Education:
Rutgers University - B.S. Chemical and Biochemical Engineering (2015)
Email: svensken[at]rutgers.edu Office: CIPR-308
About Me:I'm interested in the development of more efficient QM/MM strategies and algorithms, with applications in studying mechanisms of catalysis in ribozymes, especially of the glmS class.
Full Publications:
Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme
(2019) 25, 1439-1456 DOI:10.1261/rna.071944.119
The pistol ribozyme (Psr) is among the most recently discovered RNA enzymes, and has been the subject of experiments aimed at elucidating mechanism. Recent biochemical studies have revealed exciting clues about catalytic interactions in the active site not apparent from available crystallographic data. The present work unifies the interpretation of the existing body of structural and functional data on Psr by providing a dynamical model for the catalytically active state in solution from molecular simulation. Our results suggest that a catalytic Mg2+ ion makes inner-sphere contact with G33:N7 and outer-sphere coordination to the pro-Rp of the scissile phosphate, promoting electrostatic stabilization of the dianionic transition state and neutralization of the developing charge of the leaving group through a metal-coordinated water molecule that is made more acidic by a hydrogen bond donated from the 2’OH of P32. This model is consistent with experimental activity-pH and mutagenesis data, including sensitivity to G33(7cG) and phosphorothioate substitution/metal ion rescue. The model suggests several experimentally testable predictions including stereospecific thio substitutions and G42X (X=xanthine) mutations, some of which have appeared and been validated during the review of this work. Further, the model identifies striking similarities of Psr to the hammerhead ribozyme (HHr), including: similar global fold, organization of secondary structure around an active site 3-way junction, catalytic metal ion binding mode, and guanine general base. However, the specific binding mode and role of the Mg2+ ion, as well as a conserved 2’-OH in the active site, are inter-related but subtly different between the ribozymes.
A predictive understanding of the mechanisms of RNA cleavage is important for the design of emerging technology built from biological and synthetic molecules that have promise for new biochemical and medicinal applications. Over the past 15 years, RNA cleavage reactions involving 2′-O-transphosphorylation have been discussed using a simplified framework introduced by Breaker that consists of four fundamental catalytic strategies (designated α, β, γ, and δ) that contribute to rate enhancement. As more detailed mechanistic data emerge, there is need for the framework to evolve and keep pace. We develop an ontology for discussion of strategies of enzymes that catalyze RNA cleavage via 2′-O-transphosphorylation that stratifies Breaker’s framework into primary (1°), secondary (2°), and tertiary (3°) contributions to enable more precise interpretation of mechanism in the context of structure and bonding. Further, we point out instances where atomic-level changes give rise to changes in more than one catalytic contribution, a phenomenon we refer to as “functional blurring”. We hope that this ontology will help clarify our conversations and pave the path forward toward a consensus view of these fundamental and fascinating mechanisms. The insight gained will deepen our understanding of RNA cleavage reactions catalyzed by natural protein and RNA enzymes, as well as aid in the design of new engineered DNA and synthetic enzymes.