Many important protein functions are carried out through proton-coupled conformational
dynamics. Thus, the ability to accurately model protonation states dynamically has wide …

The impact of pH on proteins is significant but often neglected in molecular dynamics
simulations. Constant-pH Molecular Dynamics (CpHMD) is the state-of-the-art methodology …

The pH-low insertion peptides (pHLIP) are pH-dependent membrane inserting peptides,
whose function depends on the cell microenvironment acidity. Several peptide variants have …

Ions are involved in multiple biological processes and may exist bound to biomolecules or
may be associated with their surface. Although the presence of ions in nucleic acids has …

The majority of drug-like molecules contain at least one ionizable group, and many common
drug scaffolds are subject to tautomeric equilibria. Thus, these compounds are found in a …

The hallmarks of type 2 diabetes (T2D) include peripheral insulin resistance and insulin
insufficiency. Given the significance of T2D as a major public health concern, the goal of this …

Abstract β-Lactoglobulin (BLG) is an important food protein with great nutritional value. It
exists as monomeric and dimeric forms at pH 3.0 (gastric conditions) and 6.2 (small intestine …

Salts reduce the p K a of weak acids by a mechanism sensitive to ion identity and
concentration via charge screening of the deprotonated state. In this study, we utilize …

Protons participate in many reactions. In proteins, protons need paths to move in and out of
buried active sites. The vectorial movement of protons coupled to electron transfer reactions …

Periodic boundary conditions (PBCs) are a standard feature of molecular simulations, and
their mathematical and computational aspects are well-understood and relatively …