Exact reaction coordinates for flap opening in HIV-1 protease.

ABSTRACT: The primary goal of protein science is to understand how proteins function, which requires understanding the functional dynamics responsible for transitions between different functional structures of a protein. A central concept is the exact reaction coordinates that can determine the value of committor for any protein configuration, which provide the optimal description of functional dynamics. Despite intensive efforts, identifying the exact reaction coordinates (RCs) in complex molecules remains a formidable challenge. Using the recently developed generalized work functional, we report the discovery of the exact RCs for an important functional process-the flap opening of HIV-1 protease. Our results show that this process has six RCs, each one is a linear combination of ~240 backbone dihe

SUBMITTER: Wu S 

PROVIDER: S-EPMC9894123 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature