量研学術機関リポジトリ「QST-Repository」は、国立研究開発法人 量子科学技術研究開発機構に所属する職員等が生み出した学術成果（学会誌発表論文、学会発表、研究開発報告書、特許等）を集積しインターネット上で広く公開するサービスです。 Welcome to QST-Repository where we accumulates and discloses the academic research results(Journal Publications, Conference presentation, Research and Development Report, Patent, etc.) of the members of National Institutes for Quantum Science and Technology.
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We tried to predict docking structures of a complex system of an intrinsically disordered protein (IDP) with high structural flexibility and the receptor protein using Adaptive Lambda Square Dynamics (ALSD) method, which is a molecular dynamics (MD) simulation to efficiently search conformations of biomolecules. Conventionally, since docking pose search calculations mostly treat conformations of proteins and the substrates as rigid bodies, it is difficult to apply these methods to IDPs, which do not have specific conformations. In this study, we considered conformational changes of proteins and substrates and performed an exhaustive conformational search for their docking poses. Because the conformational degrees of freedom of this system are much larger than those of systems to which ALSD has been successfully applied so far, the docking structure observed in the NMR models could not be reproduced within the project period. However, this study could clarify a specific problem occurring in conformation sampling of a system with high degrees of freedom and suggested a direction to improve ALSD.
Exhaustive sampling of intrinsically disordered protein docking conformation with ALSD simulation
