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 noncanonical 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 spaces of dynamic structures and to perform robust calculations of pH-dependent properties, such as the pK_a of titratable sites. Despite growing biological evidence concerning pH regulation of certain motifs and its role in biotechnological applications, pH-sensitive in silico methods have rarely been applied to nucleic acids. Thi

SUBMITTER: Silva TFD 

PROVIDER: S-EPMC12004511 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature