RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis

Abstract

Electrostatic interactions are fundamental to RNA structure and function, and intimately influenced by solvation and the ion atmosphere. RNA enzymes, or ribozymes, are catalytic RNAs that are able to enhance reaction rates over a million-fold, despite having only a limited repertoire of building blocks and available set of chemical functional groups. Ribozyme active sites usually occur at junctions where negatively charged helices come together, and in many cases leverage this strained electrostatic environment to recruit metal ions in solution that can assist in catalysis. Similar strategies have been implicated in related artificially engineered DNA enzymes. Herein, we apply Poisson–Boltzmann, 3D-RISM, and molecular simulations to study a set of metal-dependent small self-cleaving ribozymes (hammerhead, pistol, and Varkud satellite) as well as an artificially engineered DNAzyme (8–17) to examine electrostatic features and their relation to the recruitment of monovalent and divalent metal ions important for activity. We examine several fundamental roles for these ions that include: (1) structural integrity of the catalytically active state, (2) pK a tuning of residues involved in acid–base catalysis, and (3) direct electrostatic stabilization of the transition state via Lewis acid catalysis. Taken together, these examples demonstrate how RNA electrostatics orchestrates the site-specific and territorial binding of metal ions to play important roles in catalysis.

Local Electric Fields: From Enzyme Catalysis to Synthetic Catalyst Design

“…Using computational tools, they established that the LEF of an enzyme provides a preorganized polar environment in such a way that it stabilizes the TS significantly in the enzyme relative to the same reactions without an enzymatic environment . In subsequent years, other research groups have built on this viewpoint and/or refined it. − …”

Sequence-Specific Structural Features and Solvation Properties of Transcription Factor Binding DNA Motifs: Insights from Molecular Dynamics Simulation

“…Efforts have been made to understand how DNA shape contributes to protein–DNA recognition and TF binding. Accumulating evidence showing that TF binding sites are embedded within a unique environment, specific to each TF and DNA shape features improve the search efficiency. ,,− Electrostatic interactions are found to be fundamental to nucleic acid structure and function and strongly influenced by solvation and the ion atmosphere. − Electrostatic features and their relation to the binding of monovalent and divalent metal ions are found to be important for catalytic activity of the ribozymes as well as DNAzyme . However, little is known about how the solvation properties associated with the unique shape feature of the motif contribute to the search.…”

“…52−54 Electrostatic features and their relation to the binding of monovalent and divalent metal ions are found to be important for catalytic activity of the ribozymes as well as DNAzyme. 52 However, little is known about how the solvation properties associated with the unique shape feature of the motif contribute to the search. Hydration properties of the DNA grooves and the interfacial water molecules can act as a "hydration fingerprint" for a specified DNA sequence.…”

Biomolecular Electrostatic Phenomena: An Evergreen Field

“…32 An example of exploitation of continuum models and MD for the description of the behavior of highly charged RNA systems in an ionic environment is the analysis of ribozymes. 33 The advanced electrostatic treatment adopted by the AMOEBA polarizable force field helped improve the characterization of dynamics and interaction between protein and RNA. 34 The effectiveness of a more accurate electrostatic representation in the description of protein−RNA interaction was also shown in a study on IFIT proteins, which are effectors of the innate immune system.…”

“…Most of them were directed toward biomolecules, such as nucleic acids, for instance by considering their complexation with positively charged proteins, or by considering ion-specific distributions and binding patterns to RNA and DNA . An example of exploitation of continuum models and MD for the description of the behavior of highly charged RNA systems in an ionic environment is the analysis of ribozymes . The advanced electrostatic treatment adopted by the AMOEBA polarizable force field helped improve the characterization of dynamics and interaction between protein and RNA .…”