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At least 217 records · Page 12Linked to original sources
PubMed2006

Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation.

The structure and molecular packing density of a "mismatched" solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data on comparable systems. The local density or molecular packing in DMPC-hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested a positive volume change, DeltaV(m), of 4 cm(3) mol(-1) hexanol partitioned at 310 K in good accordance with experimental values. Analysis of the apparent volumes of each component in the pure and mixed states further showed that DeltaV(m) reflects a balance between a substantial increase in the packing density of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8) is stretched by about 4%. Concomitantly, the average lateral area per chain decreases and these two effects compensate so that the overall packing density in the outer region, where the hexanol molecules are located, remains practically constant. The core of the bilayer (C9-C13) is slightly thinned. The average lateral area per chain in this region expands, resulting in a looser packing density. The net effect in the core is a 2-3% decrease in density corresponding to a total volume increase of approximately 14 cm(3) mol(-1) hexanol partitioned.

Computer Simulation↗
PubMed2006

Alkali cation extraction by calix[4]crown-6 to room-temperature ionic liquids. The effect of solvent anion and humidity investigated by molecular dynamics simulations.

We report a molecular dynamics study on the solvation of M+ (Na+ to Cs+) alkali cations and of their LM+ complexes with a calix[4]arene host (L = 1,3-dimethoxy-calix[4]arene-crown-6 in the 1,3-alternate conformation) in the [BMI][PF6] and [BMI][Tf2N] room-temperature ionic liquids "ILs" based on the BMI+ (1-butyl-3-methylimidazolium) cation. The comparison of the two liquids and the dry versus humid form of the former one (with a 1:1 ratio of H2O and BMI+PF6- species) reveals the importance of humidity: in [BMI][PF6]-dry as in the [BMI][Tf2N] liquid, the first solvation shell of the "naked" M+ ions is composed of solvent anions only (four PF6- anions, and from four to five Tf2N- anions, respectively, quasi-neutralized by a surrounding cage of BMI+ cations), while in the [BMI][PF6]-humid IL, it comprises from one to three solvent anions and about four H2O molecules. In the LM+ complexes, the cation is shielded from solvent, but still somewhat interacts with a solvent anion in the dry ILs and with water in the humid IL. We also report tests on M+ interactions with solvent anions PF6- and Tf2N- in the gas phase, showing that the AMBER results are in satisfactory agreement with QM results obtained at different levels of theory. The question of ion recognition by L is then examined by free energy perturbation studies in the three liquids, predicting a high Cs+/Na+ selectivity upon liquid extraction from an aqueous phase, in agreement with experimental results on a parent calixarene host. A similar Cs+/Na+ selectivity is predicted upon complexation in a homogeneous IL phase, mainly due to the desolvation energy of the free cations. Thus, despite their polar character, ionic liquids qualitatively behave as classical weakly polar organic liquids (e.g., choroform) as far as liquid-liquid extraction is concerned but more like polar liquids (water, alcohols) as far as complexation in a single phase is concerned.

Journal Article↗
PubMed2003

Prediction of glass transition temperature of freeze-dried formulations by molecular dynamics simulation.

PURPOSE: To examine whether the glass transition temperature (Tg) of freeze-dried formulations containing polymer excipients can be accurately predicted by molecular dynamics simulation using software currently available on the market. Molecular dynamics simulations were carried out for isomaltodecaose, a fragment of dextran, and alpha-glucose, the repeated unit of dextran. in the presence or absence of water molecules. Estimated values of Tg were compared with experimental values obtained by differential scanning calorimetry (DSC). METHODS: Isothermal-isobaric molecular dynamics simulations (NPTMD) and isothermal molecular dynamics simulations at a constant volume (NVTMD) were carried out using the software package DISCOVER (Material Studio) with the Polymer Consortium Force Field. Mean-squared displacement and radial distribution function were calculated. RESULTS: NVTMD using the values of density obtained by NPTMD provided the diffusivity of glucose-ring oxygen and water oxygen in amorphous alpha-glucose and isomaltodecaose, which exhibited a discontinuity in temperature dependence due to glass transition. Tg was estimated to be approximately 400K and 500K for pure amorphous a-glucose and isomaltodecaose, respectively, and in the presence of one water molecule per glucose unit, Tg was 340K and 360K, respectively. Estimated Tg values were higher than experimentally determined values because of the very fast cooling rates in the simulations. However, decreases in Tg on hydration and increases in Tg associated with larger fragment size could be demonstrated. CONCLUSION: The results indicate that molecular dynamics simulation is a useful method for investigating the effects of hydration and molecular weight on the Tg of lyophilized formulations containing polymer excipients. although the relationship between cooling rates and Tg must first be elucidated to predict Tg vales observed by DSC measurement. January 16.

Calorimetry, Differential Scanning↗
PubMed2006

Multibaric-multithermal ensemble molecular dynamics simulations.

We present new generalized-ensemble molecular dynamics simulation algorithms, which we refer to as the multibaric-multithermal molecular dynamics. We describe three algorithms based on (1) the Nosé thermostat and the Andersen barostat, (2) the Nosé-Poincaré thermostat and the Andersen barostat, and (3) the Gaussian thermostat and the Andersen barostat. The multibaric-multithermal simulations perform random walks widely both in the potential-energy space and in the volume space. Therefore, one can calculate isobaric-isothermal ensemble averages in wide ranges of temperature and pressure from only one simulation run. We test the effectiveness of the multibaric-multithermal algorithm by applying it to a Lennard-Jones 12-6 potential system.

Journal Article↗
PubMed1995

Structural fluctuation of methyl N,N'-diacetyl-beta-D-chitobioside in vacuo and in aqueous solution: molecular dynamics simulations and proton NMR spectroscopy.

Molecular dynamics (MD) simulations of methyl N,N'-diacetyl-beta-D-chitobioside (GlcNAc beta-(1-->4)GlcNAc beta-OMe) have been performed both in vacuo and in aqueous solution with the explicit inclusion of the solvent water molecules. The beta-(1-->4) glycosidic linkage fluctuates considerably, over a range of +/- 10 degrees, in each of the MD simulations in vacuo and in aqueous solution. The intra- and inter-residue hydrogen bonds in vacuo are replaced by intermolecular hydrogen bonds with the solvent water molecules in aqueous solution. Multiple conformations (gg and gt) exist for the exocyclic hydroxymethyl groups. The results of the MD simulations are compared with those of 1H-1H nuclear Overhauser effect measurements.

Carbohydrate Conformation↗
PubMedDate not supplied

Molecular dynamics simulations of aqueous pullulan oligomers.

Molecular dynamics (MD) simulations have been used to model small-angle X-ray scattering (SAXS) data on aqueous solutions of four oligomeric segments of the glucan pullulan: the trimer G(3) (comprising one polymer repeating unit), the hexamer (G(3))(2), the nonamer (G(3))(3), and the dodecamer (G(3))(4). The AMBER force field was used in conjunction with the GB/SA continuum solvation model to calculate both the mean global dimensions of the oligomers from the limiting small angle scattering behavior and the shorter range structural information implicit in the Debye scattering function at larger scattering angles. This same force field and solvation treatment were employed earlier by Liu et al. (Macromolecules 1999, 32, 8611-8620) with apparent success in a rotational isomeric state (RIS) treatment of the same experimental data. The present work discloses that, despite numerical success in modeling the SAXS data, the RIS treatment, which includes only the interactions within dimeric segments of the polymer chain, fails to account accurately for excluded volume effects at the range of 3-12 sugar residues in the polymer backbone. It is suggested that MD simulations using continuum solvation models can be used to circumvent errors inherent in the computationally efficient RIS treatments of polymer nano- and picosecond dynamics while at the same time avoiding the heavy computational requirements of all-atom methods.

Carbohydrate Conformation↗
PubMed1999

The third leg: molecular dynamics simulations of lipid binding proteins.

Molecular dynamics computer simulations can provide a third leg which balances the contributions of both structural biology and binding studies performed on the lipid binding protein family. In this context, these calculations help to establish a dialogue between all three communities, by relating experimental observables with details of structure. Working towards this connection is important, since experience has shown the difficulty of inferring thermodynamic properties from a single static conformation. The challenge is exemplified by ongoing attempts to interpret the impact of mutagenesis on structure and function (i.e. binding). A detailed atomic-level understanding of this system could be achieved with the support of all three legs, paving the way towards rational design of proteins with novel specificities. This paper provides an outline of the connections possible between experiment and theory concerning lipid binding proteins.

Carrier Proteins↗
PubMedDate not supplied

Molecular dynamics simulation of cyclosophoroheptadecaose (Cys-A).

The conformational preferences of cyclosophoroheptadecaose (Cys-A), which is a member of a class of cyclic (1 --> 2)-beta-D-glucan, were characterized by molecular dynamics simulations. Simulated annealing and constant temperature molecular dynamics simulations were performed on the Cys-A. The simulations produced various types of compact and asymmetrical conformations of Cys-A. Excellent agreement was found between experimental data and corresponding values predicted by molecular modeling. Most glycosidic linkages were concentrated in the lowest energy region of phi-psi energy map, and the values of radius of gyration (R(G)) and the nuclear Overhauser effect (NOE) distance data derived from our simulations were finely consistent with the reported experimental values. This result will also give novel insights for the molecular complexation mechanism of Cys-A with various guest chemicals.

Carbohydrate Conformation↗
PubMed2004

Dynamics of water molecules buried in cavities of apolipoprotein E studied by molecular dynamics simulations and continuum electrostatic calculations.

Molecular dynamics (MD) simulations of several nanoseconds each were used to monitor the dynamic behavior of the five crystal water molecules buried in the interior of the N-terminal domain of apolipoprotein E. These crystal water molecules are fairly well conserved in several apolipoprotein E structures, suggesting that they are not an artifact of the crystal and that they may have a structural and/or functional role for the protein. All five buried crystal water molecules leave the protein interior in the course of the longest simulations and exchange with water molecules from the bulk. The free energies of binding evaluated from the electrostatic binding free energy computed using a continuum model and estimates of the binding entropy changes represent shallow minima. The corresponding calculated residence times of the buried water molecules range from tens of picoseconds to hundreds of nanoseconds, which denote rather short times as for buried water molecules. Several water exchanges monitored in the simulations show that water molecules along the exit/entrance pathway use a relay of H bonds primarily formed with charged residues which helps either the exit or the entrance from or into the buried site. The exit/entrance of water molecules from/into the sites is permitted essentially by local motions of, at most, two side chains, indicating that, in these cases, complex correlated atomic motions are not needed to open the buried site toward the surface of the protein. This provides a possible explanation for the short residence times.

Apolipoproteins E↗
PubMed2005

Fluctuating charge normal modes: An algorithm for implementing molecular dynamics simulations with polarizable potentials.

A new method for performing molecular dynamics simulations with fluctuating charge polarizable potentials is introduced. In fluctuating charge models, polarizability is treated by allowing the partial charges to be variables, with values that are coupled to charges on the same molecule as well as those on other molecules. The charges can be efficiently propagated in a molecular dynamics simulation using extended Lagrangian dynamics. By making a coordinate change from the charge variables to a set of normal mode charge coordinates for each molecule, a new method is constructed in which the normal mode charge variables uncouple from those on the same molecule. The method is applied to the TIP4P-FQ model of water and compared to other methods for implementing the dynamics. The methods are compared using different molecular dynamics time steps.

Journal Article↗
PubMed2003

Molecular dynamics simulation of an electric field driven dipolar molecular rotor attached to a quartz glass surface.

Molecular dynamics simulations of the response of a dipolar azimuthal 3-chloroprop-1-ynyl rotor mounted on the surface of quartz glass to a rotating electric field were performed. The rotor motion was classified as synchronous, asynchronous, random, or hindered, based on the value of the average lag of the rotor behind the field and a comparison of the intrinsic rotational barrier V(b) with kT. A phase diagram of rotor behavior was deduced at 10, 300, and 500 K as a function of field strength and frequency. A simple model for the rotor motion was developed, containing the driving force, the temperature, the height of the torsional barrier, and the friction constant of the rotor. Defining E(bo) to be the electric field strength necessary to get rotational response from the rotor ("breakoff field") and mu to be the rotor dipole moment component in the plane of rotation, we find that E(bo) is frequency independent when 2 microE(bo) is less than either V(b) or kT (the driving force needs to overcome the more important of the two, the intrinsic barrier or random thermal motion). At higher frequencies, E(bo) is a quadratic function of the frequency and the driving force fights friction, which is dictated by intramolecular vibrational redistribution (IVR) from the pumped rotational mode to all others. Fitting the simple model to simulation data, we derived a friction constant of 0.26 ps eV x (nu - 0.5)/THz between 500 and 1000 GHz.

Journal Article↗
PubMed2003

Quasiequilibrium unfolding thermodynamics of a small protein studied by molecular dynamics simulation with an explicit water model.

The 124 independent molecular dynamics simulations are completed with total time of 196.8 ns. The calculated unfolding quasiequilibrium thermodynamics of G-IgG-binding domain B1 (GB1) shows the experimentally observed protein transitions: a coil to disordered globule transition, a disordered globule to molten globule transition, a molten globule to nativelike transition, and a nativelike to solidlike state transition. The first protein unfolding phase diagram has been constructed from molecular dynamics simulations with an explicit water model. The calculated melting temperature of GB1 agrees with early experiment. The results also agree with the recent experiment result in which GB1 has more than one intermediate.

Bacterial Proteins↗
PubMed2006

Molecular dynamics simulations of aqueous solutions of ethanolamines.

We report on molecular dynamics simulations performed at constant temperature and pressure to study ethanolamines as pure components and in aqueous solutions. A new geometric integration algorithm that preserves the correct phase space volume is employed to study molecules having up to three ethanol chains. The most stable geometry, rotational barriers, and atomic charges were obtained by ab initio calculations in the gas phase. The calculated dipole moments agree well with available experimental data. The most stable conformation, due to intramolecular hydrogen bonding interactions, has a ringlike structure in one of the ethanol chains, leading to high molecular stability. All molecular dynamics simulations were performed in the liquid phase. The interaction parameters are the same for the atoms in the ethanol chains, reducing the number of variables in the potential model. Intermolecular hydrogen bonding is also analyzed, and it is shown that water associates at low water mole fractions. The force field reproduced (within 1%) the experimental liquid densities at different temperatures of pure components and aqueous solutions at 313 K. The excess and partial molar volumes are analyzed as a function of ethanolamine concentration.

Computer Simulation↗
PubMed2004

Molecular dynamics simulations of 14 HIV protease mutants in complexes with indinavir.

The molecular mechanisms of HIV drug resistance were studied using molecular dynamics simulations of HIV-1 protease complexes with the clinical inhibitor indinavir. One nanosecond molecular dynamics simulations were run for solvated complexes of indinavir with wild type protease, a control variant and 12 drug resistant mutants. The quality of the simulations was assessed by comparison with crystallographic and inhibition data. Molecular mechanisms that contribute to drug resistance include structural stability and affinity for inhibitor. The mutants showed a range of structural variation from 70 to 140% of the wild type protease. The protease affinity for indinavir was estimated by calculating the averaged molecular mechanics interaction energy. A correlation coefficient of 0.96 was obtained with observed inhibition constants for wild type and four mutants. Based on this good agreement, the trends in binding were predicted for the other mutants and discussed in relation to the clinical data for indinavir resistance. [figure: see text]. Poincare map representation for WT protease-indinavir complex. The side chain of Tyr 59 showing the positions of hydrogen atoms.

Binding Sites↗
PubMed2006

Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations.

Two independent replica-exchange molecular dynamics (REMD) simulations with an explicit water model were performed of the Trp-cage mini-protein. In the first REMD simulation, the replicas started from the native conformation, while in the second they started from a nonnative conformation. Initially, the first simulation yielded results qualitatively similar to those of two previously published REMD simulations: the protein appeared to be over-stabilized, with the predicted melting temperature 50-150K higher than the experimental value of 315K. However, as the first REMD simulation progressed, the protein unfolded at all temperatures. In our second REMD simulation, which starts from a nonnative conformation, there was no evidence of significant folding. Transitions from the unfolded to the folded state did not occur on the timescale of these simulations, despite the expected improvement in sampling of REMD over conventional molecular dynamics (MD) simulations. The combined 1.42 micros of simulation time was insufficient for REMD simulations with different starting structures to converge. Conventional MD simulations at a range of temperatures were also performed. In contrast to REMD, the conventional MD simulations provide an estimate of Tm in good agreement with experiment. Furthermore, the conventional MD is a fraction of the cost of REMD and continuous, realistic pathways of the unfolding process at atomic resolution are obtained.

Protein Folding↗
PubMed2006

Molecular dynamics simulations of electrolyte solutions at the (100) goethite surface.

Molecular dynamics simulations of electrolyte solutions in contact with a neutral (100) goethite (alpha-FeOOH) surface were used to probe the structure of the mineral-water interface and gain insight into the adsorption properties of monovalent ions. Three electrolyte solutions were considered: NaCl, CsCl, and CsF. The electrolyte ions were chosen to cover a range of ionic sizes and affinities for the aqueous phase. The molecular dynamics simulations indicate the presence of a structured interfacial region resulting from the strong interaction of water with the mineral surface. The specific arrangement and preferred orientation of water that arise from this interaction create adsorption sites in the interfacial region, i.e., as far as 15 A away from the surface, and hence give rise to a strong correlation between the water and ion distributions. The structure of the hydrated ion, its effect on the water arrangement at the interface, and the strength of the ion-water bond are found to be key factors that determine the location and extent of ion adsorption at the interface. Additionally, in all simulations, we find a build up of positive charges near the surface due to cation adsorption, which is compensated by an accumulation of anions in the next few angströms. This creates an excess of negative charges, which is in turn compensated by an excess of positive charges, and so on. As we modeled a neutral surface, the structure of the electrolyte distribution arises from the complex interplay of the interactions between the surface, water, and the electrolyte ions rather than from the need to neutralize a surface charge. In addition, our simulations indicate that the electrolyte distribution does not resemble that of a classical electrical double layer. Indeed, our calculations predict the presence of several condensed layers and oscillations in the net charge away from the surface.

Journal Article↗
PubMed2006

Determination of the interfacial characteristics of a series of bolaamphiphilic poly(fluorooxetane) surfactants through molecular dynamics simulation.

Constant surface tension (NgammaT) and constant volume (NVT) molecular dynamics simulations have been conducted on a series of bolaamphiphilic alpha,varpi-(diammonium disulfato)poly(fluorooxetane)s and on a typical "long-chain" anionic fluorosurfactant used to improve the flow-and-leveling characteristics of aqueous coatings, to compare their behavior at a water/air interface. Recent research has shown that the poly(fluorooxetane) surfactants considered in this paper could serve as an effective substitute for traditional fluorosurfactants used in flow-and-leveling applications.(1) From molecular dynamics simulation, we have determined the saturated interfacial area per surfactant, interfacial area per surfactant as a function of surface tension, density profiles, the degree of hydration for various atoms in each surfactant, the degree of counterion binding, and order parameters. Our results for saturated interfacial area per surfactant molecule are greater than what has been obtained by other researchers through parametric fitting of interfacial area from experimental surface tension data using the Davies isotherm. Possible explanations for this difference are discussed. The low interfacial areas occupied by each poly(fluorooxetane) at the water/air interface are the result of their ability to adopt a "looped" conformation, in which the carbon and oxygen backbone of each surfactant and the attached perfluoroalkyl chains are forced into the air phase. A geometrically defined penetration parameter was calculated from the density profiles, which reveals that each poly(fluorooxetane) surfactant is more effective at separating the air and water phases than the "long-chain" anionic fluorosurfactant. The degree of hydration measured for different atoms in poly(fluorooxetane) during simulation confirms that a "looped" conformation is adopted in which the surfactant backbone and the perfluoroalkyl chains are lifted away from the water surface. Calculation of order parameters revealed a much lower degree of ordering for the perfluoroalkyl side chains in each bolaamphiphile than in the "long chain" anionic fluorosurfactant. When viewed in the context of the penetration parameter analysis, the density profiles and hydration data suggest why each poly(fluorooxetane) is capable of significantly reducing surface tension when other fluorosurfactants with similarly short perfluoroalkyl moieties provide inadequate surface tension reduction for practical flow-and-leveling applications.

Journal Article↗
PubMed1992

Molecular dynamics simulation on a network of workstations using a machine-independent parallel programming language.

Molecular dynamics simulations investigate local and global motion in molecules. Several parallel computing approaches have been taken to attack the most computationally expensive phase of molecular simulations, the evaluation of long range interactions. This paper reviews these approaches and develops a straightforward but effective algorithm using the machine-independent parallel programming language, Linda. The algorithm was run both on a shared memory parallel computer and on a network of high performance Unix workstations. Performance benchmarks were performed on both systems using two proteins. This algorithm offers a portable cost-effective alternative for molecular dynamics simulations. In view of the increasing numbers of networked workstations, this approach could help make molecular dynamics simulations more easily accessible to the research community.

Algorithms↗