Four-Body Scoring Function for Mutagenesis

Motivation: There is a need for an efficient and accurate computational method to identify the effects of single and multiple residue mutations on the stability and reactivity of proteins. Such a method should ideally be consistent and yet applicable in a widespread manner, i.e., it should be applied to various proteins under the same parameter settings, and have good predictive power for all of them. Results: We develop a Delaunay tessellation-based four-body scoring function to predict the effects of single and multiple residue mutations on the stability and reactivity of proteins. We test our scoring function on sets of single point mutations used by several previous studies. We also assemble a new, diverse set of 237 single and multiple residue mutations, from over twenty four different publications. The four-body scoring function correctly predicted the changes to the stability of 169 out of 210 mutants (80.5%), and the changes to the reactivity of 17 out of 27 mutants (63%). For the mutants that had the changes in stability/reactivity quantified (using reaction rates, temperatures etc.), an average Spearman rank correlation coefficient of 0.67 was achieved with the four-body scores. We also develop an efficient method for screening huge numbers of mutants of a protein, called combinatorial mutagenesis. In one study, 64 million mutants of a cold-shock nucleus binding domain protein 1CSQ, with six of its residues being changed to all possible (20) amino acids, were screened within a few hours on a PC, and all five stabilizing mutants reported were correctly identified as stabilizing by combinatorial mutagenesis. Availability: All lists of mutants scored, and executables of programs developed as part of this study are available from this web page