A Novel Mechanism of Biomolecular Conformational Dynamics: Energy Flow in Phase Space

Abstract

All the functionally important processes for proteins are activated processes. Understanding their mechanisms is of critical importance in both theory and applications. Most studies have focused on the barrier crossing through the transition-state region in the configuration space, which has shown limitations by recent studies. Therefore, in addition to the barrier crossing phase that can be rigorously parameterized by committor, we investigated the progress of the energy activation phase that precedes barrier crossing by introducing a new quantity, the reaction stability (ps), that can rigorously parameterize this phase.