Research Article

X-ray structural and simulation analysis of a protein mutant: The value of a combined approach

  1. Carla Mattos1,*,
  2. Justin D. Cohen2,
  3. David F. Green2,
  4. Bruce Tidor2,
  5. Martin Karplus3,4,*

Article first published online: 5 MAR 2004

DOI: 10.1002/prot.20031

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Volume 55, Issue 3, pages 733–742, 15 May 2004

Additional Information

How to Cite

Mattos, C., Cohen, J. D., Green, D. F., Tidor, B. and Karplus, M. (2004), X-ray structural and simulation analysis of a protein mutant: The value of a combined approach. Proteins, 55: 733–742. doi: 10.1002/prot.20031

Author Information

  1. 1

    Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina

  2. 2

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts

  3. 3

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts

  4. 4

    Laboratoire de Chimie Biophysique, Institut le Bel Universite Louis Pasteur, Strasbourg, France

*Department of Molecular and Structural Biochemistry, North Carolina State University, 128 Polk Hall, Raleigh, NC 27695-7622

Publication History

  1. Issue published online: 16 APR 2004
  2. Article first published online: 5 MAR 2004
  3. Manuscript Accepted: 20 OCT 2003
  4. Manuscript Received: 10 SEP 2003

Funded by

  • National Institutes of Health
  • Lord Foundation Scholarship
  • Merck Graduate Fellowship
  • Alfred P. Sloan Research Fellowship
  • Burroughs Wellcome Fund New Investigator Award in the Basic Pharmacological Sciences

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Keywords:

  • protein crystallography;
  • structure refinement;
  • computational chemistry;
  • free energy simulations

Abstract

The effect of the mutation Arg 96 to His on the stability of bacteriophage T4 lysozyme has been previously studied by calorimetric experiments, X-ray crystallography, and free energy simulation techniques. The experimental and calculated values for the difference between the free energy of denaturation of the mutant and the wild type are in reasonable agreement. However, the two approaches led to different explanations for the loss in stability. To analyze the differences, a series of refinements based on the crystallographic data were performed, a number of aspects of the simulations were reexamined, and continuum electrostatic calculations were done to complement the latter. The results of those comparisons provide a better understanding of the origin of the free energy difference in this mutant. Furthermore, they show the importance of the combined use of simulations and crystallography for interpreting the effects of mutations on the energetics of the system. Proteins 2004. © 2004 Wiley-Liss, Inc.

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