研究者詳細 - 入佐　正幸

口頭発表・ポスター発表等 - 入佐　正幸

分割表示77 件中 1 - 20 件目／全件表示 >>

QM/MM metadynamics で調べた EcoRV の DNA 加水分解の反応機構

三松美香,大西到,松田涼太郎,吉田紀生,平田文男,入佐正幸

第45回溶液化学シンポジウム溶液化学研究会

Reaction Pathways in DNA Hydrolysis of EcoRV Calculated by Quantum- Chemical Metadynamics

Mika Mitsumatsu, Itaru Onishi, Norio Yoshida, Fumio Hirata, Masayuki Irisa

International Conference on Biological Physics (ICBP2023) 2023年08月 International Union of Pure and Applied Biophysics (IUPAB)

開催期間： 2023年08月14日 - 2023年08月18日記述言語：英語開催地：Seoul, Korea 国名：大韓民国

Restriction enzyme recognizes a specific DNA sequence and selectively cuts double-stranded DNA. This hydrolysis reaction requires divalent cations. One of the type II restriction enzymes, EcoRV, is a homo dimer, subunit A and B, and requires Mg 2+ for its function. QM/MM metadynamics simulation of EcoRV–DNA complex structure was performed with a precursor structure, referred to as structure M, as the initial structure. Structure M is an equilibrium structure suitable for hydrolysis obtained from MD trajectories in our previous studies. The Potential of Mean Force (PMF) surface obtained from the QM/MM metadynamics simulations with structure M shows two pathways, a dissociative reaction pathway and an associative reaction pathway, for DNA hydrolysis by EcoRV. In this study, we made video movies to investigate proton-transfer in DNA hydrolysis of subunit B along the two pathways. In both of two pathways, we have found Asp90 and Lys92 side chains are ionized in structure M and then electrically neutralized by a proton-transfer from Lys92 to Asp90 before the nucleophile water attacks the scissile phosphate. In
a dissociative reaction pathway, a trigonal bipyramidal structure consisting of the scissile phosphate five atoms, a phosphor atom and three oxygen atoms in Ade7 and oxygen atom O3' in Thr6, and an oxygen atom in the nucleophile water, is meta-stable in the PMF surface. Two Mg 2+ ions form a chemical complex and bridges between catalytic residues, Ile91 and Asp74, and atoms in the trigonal bipyramidal structure.

Further Development of STCSB, Scala Tool for the Computational Science of Biomolecules, to Add Quantum-Chemistry Calculation and Visualization of Electron Density Distribution: An Application Example of DNA Hydrolysis by EcoRV

Ryoutarou Matsuda, Mika Mitsumatsu, Itaru Onishi, Masayuki Irisa

International Conference on Biological Physics (ICBP2023) 2023年08月 International Union of Pure and Applied Biophysics (IUPAB)

開催期間： 2023年08月14日 - 2023年08月18日記述言語：英語開催地：Seoul, Korea 国名：大韓民国

We have further developed STCSB, Scala Tool for the Computational Science of Biomolecules, to add a quantumchemistry calculation module, DFTB3/3OB calculation, by calling external libraries, DFTB+ and AMBER-sqm/sander. STCSB was made by our group and has been used for 3D-RISM calculations, molecular dynamics (MD) simulations, and QM/MM metadynamics simulations. In this study, one of the snapshot structure obtained from QM/MM metadynamics simulations of EcoRV–DNA complex, one of the type II restriction enzymes, is visualized as a 3D image of electron-density distribution in an active site of EcoRV–DNA complex. At the snapshot structure, proton-transfers occurred in hydrolysis of DNA by EcoRV. We have succeeded in showing the electron density distribution corresponding to a proton-relay consisting of two proton-transfers, one from the nucleophile water to Asp90 and the other from Asp90 to the scissile phosphate, Ade7 O1.

Scala言語を用いた生体高分子計算科学ツールSTCSBへの量子化学計算機能の追加

松田涼太郎,三松美香,大⻄到,入佐正幸

第44回溶液化学シンポジウム溶液化学研究会

EcoRV による DNA 加水分解におけるプロトン移動の量子化学計算による観察

三松美香,大⻄到,吉田紀生,平田文男,入佐正幸

第44回溶液化学シンポジウム溶液化学研究会

VRwave 改造立体視 VRML ブラウザにおける VR 空間内の滑らかな視点移動表現機能

渡邉智也,大西到,入佐正幸

第35回分子シミュレーション討論会

関数型言語 Scala のパーサコンビネータを用いた立体視 VRML ブラウザでのファイル読み込み機能の改良

川原康平,入佐正幸

第35回分子シミュレーション討論会

EcoRV による DNA 加水分解におけるプロトン移動の量子化学計算による観察

三松美香,大⻄到,吉田紀生,平田文男,入佐正幸

第43回溶液化学シンポジウム溶液化学研究会

DNA 切断直後における EcoRV–DNA 複合体中のカチオン近傍溶媒構造の計算

長野怜也,大⻄到,吉田紀生,平田文男,入佐正幸

第43回溶液化学シンポジウム溶液化学研究会

3D-RISM を⽤いた BamHI–DNA 複合体の活性部位におけるカチオンと⽔の分布の計算

⽮野佑紀，⼤⻄到，吉⽥紀⽣，平⽥⽂男，⼊佐正幸

第42回溶液化学シンポジウム溶液化学研究会

A QM/MM Metadynamics study of the DNA Hydrolysis by EcoRV Subsequent to Scissile-Phosphate Twist

⼤⻄到，吉⽥紀⽣，平⽥⽂男，⼊佐正幸

第42回溶液化学シンポジウム溶液化学研究会

拡張 scaled particle 理論によって計算した動径分布関数

生命情報工学科

日本生物物理学会第４６回年会

小さな球状蛋白質の熱容量と立体構造

生命情報工学科

日本生物物理学会第４６回年会

XSPTで計算した２種類の球状蛋白質の水和熱容量の比較

本人

溶液化学シンポジウム第31回年会

Van der Waals picture based on scaled particle theory

本人

2nd Mini-Symposium on Liquids ─Ver der Waals picture─

Heat Capacity of Protein and Hydration Entropy

情報工学科

International conference of biophysics 2008

Distribution of water molecules in hydration shell around a smallglobular protein calculated by using molecular dynamics

情報工学科

International conference of biophysics 2008

Heat Capacity of Protein and Hydration Entropy

本人

日本生物物理学会第４５回年会

Distribution of water molecules in hydration shell around a small globular protein calculated by usingmolecular dynamics

本人

日本生物物理学会第４５回年会

Distribution of water molecules in hydration shell around a smallglobular protein calculated by using molecular dynamics

情報工学科

Joint Conference of JMLG/EMLG Meeting 2007　and 30th Symposium on Solution Chemistry of Japan:Molecular Approaches to Complex Liquids System

　前のページ- 次のページ　

<入佐 正幸>

口頭発表・ポスター発表等 - 入佐 正幸

<入佐　正幸>

口頭発表・ポスター発表等 - 入佐　正幸