Statistical analysis of conformational changes of proteins

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With the help of recent advances in computer hardware and software, it is becoming possible to simulate functionally relevant conformational changes of biomolecules. On the other hand, however, the amount of simulation data is rapidly increasing and it is becoming difficult to treat such large amount of data without statistical analysis. In this study, we have developed a framework for the statistical analysis of molecular dynamics simulation data. The developed framework was successfully applied to conformational change data of two cases: (i) The most slowest degrees of freedom (involving the P-loop and a hinge region) in Adenylate Kinase was identified from 9 microseconds simulation data. (ii) Free energy differences along the conformational change pathways of multidrug transporter AcrB was successfully evaluated.