Characterizing RNA oligomers using Stochastic Titration Constant-pH Metadynamics simulations

Abstract

RNA molecules exhibit various biological functions intrinsically dependent on their diverse ecosystem of highly flexible structures. This flexibility arises from complex hydrogen-bonding networks defined by canonical and non-canonical base pairs that require protonation events to stabilize or perturb these interactions. Constant pH molecular dynamics (CpHMD) methods provide a reliable framework to explore the conformational and protonation space of dynamic structures and for robust calculations of pH-dependent properties, such as the pK$_\mathrm{a}$ of titrable sites. Despite growing biological evidence concerning pH regulation of certain motifs and in biotechnological applications, pH-sensitive in silico methods have rarely been applied to nucleic acids. In this work, we extended the stochastic titration CpHMD method to include RNA parameters from the standard $\chi$OL3 AMBER force field and highlighted its capability to depict titration events of nucleotides in single-stranded RNAs. We validated the method using trimers and pentamers with a single central titrable site while integrating a well-tempered metadynamics approach into the st-CpHMD methodology (CpH-MetaD) using PLUMED. This approach enhanced the convergence of the conformational landscape and enabled more efficient sampling of protonation-conformation coupling. Our pK$_\mathrm{a}$ estimates agree with experimental data, validating the method's ability to reproduce electrostatic changes around a titrable nucleobase in single-stranded RNA. These findings provided molecular insight into intramolecular phenomena, such as nucleobase stacking and phosphate interactions, that dictate the experimentally observed pK$_\mathrm{a}$ shifts between different strands. Overall, this work validates both the st-CpHMD and the metadynamics integration as reliable tools for studying biologically relevant RNA systems.