Understanding the dynamics of protein evolution from a biophysical-organismal perspective

Abstract

Since protein stability is imperative for a proper function, the physical properties of essential globular proteins dictate the fitness of an organism that carries them. Most globular proteins, however, possess thermodynamic margins within which their stability can be affected by mutations (either destabilizing or stabilizing) without causing an immediate effect on organismal fitness. Although these ‘neutral’ mutations can become deleterious or advantageous when combined with subsequent generational mutations, their impact on the rate and course of protein evolution remains unexplored. The goal of this project is to elucidate by a comprehensive approach, spanning the basic biophysical, molecular level, and organismal fitness level, how apparently neutral amino acid changes in essential proteins can influence the dynamics of protein evolution. To this end, the thermodynamic response of a group of E. coli’s essential proteins to a set of computationally predicted and experimentally verified neutral mutations will be measured against the fitness of competing populations in a real-time evolution experiment. Whole genomes of representative clones will be sequenced, and genomic changes responsible for buffering the stability effects of neutral mutations in evolving populations will be identified. Possible structural, functional and regulatory mechanisms that underlie these genetic changes will be tested computationally and experimentally at the single protein, functional pathway/network, and organism levels. Finally, a mathematical model that relates the thermodynamic response of proteins to neutral mutations with the rate of molecular evolution will be developed.