理化学研究所 計算科学研究センター

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第184回 第2部

第184回 第2部
日時: 2019年11月25日(月)、16:10 - 16:40
場所: R-CCS 6階講堂

・講演題目:Atomistic modeling of the alternating access mechanism of the mitochondrial ADP/ATP carrier with molecular simulations
・講演者:田村 康一(粒子系生物物理研究チーム)
※発表・スライド共に英語

講演要旨:

ADP/ATP Carrier (AAC) is a membrane transport protein embedded in the inner mitochondrial membrane and mediates a 1:1 exchange of ADP and ATP. The transporter is known to alternate between the so-called c-state and the m-state in the course of the transport cycle. The crystallographic structure of the c-state has been known since 2003, while that of the m-state is not known until 2019. In 2015, we developed a molecular dynamics (MD) technique to simulate global conformational changes of protein. The method, linear response path following (LRPF), enables us to sample large conformational changes of protein without the prior knowledge of the target conformation. The method is suitable for the study of AAC, as no structural knowledge of the m-state is available when the project is started. Using LRPF simulations, we successfully predicted a model structure for the m-state structure (Tamura and Hayashi, 2017, PLOS ONE). The predicted structure was later validated by the experimentally determined m-state structure.