Theoretical study of molecular mechanism of protein functions
| Project/Area Number |
22370058
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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 | Kyoto University |
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Principal Investigator |
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| Project Period (FY) |
2010 – 2012
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| Project Status |
Completed (Fiscal Year 2012)
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| Budget Amount *help |
¥18,590,000 (Direct Cost: ¥14,300,000、Indirect Cost: ¥4,290,000)
Fiscal Year 2012: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
Fiscal Year 2011: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
Fiscal Year 2010: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
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| Keywords | タンパク質機能 / 酵素反応 / QM/MM 法 / 分子動力学法 / 分子シミュレーション / リン酸加水分解 / 動力学法 / QM/MM-FF法 / 構造変化経路探索 / 線形応答理論 / カルモジュリン / 分散-共分散行列 / QM/MM-FE法 |
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| Research Abstract |
We have developed novel methodologies of molecular simulations to elucidate molecular mechanisms of protein functions. By the methodologies developed, we theoretically analyzed enzymatic reactions and global conformational changes of proteins. We developed a QM/MM free energy method (QM/MM RWFE-SCF) that enables one to very efficiently take into account protein structural fluctuation in analysis of enzymatic reaction paths. We revealed by the method that large conformational changes of an adjacent protein loop play a crucial role in enzymatic catalysis of □amylase. The method was also applied to structural modeling of color variants of microbial rhodopsins. For simulations of large scale conformational changes of proteins, we developed the linear response path following method based on a linear response theory. We applied the method to simulations of large scale conformational changes of calmodulin upon ion bindings, and successfully predicted the conformational changes with very short MD calculations.
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Report
(4 results)
Research Products
(45 results)
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[Journal Article] Crystal structure of the channelrhodopsin light-gated cation channel2012
Author(s)
Hideaki E. Kato, Feng Zhang, Ofer Yizhar, Charu Ramakrishnan, Tomohiro Nishizawa, Kunio Hirata, Jumpei Ito, Yusuke Aita, Tomoya Tsukazaki, Shigehiko Hayashi, Peter Hegemann, Andres D. Maturana, Ryuichiro Ishitani, Karl Deisseroth, and Osamu Nureki
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Journal Title
Nature
Volume: 482
Pages: 369-374
Related Report
Peer Reviewed
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