Simulation-Guided Conformational Space Exploration to Assess Reactive Conformations of a Ribozyme

Self-splicing ribozymes are small RNA enzymes that catalyze their own cleavage through a transphosphoesterification reaction. While this process is involved in some specific steps of viral RNA replication and splicing, it is also of importance in the context of the (putative) first autocatalytic RNA-based systems that could have preceded the emergence of modern life. The uncatalyzed phosphoesterbond formation is thermodynamically very unfavorable, and many experimental studies have focused on the understanding of the molecular features of catalysis in these ribozymes. However, chemical reaction paths are short-lived and not easily characterized by experimental approaches, so that molecular simulation approaches appear as an ideal tool to unveil the molecular details of the reaction. Here, we focus on the model hairpin ribozyme and highlight that identifying a relevant initial conformation for reactivity studies can be highly challenging due to limitations in both available X-ray and the force field accuracy, together with the necessity of extensive sampling. This is frequently overlooked in mixed quantum/classical studies that predominantly concentrate on the chemical reaction itself. These challenges stem from limitations in both available experimental structures (which are chemically altered to prevent self-cleavage) and the accuracy of force fields, together with the necessity for comprehensive sampling. We show that molecular dynamics simulations, combined with extensive conformational phase space exploration with Hamiltonian replica-exchange simulations, enable to characterize the relevant conformational basins of the minimal hairpin ribozyme in the ligated state, prior to self-cleavage. With all investigated force fields, we find that what is usually considered as a canonical reactive conformation with active site geometries and hydrogen-bond patterns that are optimal for the addition-elimination reaction with general acid/general base catalysis, is metastable and only marginally populated. The thermodynamically stable conformation appears to be consistent with the expectations of a mechanism that does not require the direct participation of ribozyme residues to the reaction. Our study therefore demonstrates that identifying the most pertinent reactant state conformation, holds equal importance alongside the accurate determination of the thermodynamics and kinetics of the chemical steps of the reaction.