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At least 523 records · Page 29Linked to original sources
PubMed2002

Molecular dynamics simulation study of DNA triplex formed by mixed sequences in solution.

The unrestrained molecular dynamics simulation of the triple helical DNA with mix sequences d(GACTGGTGAC).d(CTGACCACTG)*d (GACTGGTGAC), using the particle mesh Ewald sum, is presented here. The Ewald summation method effectively eliminates the usualcut-of of the long range interactions and allowed us to evaluate the full effect of the electrostatic forces. The AMBER5.0 force field has been used during the simulation in solvent. The MD results support a dynamically stable model of DNA triplex over the entire length of the trajectory. The duplex structure assumes the conformation, which is very close to B-DNA. In mixed sequences the purine bases occurs in both strand of DNA duplex. The bases of third strand do not favor the Hoogsteen or/and reverse Hoogsteen type of Hydrogen bonding but they form hydrogen bonds with the bases of both the strand of DNA duplex. The orientation of the third strand is parallel to one of the strand of duplex and all nucleotides (C, A, G & T) show isomorphic behavior with respect to the DNA duplex. The conformation of all the three strands is almost same except few exceptions. Due to interaction of third strand the conformational change in the duplex structure and a finite amount of displacement in the W-C base pairs have been observed. The conformational variation of the back bone torsion angles and helicoidal parameters, groove widths have been discussed. The sequence dependent effects on local conformation, helicoidal and morphological structure, width of the grooves of DNA helix may have important implication for understanding the functional energetics and specificity of interactions of DNA and its triplexes with proteins, pharmaceutical agents and other ligands.

Base Pairing↗
PubMed2004

Molecular dynamics simulations of the Ag+ or Na+ cation with an excess electron in bulk water.

The properties of an excess electron interacting with a monovalent cation in bulk water are studied by molecular dynamics simulations. Sodium and silver cations are chosen as prototypical cases because of their very different redox properties. In both cases, mixed quantum classical molecular dynamics simulations reproduce the experimental UV-Vis spectra. In the case of silver, we observe a highly polarized neutral atom, corresponding to a dipolar excitonic state. For sodium a contact cation/electron pair is observed. Free energy curves along the cation electron coordinate are calculated using quantum Umbrella Sampling technique. The relative stability of the different chemical species is discussed.

Journal Article↗
PubMed2006

Size, motion, and function of the SecY translocon revealed by molecular dynamics simulations with virtual probes.

We report a hybrid, coarse-grained and atomistic, molecular dynamics simulation study of the size, motion, and function of the SecY protein-conducting channel. Growing and pushing virtual soft ball constructs through the pore of SecY, we mimic the push-through of polypeptides, performed cotranslationally by the ribosome and posttranslationally by the SecA ATPase. Forced lateral opening of a "front gate" between transmembrane helices is also induced by the passage of the virtual probes, with implications for the membrane insertion of peptides. We conclude that the SecY channel can stretch to allow passage of peptides with transversal sizes of approximately 16 A. The observed motion of a transmembrane helical "plug" controlling the closed and open states of the channel is consistent with experimental results and confirms previous hypotheses. Additionally, the "hinge" region for front gate opening is observed to be highly mobile as postulated. Both the forced dilation of a "ring" of residues at the middle of the pore and the lateral opening of the front gate are shown to induce plug displacement, but neither accomplish a full-extent motion of the plug to the back of the channel. For probes whose passage does not destroy the resilience of the SecY, both lateral exit and full translocation are observed, despite the fact that applied forces were always in the direction along the pore axis. Lateral exit is accompanied by front gate opening and slight plug displacement, whereas full translocation is accompanied by large plug displacement but no apparent lateral opening. Simulations also reveal that dilating the pore ring is a more effective way to destabilize the plug than intercalation of a cylinder-like probe at the front gate. Based on the simulations, the existence of a family of diverse open states is proposed.

Computer Simulation↗
PubMed1999

Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex.

Molecular dynamics simulations and free energy calculations of the wild-type EcoRI-DNA complex and several variants have been performed in aqueous solvent. In general, he theoretical estimations of the free energy differences (DeltaDeltaA) qualitatively agree well with the corresponding experimental data. The modifications which were experimentally found unfavorable compared to the wild-type complex were also found to be so in theoretical estimates. The mutant where the amino group of the base Ade(6) was replaced by a hydrogen atom eliminating one H-bond between the DNA and the protein, was experimentally found to be more stable than the wild-type complex. It was speculated that the modification also caused a structural relaxation in the DNA making DeltaDeltaA favorable. Our theoretical estimate yields a positive DeltaDeltaA in this case, but the difference is small, and no significant local structural relaxation was observed. The major H-bonds between the DNA and the protein in the wild-type complex are found to be maintained in the different mutants although the specific and non-specific interaction energies between the interacting the DNA bases and the protein residues are different in different mutants. The interaction pattern of the other nearby nucleotides are significantly influenced by each modification. Thus, the alteration of the non-specific interactions may also play an indirect role in determining the specificity of the complex. The interaction of the Gua(4) of the DNA with the protein is found to be most sensitive to any alteration in the recognition site. Because Gua(4) is the nucleotide closest to the scissile bond, this extra sensitivity seems to play an important role in altering the functional activity of the complex.

Binding Sites↗
PubMed2001

Poly(gamma-glutamic acid) in aqueous solution: molecular dynamics simulations of 10- and 20-residue chains at different temperatures.

A series of molecular dynamics simulations in aqueous solution have been carried out in order to investigate the effects of the length of the peptide chain and the temperature on the helical conformation of un-ionized poly(gamma-D-glutamic acid). The results reveal that the helix is not stable for a small number of residues independent of the temperature. On the other hand, the temperature induces a conformational transition from the helical state to the random coil. Analysis of the energy of the whole system indicates that the helix is more stable than the random coil state by about 5 kcal/mol, even although the solvation potential energy is lower in the latter than in the former.

Biopolymers↗
PubMed2003

Conformational properties of penicillins: quantum chemical calculations and molecular dynamics simulations of benzylpenicillin.

Herein, we present theoretical results on the conformational properties of benzylpenicillin, which are characterized by means of quantum chemical calculations (MP2/6-31G* and B3LYP/6-31G*) and classical molecular dynamics simulations (5 ns) both in the gas phase and in aqueous solution. In the gas phase, the benzylpenicillin conformer in which the thiazolidine ring has the carboxylate group oriented axially is the most favored one. Both intramolecular CH. O and dispersion interactions contribute to stabilize the axial conformer with respect to the equatorial one. In aqueous solution, a molecular dynamics simulation predicts a relative population of the axial:equatorial conformers of 0.70:0.30 in consonance with NMR experimental data. Overall, the quantum chemical calculations as well as the simulations give insight into substituent effects, the conformational dynamics of benzylpenicillin, the frequency of ring-puckering motions, and the correlation of side chain and ring-puckering motions.

Computer Simulation↗
PubMed2005

Molecular dynamics simulation studies of the effect of phosphocitrate on crystal-induced membranolysis.

In this study, following our earlier work on calcium pyrophosphate dihydrate (CPPD) crystal-induced membranolysis, we demonstrate, using the CHARMM method of molecular dynamics simulation, the protective role of phosphocitrate (PC) against solvated dimyristoyl phosphatidylcholine phospholipid bilayer disintegration on contact with the CPPD crystal. Our molecular dynamics simulations studies show that coverage of the CPPD crystal with a layer of phosphocitrate molecules results in the conservation of phospholipid bilayer integrity. We show that the rupture of the lipid bilayer in presence of CPPD and the protective effect of PC are primarily due to electrostatic interactions. The protective role of PC, which may also play an important and potentially therapeutic function against crystal-induced membranolysis is also discussed.

Animals↗
PubMed2005

Molecular dynamics simulation of water near nanostructured hydrophobic surfaces: interfacial energies.

We present results from molecular dynamics simulations of water near structured hydrophobic surfaces. The surface structures reported herein are a planar alkane crystal as a reference and crystals with a hole and a protrusion of approximately 2.5 nm diameter and 0.5 nm depth or height. All indicators show that surface structuring increases the hydrophobicity: The water density is reduced near the structure elements, and the number of residual contacts between water and the surface decreases by about 40 % with respect to the planar surface. Thermodynamic integration shows that the interfacial energy of the structured surfaces is about 7 mJ m(-2) higher for structured surfaces than for the planar surface. The hydrophobicity increases by a similar amount for the hole and the protrusion geometries compared to the planar surface.

Alkanes↗
PubMed2005

Comparative molecular dynamics simulations of uncomplexed, 'agonist-bound' and 'antagonist-bound' alpha1A adrenoceptor models.

Molecular dynamics simulations (2 ns) were conducted on a homology model of the alpha1A adrenoceptor complexed with agonists and antagonists to examine the various receptor conformations induced. These simulations yield insights into the binding site interactions of the active and inactive states of the receptor. Furthermore, our analysis allowed for the selection of candidate sites for future mutagenesis experiments such as of Glu-180, which may be important for antagonist binding. The interactions of conserved residues of the DRY motif in TM-III and the NPxxY motif in TM-VII in the alpha1A adrenoceptor complexes were also examined. The major differences lie in the role of residue Arg-124, which for the agonist complexes formed additional interactions with residues of intracellular loops I and II. Alternatively, for the antagonist complexes, additional interactions were observed for Asn-322 with residues of TM-II and TM-VII.

Adrenergic alpha-1 Receptor Agonists↗
PubMed2005

Atomistic molecular dynamics simulation of benzene as a solute in a columnar discotic liquid crystal.

A molecular dynamics simulation study on a binary liquid-crystalline mixture, where the solvent is the typical discogen hexakis-pentyloxy-triphenylene in its columnar state, while benzene is the solute, is reported. Both discotic and benzene molecules are modeled employing an atomistic force field. Attention has been paid to the structural and dynamic properties of benzene in this unusual environment, comparing these results with available experiments on the same or similar systems and with computer simulation data on neat liquid benzene.

Journal Article↗
PubMed2005

Molecular dynamics simulation of folding of a short helical peptide with many charged residues.

A molecular dynamics simulation of the folding of conantokin-T (con-T), a short helical peptide with 5 helical turns of 21 amino acids with 10 charged residues, was carried out to examine folding pathways for this peptide and to predict the folding rate. In the 18 trajectories run at 300 K, 16 trajectories folded, with an averaged folding time of approximately 50 ns. Two trajectories did not fold in up to 200 ns simulation. The folded structure in folded trajectories is in good agreement with experimental structure. An analysis of the trajectories showed that, at the beginning of a few nanoseconds, helix formation started from residues 5-9 with assistance of a hydrophobic clustering involving Tyr5, Met8, and Leu9. The peptide formed a U-shape mainly due to charge-charge interactions between charged residues at the N- and C-terminus segments. In the next approximately 10 ns, several nonnative charge-charge interactions were broken and nonnative Gla10-Lys18 (this denotes a salt bridge between Gal10 and Lys18) and/or Gla10-Lys19 interactions appeared more frequently in this folding step and the peptide became a fishhook J-shape. From this structure, the peptide folded to the folded state in 7 of all 16 folded trajectories in approximately 15 ns. Alternatively, in approximately 30 ns, the con-T went to a conformation in an L-shape with 4 helical turns and a kink at the Arg13 and Gla14 segment in the other 9 trajectories. Con-T in the L-shape then required another approximately 15 ns to fold into the folded state. In addition, in overall folding times, the former 7 trajectories folded faster with the total folding times all shorter than 45 ns, while the latter 9 trajectories folded at a time longer than 45 ns, resulting in an average folding time of approximately 50 ns. Two major folding intermediates found in 2 nonfolded trajectories are stabilized by charge clusters of 5 and 6 charged residues, respectively. With inclusion of friction and solvent-solvent interactions, which were ignored in the present GB/SA solvation model, the folding time obtained above should be multiplied by a factor of 1.25-1.7 according to a previous, similar simulation study. This results in a folding time of 65-105 ns, slightly shorter than the folding time of 127 ns for an alanine-based peptide of the same length. This suggests that the energy barrier of folding for this type of peptides with many charged residues is slightly lower than alanine-based helical peptides by less than 1 kcal/mol.

Amino Acids↗
PubMed2006

Molecular dynamics simulation of the cation motion upon adsorption of CO2 in Faujasite zeolite systems.

Molecular Dynamics simulations have been carried out in NaX and NaY Faujasite systems to deepen understanding of the cation rearrangement during the CO2 adsorption process suggested by our recent diffusivity measurements. This study is a major contribution since the rearrangement of the cations in Faujasite, the most promising adsorbent for CO2 storage, can represent a significant breakthrough in understanding the adsorption and diffusion processes at the mircroscopic scale. For NaY, it has been shown that at low and intermediate loadings, SII cations can migrate toward the center of the supercage due to strong interactions with the adsorbates, followed by a hopping of SI'cation from the sodalite cage into the supercage to fill the vacant SII site. The SI cations are only displaced at a higher loading, leading to cation de-trapping out of the double six rings into the vacant SI' sites. For NaX, the SIII' cations which occupy the most accessible adsorption sites move significantly upon coordination to the carbon dioxide molecules. The SI' and SII cations remain consistently located in their initial sites whatever the loading. Indeed, the most probable migration mechanism involves SIII' cation displacements into nearby vacant SIII' sites.

Journal Article↗
PubMed2005

Molecular dynamics simulation of uranyl(VI) adsorption equilibria onto an external montmorillonite surface.

We used molecular dynamics simulations to study the adsorption of aqueous uranyl species (UO(2)(2+)) onto clay mineral surfaces in the presence of sodium counterions and carbonato ligands. The large system size (10,000 atoms) and long simulation times (10 ns) allowed us to investigate the thermodynamics of ion adsorption, and the atomistic detail provided clues for the observed adsorption behavior. The model system consisted of the basal surface of a low-charge Na-montmorillonite clay in contact with aqueous uranyl carbonate solutions with concentrations of 0.027 M, 0.081 M, and 0.162 M. Periodic boundary conditions were used in the simulations to better represent an aqueous solution interacting with an external clay surface. Uranyl adsorption tendency was found to decrease as the aqueous uranyl carbonate concentration was increased, while sodium adsorption remained constant. The observed behavior is explained by physical and chemical effects. As the ionic strength of the aqueous solution was increased, electrostatic factors prevented further uranyl adsorption once the surface charge had been neutralized. Additionally, the formation of aqueous uranyl carbonate complexes, including uranyl carbonato oligomers, contributed to the decreased uranyl adsorption tendency.

Adsorption↗
PubMed2004

Molecular dynamics simulation of optically trapped colloidal particles at an oil-water interface.

Using molecular dynamics simulations, we calculate the net force on a colloidal particle trapped by an optical tweezer and confined within a particle monolayer which is in motion relative to the trapped particle. The calculations are compared with recent experimental data on polystyrene particles located at an oil-water interface. Good agreement between theory and experiment is obtained over the investigated range of lattice constants for an interaction mechanism between the polystyrene particles which is dominated by an effective dipole-dipole potential. The assumed interaction mechanism is consistent with the formation of surface charge dipoles at the particle-oil interface due to the dissociaton of the hydrophilic sulfate headgroups at the surface of the polystyrene particles. A possible physical mechanism for the formation of the surface charge dipoles, involving a diffuse cloud of fully hydrated counterions, is described, and the fraction of surface groups contributing to the formation of surface charge dipoles is estimated to be of the order of 10(-1) for the present system.

Journal Article↗
PubMed2005

Test of classical nucleation theory via molecular-dynamics simulation.

A direct test of classical nucleation theory (CNT) is made using molecular-dynamics simulations. The relation between critical nucleus size and undercooling temperature is extracted and the result yields the solid-liquid interfacial energy. It is shown that the CNT, within the assumptions made for spherical nucleus in supercooled liquid, is valid in the critical regime of nucleation for a large range of undercooling and nucleus size.

Journal Article↗
PubMed2005

A molecular-dynamics simulation study of solvent-induced repulsion between C60 fullerenes in water.

Molecular-dynamics simulations of a single C(60) fullerene and pairs of C(60) fullerenes in aqueous solution have been performed for the purpose of obtaining improved understanding of the nature of solvent-induced interactions between C(60) fullerenes in water. Our simulations reveal repulsive solvent-induced interactions between two C(60) fullerenes in aqueous solution in contrast to the associative effects observed for conventional nonpolar solutes. A decomposition of the solvent-induced potential of mean force between fullerenes into entropy and energy (enthalpy) contributions reveals that the water-induced repulsion between fullerenes is energetic in origin, contrasting strongly to entropy-driven association observed for conventional nonpolar solutes. The dominance of energy in the solvent-induced interactions between C(60) fullerenes arises primarily from the high atomic density of the C(60) molecule, resulting in strong C(60)-water van der Waals attraction that is reduced upon association of the fullerenes. The water-induced repulsion is found to decrease with increasing temperature due largely to an increasing contribution from a relatively weak entropy-driven association.

Journal Article↗
PubMed1993

Molecular dynamics simulations and rigid body (TLS) analysis of aspartate carbamoyltransferase: evidence for an uncoupled R state.

In the R form of ATCase complexed with the bisubstrate analogue, N-(phosphonacetyl)-L-aspartate, large temperature factors are reported for the allosteric domains of the regulatory chains. We studied the conformational flexibility of the holoenzyme with molecular dynamics simulations and rigid body (TLS) analysis. The results of the molecular dynamics simulations suggest that, although local atomic fluctuations account for the temperature factors of the catalytic and zinc domains, they do not account for the large temperature factors of the allosteric regions. However, the temperature factors of the allosteric domains can be satisfactorily analyzed using a rigid body model. The simulations and rigid body analysis support the idea that the allosteric regions are mechanically uncoupled from the rest of the enzyme in the PALA structure. Implications of this uncoupling for allosteric regulation are discussed.

Allosteric Site↗
PubMed2002

Molecular dynamics simulation of polymer crystallization from an oriented amorphous state.

The molecular process of crystallization from an oriented amorphous state was reproduced by molecular dynamics simulation for a realistic polyethylene model. The initial oriented amorphous state was obtained by uniaxially drawing an isotropic glassy state at 100 K. By the temperature jump from 100 K to 330 K, there occurred crystallization into the fiber structure, during the process of which we observed the developments of various order parameters. The real-space image and its Fourier transform revealed that a hexagonally ordered domain was initially formed, and then a highly ordered crystalline state with stacked lamellas developed after further adjustment of the relative heights of the chains along their axes.

Journal Article↗