Toward Accurate Prediction of the Protonation Equilibrium of Nucleic Acids

The role of protonated nucleotides in modulating the pH-dependent properties of nucleic acids is one of the emerging frontiers in the field of nucleic acid biology. The recent development of a constant pH molecular dynamics simulation (CPHMDMS?D) framework for simulating nucleic acids has provided a tool for realistic simulations of pH-dependent dynamics. We enhanced the CPHMDMS?D framework with pH-based replica exchange (pH-REX), which significantly improves the sampling of both titration and spatial coordinates. The results from our pKa calculations for the GAAA tetraloop, which was predicted with lower accuracy previously due to sampling challenges, demonstrates that pH-REX reduces the average unsigned error (AUE) to 0.7 pKa units, and the error of the most poorly predicted residue A17 was drastically reduced from 2.9 to 1.2 pKa units. Lastly, we show that pH-REX CPHMDMS?D simulations can be used to identify the dominant conformation of nucleic acid structures in alternate pH environments. This work suggests that pH-REX CPHMDMS?D simulations provide a practical tool for predicting nucleic acid protonation equilibrium from first-principles and offering structural and mechanistic insight into the study of pH-dependent properties of nucleic acids.