research-article

Relationship between Dynamics of Structures and Dynamics of Hydrogen Bonds in Hras-GTP/GDP Complex

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Ryota MorikawaAuthors Info & Claims

ICBBB '20: Proceedings of the 2020 10th International Conference on Bioscience, Biochemistry and Bioinformatics

Pages 1 - 7

https://doi.org/10.1145/3386052.3386059

Published: 18 May 2020 Publication History

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Abstract

Hras protein is an intermediate for signals of cell proliferation and cell differentiation when Hras combines with guanosine triphosphate (GTP). In ordinary cells, GTP combined with Hras is hydrolyzed to guanosine diphosphate (GDP), and the structures of the protein-ligand complex strongly depend on hydrogen bonds. In such a system, hydrogen bonds exist between protein and ligand, between protein and water, and between ligand and water. In this study, we applied a relaxation mode analysis (RMA) to the trajectories of MD simulations for Hras-GTP/GDP to investigate the relationship between the dynamics of structures and those of hydrogen bonds. Different relaxation time of relaxation modes of Hras structures and Hras-solvent water hydrogen bonds were evident between Hras-GTP and Hras-GDP, and the results imply that the structure of Hras in Hras-GTP is stiffer than that in Hras-GDP. The method devised here and its interpretation can be applied to other systems focusing on objects with different stiffnesses.

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Maruyama YIgarashi RUshiku YMitsutake A(2023)Analysis of Protein Folding Simulation with Moving Root Mean Square DeviationJournal of Chemical Information and Modeling10.1021/acs.jcim.2c0144463:5(1529-1541)Online publication date: 23-Feb-2023
https://doi.org/10.1021/acs.jcim.2c01444

Index Terms

Relationship between Dynamics of Structures and Dynamics of Hydrogen Bonds in Hras-GTP/GDP Complex
1. Applied computing
  1. Life and medical sciences
    1. Bioinformatics

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ICBBB '20: Proceedings of the 2020 10th International Conference on Bioscience, Biochemistry and Bioinformatics

January 2020

160 pages

ISBN:9781450376761

DOI:10.1145/3386052

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Natl University of Singapore: National University of Singapore
RIED, Tokai Univ., Japan: RIED, Tokai University, Japan

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 18 May 2020

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ICBBB '20

ICBBB '20: 2020 10th International Conference on Bioscience, Biochemistry and Bioinformatics

January 19 - 22, 2020

Kyoto, Japan

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Maruyama YIgarashi RUshiku YMitsutake A(2023)Analysis of Protein Folding Simulation with Moving Root Mean Square DeviationJournal of Chemical Information and Modeling10.1021/acs.jcim.2c0144463:5(1529-1541)Online publication date: 23-Feb-2023
https://doi.org/10.1021/acs.jcim.2c01444

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