Computation of the reduction free energy of coenzyme in water: A novel approach within the framework of the QM/MM-ER method

Hideaki Takahashi, Hajime Ohno, Ryohei Kishi, Shin Ichi Furukawa, Masayoshi Nakano

研究成果: Conference contribution

抄録

We have computed free energy for one-electron reduction of the active site of the coenzyme (flavin adenine dinucleotide (FAD)) in aqueous solution by means of the QM/MM method combined with the theory of energy representation (QM/MM-ER). In the present work, we have proposed a novel approach that the excess electron to be attached on the FAD has been regarded as a solute, while the remaining molecules including the active site of FAD have been considered as solvent in the implementation of the method of energy representation. The efficiency and the accuracy of the method have been examined by performing the conventional simulations where the oxidized and the reduced active sites of FAD are regarded as solutes and the surrounding water molecules are treated as solvent. The present approach is computationally more advantageous and is amenable to the extension to the reaction in the protein systems as compared with the conventional one. It has been found that the reduction free energy obtained by the present method is in excellent agreement with that computed by the conventional approach, which guarantees the robustness of the method.

本文言語English
ホスト出版物のタイトルSelected Papers from ICNAAM 2007 and ICCMSE 2007 - Special Presentations Int. Conf. Numerical Analysis and Applied Mathematics 2007 and Int. Conf. Computational Methods in Science and Engineering 2007
ページ56-59
ページ数4
DOI
出版ステータスPublished - 2008 10 22
外部発表はい
イベントInternational Conference on Numerical Analysis and Applied Mathematics, ICNAAM 2007 and International Conference on Computational Methods in Science and Engineering, ICCMSE 2007 - Corfu, Greece
継続期間: 2007 9 252007 9 30

出版物シリーズ

名前AIP Conference Proceedings
1046
ISSN(印刷版)0094-243X
ISSN(電子版)1551-7616

Other

OtherInternational Conference on Numerical Analysis and Applied Mathematics, ICNAAM 2007 and International Conference on Computational Methods in Science and Engineering, ICCMSE 2007
CountryGreece
CityCorfu
Period07/9/2507/9/30

ASJC Scopus subject areas

  • Physics and Astronomy(all)

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