Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics.

ABSTRACT: Tunnels are structural conduits in biomolecules responsible for transporting chemical compounds and solvent molecules from the active site. They have been shown to be present in a wide variety of enzymes across all functional and structural classes. However, the study of such pathways is experimentally challenging, because they are typically transient. Computational methods, such as molecular dynamics (MD) simulations, have been successfully proposed to explore tunnels. Conventional MD (cMD) provides structural details to characterize tunnels but suffers from sampling limitations to capture rare tunnel openings on longer time scales. Therefore, in this study, we explored the potential of Gaussian accelerated MD (GaMD) simulations to improve the exploration of complex tunnel networks in enz

SUBMITTER: Mandal N 

PROVIDER: S-EPMC11351021 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature