Application of massively parallel measurements of protein stability to study protein evolution

A central biophysical constraint acting on proteins in evolution is thermodynamic stability.

Selection for stability impacts the type of amino acids that are compatible with a folded structure at sites in proteins.

The propensity of amino acids at a given site depends on interactions with neighboring residues in the three-dimensional structure.

The impact of an amino acid substitution can therefore change depending on the sequence background that the change occurs in, something that is called epistasis.

In this project we study how amino acid preferences change over evolutionary time and how that impacts the sequence landscapes of proteins.

We also study how correlated substitutions at different sites in proteins emerge and investigate its coupling to epistasis.

The studies of epistasis and correlated substitutions in protein evolutions is carried out by measuring the experimental stability of a large number of mutants using a high-throughput stability assay. A second aim of this project is to investigate how new protein folds may have emerged.

We create a protein design approach for engineering sequences that can switch from one fold to the next with a limited number of mutations. With this method we can map the space of switchable folds.

We then experimentally characterize folds to create a set of scaffolds that can be used as a basis to design proteins that can change conformations, something that is central for the design of the next generation of denovo proteins.