Large-scale Protein Fitness Data Reveal Fundamental Protein Properties

The ability of a protein to carry out a given function results from fundamental physicochemical properties that include the protein's structure, mechanism of action, and thermostability. Traditional approaches to study these protein properties have typically required the direct measurement of the property of interest. However, we have developed deep mutational scanning, which enables the rapid and large-scale quantification of the relationship between the sequence of a protein and its fitness in a simple assay, such as binding. We measured the fitness of 47,000 variants of a WW domain to bind to a peptide ligand and use these measurements to identify stabilizing mutations without directly assaying stability. Stabilizing mutations are found via their ability to rescue destabilizing mutations. Thus, physicochemical properties such as stability are latent within large-scale protein fitness data and can be revealed by systematic analysis. This approach represents a new direction in protein science, wherein large protein fitness data sets are used to uncover fundamental protein properties.