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Accurate Calculation of Free Energy Changes upon Amino Acid Mutation

  • Matteo AldeghiEmail author
  • Bert L. de GrootEmail author
  • Vytautas GapsysEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1851)

Abstract

Molecular dynamics based free energy calculations allow for a robust and accurate evaluation of free energy changes upon amino acid mutation in proteins. In this chapter we cover the basic theoretical concepts important for the use of calculations utilizing the non-equilibrium alchemical switching methodology. We further provide a detailed step-by-step protocol for estimating the effect of a single amino acid mutation on protein thermostability. In addition, the potential caveats and solutions to some frequently encountered issues concerning the non-equilibrium alchemical free energy calculations are discussed. The protocol comprises details for the hybrid structure/topology generation required for alchemical transitions, equilibrium simulation setup, and description of the fast non-equilibrium switching. Subsequently, the analysis of the obtained results is described. The steps in the protocol are complemented with an illustrative practical application: a destabilizing mutation in the Trp cage mini protein. The concepts that are described are generally applicable. The shown example makes use of the pmx software package for the free energy calculations using Gromacs as a molecular dynamics engine. Finally, we discuss how the current protocol can readily be adapted to carry out charge-changing or multiple mutations at once, as well as large-scale mutational scans.

Key words

Molecular dynamics free energy calculations alchemistry amino acid mutation pmx hybrid structure hybrid topology non-equilibrium transitions 

Supplementary material

426856_1_En_2_MOESM1_ESM.zip (57 kb)
1 work_distributions-checkpoint.ipynb (ZIP 57 KB)

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

Authors and Affiliations

  1. 1.Max Planck Institute for Biophysical ChemistryComputational Biomolecular Dynamics GroupGöttingenGermany

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