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| 1.
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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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| 2.
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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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| 3.
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Kurniawan, Isman ; Saito, Hiroaki ; Kawaguchi, Kazutomo ; Nagao, Hidemi
概要:
This study focus on investigating the oxidation potential fluctuation of organic molecule in the solution. The organic mo
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lecule that was investigated is 3-pentanone molecule that has oxi-dation potential 0.143 V experimentally. The oxidation potential was calculated using Born-Haber cycle approximation involving the calculation of gas phase Gibbs free energy and solvation energy of reduced and the oxidized state. The reduced state represents a neutral charge molecule and the oxidized state represents a radical cation molecule. The first, molecular dynamics (MD) simulation of both state was performed for 2 ns time. Then, 400 snapshot structures of both state molecule was captured. Gas phase Gibbs free energy and solvation energy were calculated using MP2 theory with cc-pvdz basis set and the solvation effect was approached using Polarizable Continuum Model (PCM). Normal Hydrogen Electrode (NHE), that has redox potential 4.44 V experimentally, was used as reference electrode. The result shows the different of gas phase Gibbs free energy average of both state was 756.97 ± 21.598 kJ/mol, and solvation energy average of reduced and oxidized state were -18.42 kJ/mol ± 1.482 kJ/mol, and -219.02 ± 1.094 kJ/mol respectively. Then, the oxidation potential was calculated by substituting gas phase Gibbs free energy and solvation energy into Born-Haber cycle approximation. The calculation result shows the average of oxidation po-tential value is 1.396 ± 0.225 V. The deviation of oxidation potential confirms the fluctuation of oxidation potential during the simulation.
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| 4.
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Iwayama, Masashi ; Kawaguchi, Kazutomo ; Saito, Hiroaki ; Nagao, Hidemi
概要:
Structure and hydration property of acetone and 3-pentaone in the neutral and cationic state were investigated by using molecular dynamics (MD) and free energy calculations. The force field parameters of stretching vibration, angle
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bending, and partial charges of each molecule in the neutral and cationic state were developed by using density functional theory (DFT) calculations with B3LYP method and 6-31+G** basis set. The optimized structures by using these force field parameters in gas phase were compared with the experimental data and AMBER force fields parameters (parm99). From the results, the optimized structure in the neutral state of acetone was in good agreement with the experimental data. The evaluated hydration free energy in the neutral state of acetone was closed to the experimental data, while that of 3-pentaone was little bit larger than the experimental data. The ionization effect of ketone molecule on the hydration free energies was found to be significant in both molecules.
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| 5.
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Meidy, Triana Pakpahan ; Saito, Hiroaki ; Kawaguchi, Kazutomo ; Nagao, Hidemi
概要:
Accurate methods of computing the affinity of ligand with protein target are strongly needed in the drug discovery proce
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ss. Many attempts have been made and several algorithms have been developed for this purpose. We compared the protein-ligand binding free energies (∆G) in various methods include docking score function, combining docking score function and molecular dynamics (MD) simulation with explicit and implicit solvent model, and molecular-mechanics Poisson Boltzmann surface area (MM-PBSA) approach with and without the inclusion of entropic contributions. We tested these various methods to human plasminogen kringle-3 domain protein with the ligand trans-(aminomethyl) cyclohexanecarboxylic acid (AMCHA). The results showed the comparison between these various methods and the experimental affinity value. We found that combining docking score function and MD simulation with explicit solvent model was more favorable and close to the experimental result. This indicated that combining docking score function and MD simulation with explicit solvent model could be more accurate and effective in the protein-ligand binding free energy calculation.
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| 6.
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Micke, Rusmerryani ; Takasu, Masako ; Kawaguchi, Kazutomo ; Saito, Hiroaki ; Nagao, Hidemi
概要:
Most of protein function analyses focus mainly on the physical properties of a sin-gle protein. Nevertheless, the enviro
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nments where proteins perform their biological functions are crowded with macromolecules, such as lipid, nucleic acids, and other proteins. The interactions between macromolecules may be affected by molecular crowding. Therefore, as an initial step we here investigate the protein–protein interactions for gaining insights into molecular crowding effects on protein conformational changes. Computational molecular simulation is one of the useful and important tools to study the protein interactions. Here we develop a coarse-grained model and a topology-based potential interactions to simulate dynamical properties of multiprotein complex crys-tal structure. We apply them to simulate complex crystal structure of Pseudomonas Aeruginosa azurin, a small cupredoxin, which functions as an electron carrier in bacterial respiration. Since electron transfer on azurin plays an important role in the biological system, it is important to cha-racterize the protein interactions in azurin. In our simulation, the interactions between intra- and inter- domains are treated at the residue level with the implementation of the off lattice G¯o-like model. In each domain, bonded interactions between residues are described by bond stretching, bond angle bending, and torsional angle potentials. The non-bonded interactions, which are repre-sented by short range and long range potentials, describe the interactions both among residues and between proteins. We probe the protein–protein interactions by analyzing the protein binding. A simple clustering algorithm is applied to group the bound structures of protein complex. Moreover, we can investigate the importance of the long range interaction on the multiprotein complex system. These studies will serve as valuable insights for further investigation on molecular crowding effects.
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| 7.
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Septiana Wulandari, Gia ; Rusmerryani, Micke ; Kawamoto, Shuhei ; Saito, Hiroaki ; Nishikawa, Kiyoshi ; Nagao, Hidemi
概要:
We studied the temperature effect on the dynamics of spherical micelle dimer in wa-ter solvent by using molecular dynamic
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s (MD) simulation. For this purpose, we carried out the MD simulations of 8-8 spherical POPC micelle dimer in 11,326 TIP3P water molecules under the constant NPT condition for 10 ns and continued the MD simulation under the constant NVT condition for 10 ns. We ran the MD simulations of this system at two different temperatures, 340 K and 370 K. The dynamical behavior of the micelle was analyzed by calculating ASIC parameters. We found that the effects of temperature on stuctures and dynamics of micelle were different for the constant NPT and NVT condition.
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