2004 Fiscal Year Final Research Report Summary
Structural and Informatics Basis of Channel Protein Interactions
| Project/Area Number |
12144206
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| Research Category |
Grant-in-Aid for Scientific Research on Priority Areas
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| Allocation Type | Single-year Grants |
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| Review Section |
Biological Sciences
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| Research Institution | Osaka University |
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Principal Investigator |
NAKAMURA Haruki Osaka University, Institute for Protein Research, Professor, 蛋白質研究所, 教授 (80134485)
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| Co-Investigator(Kenkyū-buntansha) |
NAKAJIMA Nobuyuki Kobe University, Clinical Genome Informatics Center, Graduate School of Medicine, Specially Appointed Instructor, 大学院医学系研究科クリニカル・ゲノム・インフォマティクスセンター, 特命講師 (60324852)
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| Project Period (FY) |
2000 – 2004
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| Keywords | Molecular Dynamics / Homology Modeling / Molecular Recognition / Simulation / Supramolecular Structure / Molecular Surface / Brownian Dynamics / Database |
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| Research Abstract |
Methods were developed for building tertiary structural models of channel proteins, by combining the inductive homology modeling method and the deductive molecular simulation for low-homologous regions. In particular, we developed a new model building method for flexible loop regions, based on the Force-Biased Multicanonical Molecular Dynamics (FB-McMD) with the implicit solvent model using the generalized Born approximation. This method could give us a precise protein model structure even for the flexible loop regions, and it was applied to modeling of actual channel proteins. In addition, protein functions with their sites and protein-protein interaction pairs were identified and predicted with the informatics technology using our new databases, eF-site and HINTdb, respectively.
In order to analyze the molecular recognition of channel proteins, we have developed a new NMR analysis method, where the complexed structure is produced by molecular dynamics simulations using the cross saturation transfer and the residual dipolar coupling signals. This method was applied to build a complexed model between KcsA K^+-channel and agitoxin-2. Brownian dynamics simulation method was also developed for computing permeation of small ions and compounds through a channel protein.
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Research Products
(92 results)
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[Book] タンパク質科学2005
Author(s)
後藤祐児 他
Total Pages
579
Publisher
化学同人
Description
「研究成果報告書概要(和文)」より
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