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Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs

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G Protein-Coupled Receptor Signaling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1947))

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.

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Acknowledgments

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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Authors and Affiliations

  1. Department of Mechanical Engineering, Keio University, Yokohama, Japan

    Katsufumi Tomobe & Kenji Yasuoka

  2. Department of System Design Engineering, Keio University, Yokohama, Japan

    Eiji Yamamoto

Authors
  1. Katsufumi Tomobe
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  2. Eiji Yamamoto
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  3. Kenji Yasuoka
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Corresponding author

Correspondence to Kenji Yasuoka .

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Editors and Affiliations

  1. Ottawa Hospital Research Institute (Neurosciences), Ottawa, ON, Canada

    Mario Tiberi

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Tomobe, K., Yamamoto, E., Yasuoka, K. (2019). Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs. In: Tiberi, M. (eds) G Protein-Coupled Receptor Signaling. Methods in Molecular Biology, vol 1947. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9121-1_2

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  • DOI: https://doi.org/10.1007/978-1-4939-9121-1_2

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9120-4

  • Online ISBN: 978-1-4939-9121-1

  • eBook Packages: Springer Protocols

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