2013 Fiscal Year Final Research Report
Quantitative computational and informatics studies on protein-protein interaction systems based on their dynamic structures
| Project/Area Number |
23370071
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Biophysics
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| Research Institution | Osaka University |
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Principal Investigator |
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| Co-Investigator(Kenkyū-buntansha) |
KINJO Akira R 大阪大学, たんぱく質研究所, 准教授 (30370117)
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| Co-Investigator(Renkei-kenkyūsha) |
HIGO Junichi 大阪大学, たんぱく質研究所, 特任研究員 (80265719)
KAMIYA Narutoshi 大阪大学, たんぱく質研究所, 特任研究員 (80420462)
YONEZAWA Yasushige 近畿大学, 先端技術総合研究所, 教授 (40248753)
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| Project Period (FY) |
2011-04-01 – 2014-03-31
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| Keywords | 構造・機能予測 / 分子シミュレーション / 蛋白質 / プロテオーム / 蛋白質間相互作用 |
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| Research Abstract |
We have newly developed the V-McMD method, performing much more effective enhanced sampling than before. This method has been combined with our new non-Ewald method for rapid molecular dynamics simulations for the periodic system, so that the quantitative analysis for the stability of the protein dimer formation was made based on the free energy landscape for the molecular system, where the backbone and the side-chain conformations change upon binding. In addition, the local structures and molecular surfaces of the protein interfaces were investigated exhaustively, and many common patches are found to be shared in proteins across the different folds. The common structural motifs were identified, and the composite motifs, which are defined as the combination of those structural motifs, correspond well with the molecular functions of proteins.
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Research Products
(28 results)
