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Interface Prediction for GPCR Oligomerization Between Transmembrane Helices

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Computational Design of Membrane Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2315))

Abstract

Oligomers of G protein-coupled receptors (GPCRs) are closely related to their biochemical and biological functions and have been conserved during the course of molecular evolution. The mechanisms of GPCR interactions and the reason why GPCRs interact between themselves have remained elusive. Accurate interface prediction is useful to generate guidelines for mutation and inhibition experiments and would accelerate investigations of the molecular mechanisms of GPCR oligomerization and signaling. We have developed a method to predict the interfaces for GPCR oligomerization. Our method detects clusters of conserved residues along the surfaces of transmembrane helices, using a multiple sequence alignment and a target GPCR or closely related structure. This chapter outlines our method and introduces some problems that occur with it, along with our future direction to extend the method for interface predictions of general membrane proteins.

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Acknowledgments

This work was supported by Grant-in-Aid for Scientific Research from the Ministry of Education Culture, Sports, Science and Technology of Japan (25870764, 18K06199).

Author information

Author notes

  1. Akira Saito

    Present address: Software Service, Inc., Osaka, Japan

Authors and Affiliations

  1. Division of Life Science, Department of Science and Engineering, School of Science and Engineering, Tokyo Denki University (TDU), Tokyo, Japan

    Wataru Nemoto & Akira Saito

  2. Division of Life Science and Engineering, Graduate School of Science and Engineering, Tokyo Denki University (TDU), Tokyo, Japan

    Wataru Nemoto

Authors
  1. Wataru Nemoto
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  2. Akira Saito
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Corresponding author

Correspondence to Wataru Nemoto .

Editor information

Editors and Affiliations

  1. Department of Life Sciences, University of Coimbra, Coimbra, Portugal

    Irina S. Moreira

  2. BioISI, University of Lisboa, Lisboa, Portugal

    Miguel Machuqueiro

  3. Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal

    Joana Mourão

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Nemoto, W., Saito, A. (2021). Interface Prediction for GPCR Oligomerization Between Transmembrane Helices. In: Moreira, I.S., Machuqueiro, M., Mourão, J. (eds) Computational Design of Membrane Proteins. Methods in Molecular Biology, vol 2315. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1468-6_6

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  • DOI: https://doi.org/10.1007/978-1-0716-1468-6_6

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1467-9

  • Online ISBN: 978-1-0716-1468-6

  • eBook Packages: Springer Protocols

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