Identifying residue–residue clashes in protein hybrids by using a second-order mean-field approach

In this article, a second-order mean-field-based approach is introduced for characterizing the complete set of residue–residue couplings consistent with a given protein structure. This information is subsequently used to classify protein hybrids with respect to their potential to be functional based on the presence/absence and severity of clashing residue–residue interactions. First, atomistic representations of both the native and denatured states are used to calculate rotamer–backbone, rotamer–intrinsic, and rotamer–rotamer conformational energies. Next, this complete conformational energy table is coupled with a second-order mean-field description to elucidate the probabilities of all possible rotamer–rotamer combinations in a minimum Helmholtz free-energy ensemble. Computational results for the dihydrofolate reductase family reveal correlation in substitution patterns between not only contacting but also distal second-order structural elements. Residue–residue clashes in hybrid proteins are quantified by contrasting the ensemble probabilities of protein hybrids against the ones of the original parental sequences. Good agreement with experimental data is demonstrated by superimposing these clashes against the functional crossover profiles of bidirectional incremental truncation libraries for Escherichia coli and human glycinamide ribonucleotide transformylases.