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At least 1,693 records · Page 94Linked to original sources
PubMed2005

Absolute free energies of binding of peptide analogs to the HIV-1 protease from molecular dynamics simulations.

The constants of binding of five peptide analogs to the active site of the HIV-1 aspartic-protease are calculated based on a novel sampling scheme that is efficient and does not introduce any approximations in addition to the energy function used to describe the system. The results agree with experiments. The squared correlation coefficient of the calculated vs. the measured values is 0.79. The sampling scheme consists of a series of molecular dynamics integrations with biases. The biases are selected based on an estimate of the probability density function of the system in a way to explore the conformational space and to reduce the statistical error in the calculated binding constants. The molecular dynamics integrations are done with a vacuum potential using a short cutoff scheme. To estimate the probability density of the simulated system, the results of the molecular dynamics integrations are combined using an extension of the weighted histogram analysis method (C. Bartels, Chem. Phys. Letters 331 (2000) 446-454). The probability density of the solvated ligand-protein system is obtained by applying a correction for the use of the short cutoffs in the simulations and by taking into account solvation with an electrostatic term and a hydrophobic term. The electrostatic part of the solvation is determined by finite difference Poisson-Boltzmann calculations; the hydrophobic part of the solvation is set proportional to the solvent accessible surface area. Setting the hydrophobic surface tension parameter equal to 8 mol(-1) K(-1) A(-2), absolute binding constants are in the muM to nM range. This is in agreement with experiments. The standard errors determined from eight repeated binding constant determinations are a factor of 14 to 411. A single determination of a binding constant is done with 499700 steps of molecular dynamics integration and 4500 finite difference Poisson-Boltzmann calculations. The simulations can be analyzed with respect to conformational changes of the active site of the HIV-1 protease or the ligands upon binding and provide information that complements experiments and can be used in the drug development process.

Algorithms↗
PubMed2006

Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations.

High-density lipoproteins (HDL) function as cholesterol transporters, facilitating the removal of excess cholesterol from the body. Due to the heterogeneity of native HDL particles (both in size and shape), the details on how these protein-lipid particles form and the structure they assume in their lipid-associated states are not well characterized. We report here a study of the self-assembly of discoidal HDL particles using coarse-grained (CG) molecular dynamics. The microsecond simulations reveal the self-assembly of HDL particles from disordered protein-lipid complexes to form structures containing many of the features of the generally accepted double-belt model for discoidal HDL particles. HDL assembly is found to proceed in two broad steps, aggregation of proteins and lipids driven by the hydrophobic effect which occurs on a approximately 1 micros time scale, followed by the optimization of the protein structure driven by increasingly specific protein-protein interactions.

Lipoproteins, HDL↗
PubMed1997

RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin.

The hydration of the tRNA(Asp) anticodon hairpin was investigated through the analysis of six 500 ps multiple molecular dynamics (MMD) trajectories generated by using the particle mesh Ewald method for the treatment of the long-range electrostatic interactions. Although similar in their dynamical characteristics, these six trajectories display different local hydration patterns reflecting the landscape of the "theoretical" conformational space being explored. The statistical view gained through the MMD strategy allowed us to characterize the hydration patterns around important RNA structural motifs such as a G-U base-pair, the anticodon U-turn, and two modified bases: pseudouridine and 1-methylguanine. The binding of ammonium counterions to the hairpin has also been investigated. No long-lived hydrogen bond between water and a 2'-hydroxyl has been observed. Water molecules with long-residence times are found bridging adjacent pro-Rp phosphate atoms. The conformation of the pseudouridine is stiffened by a water-mediated base-backbone interaction and the 1-methylguanine is additionally stabilized by long-lived hydration patterns. Such long-lived hydration patterns are essential to ensure the structural integrity of this hairpin motif. Consequently, our simulations confirm the conclusion reached from an analysis of X-ray crystal structures according to which water molecules form an integral part of nucleic acid structure. The fact that the same conclusion is reached from a static and a dynamic point of view suggests that RNA and water together constitute the biologically relevant functional entity.

Anticodon↗
PubMed2003

nMoldyn: a program package for a neutron scattering oriented analysis of molecular dynamics simulations.

We present a new implementation of the program nMoldyn, which has been developed for the computation and decomposition of neutron scattering intensities from Molecular Dynamics trajectories (Comp. Phys. Commun 1995, 91, 191-214). The new implementation extends the functionality of the original version, provides a much more convenient user interface (both graphical/interactive and batch), and can be used as a tool set for implementing new analysis modules. This was made possible by the use of a high-level language, Python, and of modern object-oriented programming techniques. The quantities that can be calculated by nMoldyn are the mean-square displacement, the velocity autocorrelation function as well as its Fourier transform (the density of states) and its memory function, the angular velocity autocorrelation function and its Fourier transform, the reorientational correlation function, and several functions specific to neutron scattering: the coherent and incoherent intermediate scattering functions with their Fourier transforms, the memory function of the coherent scattering function, and the elastic incoherent structure factor. The possibility to compute memory function is a new and powerful feature that allows to relate simulation results to theoretical studies.

Journal Article↗
PubMed2001

Structural properties of a highly polyunsaturated lipid bilayer from molecular dynamics simulations.

The structure of a fully hydrated mixed (saturated/polyunsaturated) chain lipid bilayer in the biologically relevant liquid crystalline phase has been examined by performing a molecular dynamics study. The model membrane, a 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (SDPC, 18:0/22:6 PC) lipid bilayer, was investigated at constant (room) temperature and (ambient) pressure, and the results obtained in the nanosecond time scale reproduced quite well the available experimental data. Polyunsaturated fatty acids are found in high concentrations in neuronal and retinal tissues and are essential for the development of human brain function. The docosahexaenoic fatty acid, in particular, is fundamental for the proper function of the visual receptor rhodopsin. The lipid bilayer order has been investigated through the orientational order parameters. The water-lipid interface has been explored thoroughly in terms of its dimensions and the organization of the different components. Several types of interactions occurring in the system have been analyzed, specifically, the water-hydrocarbon chain, lipid-lipid and lipid-water interactions. The distribution of dihedral angles along the chains and the molecular conformations of the polyunsaturated chain of the lipids have also been studied. Special attention has been focused on the microscopic (molecular) origin of the effects of polyunsaturations on the different physical properties of membranes.

Computer Simulation↗
PubMed2006

Molecular dynamics simulations of mass transfer resistance in grain boundaries of twinned zeolite membranes.

The net mass transfer resistance for gas molecules permeating through zeolite membranes includes contributions from intracrystalline diffusion and contributions from interfacial effects. These interfacial effects can arise either from gas-zeolite interfaces or from interfaces that exist within zeolite crystals due to grain boundaries. We present the first atomically detailed simulations that examine interfacial mass transfer resistance due to internal grain boundaries in zeolites that are relevant for membrane applications. Our calculations examine twinned silicalite crystals in crystallographic configurations that have been identified in previous experiments. We used the dual control volume grand canonical molecular dynamics method to simulate the permeance of CH(4) and CF(4) through thin twinned silicalite crystals. The magnitudes of the grain boundary resistances are quite substantial, at least for the thin crystals that are accessible in our simulations.

Journal Article↗
PubMed2000

Analysis of correlated motion in antibody combining sites from molecular dynamics simulations.

The crystal structures of the NC6.8-antisweet taste ligand complex and the uncomplexed antibody structures display significant differences in the conformations of residues in the combining site. A molecular dynamics method was employed to understand the flexibility and correlated motion of key combining site residues in the uncomplexed antibody. The simulations reveal that residues that show conformational differences between the complex and uncomplexed structures display strong dynamical correlations. Extensive analysis of the dynamics trajectory using time correlation methods is presented.

Acetates↗
PubMed2002

Unfolding of titin domains studied by molecular dynamics simulations.

Titin, a approximately 1 micron long protein found in striated muscle myofibrils, possesses unique elastic properties. The extensible behavior of titin has been demonstrated in atomic force microscopy and optical tweezer experiments to involve the reversible unfolding of individual immunoglobulin-like (Ig) domains. We have used steered molecular dynamics (SMD), a novel computer simulation method, to investigate the mechanical response of single titin Ig domains upon stress. Simulations of stretching Ig domains I1 and I27 have been performed in a solvent of explicit water molecules. The SMD approach provides a detailed structural and dynamic description of how Ig domains react to external forces. Validation of SMD results includes both qualitative and quantitative agreement with AFM recordings. Furthermore, combining SMD with single molecule experimental data leads to a comprehensive understanding of Ig domains' mechanical properties. A set of backbone hydrogen bonds that link the domains' terminal beta-strands play a key role in the mechanical resistance to external forces. Slight differences in architecture permit a mechanical unfolding intermediate for I27, but not for I1. Refolding simulations of I27 demonstrate a locking mechanism.

Amino Acid Sequence↗
PubMed1998

Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap.

Large concerted motions of proteins which span its "essential space," are an important component of protein dynamics. We investigate to what extent structure ensembles generated with standard structure calculation techniques such as simulated annealing can capture these motions by comparing them to long-time molecular dynamics (MD) trajectories. The motions are analyzed by principal component analysis and compared using inner products of eigenvectors of the respective covariance matrices. Two very different systems are studied, the beta-spectrin PH domain and the single-stranded DNA binding protein (ssDBP) from the filamentous phage Pf3. A comparison of the ensembles from NMR and MD shows significant overlap of the essential spaces, which in the case of ssDBP is extraordinarily high. The influence of variations in the specifications of distance restraints is investigated. We also study the influence of the selection criterion for the final structure ensemble on the definition of mobility. The results suggest a modified criterion that improves conformational sampling in terms of amplitudes of correlated motion.

Computer Simulation↗
PubMed2005

A molecular-dynamics simulation study on the dependence of Lennard-Jones gas-liquid phase diagram on the long-range part of the interactions.

The particle-transfer molecular-dynamics technique is adopted to construct the Lennard-Jones fluid gas-liquid phase diagram. Detailed study of the dependence of the simulation results on the system size and the cutoff distance is performed to test the validity of the simulation technique. Both the traditional cutoff plus long-range correction (CPC) and Ewald summation methods are used in the simulations to calculate the interactions. In the intermediate range of temperatures, the results with the Ewald summation method are almost the same as those with the CPC method. However, in the range close to the critical point, the results with the CPC method deviate from those with the Ewald summation. Compared with the results obtained via the Ewald summation in a smaller system, simply increasing the system size in the CPC scheme may not give better results.

Journal Article↗
PubMed2001

Molecular dynamics simulation of the fragile glass former orthoterphenyl: a flexible molecule model. II. Collective dynamics.

We present a molecular dynamics study of the collective dynamics of a model for the fragile glass former orthoterphenyl. In this model, introduced by Mossa, Di Leonardo, Ruocco, and Sampoli [Phys. Rev. E 62, 612 (2000)], the intramolecular interaction among the three rigid phenyl rings is described by a set of force constants whose value has been fixed in order to obtain a realistic isolated molecule spectrum. The interaction between different molecules is described by a Lennard Jones site-site potential. We study the behavior of the coherent scattering functions F(t)(q,t), considering the density fluctuations of both molecular and phenyl-ring centers of mass; moreover we directly simulate the neutron scattering spectra taking into account both the contributions due to carbon and hydrogens atoms. We compare our results with the main predictions of the mode-coupling theory and with the available coherent neutron scattering experimental data.

Journal Article↗
PubMed2000

Molecular dynamics simulation of structural transformation in silicon carbide under pressure

Pressure-induced structural transformation in cubic silicon carbide is studied with the isothermal-isobaric molecular-dynamics method using a new interatomic potential scheme. The reversible transformation between the fourfold coordinated zinc-blende structure and the sixfold coordinated rocksalt structure is successfully reproduced by the interatomic potentials. The calculated volume change at the transition and hysteresis are in good agreement with experimental data. The atomistic mechanisms of the structural transformation involve a cubic-to-monoclinic unit-cell transformation and a relative shift of Si and C sublattices in the 100 direction.

Journal Article↗
PubMed1993

Molecular dynamics simulation of winter flounder antifreeze protein variants in solution: correlation between side chain spacing and ice lattice.

The solution structure of the 38 amino acid C-terminal region of the precursor for the HPLC-6 antifreeze protein from winter flounder has been investigated with molecular dynamics using the AMBER software. The simulation for the peptide in aqueous solution was carried out at a constant temperature of 0 degree C and at atmospheric pressure. The simulation covered 120 ps and the results were analyzed based on data sampled upon reaching a stable equilibrium phase. Information has been obtained on the quality of constant temperature and pressure simulations, the solution structure and dynamics, the hydrogen bonding network, the helix stabilizing role of terminal charges and the interaction with the surrounding water molecules. The Lys18-Glu22 interactions and the terminal charged residues are found to stabilize a helical structure with the side chains of Thr2, Thr13, Thr24 and Thr35 equally spaced on one side of the helix. The spacing between oxygen atoms in the hydroxyl group of the threonine side chains exhibits fluctuations of the order of 2-3 A during the 120 ps of simulation, but values simultaneously close to the repeat distance of 16.6 A between oxygen atoms along the [0112] direction in ice are observed. Furthermore, two engineered variants were studied using the same simulation protocol.

Amino Acid Sequence↗
PubMed2004

Electric field induced switching of poly(ethylene glycol) terminated self-assembled monolayers: a parallel molecular dynamics simulation.

Effects of electric field on the structure of poly(ethylene glycol) (PEG) terminated alkanethiol self-assembled monolayer (SAM) on gold have been studied using parallel molecular dynamics method. An applied electric field triggers a conformational transition from all-trans to a mostly gauche conformation. The polarity of the electric field has a significant effect on the surface structure of PEG leading to a profound effect on the hydrophilicity of the surface. The electric field applied antiparallel to the surface normal causes a reversible transition to an ordered state in which the oxygen atoms are exposed. On the other hand, an electric field applied in a direction parallel to the surface normal introduces considerable disorder in the system and the oxygen atoms are buried inside. The parallel field affects the overall tilt structure of SAMs more adversely than the antiparallel field.

Adsorption↗
PubMed2005

Hydrophilic solutes in modified carbon dioxide extraction-prediction of the extractability using molecular dynamic simulation.

Super- and subcritical carbon dioxide (CO2) extractions of crude drugs were simulated by molecular modelling to predict the extractability of different hydrophilic plant constituents under various extraction conditions. The CO2 extraction fluids were simulated either with pure CO2 or with solvent modified CO2 at different pressures and temperatures. Molecular modelling resulted in three different solubility parameters: the total solubility parameter delta and the partial solubility parameters delta(d) for the van der Waals and delta(EL) for the polar forces. Thus, delta(EL) enabled the estimation of the polarity of the extraction fluids and the solute molecules. If the value of delta(EL) of the extraction fluid reached the value of the solute molecule in the crude drug, i.e. minimum extraction value, the compound was soluble at the distinct extraction conditions. For a further increase in yield of the hydrophilic solutes, the polarity of the extraction fluid had to be increased, too. That means delta(EL) of the fluid exceeded the minimum extraction value. All simulations were verified by CO2 extractions of the secondary roots of Harpagophytum procumbens (harpagoside, stachyose) and the seeds of Aesculus hippocastanum (aescin). CO2 extractions of the flowers of Matricaria recutita ((-)-alpha-bisabolol) were obtained from literature data. These four constituents with different properties, like molecular size and the allocation of polar functional groups were extracted, analysed, simulated and the extract content was correlated with the extraction fluid used, respectively.

Aesculus↗
PubMed2003

Structure of the parallel-stranded DNA quadruplex d(TTAGGGT)4 containing the human telomeric repeat: evidence for A-tetrad formation from NMR and molecular dynamics simulations.

The structure of the intermolecular DNA quadruplex d(TTAGGGT)4, based on the human telomeric DNA sequence d(TTAGGG), has been determined in solution by NMR and restrained molecular dynamics simultations. The core GGG region forms a highly stable quadruplex with G-tetrads likely stabilised by K+ ions bound between tetrad plains. However, we have focused on the conformation of the adenines which differ considerably in base alignment, stability and dynamics from those in previously reported structures of d(AGGGT)4 and d(TAGGGT)4. We show unambiguously that the adenines of d(TTAGGGT)4 are involved in the formation of a relatively stable A-tetrad with well-defined glycosidic torsion angles (anti), hydrogen bonding network (adenine 6-NH2-adenine N1) defined by interbase NOEs, and base stacking interactions with the neighbouring G-tetrad. All of these structural features are apparent from NOE data involving both exchangeable and non-exchangeable protons. Thus, context-dependent effects appear to play some role in dictating preferred conformation, stability and dynamics. The structure of d(TTAGGGT)4 provides us with a model system for exploiting in the design of novel telomerase inhibitors that bind to and stabilise G-quadruplex structures.

Base Sequence↗
PubMed2005

Associative mechanism for phosphoryl transfer: a molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates.

The ternary complex of Escherichia coli adenylate kinase (ECAK) with its substrates adenosine monophosphate (AMP) and Mg-ATP, which catalyzes the reversible transfer of a phosphoryl group between adenosine triphosphate (ATP) and AMP, was studied using molecular dynamics. The starting structure for the simulation was assembled from the crystal structures of ECAK complexed with the bisubstrate analog diadenosine pentaphosphate (AP(5)A) and of Bacillus stearothermophilus adenylate kinase complexed with AP(5)A, Mg(2+), and 4 coordinated water molecules, and by deleting 1 phosphate group from AP(5)A. The interactions of ECAK residues with the various moieties of ATP and AMP were compared to those inferred from NMR, X-ray crystallography, site-directed mutagenesis, and enzyme kinetic studies. The simulation supports the hypothesis that hydrogen bonds between AMP's adenine and the protein are at the origin of the high nucleoside monophosphate (NMP) specificity of AK. The ATP adenine and ribose moieties are only loosely bound to the protein, while the ATP phosphates are strongly bound to surrounding residues. The coordination sphere of Mg(2+), consisting of 4 waters and oxygens of the ATP beta- and gamma-phosphates, stays approximately octahedral during the simulation. The important role of the conserved Lys13 in the P loop in stabilizing the active site by bridging the ATP and AMP phosphates is evident. The influence of Mg(2+), of its coordination waters, and of surrounding charged residues in maintaining the geometry and distances of the AMP alpha-phosphate and ATP beta- and gamma-phosphates is sufficient to support an associative reaction mechanism for phosphoryl transfer.

Adenosine Monophosphate↗