Local Ion Densities can Influence Transition Paths of Molecular Binding.

ABSTRACT: Improper reaction coordinates can pose significant problems for path-based binding free energy calculations. Particularly, omission of long timescale motions can lead to over-estimation of the energetic barriers between the bound and unbound states. Many methods exist to construct the optimal reaction coordinate using a pre-defined basis set of features. Although simulations are typically conducted in explicit solvent, the solvent atoms are often excluded by these feature sets-resulting in little being known about their role in reaction coordinates, and ultimately, their role in determining (un)binding rates and free energies. In this work, analysis is done on an extensive set of host-guest unbinding trajectories, working to characterize differences between high and low probability unbindi

SUBMITTER: Roussey NM 

PROVIDER: S-EPMC9086317 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature