Computational design of a substrate specificity mutant of a protein

Abstract

The wild-type trp repressor of E. coli bound 5-methoxytryptophan, a Trp analogue, less tightly than Trp. A mutant repressor (Val58-->Ala) that should bind 5-methoxytryptophan preferentially to Trp was computationally designed by free-energy calculations accompanied by free-energy decomposition. The designed mutant was demonstrated by experiments to bind 5-methoxytryptophan more tightly than Trp, consistent with the computational prediction. This success indicates the usefulness of free energy decomposition in protein design.

Beyond the rotamer library: Genetic algorithm combined with the disturbing mutation process for upbuilding protein side‐chains

“…Side‐chain packing has an essential role in the formation of hydrophobic core and active sites in the protein folding process, and is crucial for protein stability and function. Recently, side‐chain conformation predictions have had many successful applications in protein modeling, side‐chain redesigning of known proteins,1 and protein mutation experiments 2, 3. Its increasingly wide applications demand further development of the method.…”