Chapter 8. Understanding Structure and Function of Membrane Proteins Using Free Energy Calculations

  1. Prof. Eva Pebay-Peyroula PhD professor
  1. Christophe Chipot1 and
  2. Klaus Schulten2

Published Online: 7 JAN 2008

DOI: 10.1002/9783527621224.ch8

Biophysical Analysis of Membrane Proteins: Investigating Structure and Function

Biophysical Analysis of Membrane Proteins: Investigating Structure and Function

How to Cite

Chipot, C. and Schulten, K. (2008) Understanding Structure and Function of Membrane Proteins Using Free Energy Calculations, in Biophysical Analysis of Membrane Proteins: Investigating Structure and Function (ed E. Pebay-Peyroula), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527621224.ch8

Editor Information

  1. Institut de Biologie Structurale Jean-Pierre Ebel, Université Joseph Fourier-CEA-CNRS, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France

Author Information

  1. 1

    Equipe de Dynamique des Assemblages Membranaires, UMR CNRS/UHP 7565, Université Henri Poincaré, BP 239, 54506 Vandoeuvre-lès-Nancy cedex, France

  2. 2

    Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA

Publication History

  1. Published Online: 7 JAN 2008
  2. Published Print: 24 OCT 2007

ISBN Information

Print ISBN: 9783527316779

Online ISBN: 9783527621224

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Keywords:

  • biophysical analysis;
  • molecular dynamics studies;
  • structure;
  • function;
  • free energy calculations;
  • theoretical underpinnings;
  • point mutations;
  • assisted transport phenomena across membranes

Summary

This chapter contains sections titled:

  • Introduction

  • Theoretical Underpinnings of Free Energy Calculations

    • Alchemical Transformations

      • What is Usually Implied by Small Changes?

      • How is the Coupling Parameter Defined?

      • Thermodynamic Integration

    • Free Energy Changes Along a Reaction Coordinate

      • Umbrella Sampling or Stratification?

      • Adaptive Biasing Force

      • Non-Equilibrium Simulations for Equilibrium Free Energies

  • Point Mutations in Membrane Proteins

    • Why Have Free Energy Calculations Been Applied only Sparingly to Membrane Proteins?

    • Gaining New Insights into Potassium Channels

    • Tackling the Assisted Transport of Ammonium Using FEP

    • How Relevant are Free Energy Calculations in Models of Membrane Proteins?

  • Assisted Transport Phenomena Across Membranes

    • Gramicidin: A Paradigm for Assisted Transport Across Membranes

    • Free Energy Calculations and Potassium Channels

    • Non-Equilibrium Simulations for Understanding Equilibrium Phenomena

    • Deciphering Transport Mechanisms in Aquaporins

    • Non-Equilibrium Simulations and Potassium Channels

  • Recognition and Association in Membrane Proteins

    • The “Two-Stage” Model

    • Glycophorin A: A Paradigmatic System for Tackling Recognition and Association in Membranes

  • Conclusions