Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs

Katsufumi Tomobe, Eiji Yamamoto, Kenji Yasuoka

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

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.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages21-30
Number of pages10
DOIs
Publication statusPublished - 2019 Jan 1

Publication series

NameMethods in Molecular Biology
Volume1947
ISSN (Print)1064-3745

Fingerprint

Molecular Dynamics Simulation
Rhodopsin
Water
G-Protein-Coupled Receptors
Signal Transduction
Proteins
Light

Keywords

  • Biological membrane
  • G Protein-coupled receptor
  • Molecular dynamics simulations
  • Rhodopsin
  • Water pathway

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

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

Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs. / Tomobe, Katsufumi; Yamamoto, Eiji; Yasuoka, Kenji.

Methods in Molecular Biology. Humana Press Inc., 2019. p. 21-30 (Methods in Molecular Biology; Vol. 1947).

Research output: Chapter in Book/Report/Conference proceedingChapter

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