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PubMed2006

Effect of surfactant conformation on the structures of small size nonionic reverse micelles: a molecular dynamics simulation study.

We used constant pressure (P=0.1 MPa) and temperature (T=298 K) molecular dynamics simulations to study the structures and dynamics of small size reverse micelles (RMs) with poly(ethylene glycol) alkyl ether (CmEn) surfactants. The water-to-surfactant molar ratio was 3, with decane as the apolar solvent. We focused on the effect of the two possible imposed conformations (trans vs gauche) for the surfactant headgroups on RMs structures and water dynamics. For this purpose, we built up two RMs, which only differ by their surfactant headgroup conformations. The results obtained for the two RMs were compared to what is known in the literature. Here, we show that the surfactant headgroup conformation affects mainly the water-related properties such as the water core size, the area per surfactant headgroup, the headgroup hydration, and the water core translational diffusion. The properties computed for the RM with the surfactant in trans conformation fit better with the experimental data than the gauche conformation. We further show that the surfactant hydrophilic headgroup plays a crucial role in the micellar structures, favors the entrapment of the micellar water, and reduces strongly their diffusion compared to the bulk water.

Computer Simulation↗
PubMed2002

Hidden Markov models from molecular dynamics simulations on DNA.

An enhanced bioinformatics tool incorporating the participation of molecular structure as well as sequence in protein DNA recognition is proposed and tested. Boltzmann probability models of sequence-dependent DNA structure from all-atom molecular dynamics simulations were obtained and incorporated into hidden Markov models (HMMs) that can recognize molecular structural signals as well as sequence in protein-DNA binding sites on a genome. The binding of catabolite activator protein (CAP) to cognate DNA sequences was used as a prototype case for implementation and testing of the method. The results indicate that even HMMs based on probabilistic roll/tilt dinucleotide models of sequence-dependent DNA structure have some capability to discriminate between known CAP binding and nonbinding sites and to predict putative CAP binding sites in unknowns. Restricting HMMs to sequence only in regions of strong consensus in which the protein makes base specific contacts with the cognate DNA further improved the discriminatory capabilities of the HMMs. Comparison of results with controls based on sequence only indicates that extending the definition of consensus from sequence to structure improves the transferability of the HMMs, and provides further supportive evidence of a role for dynamical molecular structure as well as sequence in genomic regulatory mechanisms.

DNA↗
PubMed1998

Deducing polymeric structure from aqueous molecular dynamics simulations of oligosaccharides: predictions from simulations of hyaluronan tetrasaccharides compared with hydrodynamic and X-ray fibre diffraction data.

Molecular dynamics simulations of the two hyaluronan tetrasaccharides in water predict that over a period of 500 ps, their central linkages populate a single primary minima. Over the same period the peripheral linkages explore this minima, but also a secondary minima. Structures constructed using the primary minima were found to be extended left-handed helices of axial rise per disaccharide (h) 0.8 to 1.0 nm and 2.8 to 4.5 disaccharides per turn (n), in good agreement with n=3 and n=4 helices found by X-ray fibre diffraction studies. We have used the predicted average conformation from molecular dynamics to calculate the translational diffusion coefficients of the oligosaccharide series up to decasaccharide, and compared these with experimental measurements obtained using the method of capillary dispersion. Our calculated values are found to be in good agreement with experiment beyond the size of a tetrasaccharide. A partial digest of hyaluronan in the molecular mass range 10 to 100 kDa was fractionated by gel chromatography. Molecular weights were determined by in-line laser light-scattering measurements, and the translational diffusion coefficients of selected fractions were determined by dynamic laser light-scattering. A similar experiment was performed on hyaluronan with a molecular mass greater than 1MDa. The data suggest a change from rod-like to stiff coil behaviour beyond a molecular weight of 10 kDa. We have also examined the conformations available using the secondary minima, found at the peripheral linkages. In contrast to the extended structures previously described we have found left and right-handed helices with high values of n (5-10) and low values of h. Although there is no experimental evidence for these structures, they are of interest as, over short stretches, they would introduce folds, loops, and turns into the hyaluronan molecule. Such shapes may play an important role in the hydrodynamics of hyaluronan and its interaction with lipids and proteins.

Carbohydrate Conformation↗
PubMed1996

The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the X-ray structure "maintained"?

We present molecular dynamics simulations on ubiquitin with explicit solvent molecules and investigate the influence of different force fields [Weiner et al. (J. Am. Chem. Soc. 106:765-784, 1984; J. Comput. Chem. 7:230-252, 1986) vs. Cornell et al. (J. Am. Chem. Soc. 117:5179-5197, 1995)], different treatments of the long-range electrostatic interaction (8 A cutoff vs. particle mesh Ewald), and different solvation models (periodic box vs. small shell of water molecules) on the structure and the dynamics of the protein. Structural data are monitored by atomic root mean square deviations (RMSDs) from the crystal structure, the radius of gyration, the solvent-accessible surface area, and the pattern of the backbone hydrogen bonds. The dynamic behavior is assessed by the atomic fluctuations and the order parameters of the N-H backbone vectors. With the Cornell et al. force field and a periodic box model, the simulated structures stay much closer to the experimental X-ray structure than with the older Weiner et al. force field. A further improvement of the simulation is found when the electrostatic interaction is evaluated with the particle mesh Ewald method; after 1.2 ns of simulation the backbone RMSD amounts to only 1.13 A. The analysis of the dynamic parameters shows that this good structural agreement is not due to a damping of internal motion in the protein. For a given length of simulation time, the shell models achieve an agreement between simulated and experimental structures that is comparable to the best models that employ a periodic box of solvent models. However, compared with the box models, the fluctuations of the protein atoms in the shell models are smaller, and only with simulation times as long as 2 ns do they become of comparable size to the experimental ones.

Computer Simulation↗
PubMed1987

Anisotropy and anharmonicity of atomic fluctuations in proteins: analysis of a molecular dynamics simulation.

Positional probability density functions (pdf) for the atomic fluctuations are determined from a molecular dynamics simulation for hen egg-white lysozyme. Most atoms are found to have motions that are highly anisotropic but only slightly anharmonic. The largest deviations from harmonic motion are in the direction of the largest rms fluctuations in the local principal axis frame. Backbone atoms tend to be more nearly harmonic than sidechain atoms. The atoms with the largest anharmonicities tend to have pdfs with multiple peaks, each of which is close to harmonic. Several model pdfs are evaluated on the basis of how well they fit probability densities from the dynamics simulations when parameterized in terms of the moments of the distribution. Gram-Charlier and Edgeworth perturbation expansions, which have been successful in describing the motions of small molecules in crystals, are shown to be inadequate for the distributions found in the dynamics of proteins. Multipeaked distribution functions are found to be more appropriate.

Animals↗
PubMed1998

Molecular Dynamic Simulations of Single, Interacting, and Sheared Double Layers.

This article presents the results of molecular dynamic simulations of double layers developing on a flat mineral surface in aqueous sodium chloride solution. This part depicts the simulation results compared to classical double layer theory. Ion distribution, solvent orientation, and potential curve were derived for this propose. Dynamical values were calculated in the steady state and used to assess the idea of two parts of a double layer, stagnant and mobile, separated by a shear plane. Copyright 1998 Academic Press.

Journal Article↗
PubMed1998

Molecular Dynamic Simulations of Single, Interacting, and Sheared Double Layers.

This article presents the results of molecular dynamic simulations of double layers developing on a flat mineral surface in aqueous sodium chloride solutions. The first part considered the configuration of the double layer in comparison to the classical point of view. This part investigates the influences of changed system properties on the double layer. For this purpose systems of different temperature, electrolyte concentration, and surface charge were simulated. The interaction of two overlapping double layers was investigated in comparison to that of single double layers. Nonequilibrium investigations using electrokinetic and rheological measurements provide findings regarding the microscopic behavior of a double layer under shear. Copyright 1998 Academic Press.

Journal Article↗
PubMed1996

Comment on a "fluctuation and cross correlation analysis of protein motions observed in nanosecond molecular dynamics simulations".

Long range positive correlations in the internal atomic motions have been observed in molecular dynamics simulations of the bovine pancreatic trypsin inhibitor. Since the results depend on the removal of overall translation and rotation (which is not unique), some care is required. It is pointed out that original use of all of the C atoms as a frame of reference is more appropriate than the selection of a particular subset. The former comes closest to reflecting the zero rotation condition in a normal mode analysis, which also shows the existence of long range correlations.

Animals↗
PubMed1998

Molecular dynamics simulations of peptide fragments from hen lysozyme: insight into non-native protein conformations.

Molecular dynamics simulations of four peptides taken from the hen lysozyme sequence have been used to generate models for non-native protein conformations. Comparisons between the different peptides and with experimental data for denatured lysozyme and peptide fragments provides insight into the characteristics of the conformational ensembles populated in these non-native states and the dependence of their structural features on the amino acid sequence. For the denatured conformers populated local contacts dominate in determining the properties observed in the trajectories, all four peptides showing similar characteristics. These include a significant increase in the number of main-chain O(i)-NH(i+2) hydrogen bonds and hydrogen bonds involving side-chain groups, this increase compensating to a large extent for the loss of hydrogen bonds involved in helical or beta-sheet secondary structure in the native fold, and the generation of a population of collapsed states with local clusterings of hydrophobic groups. The hydrophobic clusters enable at least partial burial of many side-chains exposed by the loss of tertiary contacts on denaturation and provide models that may explain the experimentally observed protection of amides from hydrogen exchange and the existence of residual secondary structure in non-native species of lysozyme. The results suggest that this approach has an important role to play in aiding the interpretation of experimental data for conformationally disordered non-native states of proteins.

Animals↗
PubMed2004

Molecular dynamics simulation of the coalescence of nanometer-sized water droplets in n-heptane.

Molecular dynamics simulations using a modified Drieding 2.21 force field were carried out to study the coalescence behavior of nanometer-sized water droplets in vacuum and in n-heptane. The coalescence mechanisms of the water droplets in the above-noted environments are fairly similar in a sense that the water droplets form a bridge linking the droplets before they merge. However, in the latter situation, due to the presence of n-heptane molecules in between the water droplets, the coalescence was observed to be slowed down considerably, especially in the first 10 ps of the process. However, once the bridge is formed, the water droplets, in both situations, spend about the same amount of time to form a single droplet. The maximum distance between the droplets above which coalescence does not occur was found to be 10 A. In terms of the dynamics, the diffusion coefficient of n-heptane in the emulsion system was very close to its value in the pure liquid form. This may be because n-heptane is the continuous phase. Nonetheless, the dynamic behavior of water in n-heptane is different from that of pure water during and after the coalescence. In particular, the self-diffusion coefficient of water molecules in n-heptane is about 20% higher than the experimental value of pure water. Due to the lack of strong attraction forces between water and n-heptane molecules, the n-heptane molecules were observed to orient themselves perpendicularly to the water/n-heptane interfaces so that the contacting area is minimized.

Journal Article↗
PubMed2004

Ab initio molecular dynamics simulations of local structure of supercooled Ni.

We report results of first-principles molecular dynamics simulations for stable and undercooled nickel liquids. The calculated structure factors as a function of temperature are discussed with respect to recent experimental measurements. In addition, structural analysis using bonding orientational order and three-dimensional pair analysis techniques have been performed in detail and the effect of undercooling on the microstructure has been analyzed. More particularly, we show the importance of fivefold symmetry local structures.

Journal Article↗
PubMed2004

Spontaneous three-dimensional nanostructure formation of perfluoroalkyl terminated liquid crystal: a molecular dynamics simulation study.

Structure formation of a perfluoroalkyl terminated liquid crystal molecule was studied by molecular dynamics simulations. Two distinct structures with smectic-C-like layers and with bundles (blocks) of collapsed layers were spontaneously formed depending on the simulation temperatures. The bundles in the latter structure were somewhat positionally ordered (with respect to the small angle spots in its structure function) and orientationally isotropic overall even though the molecules making each bundle were well oriented. These characteristics of the simulated system well correspond to the cubic phase of the real system, and an even more precisely correspond to the proposed cubic structure model with respect to its hierarchical structure.

Journal Article↗
PubMed2005

A molecular dynamics simulation of the adsorption of water molecules surrounding an Au nanoparticle.

This study uses molecular dynamics simulations performed in a parallel computing environment to investigate the adsorption of water molecules surrounding Au nanoparticles of various sizes. An observation of the oxygen and hydrogen atom distributions reveals that the adsorption of the water molecules creates two shell-like formations of water in close vicinity to the Au nanoparticle surface. These shell-like formations are found to be more pronounced around smaller Au nanoparticles. The rearrangement of water molecules in this region reduces the local hydrogen bond strength to below that which is observed in the bulk region. Finally, the simulation results indicate that the absolute value of the interaction energy between the water molecules and the Au nanoparticle is reduced when the water molecules surround a nanoparticle of larger diameter. This observation implies that a stronger adsorption effect exists between smaller Au nanoparticles and water molecules. Hence, the value of the adsorption constant increases for smaller Au nanoparticles.

Journal Article↗
PubMed2005

An approximate but fast method to impose flexible distance constraints in molecular dynamics simulations.

A fast but approximative method to apply flexible constraints to bond lengths in molecular dynamics simulations is presented and the effects of the approximation are investigated. The method is not energy conserving, but coupling to a temperature bath results in stable simulations. The high frequencies from bond-length vibrations are successfully removed from the system while maintaining the flexibility of the bonds. As a test liquid neopentane is simulated at different pressures. Energetic and dynamic properties are not affected by the new flexible constraint simulation method.

Journal Article↗
PubMed2005

Area compressibility and buckling of amphiphilic bilayers in molecular dynamics simulations.

The elastic modulus or area compressibility of a membrane is routinely calculated in molecular dynamics simulations as the proportionality constant relating surface tension and projected surface area. Recent studies, however, have revealed a marked system size dependence of these moduli, which we attribute to the neglect of thermal undulations in the area calculation. We discuss several methods, based on the Helfrich model and on numerical triangulation, to remedy this situation, and find a satisfying agreement between them. The Helfrich model also quantitatively describes a buckling transition observed for compressed bilayers.

Compressive Strength↗
PubMed2006

Molecular-dynamics simulations of the transport properties of a single polymer chain in two dimensions.

Molecular-dynamics simulations are conducted to elucidate the critical factors affecting the transport properties of isolated polymer chains in strictly two dimensions. The relevance of surface inhomogeneity is critically examined. We unequivocally find that surface inhomogeneity is critical in obtaining transport behavior consistent with the recent measurements of surface diffusion for polymers adsorbed at the solid-liquid interface. For a systematic investigation of this point, heterogeneity was introduced by decorating the surface with impenetrable elements and we find that chain diffusivity crossed over from Rouse-type behavior to reptationlike with increasing surface coverage of obstacles. This transition in behavior occurred when the mean distance between obstacles is approximately equal to the end-to-end distance, Re, of the two-dimensional chain. Our results underscore the importance of surface disorder (not only literal obstacles but by reasonable extension also to other types of disorder) in determining the transport behavior of chains adsorbed to solids.

Journal Article↗
PubMed1998

Large-scale molecular dynamics simulations of dislocation intersection in copper

The results of massively parallel three-dimensional molecular dynamics simulations of the perpendicular intersection of extended dislocations in copper are reported. The intersection process, which involves three of the four possible 111 glide planes in the face-centered cubic lattice, begins with junction formation, followed by unzipping, partial dislocation bowing, cutting, and, finally, unit jog formation. The investigation provides insights into this complex atomistic process, which is currently not accessible to experimental investigation.

Journal Article↗
PubMed2003

Molecular dynamics simulations of galectin-1-oligosaccharide complexes reveal the molecular basis for ligand diversity.

Galectin-1 is a member of a protein family historically characterized by its ability to bind carbohydrates containing a terminal galactosyl residue. Galectin-1 is found in a variety of mammalian tissues as a homodimer of 14.5-kDa subunits. A number of developmental and regulatory processes have been attributed to the ability of galectin-1 to bind a variety of oligosaccharides containing the Gal-beta-(1,4)-GlcNAc (LacNAc(II)) sequence. To probe the origin of this permissive binding, solvated molecular dynamics (MD) simulations of several representative galectin-1-ligand complexes have been performed. Simulations of structurally defined complexes have validated the computational approach and expanded upon data obtained from X-ray crystallography and surface plasmon resonance measurements. The MD results indicate that a set of anchoring interactions between the galectin-1 carbohydrate recognition domain (CRD) and the LacNAc core are maintained for a diverse set of ligands and that substituents at the nonreducing terminus of the oligosaccharide extend into the remainder of a characteristic surface groove. The anionic nature of ligands exhibiting relatively high affinities for galectin-1 implicates electrostatic interactions in ligand selectivity, which is confirmed by a generalized Born analysis of the complexes. The results suggest that the search for a single endogenous ligand or function for this lectin may be inappropriate and instead support a more general role for galectin-1, in which the lectin is able to crosslink heterogeneous oligosaccharides displayed on a variety of cell surfaces. Such binding promiscuity provides an explanation for the variety of adhesion phenomena mediated by galectin-1.

Computer Simulation↗