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PubMed1993

Molecular dynamics simulations of the unfolding of apomyoglobin in water.

Molecular dynamics simulations of apomyoglobin have been conducted in aqueous solution for 350 ps at 25 degrees C and for 500 ps in two different runs at 85 degrees C. The structures obtained at the higher temperature display properties similar to those of molten globules. Close agreement is obtained between the computed structural models and experimental data on the helical content of both native apomyoglobin and the low-pH unfolding intermediate. The results also suggest explanations for the surprising observations on the effects of mutations at the interface of the A, G, and H helices. Detailed analyses of the final structures and the unfolding pathways at high temperature clearly show that the most stable alpha-helical regions are those in contact with other helices.

Apoproteins↗

PubMed1994

Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin.

Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin in water have been performed in a sphere of 1.4-nm radius surrounded by a restrained shell of 0.8 nm. The flavin binding site, comprising the active site of the flavodoxin, was in the center of the sphere. No explicit information about protein-bound water molecules was included. An analysis is made of the motional characteristics of residues located in the active site. Positional fluctuations, hydrogen bonding patterns, dihedral angle transitions, solvent behavior, and time-dependent correlations are examined. The 375-ps trajectories show that both oxidized and reduced protein-bound flavins are immobilized within the protein matrix, in agreement with earlier obtained time-resolved fluorescence anisotropy data. The calculated time-correlated behavior of the tryptophan residues reveals significant picosecond mobility of the tryptophan side chain located close to the reduced isoalloxazine part of the flavin.

Binding Sites↗

PubMed2006

Study of the influence of temperature on the dynamics of the catalytic cleft in 1,3-1,4-beta-glucanase by molecular dynamics simulations.

The dependence of some molecular motions in the enzyme 1,3-1,4-beta-glucanase from Bacillus licheniformis on temperature changes and the role of the calcium ion in them were explored. For this purpose, two molecular dynamics simulated trajectories along 4 ns at low (300 K) and high (325 K) temperatures were generated by the GROMOS96 package. Several structural and thermodynamic parameters were calculated, including entropy values, solvation energies, and essential dynamics (ED). In addition, thermoinactivation experiments to study the influence of the calcium ion and some residues on the activity were conducted. The results showed the release of the calcium ion, which, in turn, significantly affected the movements of loops 1, 2, and 3, as shown by essential dynamics. These movements differ at low and high temperatures and affect dramatically the activity of the enzyme, as observed by thermoinactivation studies.

Bacillus↗

PubMed2000

Atomic detail peptide-membrane interactions: molecular dynamics simulation of gramicidin S in a DMPC bilayer.

Molecular dynamics simulations have been performed of the sequence-symmetric cyclic decapeptide antibiotic gramicidin S (GS), in interaction with a hydrated dimyristoylphosphatidylcholine (DMPC) bilayer, and the results compared with a "control" simulation of the system in the absence of GS. Following experimental evidence, the GS was initially set in a single antiparallel beta-sheet conformation with two Type II' beta-turns in an amphiphilic interaction with the membrane. This conformation and position remained in the 6.5 ns simulation. Main-chain dihedrals are on average approximately 26 degrees from those determined by NMR experiment on GS in dimethylsulfoxide (DMSO) solution. Sequence-symmetric main-chain and side-chain dihedral angle pairs converge to within approximately 5 degrees and approximately 10 degrees, respectively. The area per lipid, lipid tail order parameters, and quadrupole spin-lattice relaxation times of the control simulation are mostly in good agreement with corresponding experiments. The GS has little effect on the membrane dipole potential or water permeability. However, it is found to have a disordering effect (in agreement with experiment) and a fluidifying effect on lipids directly interacting with it, and an ordering effect on those not directly interacting.

Anti-Bacterial Agents↗

PubMed2003

Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation.

The suitability of three implicit solvent models for flexible protein-protein docking by procedures using molecular dynamics simulation is investigated. The three models are (i) the generalized Born (GB) model implemented in the program AMBER6.0; (ii) a distance-dependent dielectric (DDD) model; and (iii) a surface area-dependent model that we have parameterized and call the NPSA model. This is a distance-dependent dielectric model modified by neutralizing the ionizable side-chains and adding a surface area-dependent solvation term. These solvent models were first tested in molecular dynamics simulations at 300 K of the native structures of barnase, barstar, segment B1 of protein G, and three WW domains. These protein structures display a range of secondary structure contents and stabilities. Then, to investigate the performance of the implicit solvent models in protein docking, molecular dynamics simulations of barnase/barstar complexation, as well as PIN1 WW domain/peptide complexation, were conducted, starting from separated unbound structures. The simulations show that the NPSA model has significant advantages over the DDD and GB models in maintaining the native structures of the proteins and providing more accurate docked complexes.

Bacterial Proteins↗

PubMed2006

Molecular dynamics simulations of neutral chlorpromazine in zwitterionic phospholipid monolayers.

Molecular dynamics simulations have been performed to investigate the interactions between chlorpromazine (CPZ), a neuroleptic drug used in the treatment of psychiatric disorders, and dipalmitoylphosphatidylcholine (DPPC), a zwitterionic phospholipid, in Langmuir monolayers. The results from simulations carried out at different monolayer surface densities were able to capture important features of the CPZ-lipid interaction. We find that neutral (unprotonated) CPZ is preferentially located in the lipid tail region of the phospholipids, in little contact with the aqueous phase, and that the orientation of its rigid ring structure and tail conformation vary with lipid surface density. CPZ is found to promote ordering of the lipid tails for all surface densities because of a reduction in the effective surface area per lipid upon addition of the drug. Similar effects have been observed in previous studies of cholesterol in DPPC monolayers, in which lipid tails were seen to order around the solute. This feature, however, is quite distinct from what we observe for the most dense monolayer considered here (area per lipid of 50 A(2)), for which we find that CPZ promotes a local distortion of the lipid tails in its immediate vicinity and a concomitant ordering of lipid tails located further away from the solute. This view is further supported by the results obtained for an approximated nonlinear vibrational sum frequency generation susceptibility, which showed greater tail disorder close to CPZ.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed1990

Molecular dynamics simulations of active site mutants of triosephosphate isomerase.

Molecular dynamics simulations of triosephosphate isomerase (TIM) and of some active site TIM mutants were performed in an attempt to elucidate possible interactions important for catalytic activity and binding. A variety of active site residues in TIM have been altered, resulting in all cases in decreases in catalytic activity. Second-site suppressor mutants were characterized for two of these active site mutants. The pseudorevertants have increased activity compared to the single mutant from which they were derived and, surprisingly, in both cases the increase in activity is a result of the replacement of an active site serine for proline. We performed simulations of wild-type TIM and the active site mutants with the substrate dihydroxyacetone phosphate bound both noncovalently and covalently. The noncovalent complexes were used to examine interactions important to binding while the covalent complexes are models of the transition state structure for enolization, which is the rate-determining step for the mutants. The difference between these two states, then, is related to the catalytic activity. We found various protein-substrate interactions that improved in the noncovalent mutant complexes, which correlates with the experimentally observed increase in binding affinity upon mutation. In the covalent complexes we observed improved electrostatic stabilization of the transition state upon introduction of Pro, which is also consistent with the experimental data. Our simulations reproduce the highly co-operative nature of the interactions in the active site and suggest that this approach may be useful for identifying particularly promising sites for mutation.

Binding Sites↗

PubMed2006

Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane.

Multiple molecular dynamics simulations of bacterioopsin pulling from its C-terminus show that its alpha-helices unfold individually. In the first metastable state observed in the simulations, helix G is unfolded at its C-terminal segment while the rest of helix G (residues 200-216) is folded and opposes resistance because of a salt-bridge network consisting of Asp-212 and Lys-216 on helix G and Arg-82 and Asp-85 on helix C. Helix G unfolds inside the bundle because the external force is applied to its C-terminal end in a direction perpendicular to the surface of the membrane. Inversely, helix F has to flip by 180 degrees to exit from the membrane because the applied force and the helical N-C axis point in opposite directions. At the highest peak of the force, which cannot be interpreted in single-molecule force spectroscopy experiments, helix F has a pronounced kink at Pro-186. Mutation of Pro-186 and/or the charged side chains mentioned above, which are involved in very favorable electrostatic interactions in the low-dielectric region of the membrane, are expected to reduce the highest peak of the force. Helices E and D unfold in a similar way to helices G and F, respectively. Hence, the force-distance profile and sequence of events during forced unfolding of bacterioopsin are influenced by the up-and-down topology of the seven-helix bundle. The sequential extraction of individual helices from the membrane suggests that the spontaneous (un)folding of bacterioopsin proceeds through metastable bundles of fewer than seven helices. The metastable states observed in the simulations provide atomic level evidence that corroborates the interpretation of very recent force spectroscopy experiments of bacteriorhodopsin refolding.

Bacteriorhodopsins↗

PubMed2005

Thermophoresis in liquids: a molecular dynamics simulation study.

Thermophoresis in liquids is studied by molecular dynamics simulation (MD). A theory is developed that divides the problem in the way consistent with the characteristic scales. MD is then conducted to obtain the solution of each problem, which is to be all combined for macroscopic predictions. It is shown that when the temperature gradient is applied to the nonconducting liquid bath that contains neutral particles, there occurs a pressure gradient tangential to the particle surface at the particle-liquid interface. This may induce the flow in the interfacial region and eventually the particle to move. This applies to the material system that interacts through van der Waals forces and may be a general source of the thermophoresis phenomenon in liquids. The particle velocity is linearly proportional to the temperature gradient. And, in a large part of the given temperature range, the particle motion is in the direction toward the cold end and decreases with respect to the temperature. It is also shown that the particle velocity decreases or even reverses its sign in the lowest limit of the temperature range or with a particle of relatively weak molecular interactions with the liquid. The characteristics of the phenomenon are analyzed in molecular details.

Journal Article↗

PubMed2005

Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions.

We present a molecular-dynamics simulation study of the bulk and liquid-vapor interfacial properties of ethanol using a polarizable force field based on the fluctuating charge (FQ) formalism, as well as the nonpolarizable CHARMM22 force field. Both models are competitive with respect to the prediction of ambient liquid properties such as liquid density, enthalpy of vaporization, dielectric constant, and self-diffusion constants. The polarizable model predicts an average condensed-phase dipole moment of 2.2 D associated with an induced liquid-phase dipole moment of 0.6 D; though qualitatively in agreement with earlier nonadditive models as well as recent Car-Parinello calculations, the current FQ model underestimates the condensed-phase dipole moment. In terms of liquid structure, both models are in agreement with recent neutron-diffraction results of liquid ethanol structure, although the polarizable model predicts the hydroxyl-hydrogen-hydroxyl-hydrogen structure factor in closer agreement with the experimental data. In terms of interfacial properties, both models predict ambient surface tension to within 4% of the experimental value of 22.8 dyncm, while overestimating the surface excess entropy by almost a factor of 2. Both models display the characteristic preferential orientation of interfacial molecules. The polarizable model allows for a monotonic variation of the average molecular dipole moment from the bulk value to that of the vapor phase. Consequently, there is a dramatic difference in the surface potential predicted by the polarizable and nonpolarizable models. The polarizable model estimates a surface potential of -209+/-3 mV, while the nonpolarizable model yields a value of -944+/-10 mV. Finally, based on the vapor-liquid equilibrium simulation data from several temperatures, we estimate the critical properties of both models. As observed with other FQ models for associating fluids (such as water and methanol), and counter to what one would anticipate by modeling more physically the electrostatic response to local environment, the current FQ model underestimates the critical temperature and overestimates the critical density of ethanol; moreover, the FQ model is, in this respect, equivalent to the underlying fixed-charge model. These results further suggest the need to revisit polarizable models in terms of quantitative vapor-liquid equilibrium prediction.

Chemistry, Physical↗

PubMed2004

The Jahn-Teller effect of the TiIII ion in aqueous solution: extended ab initio QM/MM molecular dynamics simulations.

Combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, including only the first and the first and second hydration shells in the QM region, were performed for TiIII in aqueous solution. The hydration structure of TiIII is discussed in terms of radial distribution functions, coordination-number distributions and several angle distributions. Dynamical properties, such as librational and vibrational motions and TiIII-O vibrations, were evaluated. A fast dynamical Jahn-Teller effect of TiIII(aq) was observed in the QM/MM simulations, in particular when the second hydration shell was included into the QM region. The results justify the computational effort required for the inclusion of the second hydration shell into the QM region and show the importance of this effort for obtaining accurate hydration-shell geometries, dynamical properties, and details of the Jahn-Teller effect.

Journal Article↗

PubMed1997

Long-term molecular dynamics simulation of copper plastocyanin in water.

A long molecular dynamics simulation (1.1 ns) of fully hydrated plastocyanin has been performed and analysed to relate protein dynamics to structural elements and functional properties. The solvated structure is described in detail by the analysis of H-bond network. During all the simulation, the crystal H-bond network is maintained in the beta-sheet regions, while several H-bonds are broken or formed on the external surface of the protein. To evaluate whether such changes could be due to conformational rearrangements or to solvent competition, we have examined the average number of H-bonds between protein atoms and water molecules, and the root mean square deviations from crystal structure as a function of protein residues. Protein mobility and flexibility have been examined by positional and dihedral angle rms fluctuations. Finally, cross-correlation maps have revealed the existence of correlated motions among residues connected by hydrogen bonds.

Journal Article↗

PubMed2006

Growth mechanism of a gas clathrate hydrate from a dilute aqueous gas solution: a molecular dynamics simulation of a three-phase system.

A molecular dynamics simulation of a three-phase system including a gas clathrate, liquid water, and a gas was carried out at 298 K and high pressure in order to investigate the growth mechanism of the clathrate from a dilute aqueous gas solution. The simulation indicated that the clathrate grew on interfaces between the clathrate and the liquid water, after transfer of the gas molecules from the gas phase to the interfaces. The results suggest a two-step process for growth: first, gas molecules are arranged at cage sites, and second, H(2)O molecules are ordered near the gas molecules. The results also suggest that only the H(2)O molecules, which are surrounded or sandwiched by the gas molecules, form the stable polygons that constitute the cages of the clathrate. In addition, the growth of the clathrate from a concentrated aqueous gas solution was also simulated, and the results suggested a growth mechanism in which many H(2)O and gas molecules correctively form the structure of the clathrate. The clathrate grown from the concentrated solution contained some empty cages, whereas the formation of empty cages was not observed during the growth from the dilute solution. The results obtained by both simulations are compared with the results of an experimental study, and the growth mechanism of the clathrate in a real system is discussed.

Journal Article↗

PubMed2005

Molecular dynamics simulations of polyelectrolyte multilayering on a charged particle.

Molecular dynamics simulations of polyelectrolyte multilayering on a charged spherical particle revealed that the sequential adsorption of oppositely charged flexible polyelectrolytes proceeds with surface charge reversal and highlighted electrostatic interactions as the major driving force of layer deposition. Far from being completely immobilized, multilayers feature a constant surge of chain intermixing during the deposition process, consistent with experimental observations of extensive interlayer mixing in these films. The formation of multilayers as well as the extent of layer intermixing depends on the degree of polymerization of the polyelectrolyte chains and the fraction of charge on its backbone. The presence of ionic pairs between oppositely charged macromolecules forming layers seems to play an important role in stabilizing the multilayer film.

Adsorption↗

PubMed2006

Self-assembly of single-walled carbon nanotubes into multiwalled carbon nanotubes in water: molecular dynamics simulations.

We report discoveries from a series of molecular dynamics simulations that single-walled carbon nanotubes, with different diameters, lengths, and chiralities, can coaxially self-assemble into multiwalled carbon nanotubes in water via spontaneous insertion of smaller tubes into larger ones. The assembly process is tube-size-dependent, and the driving force is primarily the intertube van der Waals interactions. The simulations also suggest that a multiwalled carbon nanotube may be separated into single-walled carbon nanotubes under appropriate solvent conditions. This study suggests possible bottom-up self-assembly routes for the fabrication of novel nanodevices and systems.

Journal Article↗

PubMed2005

A proper approach for nonequilibrium molecular dynamics simulations of planar elongational flow.

We present nonequilibrium molecular dynamics simulations of planar elongational flow (PEF) by an algorithm proposed by Tuckerman et al. [J. Chem. Phys. 106, 5615 (1997)] and theoretically elaborated by Edwards and Dressler [J. Non-Newtonian, Fluid Mech. 96, 163 (2001)], which we shall call the proper-SLLOD algorithm, or p-SLLOD for short. [For background on names of algorithms see W. G. Hoover, D. J. Evans, R. B. Hickman, A. J. C. Ladd, W. T. Ashurst, and B. Moran, Phys. Rev. A 22, 1690 (1980) and D. J. Evans and G. P. Morriss, Phys. Rev. A 30, 1528 (1984).] We show that there are two sources for the exponential growth in PEF of the total linear momentum of the system in the contracting direction, which has been previously observed using the so-called SLLOD algorithm. The first comes from the SLLOD algorithm itself, and the second from the implementation of the Kraynik and Reinelt [Int. J. Multiphase Flow 18, 1045 (1992)] boundary conditions. Using the p-SLLOD algorithm (to eliminate the first source) implemented with our simulation strategy (to eliminate the second) in PEF simulations, we no longer observe the exponential growth. By analyzing the equations of motion, we also demonstrate that both the SLLOD and the DOLLS algorithms are intrinsically unsuitable for representing a nonequilibrium system with elongational flow. However, the p-SLLOD algorithm has a rigorously canonical structure in laboratory phase space, and thus can represent a nonequilibrium system not only for elongational flow but also for a general flow.

Journal Article↗

PubMed2005

Molecular dynamics simulations of cluster nucleation during inert gas condensation.

Molecular dynamics simulations of vapor-phase nucleation of germanium in an argon atmosphere were performed and a unexpected channel of nucleation was observed. This channel, vapor-induced cluster splitting, is important for more refractory materials since the critical nucleus size can fall below the size of a dimer. As opposed to conventional direct vapor nucleation of the dimer, which occurs by three-body collisions, cluster-splitting nucleation is a second-order reaction. The most important cluster-splitting reaction is the collision of a vapor atom and a trimer that leads to the formation of two dimers. The importance of the cluster-splitting nucleation channel relative to the direct vapor nucleation channel is observed to increase with decreasing vapor density and increasing ratio of vapor to carrier gas atoms.

Journal Article↗

PubMed2005

Ab initio molecular dynamics simulation of liquid Al88Si12 alloys.

First-principles molecular dynamics simulations are carried out to study the structures, dynamics, and electronic properties of liquid Al88Si12 in the temperature ranging from 898 to 1298 K. The temperature dependence of static structure factors, pair correlation functions, and electronic density-of-states are investigated. The structural properties obtained from the simulations are in good agreement with the x-ray diffraction experimental results.

Journal Article↗