Enhanced and Efficient Predictions of Dynamic Ionization through Constant-pH Adiabatic Free Energy Dynamics.

ABSTRACT: Dynamic or structurally induced ionization is a critical aspect of many physical, chemical, and biological processes. Molecular dynamics (MD) based simulation approaches, specifically constant pH MD methods, have been developed to simulate ionization states of molecules or proteins under experimentally or physiologically relevant conditions. While such approaches are now widely utilized to predict ionization sites of macromolecules or to study physical or biological phenomena, they are often computationally expensive and require long simulation times to converge. In this article, using the principles of adiabatic free energy dynamics, we introduce an efficient technique for performing constant pH MD simulations within the framework of the adiabatic free energy dynamics (AFED) approach. We

SUBMITTER: Hong RS 

PROVIDER: S-EPMC11603612 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature