Energy transport pathway in proteins: Insights from non-equilibrium molecular dynamics with elastic network model.

ABSTRACT: Intra-molecular energy transport between distant functional sites plays important roles in allosterically regulating the biochemical activity of proteins. How to identify the specific intra-molecular signaling pathway from protein tertiary structure remains a challenging problem. In the present work, a non-equilibrium dynamics method based on the elastic network model (ENM) was proposed to simulate the energy propagation process and identify the specific signaling pathways within proteins. In this method, a given residue was perturbed and the propagation of energy was simulated by non-equilibrium dynamics in the normal modes space of ENM. After that, the simulation results were transformed from the normal modes space to the Cartesian coordinate space to identify the intra-protein energy tr

SUBMITTER: Wang WB 

PROVIDER: S-EPMC6015066 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature