The Role of Dynamics in Protein Evolution

Abstract

Protein evolution has most commonly been studied either theoretically, by analyzing the sequence of the protein, or experimentally, by resurrecting ancestral proteins in the lab and performing ligand binding studies to determine function. Thus far, structural and dynamic evolution have largely been left out of molecular evolution studies. Here we incorporate both structure and dynamics to elucidate the molecular principles behind the divergence in the evolutionary path of the gluccocorticoid and mineralocorticoid steroid receptor proteins. We begin by determining the likely structure of three evolutionary diverged, ancestral steroid receptor proteins using the Zipping and Assembly Method with FRODA (ZAMF). Our predictions are within 1.9A RMSD of the crystal structure of ancestral corticoid steroid receptor. Beyond comparing static structure prediction, the main advantage of ZAMF is that it allows us to observe protein dynamics. Therefore we can investigate differences in the diverged proteins’ available dynamic space by performing Principle Component Analysis (PCA) on the last .5ns of the converged MD trajectories obtained from ZAMF. We then analyze fluctuation profiles and cross-correlation maps from the slowest modes. This analysis enables us to identify critical mutations that most affect dynamics, therefore it shows the critical mutations leading to a divergence in function. We observe evolutionary diverged proteins do not share the same dynamic subspace. As this affects phenotype, we then compare binding specificities of these predicted structures to experimentally determined values by docking different ligands using ROSETTALIGAND and DrugScore online server.