experiments indicate a rather small corrugation. The potential energy surface is indeed strongly corrugated which leads to a pronounced dependence of the sticking probability on the angle of incidence. The scattered O(2) molecules, however, experience a rather flat surface due to the fact that they are predominantly scattered at the repulsive tail of the potential.

Journal Article↗
PubMed1987

Molecular dynamics simulations of fluorescence polarization of tryptophans in myoglobin.

The fluorescence of heme proteins is influenced by energy transfer from the excited tryptophan to the heme. Molecular dynamics simulations of the tryptophan and heme motions in sperm whale myoglobin were used to calculate the fluorescence intensity and anisotropy decays. The side chains underwent both small rapid orientational fluctuations and large infrequent transitions between conformations. The predicted motions of the tryptophans and the heme produce large fluctuations in the instantaneous rate of energy transfer, but no stable conformations in which energy transfer is suppressed were found. The calculated fluorescence anisotropies exhibited a large subpicosecond decay, corresponding to nondiffusive side-chain motions. The calculations adequately predict the observed fluorescence decay curve for myoglobin and the total anisotropy decay at 16-ps time resolution. The subnanosecond decays of anisotropy for tryptophan-14 in tuna myoglobin are not reproduced by the calculation.

Animals↗
PubMed2001

Molecular dynamics simulation of the antimicrobial salivary peptide histatin-5 in water and in trifluoroethanol: a microscopic description of the water destructuring effect.

The results of 520 ps molecular dynamics simulation of histatin-5, a small peptide present in human saliva and possessing antimicrobial activity, dissolved in water and in 2,2,2-trifluoroethanol, are reported. The simulations indicate that histatin-5 is destabilized in water and begins to unfold after 250 ps, while in organic solvent it maintains a regular secondary structure throughout the trajectory. Analysis of the peptide-solvent hydrogen bonds indicates that 2,2,2-trifluoroethanol is a poorer proton acceptor than water. The fluorine atom of the alcohol is almost never engaged in a hydrogen bond and the organic solvent interacts mainly with the peptide through its hydroxyl group. For some residues analysis of the solvent residence time indicated longer values for 2,2,2-trifluoroethanol than for water. The most striking difference is related to the number of times the solvent enters and leaves the first coordination shell of the peptide. This value was more than one order of magnitude higher for water than for the alcohol, suggesting that this may be the main cause of alpha-helix destabilization perpetrated by water.

Amino Acid Sequence↗
PubMed1988

Molecular-dynamics simulations of [Met5]- and [D-Ala2,Met5]-enkephalins. Biological implication of monomeric folded and dimeric unfolded conformations.

To investigate the biologically active conformation of enkephalin, molecular-dynamics simulations were applied to [Met5]- and [D-Ala2,Met5]-enkephalins. The dynamic trajectory of monomeric extended [Met5]-enkephalin was analysed in terms of relative mobility between respective torsions of backbone chain. After 10 ps of the dynamics simulation, the conformational transition was converged into a stationary state among the beta-bend folded forms, where they are stabilized by several intramolecular hydrogen-bond formations. Similar conformational transition was also observed in the dynamics simulation of [D-Ala2,Met5]enkephalin, which is a more mu-receptor-specific peptide than [Met5]enkephalin. The geometrical correspondence between the monomeric enkephalin conformation in the stationary state and morphine molecule (a mu-specific rigid opiate) was surveyed by virtue of the triangular substructures generated by choosing three functional atoms in each molecule, and good resemblances were observed. On the other hand, the dynamics simulation of the antiparallel extended [Met5]enkephalin dimer showed a trajectory different from that of the monomeric one. Two intermolecular hydrogen bonds at Tyr1 (NH3+)...Met5(CO2-) end residues were held throughout the 100 ps simulation, the dimeric structure being consequently kept. The conformational transition of the backbone chains from the antiparallel extended form to the twisted one took place via an intermediate state. Many conformations revealed during the dynamics simulation showed that the relative orientations of each two Tyr1, Gly3, Phe4 and Met5 residues in the dimer are nearly related by a pseudo-C2-symmetry respectively, and both halves of the dimer structure could be further fitted to the monomeric folded enkephalin conformation. The monomeric and dimeric conformations of enkephalin at their stationary states are discussed in relation to the substrate-specificity for mu- and delta-opioid receptors.

Computer Simulation↗