星野 忠次

A typical docking simulation provides information on the structure of ligand-receptor complexes and their binding affinity in terms of a docking energy. We have developed a potent method combining a docking simulation with cluster analysis to extract adequate docking structures from the many possible output structures of the simulation. First, we tried to predict the structure of basic fibroblast growth factor (bFGF) bound to heparin, using the docking simulation program AutoDock 3.0. Two X-ray crystal structures had already been obtained for bFGF. One was a complex of the protein and heparin, a kind of glycosaminoglycan, and the other, only the protein itself, hereafter called a simplex. We docked a heparin molecule onto the protein simplex and generated many trial structures for the bFGF-heparin complex. The structures of those docked complexes were optimized through energy minimization by AMBER8. Although neither the docking energy calculated by AMBER8 nor that calculated by AutoDock 3.0 could be used satisfactorily by themselves to select a proper heparin-binding complex from the output structures, the majority of the structures generated by AutoDock 3.0 were fairly close to each other in atom geometry, and the averaged geometry over these structures was also close to that of the crystal. Hence, we utilized only the atom geometry for evaluation and carried out cluster analysis with the collection of geometries. This procedure enabled selection of a structure considerably close to the crystal's. We applied this approach to two other heparin-binding proteins:  antithrombin and annexin V. Two crystal structures, a complex and a simplex, had been elucidated for these proteins as well as for bFGF. Our trials gave an exact prediction of the heparin-binding structures of these proteins, showing the approach in this study is effective in studying the docking of ligands that have a variety of docking conformations due to the presence of multiple rotatable bonds and charged chemical groups.

By investigating the interactions between luciferase and Si substrates using molecular dynamics (MD) simulation, we got the following results. Luciferase adsorbs directly on the hydrophobic Si substrate, and via water molecules on the hydrophilic one. Luciferase adsorbs more strongly on the hydrophobic Si substrate than on the hydrophilic one. Flexibility of luciferase is reduced when luciferase adsorbs on the Si substrate.

The intermediate structures appearing until compound I formation in the monooxygenation reaction cycle by cytochrome P450 were determined by using the density functional theory. Protons were attached to an O-2 molecule binding to the heme iron in a reduced oxy-ferrous state. When two protons were attached to the distal O atom, O-O bond cleavage occurred, and the compound I structure was formed. The structure had an energetic advantage compared to the situation in which one proton each was connected to the proximal and distal O atoms, and the structure would catalyze oxidation of a substrate. The calculated interaction energies between substrate and oxygen ligand of heme were 3-10 kcal/mol and suggests that an interaction between the substrate and the oxygen ligand of heme was maintained through the reaction process from the O-2 incorporation to the generation of the compound I and that it contributed the stability of the reaction system.

The intermediate structures appearing until compound I formation in the monooxygenation reaction cycle by cytochrome P450 were determined by using the density functional theory. Protons were attached to an O-2 molecule binding to the heme iron in a reduced oxy-ferrous state. When two protons were attached to the distal O atom, O-O bond cleavage occurred, and the compound I structure was formed. The structure had an energetic advantage compared to the situation in which one proton each was connected to the proximal and distal O atoms, and the structure would catalyze oxidation of a substrate. The calculated interaction energies between substrate and oxygen ligand of heme were 3-10 kcal/mol and suggests that an interaction between the substrate and the oxygen ligand of heme was maintained through the reaction process from the O-2 incorporation to the generation of the compound I and that it contributed the stability of the reaction system.

Binding of 1-methylimidazole to five-coordinate iodo-Fe(III) complexes of porphyrin and three porphyrin isomers was spectrophotometrically examined in benzene at 20degreesC. The result demonstrates that the geometry of the metallocavity is important to control both iron movement through the aromatic plane and magnitude of the Fe-I interactions.

Binding of 1-methylimidazole to five-coordinate iodo-Fe(III) complexes of porphyrin and three porphyrin isomers was spectrophotometrically examined in benzene at 20degreesC. The result demonstrates that the geometry of the metallocavity is important to control both iron movement through the aromatic plane and magnitude of the Fe-I interactions.

Binding of 1-methylimidazole to five-coordinate iodo-Fe(III) complexes of porphyrin and three porphyrin isomers was spectrophotometrically examined in benzene at 20degreesC. The result demonstrates that the geometry of the metallocavity is important to control both iron movement through the aromatic plane and magnitude of the Fe-I interactions.

Human 8-oxoguanine DNA glycosylase 1(hOGG1) plays a significant role of repairing oxidized genomic DNAs. The repair process includes the cleavage reaction of N-glycosidic linkage between 8-oxoguanine (8-oxoG) and the deoxyribose. To clarify the atomic-scale reaction mechanism of the N-glycosidic linkage cleavage, quantum chemical (QM) calculation at B3LYP/6-31G(d,p) was performed with a reaction model that consists of the catalytic Lys249 and guanosine that includes the 8-oxoG. It has been found from the QM calculation that the cleavage mechanism proceeds via three elementary reactions. In the first elementary reaction, a proton in the ammonium group of Lys249 is removed by the oxygen atom of 8-oxoG (8O) in concert with the generation of a new hydrogen bond between 8O and O4' of deoxyribose. In the second elementary reaction, N atom in Lys249 side chain (Nζ) nucleophilically attacks on C1' of the deoxyribose in concert with the spontaneous proton migration from 8O to O4'. The proton migration induces the dissociation of ether bond between O4' and C1'. Finally, a proton migrates from Nζ to N9 in 8-oxoG via 8O. N-glycosidic linkage between C1' and N9 is completely cloven in the final elementary reaction. It was confirmed that Schiff base appeared in products of the final reaction. According to the obtained base excision mechanism, 8O participates in the first and second elementary reactions. Therefore, this enzymatic reaction is a substrate-assisted catalysis. It was also found that the reaction path requires large activation energy (&lt 42kcal/mol). This result finely reflects the experimental finding that the enzymatic activity of hOGG1 is not so high. Copyright 2004 Chem-Bio Informatics Society.

We report the molecular dynamics (MD) simulations of an asymmetric and mixed phospholipid bilayer with NaCl and cholesterols, and that with NaCl and no cholesterol. The extracellular sides of the membranes were constructed with phosphatidylcholine (POPC) molecules and the intracellular sides were phosphatidylethanolamine (POPE) and phosphatidylserine (POPS). The results showed that the cholesterol functioned to stabilize the phospholipid-mixed asymmetric membranes by making the lipid molecules more ordered and extended. In addition, it was revealed that the asymmetric feature affected the distribution of water molecules and the thickness of the membranes. The mixed phospholipid species dominated the ion distribution, such that Na+ ions were found more frequently on the intracellular side along the distribution of the POPS molecules. These results suggested that the asymmetric and mixed characters had a significant influence on the environment around the membrane, which would also affect the membrane proteins. Copyright 2004 Chem-Bio Informatics Society.

Human 8-oxoguanine DNA glycosylase 1(hOGG1) plays a significant role of repairing oxidized genomic DNAs. The repair process includes the cleavage reaction of N-glycosidic linkage between 8-oxoguanine (8-oxoG) and the deoxyribose. To clarify the atomic-scale reaction mechanism of the N-glycosidic linkage cleavage, quantum chemical (QM) calculation at B3LYP/6-31G(d,p) was performed with a reaction model that consists of the catalytic Lys249 and guanosine that includes the 8-oxoG. It has been found from the QM calculation that the cleavage mechanism proceeds via three elementary reactions. In the first elementary reaction, a proton in the ammonium group of Lys249 is removed by the oxygen atom of 8-oxoG (8O) in concert with the generation of a new hydrogen bond between 8O and O4' of deoxyribose. In the second elementary reaction, N atom in Lys249 side chain (Nζ) nucleophilically attacks on C1' of the deoxyribose in concert with the spontaneous proton migration from 8O to O4'. The proton migration induces the dissociation of ether bond between O4' and C1'. Finally, a proton migrates from Nζ to N9 in 8-oxoG via 8O. N-glycosidic linkage between C1' and N9 is completely cloven in the final elementary reaction. It was confirmed that Schiff base appeared in products of the final reaction. According to the obtained base excision mechanism, 8O participates in the first and second elementary reactions. Therefore, this enzymatic reaction is a substrate-assisted catalysis. It was also found that the reaction path requires large activation energy (&lt 42kcal/mol). This result finely reflects the experimental finding that the enzymatic activity of hOGG1 is not so high. Copyright 2004 Chem-Bio Informatics Society.

First-principles quantum chemical calculations have been performed to reveal the adhesion mechanisms of metal impurities (Al or Fe! onto the Si wafer surface in alkali solution. As typical hydroxyl complexes of these metals, Al(OH)(4)(-), Fe(OH)(3) . 3H(2)O, or [Fe(OH)(4) . 2H(2)O](-) are used in computation. The lowest energy paths of the adhesion reaction have been obtained for the respective complex when the Si surface is terminated with OH groups and develops into a hydrophilic condition. The potential energy changes along these reaction paths were evaluated and the probabilities of the metal adhesion were compared. The detaching mechanism was also investigated for Al or Fe hydroxyl complex compounds in which a water molecule attacks the Si-O or O-metal bond at the interface between the complex and the surface. The results are discussed in comparison with recent experimental findings. (C) 2004 The Electrochemical Society.

We report the molecular dynamics (MD) simulations of an asymmetric and mixed phospholipid bilayer with NaCl and cholesterols, and that with NaCl and no cholesterol. The extracellular sides of the membranes were constructed with phosphatidylcholine (POPC) molecules and the intracellular sides were phosphatidylethanolamine (POPE) and phosphatidylserine (POPS). The results showed that the cholesterol functioned to stabilize the phospholipid-mixed asymmetric membranes by making the lipid molecules more ordered and extended. In addition, it was revealed that the asymmetric feature affected the distribution of water molecules and the thickness of the membranes. The mixed phospholipid species dominated the ion distribution, such that Na+ ions were found more frequently on the intracellular side along the distribution of the POPS molecules. These results suggested that the asymmetric and mixed characters had a significant influence on the environment around the membrane, which would also affect the membrane proteins. Copyright 2004 Chem-Bio Informatics Society.

Human 8-oxoguanine DNA glycosylase 1(hOGG1) plays a significant role of repairing oxidized genomic DNAs. The repair process includes the cleavage reaction of N-glycosidic linkage between 8-oxoguanine (8-oxoG) and the deoxyribose. To clarify the atomic-scale reaction mechanism of the N-glycosidic linkage cleavage, quantum chemical (QM) calculation at B3LYP/6-31G(d,p) was performed with a reaction model that consists of the catalytic Lys249 and guanosine that includes the 8-oxoG. It has been found from the QM calculation that the cleavage mechanism proceeds via three elementary reactions. In the first elementary reaction, a proton in the ammonium group of Lys249 is removed by the oxygen atom of 8-oxoG (8O) in concert with the generation of a new hydrogen bond between 8O and O4' of deoxyribose. In the second elementary reaction, N atom in Lys249 side chain (Nζ) nucleophilically attacks on C1' of the deoxyribose in concert with the spontaneous proton migration from 8O to O4'. The proton migration induces the dissociation of ether bond between O4' and C1'. Finally, a proton migrates from Nζ to N9 in 8-oxoG via 8O. N-glycosidic linkage between C1' and N9 is completely cloven in the final elementary reaction. It was confirmed that Schiff base appeared in products of the final reaction. According to the obtained base excision mechanism, 8O participates in the first and second elementary reactions. Therefore, this enzymatic reaction is a substrate-assisted catalysis. It was also found that the reaction path requires large activation energy (&lt 42kcal/mol). This result finely reflects the experimental finding that the enzymatic activity of hOGG1 is not so high. Copyright 2004 Chem-Bio Informatics Society.

近年、多くの感染症において、薬が効かなくなるという薬剤耐性という問題がある。この薬剤耐性とは遺伝子の変異による薬物-標的蛋白質間の結合力の低下が大きな要因である。従来の薬剤耐性検査に加えて、この結合力を構造の観点から測定するという新しい検査法を開発している。今回薬物-蛋白質間の結合力をエネルギー値として評価するために、その相互作用を5つの項目から構成されていると考え、これらの合計を結合力とした。また、実験で得られている結合力と比較し、この検査法の信頼性の検証を試みた。

Quantum chemical calculations were carried out to investigate the hydrolysis reaction of GTP --> GDP by Gialpha1. Gialpha1 is one kind of G protein and contains a GTPase-activating protein (GAP) inside it. The reason for the increase in GTPase activity in the presence of GAP was examined in detail. Geometry optimization was performed at the Hartree-Fock level using the 3-21G** basis functional set. The energy levels required for all optimized structures of stable and transition states were re-estimated by the density functional theory (B3LYP) method using the 6-31G** basis set. It was revealed that the GTP --> GDP hydrolysis reaction proceeds through a proton relay process assisted by a Lys residue. This reaction is a one-step reaction and gives an activation-energy barrier of 35 kcal/mol. A Gln residue, a part of GAP, plays a role in maintaining the position of an H2O molecule near the gamma-phosphate of GTP, and the H2O molecule is therefore kept in an appropriate position for initiating the hydrolysis.