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X‐ray structural and simulation analysis of a protein mutant: The value of a combined approach
Author(s) -
Mattos Carla,
Cohen Justin D.,
Green David F.,
Tidor Bruce,
Karplus Martin
Publication year - 2004
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20031
Subject(s) - mutant , lysozyme , stability (learning theory) , crystallography , complement (music) , chemistry , materials science , physics , thermodynamics , computer science , biochemistry , gene , machine learning , complementation
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.