How function shapes dynamics in evolution of protein molecules
We plan to develop unique exploratory research at the interface of two seemingly disparate fields of science, evolutionary genomics and molecular dynamics. One studies universal processes of molecular change throughout biological history. The other looks at change occurring at nanosecond–to-microsecond level. Our central goal is to explore evolutionary principles behind the structure and dynamics of protein molecules and their link to molecular functions. Flexible structural regions of proteins determine their molecular functions. This flexibility is constrained by evolution, which often makes these regions conserved across homologous proteins. Since flexibility correlates with the dynamics of the molecules, the objective of our investigation is to seek specific patterns of motions of loop regions that are associated with protein function and to study their evolution. Here we propose to extend our initial molecular dynamics simulation of loops of metaconsensus enzymes to proteins with molecular functions representative of the Gene Ontology annotations defined at a domain-centric sub-ontology level, which encompass 14 broad categories.