| 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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| 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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