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Topological data analysis of protein structure and inter/intra-molecular interaction changes attributable to amino acid mutations.
Koseki, Jun; Hayashi, Shuto; Kojima, Yasuhiro; Hirose, Haruka; Shimamura, Teppei.
Afiliação
  • Koseki J; Division of Systems Biology, Graduate School of Medicine, Nagoya University, Aichi 466-8550, Japan.
  • Hayashi S; Division of Systems Biology, Graduate School of Medicine, Nagoya University, Aichi 466-8550, Japan.
  • Kojima Y; Department of Computational and Systems Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan.
  • Hirose H; Division of Systems Biology, Graduate School of Medicine, Nagoya University, Aichi 466-8550, Japan.
  • Shimamura T; Department of Computational and Systems Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan.
Comput Struct Biotechnol J ; 21: 2950-2959, 2023.
Article em En | MEDLINE | ID: mdl-37228703
ABSTRACT
The presence of some amino acid mutations in the amino acid sequence that determines a protein's structure can significantly affect that 3D structure and its biological function. However, the effects upon structural and functional changes differ for each displaced amino acid, and it is very difficult to predict these changes in advance. Although computer simulations are very effective at predicting conformational changes, they struggle to determine whether the amino acid mutation of interest induces sufficient conformational changes, unless the researcher is a specialist in molecular structure calculations. Therefore, we created a framework that efficiently utilizes molecular dynamics and persistent homology methods to identify amino acid mutations that induce structural changes. We show that this framework can be used not only to predict conformational changes produced by amino acid mutations but also to extract groups of mutations that significantly alter similar molecular interactions, by capturing the resultant protein-protein interaction changes.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: Comput Struct Biotechnol J Ano de publicação: 2023 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: Comput Struct Biotechnol J Ano de publicação: 2023 Tipo de documento: Article