Computational design of conformation-biasing mutations to alter protein functions

Most natural proteins alternate between distinct conformational states, each associated with specific functions. Intentional manipulation of conformational equilibria could lead to improved or altered protein properties. Here we develop Conformational Biasing (CB), a rapid and streamlined computational method that utilizes contrastive scoring by inverse folding models to predict variants biased towards desired conformational states. We validated CB across seven diverse deep mutational scanning datasets, successfully predicting variants of K-Ras, SARS-CoV-2 spike, β2 adrenergic receptor, and Src kinase with improved conformation-specific functions including enhanced effector binding or enzymatic activity. Furthermore, applying CB to lipoic acid ligase, a conformation-switching bacterial enzyme that has been used for the development of protein labeling technologies, revealed a previously unknown mechanism for conformational gating of sequence-specificity. Variants biased toward the “open” conformation were highly promiscuous, while “closed” conformation-biased variants were even more specific than wild-type, enhancing the utility of LplA for site-specific protein labeling with fluorophores in living cells. The speed, simplicity, and versatility of CB (available at: https://github.com/alicetinglab/ConformationalBiasing/ ) suggest that it may be broadly applicable for understanding and engineering protein conformational dynamics, with implications for basic research, biotechnology, and medicine.