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PubMed2005

Molecular dynamics simulations of atmospheric oxidants at the air-water interface: solvation and accommodation of OH and O3.

A comparative study of OH, O3, and H2O equilibrium aqueous solvation and gas-phase accommodation on liquid water at 300 K is performed using a combination of ab initio calculations and molecular dynamics simulations. Polarizable force fields are developed for the interaction potential of OH and O3 with water. The free energy profiles for transfer of OH and O3 from the gas phase to the bulk liquid exhibit a pronounced minimum at the surface, but no barrier to solvation in the bulk liquid. The calculated surface excess of each oxidant is comparable to calculated and experimental values for short chain, aliphatic alcohols. Driving forces for the surface activity are discussed in terms of the radial distribution functions and dipole orientation distributions for each molecule in the bulk liquid and at the surface. Simulations of OH, O3, and H2O impinging on liquid water with a thermal impact velocity are used to calculate thermal accommodation (S) and mass accommodation (alpha) coefficients. The values of S for OH, O3, and H2O are 0.95, 0.90, and 0.99, respectively. The approaching molecules are accelerated toward the liquid surface when they are approximately 5 angstroms above it. The molecules that reach thermal equilibrium with the surface do so within 2 ps of striking the surface, while those that do not scatter into the gas phase with excess translational kinetic energy in the direction perpendicular to the surface. The time constants for absorption and desorption range from approximately 35 to 140 ps, and the values of alpha for OH, O3, and H2O are 0.83, 0.047, and 0.99, respectively. The results are consistent with previous formulations of gas-phase accommodation from simulations, in which the process occurs by rapid thermal and structural equilibration followed by diffusion on the free energy profile. The implications of these results with respect to atmospheric chemistry are discussed.

Air↗
PubMed2006

Molecular dynamics simulation study of the structure of poly(ethylene oxide) brushes on nonpolar surfaces in aqueous solution.

The structure of poly(ethylene oxide) (PEO, M(w) = 526) brushes of various grafting density (sigma) on nonpolar graphite and hydrophobic (oily) surfaces in aqueous solution has been studied using atomistic molecular dynamics simulations. Additionally, the influence of PEO-surface interactions on the brush structure was investigated by systematically reducing the strength of the (dispersion) attraction between PEO and the surfaces. PEO chains were found to adsorb strongly to the graphite surface due primarily to the relative strength of dispersion interactions between PEO and the atomically dense graphite compared to those between water and graphite. For the oily surface, PEO-surface and water-surface dispersion interactions are much weaker, greatly reducing the energetic driving force for PEO adsorption. This reduction is mediated to some extent by a hydrophobic driving force for PEO adsorption on the oily surface. Reduction in the strength of PEO-surface attraction results in reduced adsorption of PEO for both surfaces, with the effect being much greater for the graphite surface where the strong PEO-surface dispersion interactions dominate. At high grafting density (sigma approximately 1/R(g)(2)), the PEO density profiles exhibited classical brush behavior and were largely independent of the strength of the PEO-surface interaction. With decreasing grafting density (sigma < 1/R(g)(2)), coverage of the surface by PEO requires an increasingly large fraction of PEO segments resulting in a strong dependence of the PEO density profile on the nature of the PEO-surface interaction.

Journal Article↗
PubMed2006

Molecular dynamics simulations of a chemical reaction; conditions for local equilibrium in a temperature gradient.

We have examined a simple chemical reaction in a temperature gradient; 2F <==> F2. A mechanical model was used, based on Stillinger and Weber's 2- and 3-body potentials. Equilibrium and non-equilibrium molecular dynamics simulations showed that the chemical reaction is in local thermodynamic as well as in local chemical equilibrium (delta(r)G = 0) in the supercritical fluid, for temperature gradients up to 10(12) K m(-1). The reaction is thus diffusion-controlled. The velocity distributions of both components were everywhere close to being Maxwellian. The peak distributions were shifted slightly up or down from the average velocity of all particles. The shift depended on the magnitude of the temperature gradient. The results support the assumption that the entropy production of the reacting mixture can be written as a product sum of fluxes and forces. The temperature gradient promotes interdiffusion of components in the stationary state, a small reaction rate and an accumulation of the molecule in the cold region and the atom in the hot region.

Journal Article↗
PubMed2003

Molecular-dynamics simulations of carbon nanotubes as gigahertz oscillators.

Recently, Zheng and Jiang [Phys. Rev. Lett. 88, 045503 (2002)]] have proposed that multiwalled carbon nanotubes could be the basis for a new generation of nano-oscillators in the several gigahertz range. In this Letter, we present the first molecular dynamics simulation for these systems. Different nanotube types were considered in order to verify the reliability of such devices as gigahertz oscillators. Our results show that these nano-oscillators are dynamically stable when the radii difference values between inner and outer tubes are of approximately 3.4 A. Frequencies as large as 38 GHz were observed, and the calculated force values are in good agreement with recent experimental investigations.

Journal Article↗
PubMed2006

Insights on HIV-1 Tat:P/CAF bromodomain molecular recognition from in vivo experiments and molecular dynamics simulations.

Structural and functional studies indicate that, through its bromodomain, the cellular acetyltransferase P/CAF binds the acetylated Tat protein of human immunodeficiency virus type 1 (HIV-1) and promotes transcriptional activation of the integrated provirus. Based on the NMR structure of P/CAF complexed with an acetylated Tat peptide, here we use molecular dynamics simulations to construct a model describing the interaction between full length Tat and the P/CAF bromodomain. Our calculations show that the protein-protein interface involves hydrophobic interactions between the P/CAF ZA loop and the Tat core domain. In particular, tyrosines 760 and 761 of P/CAF, two residues that are highly conserved in most known bromodomains, play an essential role for the binding. Fluorescence resonance energy transfer (FRET) experiments performed in this work demonstrate that P/CAF proteins in which these tyrosines are mutated into hydrophilic residues neither bind to Tat inside the cells nor mediate Tat transactivation. The combination of theoretical and in vivo studies provides new insights into the specificity of bromodomain recognition.

Binding Sites↗
PubMed2006

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations.

Biomolecules often undergo large-amplitude motions when they bind or release other molecules. Unlike macroscopic machines, these biomolecular machines can partially disassemble (unfold) and then reassemble (fold) during such transitions. Here we put forward a minimal structure-based model, the "multiple-basin model," that can directly be used for molecular dynamics simulation of even very large biomolecular systems so long as the endpoints of the conformational change are known. We investigate the model by simulating large-scale motions of four proteins: glutamine-binding protein, S100A6, dihydrofolate reductase, and HIV-1 protease. The mechanisms of conformational transition depend on the protein basin topologies and change with temperature near the folding transition. The conformational transition rate varies linearly with driving force over a fairly large range. This linearity appears to be a consequence of partial unfolding during the conformational transition.

Carrier Proteins↗
PubMed2005

Comparison of the glass transition temperature and fragility parameter of isomalto-olygomer predicted by molecular dynamics simulations with those measured by differential scanning calorimetry.

The purpose of this study is to examine whether molecular dynamics (MD) simulations using a commercially available software for personal computers can estimate the glass transition temperature (Tg) of amorphous systems containing pharmaceutically-relevant excipients. MD simulations were carried out with an amorphous matrix model constructed from isomaltoheptaose, and the Tg estimated from the calculated density versus temperature profile was compared with the Tg measured by differential scanning calorimetry (DSC) for freeze-dried isomalto-oligomer having an average molecular weight close to that of isomaltoheptaose. The Tg values determined by DSC were lower by 10 to 20 K than those extrapolated from the Tg values estimated by MD simulation. Fragility parameter was estimated to be 56 and 51 from MD simulation and from DSC measurement, respectively. Thus, the results suggest that MD simulation can provide approximate estimates for the Tg and fragility parameter of amorphous formulations. However, a reduction of the cooling rate, achievable by sufficiently elongating the simulation duration, is necessary for more accurate estimation.

Algorithms↗
PubMed2006

A combined QM/MM molecular dynamics simulations study of nitrate anion (NO3-) in aqueous solution.

The structural and dynamical properties of NO3- in dilute aqueous solution have been investigated by means of two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely HF/MM and B3LYP/MM, in which the ion and its surrounding water molecules were treated at HF and B3LYP levels of accuracy, respectively, using the DZV+ basis set. On the basis of both HF and B3LYP methods, a well-defined first hydration shell of NO3- is obtainable, but the shell is quite flexible and the hydrogen-bond interactions between NO3- and water are rather weak. With respect to the detailed analysis of the geometrical arrangement and vibrations of NO3-, the experimentally observed solvent-induced symmetry breaking of the ion is well reflected. In addition, the dynamical information, i.e., the bond distortions and shifts in the corresponding bending and stretching frequencies as well as the mean residence time of water molecules surrounding the NO3- ion, clearly indicates the "structure-breaking" ability of this ion in aqueous solution. From a methodical point of view it seems that both the HF and B3LYP methods are not too different in describing this hydrated ion by means of a QM/MM simulation. However, the detailed analysis of the dynamics properties indicates a better suitability of the HF method compared to the B3LYP-DFT approach.

Anions↗
PubMed1995

Methodological advances in molecular dynamics simulations of biological systems.

New advances in the techniques used to simulate specific statistical ensembles provide molecular dynamics algorithms that permit rigorous connections to be made between thermodynamic observables and calculated quantities in simulations of biological molecules. The complete inclusion of electrostatic forces in simulations also improves the comparison between calculations of simple structural measures in crystals and X-ray crystallographic results. These advances coupled with the ongoing development of more accurate inter/intramolecular forcefields with enhanced accuracy provide guidelines and benchmarks for comparison as we move to study more complicated biological problems.

Algorithms↗
PubMed2000

Multicopy molecular dynamics simulations suggest how to reconcile crystallographic and product formation data for camphor enantiomers bound to cytochrome P-450cam.

Multiple ligand binding modes are possible in many enzyme active sites; their presence in cytochrome P450cam (P450cam) is evident from crystallographic studies of the binding of thiocamphor and phenylimidazoles. Here, we use multicopy molecular dynamics simulations to compare the binding modes of (1R)- and (1S)-camphor in the active site of P450cam. Simulations with (1R)-camphor, the natural substrate, serve to calibrate our protocol: 19 out of 20 copies of (1R)-camphor converged to coordinates very close to those observed for (1R)-camphor in its crystallographic complex with P450cam during the simulations. Simulations with the (1S)-camphor enantiomer showed greater mobility of the substrate, consistent with spectroscopic data, and resulted in 3 major binding modes. One of these is similar to the major conformation (of the two conformations assigned) in a recently determined crystal structure, but this conformation is not correctly oriented for regiospecific hydroxylation at C-5. The simulations, however, provide evidence for reorientation of (1S)-camphor upon formation of the reactive Fe-O intermediate to an orientation suitable for hydroxylation. The simulations thus permit rationalisation of the apparent inconsistency between the crystal structure and the reaction products.

Binding Sites↗
PubMed2006

Molecular-dynamics simulations of pyronine 6G and rhodamine 6G dimers in aqueous solution.

We have carried out molecular-dynamics (MD) simulations on dimers of the positively charged laser dyes pyronine 6G (P6G) and rhodamine 6G (R6G) in aqueous solution, generating trajectories of 2.5 ns for various computational protocols. We discuss how the choice of atomic partial charges and the length of the trajectories affect the predicted structures of the dimers and compare our results to those of earlier MD-simulations, which were restricted to only 0.7 ns. Our results confirm that monomers of P6G easily undergo relative rotations within the dimer, but we found new conformations of the R6G dimer at longer simulation times. In addition, we analyzed in detail the energy change during the formation of dimers. With suitable corrections, the electrostatic energy from an Ewald treatment agrees with the results from an approach relying on a residue-based cutoff. For P6G, we show that the strong solvent-mediated electrostatic attraction between the monomers is counteracted by an almost equally large solvent-induced entropy contribution to yield a small driving force to dimer formation, in very good agreement with the free-energy change from a thermodynamic-integration procedure. Thus, earlier rationalizations of the dimer formation, based only on energy arguments, yield a qualitatively wrong picture.

Computer Simulation↗
PubMed2003

Molecular dynamics simulations of an oligosaccharide using a force field modified for carbohydrates.

Parameterization of the phi and omega torsion angles in pyranosidic saccharides was performed based on density functional theory calculations. The modified CHARMM force field, which is referred to as PARM22/SU01, was tested on a glucosyl trisaccharide. A molecular dynamics simulation of the oligosaccharide with explicit water as solvent was performed to investigate the conformational flexibility. Protonz.sbnd;proton distances and heteronuclear spin-spin coupling constants were calculated from the trajectories and showed good agreement to those previously determined by NMR spectroscopy.

Carbohydrate Conformation↗
PubMed1999

Bacteriorhodopsin in a periodic boundary water-vacuum-water box as an example towards stable molecular dynamics simulations of G-protein coupled receptors.

This study presents an optimised set-up for molecular dynamics (MD) simulations of G-protein coupled receptors (GPCR). Such simulations are complicated because (1) the experimental template structure for GPCRs (bovine rhodopsin) is of low resolution, (2) the receptor surroundings are irregular (water exposed loops vs. lipid exposed transmembrane regions) and (3) the protonation and solvation states of the inner core receptor residues are unknown. We compared various simulations of the experimentally derived and refined electron density structure of the seven helical transmembrane protein bacteriorhodopsin (bR) under different MD conditions using AMBER 4.1. Our results demonstrate that the optimal MD set-up with minimal computational effort is a periodic boundary (PB) box containing two water shells solvating the extra- and intracellular loops separated by a vacuum layer surrounding the helical transmembrane (TM) regions. It was found that the vacuum layer and water layers are stable under periodic boundary conditions during at least 1 ns of MD simulation. In this set-up the bR structure is stable without any restraints. The average bR structure during the last 500 ps of the MD run has an excellent RMSD value relative to the original bR structure (RMSD = 1.66 A for the C alpha atoms within the TM domains) and shows a very high helical stability within the TM regions (88.8% helix). The use of this MD set-up for simulations of GPCRs is discussed.

Animals↗
PubMed1994

Molecular dynamics simulation of MHC-peptide complexes as a tool for predicting potential T cell epitopes.

The class I major histocompatibility complex-encoded HLA-B*2705 protein was simulated in complex with six different peptides exhibiting unexpected structure-activity relationships. Various structural and dynamical properties of the solvated protein-peptide complexes (atomic fluctuations, solvent-accessible surface areas, hydrogen bonding pattern) were found to be in qualitative agreement with the available binding data. Peptides that have been experimentally shown to bind to the protein remained tightly anchored to the MHC molecule, whereas nonbinders were significantly more weakly complexes to the protein and progressively dissociate from it at their N- and C-terminal ends. The molecular dynamics simulations emphasize the unexpectedly important role of secondary anchors (positions 1 and 3) in influencing the MHC-bound conformation of antigenic nonapeptides. Furthermore, it confirms that dominant anchor residues cannot solely account for peptide binding to a class I MHC molecule. The molecular dynamics method could be used as a complementary tool to T cell epitope predictions from the primary sequences of proteins of immunological interest. It is better suited to MHC proteins for which a crystal structure already exists. Furthermore, it may facilitate the engineering of T cell epitopes as well as the rational design of new MHC inhibitors designed to fit optimally the peptide binding cleft.

Amino Acid Sequence↗
PubMed2004

Molecular dynamics simulations of peptides containing an unnatural amino acid: dimerization, folding, and protein binding.

We have performed molecular dynamics (MD) simulations to study the dimerization, folding, and binding to a protein of peptides containing an unnatural amino acid. NMR studies have shown that the substitution of one residue in a tripeptide beta-strand by the unnatural amino acid Hao (5-HO2CCONH-2-MeO-C6H3-CO-NHNH2) modifies the conformational flexibility of the beta-strand and the hydrogen-bonding properties of its two edges: The number of hydrogen-bond donors and acceptors increases at one edge, whereas at the other, they are sterically hindered. In simulations in chloroform, the Hao-containing peptide 9 (i-PrCO-Phe-Hao-Val-NHBu) forms a beta-sheet-like hydrogen-bonded dimer, in good agreement with the available experimental data. Addition of methanol to the solution induces instability of this beta-sheet, as confirmed by the experiments. MD simulations also reproduce the folding of the synthetic peptide 1a (i-PrCO-Hao-Ut-Phe-Ile-Leu-NHMe) into a beta-hairpin-like structure in chloroform. Finally, the Hao-containing peptide, Ac-Ala-Hao-Ala-NHMe, is shown to form a stable complex with the Ras analogue, Rap1 A, in water at room temperature. Together with the available experimental data, these simulation studies indicate that Hao-containing peptides may serve as inhibitors of beta-sheet interactions between proteins.

Amino Acids, Aromatic↗
PubMed2004

Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations.

The conversion of mechanical stress into a biochemical signal in a muscle cell requires a force sensor. Titin kinase, the catalytic domain of the elastic muscle protein titin, has been suggested as a candidate. Its activation requires major conformational changes resulting in the exposure of its active site. Here, force-probe molecular dynamics simulations were used to obtain insight into the tension-induced activation mechanism. We find evidence for a sequential mechanically induced opening of the catalytic site without complete domain unfolding. Our results suggest the rupture of two terminal beta-sheets as the primary unfolding steps. The low force resistance of the C-terminal relative to the N-terminal beta-sheet is attributed to their different geometry. A subsequent rearrangement of the autoinhibitory tail is seen to lead to the exposure of the active site, as is required for titin kinase activity. These results support the hypothesis of titin kinase as a force sensor.

Computer Simulation↗
PubMed2004

A molecular dynamics simulation study of polyamine- and sodium-DNA. Interplay between polyamine binding and DNA structure.

Four different molecular dynamics (MD) simulations have been performed for infinitely long ordered DNA molecules with different counterions, namely the two natural polyamines spermidine(3+) (Spd3+) and putrescine(2+) (Put2+), the synthetic polyamine diaminopropane(2+) (DAP2+), and the simple monovalent cation Na+. All systems comprised a periodical hexagonal cell with three identical DNA decamers, 15 water molecules per nucleotide, and counterions balancing the DNA charge. The simulation setup mimics the DNA state in oriented DNA fibers, previously studied using NMR and other experimental methods. In this paper the interplay between polyamine binding and local DNA structure is analyzed by investigating how and if the minor groove width of DNA depends on the presence and dynamics of the counterions. The results of the MD simulations reveal principal differences in the polyamine-DNA interactions between the natural [spermine(4+), Spd3+, Put2+] and the synthetic (DAP2+) polyamines.

Base Sequence↗
PubMed2001

Investigation of aromatic-backbone amide interactions in the model peptide acetyl-Phe-Gly-Gly-N-methyl amide using molecular dynamics simulations and protein database search.

Weakly polar interactions between the side-chain aromatic rings and hydrogens of backbone amides (Ar-HN) are found in unique conformational regions. To characterize these conformational regions and to elucidate factors that determine the conformation of the Ar-HN interactions, four 4-ns molecular dynamics simulations were performed using four different low-energy conformations obtained from simulated annealing and one extended conformation of the model tripeptide Ac-Phe-Gly-Gly-NH-CH(3) as starting structures. The Ar(i)-HN(i+1) interactions were 4 times more frequent than were Ar(i)-HN(i+2) interactions. Half of the conformations with Ar(i)-HN(i+2) interactions also contained an Ar(i)-HN(i+1) interaction. The solvent access surface area of the Phe side chain and of the amide groups of Phe1, Gly2, and Gly3 involved in Ar-HN interactions was significantly smaller than in residues not involved in such interactions. The number of hydrogen bonds between the solvent and Phe1, Gly2, and Gly3 amide groups was also lower in conformations with Ar-HN interactions. For each trajectory, structures that contained Ar(i)-HN(i), Ar(i)-HN(i+1), and Ar(i)-HN(i+2) interactions were clustered on the basis of similarity of selected torsion angles. Attraction energies between the aromatic ring and the backbone amide in representative conformations of the clusters ranged from -1.98 to -9.24 kJ mol(-1) when an Ar-HN interaction was present. The most representative conformations from the largest clusters matched well with the conformations from the Protein Data Bank of Phe-Gly-Gly protein fragments containing Ar-HN interactions.

Amides↗