Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs

  • Katsufumi Tomobe
  • Eiji Yamamoto
  • Kenji YasuokaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1947)


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.

Key words

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



This work is supported in part by MEXT (Ministry of Education, Culture, Sports, Science and Technology) Grant-in-Aid for the Program for Leading Graduate Schools, Keio University Doctorate Student Grant-in-Aid Program, and a Bilateral Program JSPS. E.Y. was supported by MEXT Grant-in-Aid for the “Building of Consortia for the Development of Human Resources in Science and Technology”.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Katsufumi Tomobe
    • 1
  • Eiji Yamamoto
    • 2
  • Kenji Yasuoka
    • 1
    Email author
  1. 1.Department of Mechanical EngineeringKeio UniversityYokohamaJapan
  2. 2.Department of System Design EngineeringKeio UniversityYokohamaJapan

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