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Ekesan Ş, York DM. Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme. Org Biomol Chem 2022; 20:6219-6230. [PMID: 35452066 PMCID: PMC9378597 DOI: 10.1039/d2ob00234e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The pistol ribozyme (Psr) is one among the most recently discovered classes of small nucleolytic ribozymes that catalyze site-specific RNA self-cleavage through 2'-O-transphosphorylation. The Psr contains a conserved guanine (G40) that in crystal structures is in a position suggesting it plays the role of the general base to abstract a proton from the nucleophile to activate the reaction. Although some functional data is consistent with this mechanistic role, a notable exception is 2-aminopurine (2AP) substitution which has no effect on the rate, unlike similar substitutions across other so-called "G + M" and "G + A" ribozyme classes. Herein we postulate that an alternate conserved guanine, G42, is the primary general base, and provide evidence from molecular simulations that the active site of Psr can undergo local refolding into a structure that is consistent with the common "L-platform/L-scaffold" architecture identified in G + M and G + A ribozyme classes with Psr currently the notable exception. We summarize the key currently available experimental data and present new classical and combined quantum mechanical/molecular mechanical simulation results that collectively suggest a new hypothesis. We hypothesize that there are two available catalytic pathways supported by different conformational states connected by a local refolding of the active site: (1) a primary pathway with an active site architecture aligned with the L-platform/L-scaffold framework where G42 acts as a general base, and (2) a secondary pathway with the crystallographic active site architecture where G40 acts as a general base. We go on to make several experimentally testable predictions, and suggest specific experiments that would ultimately bring closure to the mystery as to "who stole the proton in the pistol ribozyme?".
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Affiliation(s)
- Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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2
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Harish B, Wang J, Hayden EJ, Grabe B, Hiller W, Winter R, Royer CA. Hidden intermediates in Mango III RNA aptamer folding revealed by pressure perturbation. Biophys J 2022; 121:421-429. [PMID: 34971617 PMCID: PMC8822612 DOI: 10.1016/j.bpj.2021.12.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 11/12/2021] [Accepted: 12/23/2021] [Indexed: 02/03/2023] Open
Abstract
Fluorescent RNA aptamers have the potential to enable routine quantitation and localization of RNA molecules and serve as models for understanding biologically active aptamers. In recent years, several fluorescent aptamers have been selected and modified to improve their properties, revealing that small changes to the RNA or the ligands can modify significantly their fluorescent properties. Although structural biology approaches have revealed the bound, ground state of several fluorescent aptamers, characterization of low-abundance, excited states in these systems is crucial to understanding their folding pathways. Here we use pressure as an alternative variable to probe the suboptimal states of the Mango III aptamer with both fluorescence and NMR spectroscopy approaches. At moderate KCl concentrations, increasing pressure disrupted the G-quadruplex structure of the Mango III RNA and led to an intermediate with lower fluorescence. These observations indicate the existence of suboptimal RNA structural states that still bind the TO1-biotin fluorophore and moderately enhance fluorescence. At higher KCl concentration as well, the intermediate fluorescence state was populated at high pressure, but the G-quadruplex remained stable at high pressure, supporting the notion of parallel folding and/or binding pathways. These results demonstrate the usefulness of pressure for characterizing RNA folding intermediates.
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Affiliation(s)
| | - Jinqiu Wang
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy
| | | | - Bastian Grabe
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Wolf Hiller
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Catherine A. Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy,Corresponding author
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3
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Yu K, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. A hexameric ribozyme nanostructure formed by double-decker assembly of a pair of triangular ribozyme trimers. Chembiochem 2022; 23:e202100573. [PMID: 35088928 DOI: 10.1002/cbic.202100573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/29/2021] [Indexed: 11/12/2022]
Abstract
The modular architecture of naturally occurring ribozymes makes them a promising class of structural platforms to design and assemble three-dimensional (3D) RNA nanostructures, into which the catalytic ability of the platform ribozyme can be installed. We have constructed and analyzed RNA nanostructures with polygonal-shaped (closed) ribozyme oligomers by assembling unit RNAs derived from the Tetrahymena group I intron with a typical modular architecture. In this study, we dimerized ribozyme trimers with a triangular shape by introducing three pillar units. The resulting double-decker nanostructures containing six ribozyme units were characterized biochemically and their structures were observed by atomic force microscopy. The double-decker hexamers exhibited higher catalytic activity than the parent ribozyme trimers.
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Affiliation(s)
- Kai Yu
- University of Toyama: Toyama Daigaku, Department of Chemistry, JAPAN
| | - Kumi Hidaka
- Kyoto University: Kyoto Daigaku, Department of Chemistry, JAPAN
| | | | | | | | - Yoshiya Ikawa
- University of Toyama, Chemistry, Gofuku 3190, 930-8555, Toyama, JAPAN
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4
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Sengupta RN, Herschlag D. Enhancement of RNA/Ligand Association Kinetics via an Electrostatic Anchor. Biochemistry 2019; 58:2760-2768. [PMID: 31117387 PMCID: PMC6586055 DOI: 10.1021/acs.biochem.9b00231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
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The diverse biological
processes mediated by RNA rest upon its
recognition of various ligands, including small molecules and nucleic
acids. Nevertheless, a recent literature survey suggests that RNA
molecular recognition of these ligands is slow, with association rate
constants orders of magnitude below the diffusional limit. Thus, we
were prompted to consider strategies for increasing RNA association
kinetics. Proteins can accelerate ligand association via electrostatic
forces, and here, using the Tetrahymena group I ribozyme,
we provide evidence that electrostatic forces can accelerate RNA/ligand
association. This RNA enzyme (E) catalyzes cleavage of an oligonucleotide
substrate (S) by an exogenous guanosine (G) cofactor. The G 2′-
and 3′-OH groups interact with an active site metal ion, termed
MC, within E·S·G, and we perturbed each of these
contacts via −NH3+ substitution. New
and prior data indicate that G(2′NH3+) and G(3′NH3+) bind as strongly as
G, suggesting that the −NH3+ substituents
of these analogues avoid repulsive interactions with MC and make alternative interactions. Unexpectedly, removal of the
adjacent −OH via −H substitution to give G(2′H,3′NH3+) and G(2′NH3+,3′H) enhanced binding, in stark contrast to the deleterious
effect of these substitutions on G binding. Pulse–chase experiments
indicate that the −NH3+ moiety of G(2′H,3′NH3+) increases the rate of G association. These results
suggest that the positively charged −NH3+ group can act as a molecular “anchor” to increase
the residence time of the encounter complex and thereby enhance productive
binding. Electrostatic anchors may provide a broadly applicable strategy
for the development of fast binding RNA ligands and RNA-targeted therapeutics.
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Affiliation(s)
- Raghuvir N Sengupta
- Department of Biochemistry , Stanford University , Stanford , California 94305 , United States
| | - Daniel Herschlag
- Department of Biochemistry , Stanford University , Stanford , California 94305 , United States.,Departments of Chemical Engineering and Chemistry , Stanford University , Stanford , California 94305 , United States.,Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health) , Stanford University , Stanford , California 94305 , United States
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5
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Zhao F, Lee EY, Shin Y. Improved Reversible Cross-Linking-Based Solid-Phase RNA Extraction for Pathogen Diagnostics. Anal Chem 2018; 90:1725-1733. [DOI: 10.1021/acs.analchem.7b03493] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Fei Zhao
- Department of Convergence Medicine, Asan Medical Center,
University of Ulsan College of Medicine, and Biomedical Engineering
Research Center, Asan Institute of Life Sciences, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Eun Yeong Lee
- Department of Convergence Medicine, Asan Medical Center,
University of Ulsan College of Medicine, and Biomedical Engineering
Research Center, Asan Institute of Life Sciences, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Center,
University of Ulsan College of Medicine, and Biomedical Engineering
Research Center, Asan Institute of Life Sciences, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
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van Schie SNS, Sengupta RN, Herschlag D. Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes. PLoS One 2016; 11:e0160457. [PMID: 27501145 PMCID: PMC4976970 DOI: 10.1371/journal.pone.0160457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 07/19/2016] [Indexed: 11/18/2022] Open
Abstract
Molecular recognition is central to biology and a critical aspect of RNA function. Yet structured RNAs typically lack the preorganization needed for strong binding and precise positioning. A striking example is the group I ribozyme from Tetrahymena, which binds its guanosine substrate (G) orders of magnitude slower than diffusion. Binding of G is also thermodynamically coupled to binding of the oligonucleotide substrate (S) and further work has shown that the transition from E•G to E•S•G accompanies a conformational change that allows G to make the active site interactions required for catalysis. The group I ribozyme from Azoarcus has a similarly slow association rate but lacks the coupled binding observed for the Tetrahymena ribozyme. Here we test, using G analogs and metal ion rescue experiments, whether this absence of coupling arises from a higher degree of preorganization within the Azoarcus active site. Our results suggest that the Azoarcus ribozyme forms cognate catalytic metal ion interactions with G in the E•G complex, interactions that are absent in the Tetrahymena E•G complex. Thus, RNAs that share highly similar active site architectures and catalyze the same reactions can differ in the assembly of transition state interactions. More generally, an ability to readily access distinct local conformational states may have facilitated the evolutionary exploration needed to attain RNA machines that carry out complex, multi-step processes.
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Affiliation(s)
- Sabine N. S. van Schie
- Department of Biochemistry, Stanford University, Stanford, California, 94305, United States of America
- Leiden Institute of Chemistry, Leiden University, Leiden, 2333 CC, the Netherlands
| | - Raghuvir N. Sengupta
- Department of Biochemistry, Stanford University, Stanford, California, 94305, United States of America
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California, 94305, United States of America
- Departments of Chemical Engineering and Chemistry, Stanford University, Stanford, California, 94305, United States of America
- Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford University, Stanford, California, 94305, United States of America
- * E-mail:
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