Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering.

ABSTRACT: Buried ionizable groups in proteins often play important structural and functional roles. However, it is generally challenging to study the detailed molecular mechanisms solely based on experimental measurements. Free energy calculations using atomistic simulations, on the other hand, complement experimental studies and can provide high temporal and spatial resolution information that can lead to mechanistic insights. Nevertheless, it is also well recognized that sufficient sampling of such atomistic simulations can be challenging, considering that structural changes related to the buried charges may be very slow. In the present study, we describe a simple but effective enhanced sampling technique called replica exchange with charge tempering (REChgT) with a novel free energy method, multi

SUBMITTER: Liu X 

PROVIDER: S-EPMC11275198 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature