Simulation Analysis of the Stability Mutants R96H of Bacteriophage T4 Lysozyme and I96A of Barnase

  1. Derek J. Chadwick Organizer and
  2. Kate Widdows
  1. Martin Karplust1,
  2. Martine Prévost1,2,
  3. Bruce Tidor1,† and
  4. Shoshana Wodak2

Published Online: 28 SEP 2007

DOI: 10.1002/9780470514146.ch5

Ciba Foundation Symposium 161 - Protein Conformation

Ciba Foundation Symposium 161 - Protein Conformation

How to Cite

Karplust, M., Prévost, M., Tidor, B. and Wodak, S. (2007) Simulation Analysis of the Stability Mutants R96H of Bacteriophage T4 Lysozyme and I96A of Barnase, in Ciba Foundation Symposium 161 - Protein Conformation (eds D. J. Chadwick and K. Widdows), John Wiley & Sons, Ltd., Chichester, UK. doi: 10.1002/9780470514146.ch5

Author Information

  1. 1

    Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138, USA

  2. 2

    Unité Conformation des Macromolécules Biologiques, Universté Libre de Bruxelles, Avenue Paul Héger-CP160, B-1050 Brussels, Belgium

  1. Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA

Publication History

  1. Published Online: 28 SEP 2007

ISBN Information

Print ISBN: 9780471929697

Online ISBN: 9780470514146

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Keywords:

  • simulation analysis;
  • stability mutants;
  • free energy simulation;
  • amino acid mutation;
  • thermodynamics

Summary

Free energy simulation methods are used to analyse the effects of the mutation Arg-96[RIGHTWARDS ARROW]His on the stability of bacteriophage T4 lysozyme and of Ile-96[RIGHTWARDS ARROW]Ala on the stability of barnase. By use of thermodynamic integration, the contributions of specific interactions to the free energy change are evaluated. It is shown that a number of contributions that stabilize the wild-type or the mutant partially cancel in the overall free energy difference; some of these involve the unfolded state. Comparison of the results with conclusions based on structural and thermodynamic data leads to new insights into the origin of the stability difference between wild-type and mutant proteins. For the charged-to-charged amino acid mutation in T4 lysozyme, the importance of the contributions of more distant residues, solvent water and the covalent linkage involving the mutated amino acid are of particular interest. Also, the analysis of the Arg-96 to His mutation with respect to the interactions with the C-terminal end of a helix (residues 82–90) indicates that the nearby carbonyl groups (Tyr-88 and Asp-89) make the dominant contribution, that the amide groups do not contribute significantly and that the helix dipole model is inappropriate for this case. For the non-polar-to-non-polar amino acid mutation in barnase, the solvent contribution is unimportant, and covalent terms are shown to be significant because they do not cancel between the folded and unfolded state.