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PubMed2006

Conformational features of an actuator containing calix[4]arene and thiophene: a molecular dynamics study.

Molecular dynamics simulations have been performed for poly(calix[4]arene bis(bithiophene)) in dichloromethane solution. This material responds to its electronic structure variations with significant conformational changes, producing contraction-expansion movements. Simulations have been performed for the three states of this molecular actuator (reduced, oxidized-nondeprotonated, and oxidized-deprotonated), a specific force-field being developed for each case. Results, which are fully consistent with previous ab initio quantum mechanical calculations on an isolated actuating unit, have revealed important findings about the dynamics of the system. Analyses of the flexibility/rigidity of the molecular chain with the state, the interaction of the polymer with the solvent molecules and the influence of environmental factors (as the viscosity of solvent, the counterions and the thermal agitation) on the dynamics have provided important insights to the actuation mechanism.

Journal Article↗

PubMed2007

Stereoselectivity by enantiomeric inhibitors of matrix metalloproteinase-8: new insights from molecular dynamics simulations.

Molecular Dynamics simulations in aqueous solution were performed for the matrix metalloproteinase-8 (MMP-8) free catalytic domain and for its complexes with the (R)- and (S)-[1-(4'-methoxybiphenyl-4-sulfonylamino)-2-methylpropyl] phosphonate. The 144-155 loop of the enzyme undergoes a drastic decrease of mobility once complexed with both enantiomers. The two enantiomers induce a different decrease of conformational entropy upon complexation. The higher affinity of the R-enantiomer can be related to the lower loss of conformational entropy accompanying its binding. The differences in the dynamical behavior of the protein induced by the two enantiomers are discussed at molecular level and the mode of binding of the simulated complexes is compared with that previously determined by X-ray crystallography.

Biphenyl Compounds↗

PubMed2006

Vibrational analysis of the H5O2+ infrared spectrum using molecular and driven molecular dynamics.

Standard molecular and driven molecular dynamics are used to analyze prominent spectral features in the H5O2+ infrared spectrum. In the driven method, the molecular Hamiltonian is augmented with a time-dependent term, mu x epsilon(0) sin(omegat), where mu is the dipole moment of H5O2+, epsilon0 is the electric field, and omega is the frequency. The magnitude of the electric field determines whether the driving is mild (the harmonic limit) or strong (anharmonic motion and mode coupling). We analyze the spectrum in the wavenumber range from 600 to 1900 cm(-1), where recent experimental measurements are available for H5O2+. On the basis of the simulations, we have assigned the broad feature around 1000 cm(-1) to the proton transfer coupled with the torsion motion. Intense absorption near 1780 cm(-1) is assigned to the H2O monomer bend coupled with proton transfer.

Models, Chemical↗

PubMed2006

Understanding the population, coordination, and orientation of water species contributing to the nonlinear optical spectroscopy of the vapor-water interface through molecular dynamics simulations.

Molecular dynamics simulations are used to deconvolve the vibrational spectral features of the vapor-water interface based on molecular environment. A simple geometric description of hydrogen bonding is deployed to identify the OH stretch modes that comprise the vibrational sum-frequency spectrum of the vapor-water interface with direct comparison to our experimental results. The population densities of different species of water molecules are presented as functions of interfacial depth and orientation. It is found that surface water molecules that possess one proton donor bond and one proton acceptor bond make the dominant contribution to both the SSP- and SPS-polarized spectral responses and are located within an angstrom of the Gibbs dividing surface.

Journal Article↗

PubMed2005

Effects of environment on the structure of Pyrococcus furiosus rubredoxin: a molecular dynamics study.

Molecular dynamics simulations based on a 0.95-A resolution crystal structure of Pyrococcus furiosus have been performed to elucidate the effects of the environment on the structure of rubredoxin, and proteins in general. Three 1-ns simulations are reported here: two crystalline state simulations at 123 and 300 K, and a solution state simulation at 300 K. These simulations show that temperature has a greater impact on the protein structure than the close molecular contacts of the crystal matrix in rubredoxin, although both have an effect on its dynamic properties. These results indicate that differences between NMR solution structures and X-ray crystal structures will be relatively minor if they are done at similar temperatures. In addition, the crystal simulations appears to mimic previous crystallographic experiments on the effects of cryo-temperature on temperature factors, and might provide a useful tool in the structural analysis of protein structures solved at cryo-temperatures.

Bacterial Proteins↗

PubMed1996

Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation.

Molecular dynamics (MD) simulations of 100 ps have been carried out to study the active-site behaviour of the Cu,Zn superoxide dismutase dimer (SOD) in water. The active site of each subunit was monitored during the whole simulation by calculating the distances between functional residues and the catalytic copper. The results indicate that charge orientation is maintained at each active site but the solvent accessibility varies. Analysis of the MD simulation, carried out by using the atomic displacement covariance matrix, has shown a different intra-subunit correlation pattern for the two monomers and the presence of inter-subunit correlations. The MD simulation presented here indicates an asymmetry in the two active sites and different dynamic behaviour of the two SOD subunits.

Animals↗

PubMed1989

The dynamic properties of melittin in solution. Investigations by NMR and molecular dynamics.

Molecular dynamics simulations are described for the peptide melittin. The atomic trajectories are calculated both with normal potential energy functions and with additional distance restraints deduced from nuclear Overhauser effects observed in NMR experiments. The results are compared with NMR data on coupling constants and amide exchange rates and with B-factors from X-ray crystallography. The observed correlations between experiment and molecular dynamics simulations suggest a relatively mobile C-terminus and relatively high flexibility around residue 11. It is noted that the high conformational variation around residue 11 is due in part to the presence of a proline at position 14 which results in a "missing" H-bond in the largely alpha-helical structure. It is also noted that a proline is a common feature of many putative membrane spanning helices. A role for such prolines is suggested.

Bee Venoms↗

PubMed2001

Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations.

Molecular dynamics simulations have been applied to the DNA octamer d(GCGCA-GAAC). d(GTTCGCGC), which has an adenine bulge at the center to determine the pathway for interconversion between the stacked and extended forms. These forms are known to be important in the molecular recognition of bulges. From a total of ~35 ns of simulation time with the most recent CHARMM27 force field a variety of distinct conformations and subconformations are found. Stacked and fully looped-out forms are in excellent agreement with experimental data from NMR and x-ray crystallography. Furthermore, in a number of conformations the bulge base associates with the minor groove to varying degrees. Transitions between many of the conformations are observed in the simulations and used to propose a complete transition pathway between the stacked and fully extended conformations. The effect on the surrounding DNA sequence is investigated and biological implications of the accessible conformational space and the suggested transition pathway are discussed, in particular for the interaction of the MS2 replicase operator RNA with its coat protein.

Adenine↗

PubMed2004

Characterization of polyethylene crystallization from an oriented melt by molecular dynamics simulation.

Molecular dynamics is used to characterize the process of crystallization for a united atom model of polyethylene. An oriented melt is produced by uniaxial deformation under constant load, followed by quenching below the melting temperature at zero load. The development of crystallinity is monitored simultaneously using molecular-based order parameters for density, energy, and orientation. For crystallization temperatures ranging from 325 to 375 K, these simulations clearly show the hallmarks of crystal nucleation and growth. We can identify multiple nucleation events, lamellar growth up to the limit imposed by periodic boundaries of the simulation cell, and lamellar thickening. We observe a competition between the rate of nucleation, which results in multiple crystallites, the rate of chain extension, which results in thicker lamellae, and the rate of chain conformational relaxation, which is manifested in lower degrees of residual order in the noncrystalline portion of the simulation. The temperature dependence of lamellar thickness is in accord with experimental data. At the higher temperatures, tilted chain lamellae are observed to form with lamellar interfaces corresponding approximately to the [201] facet, indicative of the influence of interfacial energy.

Journal Article↗

PubMed2002

Molecular dynamics simulations.

Molecular dynamics simulations have become a standard tool for the investigation of biomolecules. Simulations are performed of ever bigger systems using more realistic boundary conditions and better sampling due to longer sampling times. Recently, realistic simulations of systems as complex as transmembrane channels have become feasible. Simulations aid our understanding of biochemical processes and give a dynamic dimension to structural data; for example, the transformation of harmless prion protein into the disease-causing agent has been modeled.

Cell Membrane↗

PubMed2002

Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations.

Molecular dynamics simulations (MD) have been performed on variant crystal and NMR-derived structures of the glucocorticoid receptor DNA-binding domain (GR DBD). A loop region five residues long, the so-called D-box, exhibits significant flexibility, and transient perturbations of the tetrahedral geometry of two structurally important Cys4 zinc finger are seen, coupled to conformational changes in the D-box. In some cases, one of the Cys ligands to zinc exchanges with water, although no global distortion of the protein structure is observed. Thus, from MD simulation, dynamics of the D-box could partly be explained by solvent effects in conjunction with structural reformation of the zinc finger.

Amino Acid Sequence↗

PubMed2005

Role of water molecules in the KcsA protein channel by molecular dynamics calculations.

Molecular dynamics simulations supported by electrostatic calculations have been conducted on the KcsA channel to determine the role of water molecules in the pore. Starting from the X-ray structure of the KcsA channel in its closed state at 2.0 angstroms resolution, the opening of the pore towards a conformation built on the basis of EPR results is studied. We show that water molecules act as a structural element for the K+ ions inside the filter and the hydrophobic cavity of the channel. In the filter, water tends to enhance the depth of the wells occupied by the K+ ions, while in the cavity there is a strong correlation between the water molecules and the cavity ion. As a consequence, the protein remains very stable in the presence of three K+ ions in the selectivity filter and one in the cavity. The analysis of the dynamics of water molecules in the cavity reveals preferred orientations of the dipoles along the pore axis, and a correlated behavior between this dipole orientation and the displacement of the K+ ion during the gating process.

Bacterial Proteins↗

PubMed2003

Solvent reorganization in electron and ion transfer reactions near a smooth electrified surface: a molecular dynamics study.

Molecular dynamics simulations of electron and ion transfer reactions near a smooth surface are presented, analyzing the effect of the geometrical constraint of the surface and the interfacial electric field on the relevant solvation properties of both a monovalent negative ion and a neutral atom. The simulations show that, from the solvation point of view, ion adsorption is an uphill process due to the need to shed off the ion's solvation shell and displace water from the surface. Atom adsorption, on the other hand, has only a small barrier, related to the molecularity of the solvent. Both the electrostatic interaction of the ion with the solvent and the ion's solvent reorganization energy (the relevant parameter in the Marcus electron transfer theory) decrease as the surface is approached, whereas these parameters are not sensitive to the distance from the surface for the atom. This is a consequence of the importance of long-range electrostatic interactions for ion solvation and the importance of short-range interactions for atom solvation. The electric field either attracts or repels an ion to or from the surface, but the field has no influence on the solvent reorganization energy. By including the quantum-mechanical electron transfer between the metal surface and the ion/atom in solution in the MD simulation by using a model Hamiltonian, we calculated two-dimensional free energy surfaces for ion adsorption allowing for partial charge transfer, based on a fully molecular picture of ion solvation near the surface.

Journal Article↗

PubMed1997

Domain motions in dihydrofolate reductase: a molecular dynamics study.

Molecular dynamics simulations have been carried out on the enzyme dihydrofolate reductase from Lactobacillus casei complexed with methotrexate, NADPH and 264 crystallographic water molecules. Analysis of correlations in atomic fluctuations reveal the presence of highly correlated motion (correlation coefficient > 0.6) in the region between residues 30 to 35 and 85 to 90 leading to the identification of two domains, an "adenosine-binding domain" and a "large domain", which rotate by 3 to 4 degrees with respect to each other. The strongest correlation (> 0.6) within the large domain involves a coupling between the motions of the "teen-loop", and the spatially contiguous loops linking beta 6-beta 7 and beta 7-beta 8. Moreover, there is a significant correlation (approximately 0.5) between the adenosine fragment of NADPH and the pteridine and p-aminobenzoyl fragments of methotrexate, which are separated by approximately 17 A, and is lost on removal of "rigid-body" motion from the original trajectory. This provides support for the idea that the relative motion of the two domains is a means by which the occupation of the binding site for the adenosine end of the coenzyme can affect methotrexate binding and vice versa. Quasiharmonic vibrational analysis of the trajectory reveals that the overall dynamics of the system are governed by domain motions whose contributions are dominant at low frequencies. In addition, different low-frequency modes are responsible for separately coupling the adenosine-binding site and parts of methotrexate.

Binding Sites↗

PubMed2001

GD1a in phospholipid bilayer: a molecular dynamics simulation.

Molecular dynamics simulation of ganglioside GD1a attached to the upper layer of a fully hydrated lipid bilayer of dimyristoyl phosphatidyl choline (DMPC) at room temperature under periodic boundary conditions was performed. The time average conformation of GD1a reveals that the terminal sialic acid is more exposed into the solvent than the internal branched one. Many interresidual contacts between N-acetyl galactosamine-internal branched sialic acid; external Gal-external sialic acid; N-acetyl galactosamine-internal gal are also observed. The conformation of the GD1-hexasaccharide is stabilized by a number of intra molecular hydrogen bonds that were previously observed experimentally. The simulation results indicate that the presence of a single GD1a molecule has local effects on the bilayer. A local disorder in the arrangement of the acyl chains as well as the head groups is evident in the upper layer due to the presence of GD1a.

Acetylgalactosamine↗

PubMed2005

Internal cavities and ligand passageways in human hemoglobin characterized by molecular dynamics simulations.

Molecular dynamics simulations of the unliganded T state of human hemoglobin showed the existence of a spontaneous, very wide cavity on the distal side of the alpha subunit. This cavity consists of three tunnels spreading from the vicinity of the iron atom (the ligand binding site) to the surface of the subunit, constituting possible passageways for the entrance of the ligand. A fourth passageway was characterized due to the trajectory of water molecules entering or leaving the heme pocket. Analogous passages were observed in the beta subunits. They all appear and disappear dynamically, although some parts of them are more persistent along the trajectories. The most persistent regions within these tunnels correspond to all the xenon docking sites of human cytoglobin and to some of those of sperm whale and horse heart myoglobins and group I truncated hemoglobins.

Binding Sites↗

PubMed2000

Molecular dynamics and (2)H-NMR study of the influence of an amphiphilic peptide on membrane order and dynamics.

A molecular dynamics simulation of a fully hydrated model membrane consisting of 12 molecules of 1, 2-dimyristoyl-sn-glycero-3-phosphocholine, one amphiphilic peptide with the sequence acetyl-Lys-Lys-Gly-Leu(16)-Lys-Lys-Ala-amide, and 593 water molecules was performed for 1.06 ns (Belohorcova, K., J. H. Davis, T. B. Woolf, and B. Roux. 1997. Biophys. J. 73:3039-3055). The analysis presented here is primarily focused on the phospholipid component and the results are compared with experimental (2)H-NMR studies of the lipid component of mixtures of the same peptide and lipid at a molar ratio of 1:32, and with earlier studies of closely related peptide/lipid mixtures. The phospholipid chain and headgroup isomer populations and isomerization rates compare favorably with previous simulations and experimental measurements. Of particular interest is the effect of the peptide on the phospholipid headgroup and hydrocarbon chain orientational order calculated from the simulation, which also agree well with experimental measurements performed on this and closely related systems. Comparison of the experimental results with the simulations not only shows that there is significant agreement between the two methods, but also provides new insight into the effect of the peptide on the lipid dynamics. In particular, these results confirm that a membrane spanning peptide has little effect on lipid chain order, and bilayer thickness if its hydrophobic length closely matches the lipid hydrocarbon thickness. In addition, we find that the peptide can have a strong ordering effect if it is longer than the lipid hydrophobic thickness.

Amino Acid Sequence↗

PubMed2001

Structure and stability of the insulin dimer investigated by molecular dynamics simulation.

Molecular dynamics simulation indicates that the dynamical behaviour of the insulin dimer is asymmetric. Atomic level knowledge of the interaction modes and protein conformation in the solvation state identifies dynamical structures, held by hydrogen bonds that stabilize, mainly in one monomer, the interaction between the chains. Dynamic cross-correlation analysis shows that the two insulin monomers behave asymmetrically and are almost independent. Solvation energy, calculated to evaluate the contribute of each interface residue to the dimer association pattern, well compares with the experimental association state found in protein mutants indicating that this parameter is an important factor to explain the association properties of mutated insulin dimers.

Computer Simulation↗