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PubMed2004

Effects of resolution and friction in the interpretation of QHAS measurements.

We use Langevin molecular dynamics (MD) simulations to improve the picture of the processes that contribute to QHAS broadening, as a function of momentum transfer at the crystal. We use a simulation of realistic damped vibrational motion in a harmonic well to establish the contributions to QHAS measurements due to both vibrational motion and intracell diffusion (usually referred to as vibrational dephasing). We demonstrate the experimental conditions under which such contributions are likely to be important. These results are compared with those from a simulation of thermal diffusion over a sinusoidally corrugated potential. We show that resolution and atom-surface "friction" play an important role in determining the form of QHAS measurements and we demonstrate that there is no simple relationship between the "activation energy" derived from an Arrhenius plot of QHAS data and the adiabatic potential barrier height. MD simulations are therefore necessary to perform a complete analysis of the data. Finally, we discuss the application of our results to more sophisticated potentials, particularly those with multiple adsorption sites.

Journal Article↗
PubMed2005

Homology modeling based solution structure of Hoxc8-DNA complex: role of context bases outside TAAT stretch.

The 3D structure of neither Hoxc8 nor Hoxc8-DNA complex is known. The repressor protein Hoxc8 binds to the TAAT stretch of the promoter of the osteopontin gene and modulates its expression. Over expression of the osteopontin gene is related to diseases like osteoporosis, multiple sclerosis, cancer et cetera. In this paper we have proposed a 3D structure of Hoxc8-DNA complex obtained by Homology modeling and molecular dynamics (MD) simulation in explicit water. The crystal structure (9ant.pdb) of Antennapedia homeodomain in complex with its DNA sequence was chosen as the template based on (i) high sequence identity (85% for the protein and 60% for the DNA) and (ii) the presence of the TAAT stretch in interaction with the protein. The resulting model was refined by MD simulation for 2.0ns in explicit water. This refined model was then characterized in terms of the structural and the interactional features to improve our understanding of the mechanism of Hoxc8-DNA recognition. The interaction pattern shows that the residues Ile(195), Gln(198), and Asn(199), and the bases S2-(4)TAATG(8) are most important for recognition suggesting the stretch TAATG as the "true recognition element" in the present case. A strong and long-lived water bridge connecting Gln(198) and the base of S1-C(7) complementary to S2-G(8) was observed. Our predicted model of Hoxc8-DNA complex provides us with features that are consistent with the available experimental data on Hoxc8 and the general features of other homeodomain-DNA complexes. The predictions based on the model are also amenable to experimental verification.

Amino Acid Sequence↗
PubMed1999

Structure and dynamics of the fatty acid binding cavity in apo rat intestinal fatty acid binding protein.

The structure and dynamics of the fatty acid binding cavity in I-FABP (rat intestinal fatty acid binding protein) were analyzed. In the crystal structure of apo I-FABP, the probe occupied cavity volume and surface are 539+/-8 A3 and 428 A2, respectively (1.4 A probe). A total of 31 residues contact the cavity with their side chains. The side-chain cavity surface is partitioned according to the residue type as follows: 36-39% hydrophobic, 21-25% hydrophilic, and 37-43% neutral or ambivalent. Thus, the cavity surface is neither like a typical protein interior core, nor is like a typical protein external surface. All hydrophilic residues that contact the cavity-with the exception of Asp74-are clustered on the one side of the cavity. The cavity appears to expand its hydrophobic surface upon fatty acid binding on the side opposite to this hydrophilic patch. In holo I-FABP the fatty acid chain interactions with the hydrophilic side chains are mediated by water molecules. Molecular dynamics (MD) simulation of fully solvated apo I-FABP showed global conformational changes of I-FABP, which resulted in a large, but seemingly transient, exposure of the cavity to the external solvent. The packing density of the side chains lining the cavity, studied by Voronoi volumes, showed the presence of two distinctive small hydrophobic cores. The MD simulation predicts significant structural perturbations of the cavity on the subnanosecond time scale, which are capable of facilitating exchange of I-FABP internal water.

Animals↗
PubMed2003

Protein stability and plasticity of the hydrophobic cavity in wheat ns-LTP.

Plant ns-LTPs display an original structure with four helices and a flexible C-terminus, maintained together by four disulphide bridges and delineating an elongated central hydrophobic cavity. In order to relate these structural features to the protein stability and plasticity, combined molecular mechanics and simulated annealing calculations were undertaken on a wheat ns-LTP "mutant" with Cys-Ala replacement and with the application of core inter-residue restraints up to 2 A, reducing the cross-section size of the hydrophobic cavity. Analysis of the energy-minimized structures shows that removal of the disulphide bridges results in structures with a lower total energy and a smaller cavity volume. A 1-ns MD simulation at 300K in water, underlines that, despite the absence of a well-packed hydrophobic core, the native structure is extremely stable at room temperature and the cavity is not hydrated. This confirms that the disulphide bridges are essential for the existence of the cavity, whereas its plasticity depends both on the hydrophobic chain lining the cavity and on the C-terminal flexibility. A high temperature (500K) MD simulation confirms the stability of the secondary structure elements and the flexibility of the loops and of the C-terminal segment. Two important structural transitions during this simulation are discussed and possible routes for the insertion and release of hydrophobic ligands are suggested.

Alanine↗
PubMed2000

On the similarity of properties in solution or in the crystalline state: a molecular dynamics study of hen lysozyme.

As protein crystals generally possess a high water content, it is assumed that the behaviour of a protein in solution and in crystal environment is very similar. This assumption can be investigated by molecular dynamics (MD) simulation of proteins in the different environments. Two 2ns simulations of hen egg white lysozyme (HEWL) in crystal and solution environment are compared to one another and to experimental data derived from both X-ray and NMR experiments, such as crystallographic B-factors, NOE atom-atom distance bounds, 3J(H N alpha)-coupling constants, and 1H-15N bond vector order parameters. Both MD simulations give very similar results. The crystal simulation reproduces X-ray and NMR data slightly better than the solution simulation.

Animals↗
PubMed1999

Homology modeling of gelatinase catalytic domains and docking simulations of novel sulfonamide inhibitors.

Three-dimensional models for the catalytic domain of gelatinases (MMP-9 and -2) have been constructed based on the X-ray crystal structure of MMP-3. Conformations of the loop segment which forms the bottom half of the S1' subsite but shows conformational diversity among the crystal structures of other MMPs have been explored by simulated annealing of each gelatinase model complexed with two highly potent "probe" inhibitors. Representative catalytic domain models have been selected for each gelatinase from the set of generated conformations based on shape complementarity of the loop to the probe inhibitors. The single model selected for MMP-9 was utilized to explain the structure-activity relationship of our novel sulfonamide inhibitors. Molecular dynamics (MD) simulations of the complex models revealed important features of the binding mechanism of our inhibitors: (i) the ligand carboxylate group coordinating to the catalytic zinc ion and hydrogen bonding to the Glu219 side chain, (ii) one of the sulfonyl oxygens forming hydrogen bonds with the main chain NHs (Leu181 and Ala182), (iii) the sulfonyl substituent making extensive hydrophobic contact with the S1' subsite. The gauche conformation exclusively adopted by the sulfonamide C-N-S-C torsion plays an important role in achieving the third binding feature by properly directing the substituent into the S1' subsite. Improvement of the inhibitory activity according to straight elongation of the sulfonyl substituent was attributed to an increase of the hydrophobic contact between the substituent and the S1' subsite. Structural modifications which alter the straight shape of the substituent lead to deterioration of the activity. On the other hand, the two candidate models selected for MMP-2 differ in the bottom shape of the S1' subsite: one with a channel-like subsite and the other with a pocket-like subsite resembling that of the MMP-9 model. The bottom shape was experimentally probed by chemical synthesis of inhibitors having elongated sulfonyl substituents whose terminal alkyl groups were shown by MD simulations to protrude from the S1' subsite bottom into the solvent. Gelatinase assays of these inhibitors showed that elongation of the substituent significantly reduces activity against MMP-9 while retaining activity against MMP-2, consequently increasing the selectivity between MMP-2 and -9. The results confirm that MMP-9 has a pocket-like S1' subsite with a floorboard and MMP-2 has a channel-like S1' subsite.

Amino Acid Sequence↗
PubMed2005

Computational analysis of mutations in the transmembrane region of Vpu from HIV-1.

Vpu is an 81 amino acid integral membrane protein encoded by HIV-1. Its alpha-helical transmembrane (TM) domain (residues approximately 6-28) enhances virion release by oligomerizing into bundles and forming ion-conducting channels across the plasma membrane. Its cytoplasmic domain (residues approximately 29-81) is also alpha-helical and binds to the transmembrane protein CD4, inducing its degradation. Mutations within the TM domain have been found to abrogate enhanced particle release from the infected cell (Tiganos et al. Virology (1998) 251 96-107). A series of computational models of monomeric, pentameric and hexameric Vpu(1-31) mutants have been constructed, embedded in fully hydrated lipid bilayers and subjected to a 3 ns molecular dynamics (MD) simulation. None of the mutations has any destabilizing effect on the secondary and tertiary structure. One of the mutants, in which the position of a tryptophan residue within the TM domain is altered, is known not to induce CD4 degradation; an extended kinked model of this mutant has been generated (Vpu(1-52)IVW-k) and during subsequent MD simulations, the bend between the TM and a part of the cytoplasmic domain is found to unwind and a complex salt bridge involving Lys-37 is formed.

Amino Acid Sequence↗
PubMed2004

Prediction of HIV-1 integrase/viral DNA interactions in the catalytic domain by fast molecular docking.

This study details the separate analyses of binding specificity of HIV-1 integrase (IN) and viral B-DNA forms through ligand-receptor docking studies by means of a fast molecular docking method. The application of solvated electrostatics with the University of Houston Brownian Dynamics Program (UHBD) and configurational sampling by the Daughter of Turnip (DOT) docking program resulted in the computation of energies of more than 113 billion configurations for each ligand-receptor docking study, a procedure considered computationally intractable a few years ago. A specific binding pattern of viral DNA to the IN catalytic domain region has been predicted as a result of these calculations. In a representative docked configuration, we observe the 3'-hydroxyl of the conserved deoxyadenosine to be close to one of the two divalent metal ions that are necessary for catalysis. A superimposition of our energy-minimized docked complex on representative structures from a molecular dynamics (MD) simulation of a crystallographically resolved IN/inhibitor complex revealed an overlap of viral DNA with the inhibitor, indicating that the bound inhibitor might operate by blocking substrate binding. The DOT docking calculation also identified a second, adjacent DNA-binding site, which we believe is the nonspecific host DNA binding site. The binding pattern predicted by DOT complements previous electrostatics, MD simulation, photo-cross-linking, and mutagenesis studies and also provides a further refinement of the IN/viral DNA binding interaction as a basis for new structure-based design efforts.

Catalytic Domain↗
PubMed2006

Pressure affects the structure and the dynamics of the D-galactose/D-glucose-binding protein from Escherichia coli by perturbing the C-terminal domain of the protein.

The effect of the pressure on the structure and stability of the D-galactose/D-glucose binding protein from Escherichia coli in the absence (GGBP) and in the presence (GGBP/Glc) of glucose was studied by Fourier transform infrared (FT-IR) spectroscopy and molecular dynamic (MD) simulations. FT-IR spectroscopy experiments showed that the protein beta-structures are more resistant than alpha-helices structures to pressure value increases. In addition, the infrared data indicated that the binding of glucose stabilizes the protein structure against high pressure values, and the protein structure does not completely unfold up to pressure values close to 9000 bar. MD simulations allow a prediction of the most probable configuration of the protein, consistent with the increasing pressures on the two systems. The detailed analysis of the structures at molecular level confirms that, among secondary structures, alpha-helices are more sensitive than beta-structures to the destabilizing effect of high pressure and that glucose is able to preserve the structure of the protein in the complex. Moreover, the evidence of the different resistance of the two domains of this protein to high pressure is investigated and explained at a molecular level, indicating the importance of aromatic amino acid in protein stabilization.

Escherichia coli↗
PubMed2006

Development of many-body polarizable force fields for Li-battery applications: 2. LiTFSI-doped Oligoether, polyether, and carbonate-based electrolytes.

A quantum chemistry study of Li(+) interactions with ethers, carbonates, alkanes, and a trifluoromethanesulfonylimide anion (TFSI(-)) was performed at the MP2, B3LYP, and HF levels using the aug-cc-pvDz basis set for solvents and TFSI(-) anion, and [8s4p3d/5s3p2d]-type basis set for Li. A classical many-polarizable force field was developed for the LiTFSI salt interacting with ethylene carbonate (EC), gamma-butyrolactone (GBL), dimethyl carbonate (DMC), acetone, oligoethers, n-alkanes, and perfluoroalkanes. Molecular dynamics (MD) simulations were performed for EC/LiTFSI, PC/LiTFSI, GBL/LiTFSI, DMC/LiTFSI, 1,2-dimethoxyethane/LiTFSI, pentaglyme/LiTFSI, and poly(ethylene oxide) (MW = 2380)/LiTFSI electrolytes at temperatures from 298 to 423 K and salt concentrations from 0.3 to 5 M. The ion and solvent self-diffusion coefficients, electrolyte conductivity, electrolyte density, LiTFSI apparent molar volumes, and structure of the Li(+) cation environment predicted by MD simulations were found in good agreement with experimental data.

Journal Article↗
PubMed2006

Molecular dynamics study of the thermodynamics and transport coefficients of hard hyperspheres in six and seven dimensions.

Molecular dynamics (MD) simulations are performed for six- and seven-dimensional hard-hypersphere fluids. The equation of state, velocity autocorrelation function, self-diffusion coefficient, shear viscosity, and thermal conductivity are determined as a function of density. The molecular dynamics results for the equation of state are found to be in excellent agreement with values obtained from theoretical approaches and previous MD simulations in seven dimensions. The short-time behavior of the velocity autocorrelation function is well described by the Enskog exponential approximation. The Enskog predictions for the self-diffusion coefficient and the viscosity agree fairly well with the simulation data at low densities, but underestimate these quantities at higher densities. Data for the thermal conductivity are in fine agreement with Enskog theory for all densities and dimensions studied.

Journal Article↗
PubMed2004

Quantitative analysis of XANES spectra of disordered systems based on molecular dynamics.

A general procedure which computes X-ray absorption near-edge structure (XANES) spectra starting from the individual configurations obtained from molecular dynamics (MD) simulations has been developed. This method allows one to perform a quantitative analysis of the XANES spectra of disordered systems and to estimate the effect of disorder on the low-energy region of the X-ray absorption spectra. As a test case, a Ni2+ aqueous solution has been investigated. The configurational averaged XANES theoretical spectrum obtained from the MD configurations compares well with the experimental data. This confirms simultaneously the reliability of the procedure and of the structural results obtained from the MD simulation.

Metalloproteins↗
PubMed2003

Investigation of the induced-fit mechanism and catalytic activity of the human cytomegalovirus protease homodimer via molecular dynamics simulations.

Human cytomegalovirus (HCMV) is a highly species-specific DNA virus infecting up to 80% of the general population. The viral genome contains the open reading frame UL80, which encodes the full-length 80 kDa HCMV serine protease and its substrate. Full-length HCMV protease is composed of an N-terminal 256-amino-acid proteolytic domain, called assemblin, a linker region, and a C-terminal structural domain, the assembly protein precursor. Biochemical studies have shown that dimerization activates assemblin because of an induced stabilization of the oxyanion hole (Arg166). Thus, we performed here molecular dynamics (MD) simulations on HCMV protease models to study the induced-fit mechanism of the enzyme upon the binding of substrates and peptidyl inhibitors, and structural and energetic factors that are responsible for the catalytic activity of the enzyme dimer. Long and stable trajectories were obtained for the models of the monomeric and dimeric states, free in solution and bound to a peptidyl-activated carbonyl inhibitor, with very good agreement between theoretical and experimental results. Our results suggest that HCMV protease is indeed a novel example of serine protease that operates by an induced-fit mechanism. Also, in agreement with mutagenesis studies, our MD simulations suggest that the dimeric form is necessary to activate the enzyme because of an induced stabilization of the oxyanion hole.

Arginine↗
PubMed2004

A combined molecular dynamics+quantum mechanics method for investigation of dynamic effects on local surface structures.

A combined molecular dynamics (MD)+quantum mechanics (QM) method for studying processes on ionic surfaces is presented. Through the combination of classical MD and ab initio embedded-cluster calculations, this method allows the modeling of surface processes involving both the structural and dynamic features of the substrate, even for large-scale systems. The embedding approach used to link the information from the MD simulation to the cluster calculation is presented, and rigorous tests have been carried out to ensure the feasibility of the method. The electrostatic potential and electron density resulting from our embedded-cluster model have been compared with periodic slab results, and confirm the satisfying quality of our embedding scheme as well as the importance of applying embedding in our combined MD+QM approach. We show that a highly accurate representation of the Madelung potential becomes a prerequisite when the embedded-cluster approach is applied to temperature-distorted surface snapshots from the MD simulation.

Journal Article↗
PubMed2004

Mutational and structural-based analyses of the osmolyte effect on protein stability.

It is known that several naturally occurring substances known as osmolytes increase the conformational stability of proteins. Bolen and co-worker proposed the osmophobic theory, which asserts the osmolyte effect occurs because of an unfavorable interaction of osmolytes mainly with the protein backbone, based on the results on the transfer Gibbs energy of amino acids (Deltag) [Bolen and Baskakov (2001) J. Mol. Biol. 310, 955-963]. In this paper, we report the effect of sarcosine on the conformational stability (DeltaG) of RNase Sa (96 residues and one disulfide bond) and four mutant proteins. The thermal denaturation curves for RNase Sa in sarcosine fitted a two-state model on nonlinear least-squares analysis. All the RNase Sa proteins were stabilized by sarcosine. For example, the increase in stability of the wild-type protein in 4 M sarcosine due to the osmolyte effect (Delta(o)DeltaG) is 3.2 kcal/mol. Mutational analysis of the osmolyte effect indicated that the changed Delta(o)DeltaG values upon mutation (Delta(m)Delta(o)DeltaG), as estimated from the Deltag values, are similar to the experimental values. Structural-based analysis of the osmolyte effect was also performed using model denatured structures: (a) a fully extended model (single chain) with no disulfide bond, (b) two-part, unfolded models (two chains) with a disulfide bond constructed through molecular dynamic (MD) simulation, and (c) a two-part, folded model (two chains). The two-part, unfolded models were expected to be more suitable as denatured structures. The Delta(o)DeltaG values calculated using the two-part, unfolded models were more consistent with experimental values than those calculated using the fully extended and two-part, folded models. This suggests that MD simulation is useful for testing denatured structures. These results indicate that the osmophobic theory can explain the osmolyte effect on protein stability.

Circular Dichroism↗
PubMed2001

Proline-induced hinges in transmembrane helices: possible roles in ion channel gating.

A number of ion channels contain transmembrane (TM) alpha-helices that contain proline-induced molecular hinges. These TM helices include the channel-forming peptide alamethicin (Alm), the S6 helix from voltage-gated potassium (Kv) channels, and the D5 helix from voltage-gated chloride (CLC) channels. For both Alm and KvS6, experimental data implicate hinge-bending motions of the helix in an aspect of channel gating. We have compared the hinge-bending motions of these TM helices in bilayer-like environments by multi-nanosecond MD simulations in an attempt to describe motions of these helices that may underlie possible modes of channel gating. Alm is an alpha-helical channel-forming peptide, which contains a central kink associated with a Gly-x-x-Pro motif in its sequence. Simulations of Alm in a TM orientation for 10 ns in an octane slab indicate that the Gly-x-x-Pro motif acts as a molecular hinge. The S6 helix from Shaker Kv channels contains a Pro-Val-Pro motif. Modeling studies and recent experimental data suggest that the KvS6 helix may be kinked in the vicinity of this motif. Simulations (10 ns) of an isolated KvS6 helix in an octane slab and in a POPC bilayer reveal hinge-bending motions. A pattern-matching approach was used to search for possible hinge-bending motifs in the TM helices of other ion channel proteins. This uncovered a conserved Gly-x-Pro motif in TM helix D5 of CLC channels. MD simulations of a model of hCLC1-D5 spanning an octane slab suggest that this channel also contains a TM helix that undergoes hinge-bending motion. In conclusion, our simulations suggest a model in which hinge-bending motions of TM helices may play a functional role in the gating mechanisms of several different families of ion channels.

Alamethicin↗
PubMed2006

A combined NMR and molecular dynamics study of the transmembrane solubility and diffusion rate profile of dioxygen in lipid bilayers.

The transmembrane profile of oxygen solubility and diffusivity in a lipid bilayer was assessed by (13)C NMR of the resident lipids (sn-2-perdeuterio-1-myristelaidoyl-2-myristoyl-sn-glycero-3-phosphocholine) in combination with molecular dynamics (MD) simulations. At an oxygen partial pressure of 50 atm, distinct chemical shift perturbations of a paramagnetic origin were observed, spanning a factor of 3.2 within the sn-1 chain and an overall factor of 10 from the headgroup to the hydrophobic interior. The distinguishing feature of the (13)C NMR shift perturbation measurements, in comparison to ESR and fluorescence quenching measurements, is that the local accessibility of oxygen is achieved for nearly all carbon atoms in a single experiment with atomic resolution and without the use of a probe molecule. MD simulations of an oxygenated and hydrated lipid bilayer provided an immersion depth distribution of all carbon nuclei, in addition to the distribution of oxygen concentration and diffusivity with immersion depth. All oxygen-induced (13)C NMR chemical shift perturbations could be reasonably approximated by simply accounting for the MD-derived immersion depth distribution of oxygen in the bilayer, appropriately averaged according to the immersion depth distribution of the (13)C nuclei. Second-order effects in the paramagnetic shift are attributed to the collisionally accessible solid angle or to the propensity of the valence electrons in the vicinity of a given nuclear spin to be polarized or delocalized by oxygen. A method is presented to measure such effects. The excellent agreement between MD and NMR provides an important cross-validation of the two techniques.

Diffusion↗
PubMed2004

Power-law slip profile of the moving contact line in two-phase immiscible flows.

Large-scale molecular dynamics (MD) simulations on two-phase immiscible flows show that, associated with the moving contact line, there is a very large 1/x partial-slip region where x denotes the distance from the contact line. This power-law partial-slip region is verified in large-scale adaptive continuum calculations based on a local, continuum hydrodynamic formulation, which has proved successful in reproducing MD results at the nanoscale. Both MD simulations and numerical solutions of continuum equations indicate the existence of a universal slip profile in the Stokes-flow regime.

Journal Article↗