Predicting residue ionization of OmpF channel using Constant pH Molecular Dynamics as benchmark.

ABSTRACT: Electrostatic interactions are crucial for protein structure and function, especially in mesoscopic protein channels where ion selectivity is largely governed by the protein's electrostatic properties. Understanding the protonation state of ionizable residues across pH values -often described by their pKa- is key to linking structure and function. However, experimental pKa determination is challenging, typically carried out using Nuclear Magnetic Resonance only in a limited number of membrane proteins. Thus, computational methods are the primary alternative. Constant pH Molecular Dynamics (CpHMD) simulation is one of the most accurate pKa prediction methods in proteins that contain many charged residues since it captures the coupling between conformational dynamics and residue protonation.

SUBMITTER: Tavares-Neto E 

PROVIDER: S-EPMC12578334 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature