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Membrane Protein Structure and Function Characterization pp 383–416Cite as

Molecular Modeling of Transporters: From Low Resolution Cryo-Electron Microscopy Map to Conformational Exploration. The Example of TSPO

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1635))

Abstract

This chapter describes a protocol to establish a three-dimensional (3D) model of a protein and to explore its conformational landscape. It combines predictions from up-to-date bioinformatics methods with low-resolution experimental data. It also proposes to examine rapidly the dynamics of the protein using molecular dynamics simulations with a coarse-grained force field. Tools for analyzing these trajectories are suggested as well as those for constructing all-atoms models. Thus, starting from a protein sequence and using free software, the user can get important conformational information, which might improve the knowledge about the protein function.

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Authors and Affiliations

  1. Unité INSERM UMRS1134, Laboratory of Excellence, Institut National de la Transfusion Sanguine, Université Paris-Diderot, Sorbonne Paris Cité, Université de la Réunion, 6 rue Alexandre Cabanel, 75015, Paris Cedex 15, France

    Aurore Vaitinadapoule & Catherine Etchebest

Authors
  1. Aurore Vaitinadapoule
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  2. Catherine Etchebest
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Correspondence to Catherine Etchebest .

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Editors and Affiliations

  1. Département de Chimie, CNRS UMR 7203 LBM, Sorbonne Universités—UPMC Univ Paris 06, École Normale Supérieure—PSL Research University, Paris, France

    Jean-Jacques Lacapere

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Vaitinadapoule, A., Etchebest, C. (2017). Molecular Modeling of Transporters: From Low Resolution Cryo-Electron Microscopy Map to Conformational Exploration. The Example of TSPO. In: Lacapere, JJ. (eds) Membrane Protein Structure and Function Characterization. Methods in Molecular Biology, vol 1635. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7151-0_21

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  • DOI: https://doi.org/10.1007/978-1-4939-7151-0_21

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7149-7

  • Online ISBN: 978-1-4939-7151-0

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