2006 Fiscal Year Final Research Report Summary
Flexible dynamics of proteins and their functions
| Project/Area Number |
16207008
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| Research Category |
Grant-in-Aid for Scientific Research (A)
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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 | Nagoya University |
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Principal Investigator |
SASAI Masaki Nagoya University, Graduate School of Engineering, Professor, 大学院工学研究科, 教授 (30178628)
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| Co-Investigator(Kenkyū-buntansha) |
TAKANO Mitsunori Waseda University, Graduate School of Science and Engineering, Associate Professor, 理工学術院, 助教授 (40313168)
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| Project Period (FY) |
2004 – 2006
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| Keywords | Coarse-grained simulation / Functional funnel / Principal component analyses / Energy landscape / Molecular motor |
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| Research Abstract |
Trough the 3-year project, we have developed new methods of computation of protein dynamics and investigated processes of protein functioning.
(1) A coarse-grained method to simulate protein dynamics was newly developed and applied to the force-generation process of actomyosin system. Cooperative effects of the lever-arm swinging motion and the sliding motion of myosin head were found.
(2) Folding process of proteins were investigated by using GO-like models. Complexity in the folding process of nearly symmetrical proteins was revealed by showing the co-existence of multiple pathways and the mechanism of selection of specific routes among them.
(3) A novel concept of functional funnel was introduced by analyzing the functioning process of a photo-sensing protein.
(4) 3-D structures of proteins were predicted from sequences by developing a new method to simulate the folding process. We attended the international contest for structure prediction, CASP7, and acquired fairly good scores in a category of new-fold prediction.
(5) Sequence selection was simulated by computer. We found that by selecting sequences which have desired local configuration at the active-site, random sequences can evolve into the foldable protein-like sequences.
(6) Hydrophobic hydration around the nano-meter size solutes were investigated by molecular dynamics simulation and the topology-sensitive hydration and hydrophobic interaction were found.
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