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Specific interactions and binding free energies between thermolysin and dipeptides: Molecular simulations combined with Ab initio molecular orbital and classical vibrational analysis

2011; Wiley; Volume: 32; Issue: 14 Linguagem: Inglês

10.1002/jcc.21887

1096-987X

Kenichi Dedachi, Tatsuya Hirakawa, Seiya Fujita, Mahmud Tareq Hassan Khan, Ingebrigt Sylte, Noriyuki Kurita,

Antimicrobial Peptides and Activities

Journal of Computational ChemistryVolume 32, Issue 14 p. 3047-3057 Original Article Specific interactions and binding free energies between thermolysin and dipeptides: Molecular simulations combined with Ab initio molecular orbital and classical vibrational analysis Kenichi Dedachi, Kenichi Dedachi Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Aichi 441-8580, JapanSearch for more papers by this authorTatsuya Hirakawa, Tatsuya Hirakawa Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Aichi 441-8580, JapanSearch for more papers by this authorSeiya Fujita, Seiya Fujita Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Aichi 441-8580, JapanSearch for more papers by this authorMahmud Tareq Hassan Khan, Mahmud Tareq Hassan Khan Medical Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, 9037 Tromsø, NorwaySearch for more papers by this authorIngebrigt Sylte, Ingebrigt Sylte Medical Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, 9037 Tromsø, NorwaySearch for more papers by this authorNoriyuki Kurita, Corresponding Author Noriyuki Kurita kurita@cs.tut.ac.jp Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Aichi 441-8580, Japan Fax: +81-532-44-6875Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Aichi 441-8580, JapanSearch for more papers by this author Kenichi Dedachi, Kenichi Dedachi Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Aichi 441-8580, JapanSearch for more papers by this authorTatsuya Hirakawa, Tatsuya Hirakawa Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Aichi 441-8580, JapanSearch for more papers by this authorSeiya Fujita, Seiya Fujita Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Aichi 441-8580, JapanSearch for more papers by this authorMahmud Tareq Hassan Khan, Mahmud Tareq Hassan Khan Medical Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, 9037 Tromsø, NorwaySearch for more papers by this authorIngebrigt Sylte, Ingebrigt Sylte Medical Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, 9037 Tromsø, NorwaySearch for more papers by this authorNoriyuki Kurita, Corresponding Author Noriyuki Kurita kurita@cs.tut.ac.jp Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Aichi 441-8580, Japan Fax: +81-532-44-6875Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Aichi 441-8580, JapanSearch for more papers by this author First published: 03 August 2011 https://doi.org/10.1002/jcc.21887Citations: 11 Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Abstract Thermolysin (TLN) is a metalloprotease widely used as a nonspecific protease for sequencing peptide and synthesizing many useful chemical compounds by the chemical industry. It was experimentally shown that the activity and functions of TLN are inhibited by the binding of many types of amino acid dipeptides. However, the binding mechanisms between TLN and dipeptides have not been clarified at the atomic and electronic levels. In this study, we investigated the binding mechanisms between TLN and four dipeptides. Specific interactions and binding free energies (BFEs) between TLN and the dipeptides were calculated using molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital (FMO) methods. The molecular systems were embedded in solvating water molecules during calculations. The calculated BFEs were qualitatively consistent with the trend of the experimentally observed inhibition of TLN activity by binding of the dipeptides. In addition, the specific interactions between the dipeptides and each amino acid residue of TLN or solvating water molecules were elucidated by the FMO calculations. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011 Citing Literature Volume32, Issue1415 November 2011Pages 3047-3057 RelatedInformation