Redesigning methionyl-tRNA synthetase forβ-methionine activity with adaptive landscape flattening and experiments

Abstract

AbstractAmino acids (AAs) with a noncanonical backbone would be a valuable tool for protein engineering, enabling new structural motifs and building blocks. To incorporate them into an expanded genetic code, the first, key step is to obtain an appropriate aminoacyl-tRNA synthetase (aaRS). Currently, directed evolution is not available to optimize such AAs, since an appropriate selective pressure is not available. Computational protein design (CPD) is an alternative. We used a new CPD method to redesign MetRS and increase its activity towardsβ-Met, which has an extra backbone methylene. The new method considered a few active site positions for design and used a Monte Carlo exploration of the corresponding sequence space. During the exploration, a bias energy was adaptively learned, such that the free energy landscape of the apo enzyme was flattened. Enzyme variants could then be sampled, in the presence of the ligand and the bias energy, according to theirβ-Met binding affinities. Eleven predicted variants were chosen for experimental testing; all exhibited detectable activity forβ-Met adenylation. Top predicted hits were characterized experimentally in detail. Dissociation constants, catalytic rates, and Michaelis constants for bothα-Met andβ-Met were measured. The best mutant retained a preference forα-Met overβ-Met; however, the preference was reduced, compared to the wildtype, by a factor of 29. For this mutant, high resolution crystal structures were obtained in complex with bothα-Met andβ-Met, indicating that the predicted, active conformation ofβ-Met in the active site was retained.Author summaryAmino acids (AAs) with a noncanonical backbone would be valuable for protein engineering, enabling new structural motifs. To incorporate them into an expanded genetic code, the key step is to obtain an appropriate aminoacyl-tRNA synthetase (aaRS). Currently, directed evolution is not available to optimize such AAs. Computational protein design is an alternative. We used a new method to redesign MetRS and increase its activity towardsβ-Met, which has an extra backbone methylene. The method considered a few active site positions for design and used a Monte Carlo exploration of sequence space, during which a bias energy was adaptively learned, such that the free energy landscape of the apo enzyme was flattened. Enzyme variants could then be sampled, in the presence of the ligand and the bias energy, according to theirβ-Met binding affinities. Eleven predicted variants were chosen for experimental testing; all exhibited detectableβ-Met adenylation activity. Top hits were characterized experimentally in detail. The best mutant had its preference forα-Met overβ-Met reduced by a factor of 29. Crystal structures indicated that the predicted, active conformation ofβ-Met in the active site was retained.