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| 1.
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KURNIAWAN, Isman ; Kawaguchi, Kazutomo ; SUGIMORI, Kimikazu ; SAKURAI, Takeshi ; Nagao, Hidemi
概要:
We present a cluster model representing type I copper (T1Cu) center of copperprotein, which corrsponds to Multicopper Oxidases, Azurin, Stelacyanin and so on. Theelectronic structure and physical properties such as molecular
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orbital, atomic partial charge,partial spin densities, ionization energy (IP) of reduced T1Cu, electron affinity (EA) of oxidizedT1Cu, the bond and the angle constants etc. are calculated by using two typicalDensity Functional Theory (DFT) functionals, which are B3LYP and M06, with 6-31G(d)basis set. We find the dependency of several properties such as atomic partial charge, partialspin densities, IP, and EA on the DFT functionals. We also find that the DFT functionals givea better contribution to bond constants, especially in case of the interaction between copperand the axial ligand. We calculate the maximum absorption wavelength of T1Cu center andfind relatively a good agreement with experimental data.
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| 2.
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ARWANSYAH, MS ; KODAMA, Koichi ; KURNIAWAN, Isman ; KATAOKA, Tatsuki ; Kawaguchi, Kazutomo ; Nagao, Hidemi
概要:
We investigate the binding/dissociation process of ligand molecule from carbonicanhydrase (CA) I carbonic anhydrase (CA) I enzyme by using all-atom moleculardynamics simulation. The force field parameters of zinc ion in the CA I
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active site are estimatedby quantum chemical calculations and are summarized in this paper. The free energyprofile for binding/dissociation process of ligand from CA I active site is calculated by thethermodynamic integration combined with the all-atom molecular dynamics simulation. Thebinding free energy as a function of the distance between the center of mass positions of CAI active site and the ligand molecule is estimated. The radial distribution function of theCA I-ligand complex is calculated from the trajectory of all-atom molecular dynamics (MD)simulation. We estimate the free energy surface from the radial distribution function. Wecan obtain the bond constant of the equilibrium state from the value of the free energy surface.We discuss the binding/dissociation process of ligand molecule by calculating the freeenergy profile to know the stability of the CA I-ligand complex with some thermodynamicproperties such as the binding free energy, the equilibrium state of the free energy surfaceand so on.
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| 3.
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Sugimori, Kimikazu ; Shuku, Tomofumi ; Sugiyama, Ayumu ; Nagao, Hidemi ; Sakurai, Takeshi ; Nishikawa, Kiyoshi
概要:
We present a cluster model for the active site of oxidized azurin, and investigate the electronic structure of the activ
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e site of oxidized azurin by using density functional calculations with polarizable continuum model. The singly occupied molecular orbital and spin density in the model widely distribute around the Cu 3dx2-y2 and S(Cys112) 3p orbitals. The dependency of electronic properties such as partial charge density and spin density on the dielectric constant is discussed. We find that partial spin density and charge density on the copper ion become larger, when the dielectric constant increases. © 2005 Elsevier Ltd. All rights reserved.<br />Embargo Period 24 months
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| 4.
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Oda, Tatsuki ; Sugimori, K. ; Nagao, Hidemi ; Hamada, I. ; Kagayama, S. ; Geshi, M. ; Nagara, H. ; Kusakabe, K. ; Suzuki, N.
概要:
金沢大学大学院自然科学研究科計算科学<br />金沢大学工学部<br />We have studied the ζ-phase of solid oxygen using the generalized gradient approxim
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ation in the density functional approach. Calculations of total energies and pressures have been carried out for the prototype of diatomic ζ-phase and other hypothetical monoatomic crystal structures. The diatomic phase was found to be stable over a wide range of pressure (100-2000GPa). The stacking of molecular layers is discussed in comparison with the available experimental data. © IOP Publishing Ltd.
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| 5.
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Takamatsu, Yuichiro ; Sugiyama, Ayumu ; Purqon, Acep ; Nagao, Hidemi ; Nishikawa, Kiyoshi
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金沢大学大学院自然科学研究科計算科学<br />金沢大学理学部<br />Recently, much attention has been directed to calculational prediction for binding
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free energy and structural analysis for biomolecule complex in solvate state. We investigated Influenza Hemagglutinin (wild type HA), mutated HA and its neutralize antibody Fab fragment complex in explicit solvent water molecules by molecular dynamics simulation(MD). B-factor and binding free energy of loop structures in the complex structure are calculated. The calculation result supports the experimental result in a qualitative tendency. MD calculation also shows that hydrogen bond distance differs between wild type HA and mutated HA, which contributes to the difference of binding free energy and structural stability. These result suggests that pattern of making hydrogen bonds in crystal structure are almost kept even in solvate state. © 2006 American Institute of Physics.
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| 6.
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Sugiyama, Ayumu ; Takamatsu, Yuichiro ; Purqon, Acep ; Mizukami, Taku ; Nagao, Hidemi ; Nishikawa, Kiyoshi
概要:
金沢大学大学院自然科学研究科計算科学<br />金沢大学理学部<br />We carry out the molecular dynamics(MD) simulation of type 1 blue copper protein az
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urin in room and some lower temperatures to investigate the behavior of hydration water molecules in the protein surface. In this study, we find the anomalous behavior of the water molecules, which depend on the system temperatures. These water molecules have hydrogen bond to the protein surface residues. We specify the residues type, being classified as the hydration donor and the hydration acceptor of water molecules. We analyze the residue type, and the bond length and bond strength between solvent water molecules in each temperature. Moreover, we estimate the B-factor of these residues which indicates the fluctuation of hydration residues in each temperature. B-factor values depend on the system temperatue althought the number of hydration residue do not depend on the temperature. © 2006 American Institute of Physics.
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| 7.
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Purqon, Acep ; Sugiyama, Ayumu ; Takamatsu, Yuichiro ; Nagao, Hidemi ; Nishikawa, Kiyoshi
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金沢大学大学院自然科学研究科計算科学<br />金沢大学理学部<br />Some proteins in blue copper proteins have similar properties. In some cases it is
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not easy to distinguish the proteins each other. The study to recognize and classify in blue copper proteins has important roles to recognize the difference of similar properties, for examples, structures and residue sequences in blue copper proteins. There are many methods being developed to predict protein structure from many approachs, which one still not satisfactory yet. Therefore it is a challenge for scientists to develop or improve their methods. One of promising method is artificial neural networks (ANN). ANN is learning machine methods consisted of input, hidden and output layer. ANN is tested to recognize secondary structure in blue copper protein. It is found that ANN can distinguish for 7-type of secondary structure and recognize 72% secondary structure in blue copper protein. © 2006 American Institute of Physics.
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| 8.
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Oda, Tatsuki ; Sugimori, K. ; Nagao, Hidemi ; Hamada, I. ; Kagayama, S. ; Geshi, M. ; Nagara, H. ; Kusakabe, K. ; Suzuki, N.
概要:
金沢大学理工研究域 数物科学系<br />We have studied the ζ-phase of solid oxygen using the generalized gradient approximation in the den
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sity functional approach. Calculations of total energies and pressures have been carried out for the prototype of diatomic ζ-phase and other hypothetical monoatomic crystal structures. The diatomic phase was found to be stable over a wide range of pressure (100-2000GPa). The stacking of molecular layers is discussed in comparison with the available experimental data. © IOP Publishing Ltd.
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| 9.
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Sri, R. Natasia ; Saito, Hiroaki ; Mizukami, Taku ; Kawaguchi, Kazutomo ; Nagao, Hidemi
概要:
Solvation free energy has valuable role as represents the desolvation cost of a molecu-lar binding interaction, which is
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very important in a variety of chemical and biological processes. Therefore, many computational methods have been explored to predict this value. In this study, we attempted to find the correlation between experimental and calculated value of solvation free energy of proteins, containing organic molecules, by using quantitative structure property relation-ship (QSPR) model. To obtained a comparable value of solvation free energy which will be used as reference in QSPR model, we adopted energy representation (ER) method. And as this method works through molecular dynamic (MD) simulation, we then performed the MD simulation prior to the calculation by ER method. The results showed that the predicted solvation free energies were quite close to calculated values by ER method. We also found that the values of solvation free energy, both in MD simulation and ER method, were well correlated to solvent accessible surface area of hydrophobic portion.<br />Selected Papers from the International Symposium on Computational Science - International Symposium on Computational Science Kanazawa University, Japan
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| 10.
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Iwayama, Masashi ; Kawafuchi, Kazutomo ; Saito, Hiroaki ; Nagao, Hidemi
概要:
We have been applied the conventional approach based on the molecular dynamics simulation to estimate the redox potential so far. In this study, we have focused the computational conditions in order to estimate standard redox
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potential by using the energy representation method: we calculate excess chemical potential increasing the number of solvent molecules and sampling data for the preparation of energy distribution functions. From these results, we have found that the computational value of the standard redox potential is close to the experimental value in the case of the system with larger number of solvent molecules unaffected by the behavior of counter-ion when we take a sufficient sampling data for the energy distribution functions.<br />Selected Papers from the International Symposium on Computational Science - International Symposium on Computational Science Kanazawa University, Japan
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