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The 184th R-CCS Cafe -partⅡ

The 184th R-CCS Cafe -partⅡ
Date and Time: Mon. Nov. 25, 2019, 16:10 - 16:40
Place: Lecture Hall (6th floor) at R-CCS

Title: Atomistic modeling of the alternating access mechanism of the mitochondrial ADP/ATP carrier with molecular simulations
Speaker: Koichi Tamura (Computational Biophysics Research Team)

Presentation Language: English
Presentation Material: English

Abstract:

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.