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Fumio Hirata

Publications and source records attributed to Fumio Hirata.

13 recordsLinked to original sources
PubMed2007

Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation.

Water molecules confined in protein cavities are of great importance in understanding the protein structure and functions. However, it is a nontrivial task to locate such water molecules in protein by the ordinary molecular simulation and modeling techniques as well as experimental methods. The present study proves that the three-dimensional reference interaction site model (3D-RISM) theory, a recently developed statistical-mechanical theory of molecular solvation, has an outstanding advantage in locating such water molecules. In this paper, we demonstrate that the 3D-RISM theory is able to reproduce the structure and the number of water molecules in cavities of hen egg-white lysozyme observed commonly in the X-ray structures of different resolutions and conditions. Furthermore, we show that the theory successfully identified a water molecule in a cavity, the existence of which has been ambiguous even from the X-ray results. In contrast, we confirmed that molecular dynamics simulation is helpless at present to find such water molecules because the results substantially depend on the initial coordinates of water molecules. Possible applications of the theory to problems in the fields of biochemistry and biophysics are also discussed.

Computational Biology↗
PubMed2006

Conformational equilibrium of 1,2-dichloroethane in water: comparison of PCM and RISM-SCF methods.

The RISM-SCF and polarizable continuum model (PCM) approaches have been applied to study the conformational equilibrium of 1,2-dichloroethane (DCE) in water. Both the electron correlation effect and basis sets play an important role in the relative energies of the gauche and trans conformers in gas and solution phases. Both PCM and RISM-MP2 methods resulted in a consistent trend with the previous experimental and theoretical studies that the population of the gauche conformer increases in going from the gas phase to the aqueous solution. However, the PCM treatment could not describe the solvent effect completely in that the sign of the relative free energy of the gauche and trans forms is opposite to the most recent experimental and theoretical data, while the RISM-MP2 gives the right sign in the free energy difference. We found that the larger excess chemical potential gain (by ca. -4.1 kcal/mol) for the gauche conformer is large enough to result in the gauche preference of DCE in water, though it has to compensate for more solute reorganization energy (approximately 1.6 kcal/mol) and overcome the energy difference (approximately 1.6 kcal/mol) in the gas phase. The radial distribution functions between DCE and the nearest water shows that the electrostatic repulsion between chlorine and oxygen atoms is higher in the trans conformer than in the gauche one, while the attractive interaction between chlorine and hydrogen of water is higher in the gauche conformer.

Ethylene Dichlorides↗
PubMed2006

A theoretical analysis on hydration thermodynamics of proteins.

The hydration free energy (HFE) of several proteins modeled using the all-atom force field is calculated by employing the three-dimensional reference interaction site model theory, a recently developed integral equation theory of molecular solvation. The HFE is decomposed into the energetic and entropic components under the isochoric condition. The former comprises the protein-water interaction energy and the water reorganization energy arising from the structural changes induced in water. Each component is further decomposed into the nonelectrostatic and electrostatic contributions. It is found that the HFE is governed by the nonelectrostatic hydration entropy and the electrostatic hydration energy. The nonelectrostatic hydration entropy is almost exclusively ascribed to the translational entropy loss of water upon the protein insertion. It asymptotically becomes proportional to the excluded volume (EV) for water molecules as the protein size increases. The hydration energy is determined by the protein-water interaction energy which is half compensated by the water reorganization energy. These energy terms are approximately proportional to the water-accessible surface area (ASA). The energetic and entropic contributions are balanced with each other and the HFE has no apparent linear relation with the EV and ASA.

Biophysics↗
PubMed2006

Theoretical study of volume changes accompanying xenon-lysozyme binding: implications for the molecular mechanism of pressure reversal of anesthesia.

The change in partial molar volume (PMV) accompanying the xenon-lysozyme binding was investigated for elucidating the molecular mechanism of the pressure reversal of general anesthesia, using the three-dimensional reference interaction site model theory of molecular solvation. An increase of the PMV from xenon binding to the substrate binding site of lysozyme was found, and the binding is suppressed by pressure, while the internal site binding did not change the PMV. The PMV change was analyzed by decomposing it into several contributions from geometry and hydration. We also analyzed the hydration change due to the binding. From the results, we draw a molecular picture of the PMV change accompanying xenon-lysozyme binding, which gives a possible mechanism of pressure reversal of anesthesia.

Anesthesia, General↗
PubMed2006

Ab initio theoretical study of temperature and density dependence of molecular and thermodynamic properties of water in the entire fluid region: autoionization processes.

The temperature and density dependence of the molecular and thermodynamic properties of water is investigated theoretically by means of the ab initio electronic structure theory combined with the reference interaction site model method, so-called RISM-SCF. We consider the autoionization process (H2O + H2O right harpoon over left harpoon H3O+ + OH-) by regarding H2O, H3O+, and OH- as "solute" molecules in an aqueous solution and evaluate molecular geometry, electronic structure, solvation structure, and the ionic product of water (pKw) of these species as functions of thermodynamic conditions. In our previous paper, we calculated these properties by using essentially the same method in a wide range of density values (0.6-1.4 g/cm3). However, the calculation was limited at rather higher density (>0.6 g/cm3) due to the difficulty of convergence, which is inherent to the hypernetted-chain (HNC) closure. The problem is overcome in this study by employing the Kovalenko-Hirata (KH) closure which hybridizes the HNC and the mean-spherical approximation (MSA). Here, we present the results for the thermodynamic range of densities from 0.025 to 1.0 g/cm3 and for temperatures from 300 to 800 K including the supercritical point.

Journal Article↗
PubMed2006

A new method to determine electrostatic potential around a macromolecule in solution from molecular wave functions.

The three-dimensional reference interaction site model integral equation theory (3D-RISM) combined with the ab initio molecular orbital method (3D-RISM-SCF) is applied to a solvated macromolecular system. The solvation structure around a solute molecule is obtained from the 3D-RISM integral equation under the electrostatic potential of the solute molecule, calculated by the ab initio molecular orbital theory. The electrostatic potential should be calculated on each grid point in the three-dimensional real space. Therefore, the calculation of the electrostatic potential is the most time consuming part in this method. In this article, we propose a new procedure to save the computational cost for calculating the electrostatic potential and the solvated fock matrix. The strategy of this procedure is to evaluate the electrostatic potential and the solvated fock matrix in different ways, depending on the distance between solute and solvent. Inside the repulsive cores of solute atoms, it is possible to avoid the calculation of electrostatic potential and solvated Fock matrix by assuming the potential to be infinity. In the region sufficiently far from solute, they are evaluated classically by putting the effective point charge on each atom. In the intermediate region, the electrostatic potential is evaluated directly by integrating the molecular orbitals of the solute molecule. The electronic structure and the energy gradient of Methionine-Enkephalin and solvation structure are estimated by using this procedure in aqueous solution, and are compared with the results from other procedures. The results are compared also with those from the continuum model.

Algorithms↗
PubMed2005

Water molecules in a protein cavity detected by a statistical-mechanical theory.

Four water molecules confined in a small cavity of hen egg-white lysozyme were detected by means of the three-dimensional (3D) RISM theory, a statistical-mechanical theory of molecular solutions. This is the first theoretical realization of confined molecules in a protein without making nonsense tricks, such as placing the molecules in the space a priori. Possible impacts which the result may have on biochemistry and biophysics, including the molecular recognition, enzymatic reactions, etc., are discussed.

Animals↗
PubMed2005

Theoretical study of volume changes associated with the helix-coil transition of an alanine-rich peptide in aqueous solution.

The changes in the partial molar volume (PMV) associated with the conformational transition of an alanine-rich peptide AK16 from the alpha-helix structure to various random coil structures are calculated by the three-dimensional interaction site model (3D-RISM) theory coupled with the Kirkwood-Buff theory. The volume change is analyzed by decomposing it into contributions from geometry and hydration: the changes in the van der Waals, void, thermal, and interaction volume. The total change in the PMV is positive. This is primarily due to the growth of void space within the peptide, which is canceled in part by the volume reduction resulting from the increase in the electrostatic interaction between the peptide and water molecules. The changes in the void and thermal volume of the coil structures are widely distributed and tend to compensate each other. Additionally, the relations between the hydration volume components and the surface properties are investigated. We categorize coil structures into extended coils with the PMV smaller than helix and general coils with the PMV larger than helix. The pressure therefore can both stabilize and destabilize the coil structures. The latter seems to be a more proper model of random coil structures of the peptide.

Alanine↗
PubMed2005

Criticality of a liquid-vapor interface from an inhomogeneous integral equation theory.

A microscopic theory is developed to study the liquid-vapor interfacial properties of simple fluids with ab initio treatment of the inhomogeneous two-body correlation functions, without any interpolation. It consists of the inhomogeneous Ornstein-Zernike equation coupled with the Duh-Henderson-Verlet closure and the Lovett-Mou-Buff-Wertheim equation. For the liquid-vapor interface of the Lennard-Jones fluid, we obtained the density profile and the surface tension, as well as their critical behaviour. In particular, we identified non-classical critical exponents. The theory accurately predicts the phase diagram and the interfacial properties in a very good agreement with simulations. We also showed that the method leads to true capillary-wave asymptotics in the macroscopic limit.

Computer Simulation↗
PubMed2005

Site-site memory equation approach in study of density/pressure dependence of translational diffusion coefficient and rotational relaxation time of polar molecular solutions: acetonitrile in water, methanol in water, and methanol in acetonitrile.

We present results of the theoretical study and numerical calculation of the dynamics of molecular liquids based on the combination of the memory equation formalism and the reference interaction site model (RISM). Memory equations for the site-site intermediate scattering functions are studied in the mode-coupling approximation for the first-order memory kernels, while equilibrium properties such as site-site static structure factors are deduced from RISM. The results include the temperature-density (pressure) dependence of translational diffusion coefficients D and orientational relaxation times tau for acetonitrile in water, methanol in water, and methanol in acetonitrile--all in the limit of infinite dilution. Calculations are performed over the range of temperatures and densities employing the extended simple point charge model for water and optimized site-site potentials for acetonitrile and methanol. The theory is able to reproduce qualitatively all main features of temperature and density dependences of D and tau observed in real and computer experiments. In particular, anomalous behavior, i.e, the increase in mobility with density, is observed for D and tau of methanol in water, while acetonitrile in water and methanol in acetonitrile do not show deviations from the ordinary behavior. The variety exhibited by the different solute-solvent systems in the density dependence of the mobility is interpreted in terms of the two competing origins of friction, which interplay with each other as density increases: the collisional and dielectric frictions which, respectively, increase and decrease with increasing density.

Journal Article↗
PubMed2005

Partial molar volume of proteins studied by the three-dimensional reference interaction site model theory.

The three-dimensional reference interaction site model (3D-RISM) theory is applied to the analysis of hydration effects on the partial molar volume of proteins. For the native structure of some proteins, the partial molar volume is decomposed into geometric and hydration contributions using the 3D-RISM theory combined with the geometric volume calculation. The hydration contributions are correlated with the surface properties of the protein. The thermal volume, which is the volume of voids around the protein induced by the thermal fluctuation of water molecules, is directly proportional to the accessible surface area of the protein. The interaction volume, which is the contribution of electrostatic interactions between the protein and water molecules, is apparently governed by the charged atomic groups on the protein surface. The polar atomic groups do not make any contribution to the interaction volume. The volume differences between low- and high-pressure structures of lysozyme are also analyzed by the present method.

Binding Sites↗
PubMed2005

Hydrophobic effects on partial molar volume.

The hydrophobic effects on partial molar volume (PMV) are investigated as a PMV change in the transfer of a benzenelike nonpolar solute from the nonpolar solvent to water, using an integral equation theory of liquids. The volume change is divided into two effects. One is the "packing" effect in the transfer from the nonpolar solvent to hypothetical "nonpolar water" without hydrogen bonding networks. The other is the "iceberg" effect in the transfer from nonpolar water to water. The results indicate that the packing effect is negative and a half compensated by the positive iceberg effect. The packing effect is explained by the difference in the solvent compressibility. Further investigation shows that the sign and magnitude of the volume change depend on the solute size and the solvent compressibility. The finding gives a significant implication that the exposure of a hydrophobic residue caused by protein denaturation can either increase or decrease the PMV of protein depending on the size of the residue and the fluctuation of its surroundings.

Journal Article↗