Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs

Katsufumi Tomobe, Eiji Yamamoto, Kenji Yasuoka

研究成果: Chapter

抜粋

Rhodopsin is a light-driven G protein-coupled receptor mediating signal transduction in eyes. The molecular dynamics (MD) simulations are powerful computational tools to investigate molecular behavior of proteins and internal water molecules which are related to the function of proteins; however, the MD simulations of the rhodopsin require several technical setups for accurate calculations. This chapter discusses practical methods for setting up the MD simulations of the rhodopsin [preparation of initial systems, condition files for MD simulation package GROMACS, and data analysis]. The data analysis includes the root mean square deviation (RMSD) and mapping of accessibility of water molecules.

元の言語English
ホスト出版物のタイトルMethods in Molecular Biology
出版者Humana Press Inc.
ページ21-30
ページ数10
DOI
出版物ステータスPublished - 2019 1 1

出版物シリーズ

名前Methods in Molecular Biology
1947
ISSN(印刷物)1064-3745

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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  • これを引用

    Tomobe, K., Yamamoto, E., & Yasuoka, K. (2019). Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs. : Methods in Molecular Biology (pp. 21-30). (Methods in Molecular Biology; 巻数 1947). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-9121-1_2