1
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Pierce S. Life's Mechanism. Life (Basel) 2023; 13:1750. [PMID: 37629607 PMCID: PMC10455287 DOI: 10.3390/life13081750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/02/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of 'being alive'. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic of intrinsic functioning. Empirical studies demonstrate that biomolecules including ratcheting or rotating enzymes and ribozymes undergo repetitive conformation state changes driven either directly or indirectly by thermodynamic gradients. They exhibit disparate structures, but govern processes relying on directional physical motion (DNA transcription, translation, cytoskeleton transport) and share the principle of repetitive uniplanar conformation changes driven by thermodynamic gradients, producing dependable unidirectional motion: 'heat engines' exploiting thermodynamic disequilibria to perform work. Recognition that disparate biological molecules demonstrate conformation state changes involving directional motion, working in self-regulating networks, allows a mechanistic definition: life is a self-regulating process whereby matter undergoes cyclic, uniplanar conformation state changes that convert thermodynamic disequilibria into directed motion, performing work that locally reduces entropy. 'Living things' are structures including an autonomous network of units exploiting thermodynamic gradients to drive uniplanar conformation state changes that perform work. These principles are independent of any specific chemical environment, and can be applied to other biospheres.
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Affiliation(s)
- Simon Pierce
- Department of Agricultural and Environmental Sciences (DiSAA), University of Milan, Via Celoria 2, 20133 Milano, Italy
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2
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Dagenais P, Desjardins G, Legault P. An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme. Nucleic Acids Res 2021; 49:11959-11973. [PMID: 34718697 PMCID: PMC8599749 DOI: 10.1093/nar/gkab963] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022] Open
Abstract
The divide-and-conquer strategy is commonly used for protein structure determination, but its applications to high-resolution structure determination of RNAs have been limited. Here, we introduce an integrative approach based on the divide-and-conquer strategy that was undertaken to determine the solution structure of an RNA model system, the Neurospora VS ribozyme. NMR and SAXS studies were conducted on a minimal trans VS ribozyme as well as several isolated subdomains. A multi-step procedure was used for structure determination that first involved pairing refined NMR structures with SAXS data to obtain structural subensembles of the various subdomains. These subdomain structures were then assembled to build a large set of structural models of the ribozyme, which was subsequently filtered using SAXS data. The resulting NMR-SAXS structural ensemble shares several similarities with the reported crystal structures of the VS ribozyme. However, a local structural difference is observed that affects the global fold by shifting the relative orientation of the two three-way junctions. Thus, this finding highlights a global conformational change associated with substrate binding in the VS ribozyme that is likely critical for its enzymatic activity. Structural studies of other large RNAs should benefit from similar integrative approaches that allow conformational sampling of assembled fragments.
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Affiliation(s)
- Pierre Dagenais
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
| | - Geneviève Desjardins
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
| | - Pascale Legault
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
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3
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Chakraborty D, Ghosh S. Demonstration of a Ribozyme in Epsilon Domain of Hepatitis B Virus RNA. Methods Mol Biol 2021; 2167:45-59. [PMID: 32712914 DOI: 10.1007/978-1-0716-0716-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The epsilon domain of Hepatitis B virus plays a crucial role in encapsidation of viral pregenomic RNA and its partial NMR structure has been determined. However, we recently described a potassium-dependent ribonucleolytic activity associated with this region, so that a 53 nt long RNA containing the epsilon domain could release itself and cleaved other RNAs. We describe here the experimental methodologies for setting up the reactions and outline a general strategy for initial demonstration of this self-cleaving ribozyme activity.
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Affiliation(s)
| | - Sagarmoy Ghosh
- Department of Microbiology, University of Calcutta, University College of Science and Technology, Kolkata, India.
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4
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An RNA-centric historical narrative around the Protein Data Bank. J Biol Chem 2021; 296:100555. [PMID: 33744291 PMCID: PMC8080527 DOI: 10.1016/j.jbc.2021.100555] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/17/2021] [Accepted: 03/16/2021] [Indexed: 01/06/2023] Open
Abstract
Some of the amazing contributions brought to the scientific community by the Protein Data Bank (PDB) are described. The focus is on nucleic acid structures with a bias toward RNA. The evolution and key roles in science of the PDB and other structural databases for nucleic acids illustrate how small initial ideas can become huge and indispensable resources with the unflinching willingness of scientists to cooperate globally. The progress in the understanding of the molecular interactions driving RNA architectures followed the rapid increase in RNA structures in the PDB. That increase was consecutive to improvements in chemical synthesis and purification of RNA molecules, as well as in biophysical methods for structure determination and computer technology. The RNA modeling efforts from the early beginnings are also described together with their links to the state of structural knowledge and technological development. Structures of RNA and of its assemblies are physical objects, which, together with genomic data, allow us to integrate present-day biological functions and the historical evolution in all living species on earth.
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5
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Dagenais P, Legault P. In Vitro Selection of Varkud Satellite Ribozyme Variants that Cleave a Modified Stem-Loop Substrate. Methods Mol Biol 2021; 2167:61-77. [PMID: 32712915 DOI: 10.1007/978-1-0716-0716-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In vitro selection is an established approach to create artificial ribozymes with defined activities or to modify the properties of naturally occurring ribozymes. For the Varkud satellite ribozyme of Neurospora, an in vitro selection protocol based on its phosphodiester bond cleavage activity has not been previously reported. Here, we describe a simple protocol for cleavage-based in vitro selection that we recently used to identify variants of the Varkud satellite ribozyme able to target and cleave a non-natural stem-loop substrate derived from the HIV-1 TAR RNA. It allows quick selection of active ribozyme variants from the transcription reaction based on the size of the self-cleavage product without the need for RNA labeling. This results in a streamlined procedure that is easily adaptable to engineer ribozymes with new activities.
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Affiliation(s)
- Pierre Dagenais
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada.
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6
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Kumar N, Marx D. Deciphering the Self-Cleavage Reaction Mechanism of Hairpin Ribozyme. J Phys Chem B 2020; 124:4906-4918. [PMID: 32453954 DOI: 10.1021/acs.jpcb.0c03768] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hairpin ribozyme catalyzes the reversible self-cleavage of phosphodiester bonds which plays prominent roles in key biological processes involving RNAs. Despite impressive advances on ribozymatic self-cleavage, critical aspects of its molecular reaction mechanism remain controversially debated. Here, we generate and analyze the multidimensional free energy landscape that underlies the reaction using extensive QM/MM metadynamics simulations to investigate in detail the full self-cleavage mechanism. This allows us to answer several pertinent yet controversial questions concerning activation of the 2'-OH group, the mechanistic role of water molecules present in the active site, and the full reaction pathway including the structures of transition states and intermediates. Importantly, we find that a sufficiently unrestricted reaction subspace must be mapped using accelerated sampling methods in order to compute the underlying free energy landscape. It is shown that lower-dimensional sampling where the bond formation and cleavage steps are coupled does not allow the system to sufficiently explore the landscape. On the basis of a three-dimensional free energy surface spanned by flexible generalized coordinates, we find that 2'-OH is indirectly activated by adjacent G8 nucleobase in conjunction with stabilizing H-bonding involving water. This allows the proton of the 2'-OH group to directly migrate toward the 5'-leaving group via a nonbridging oxygen of the phosphodiester link. At variance with similar enzymatic processes where water wires connected to protonable side chains of the protein matrix act as transient proton shuttles, no such de/reprotonation events of water molecules are found to be involved in this ribozymatic transesterification. Overall, our results support an acid-catalyzed reaction mechanism where A38 nucleobase directly acts as an acid whereas G8, in stark contrast, participates only indirectly via stabilizing the nascent nucleophile for subsequent attack. Moreover, we conclude that self-cleavage of hairpin ribozyme follows an AN + DN two-step associative pathway where the rate-determining step is the cleavage of the phosphodiester bond. These results provide a major advancement in our understanding of the unique catalytic mechanism of hairpin ribozyme which will fruitfully impact on the design of synthetic ribozymes.
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Affiliation(s)
- Narendra Kumar
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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7
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Abstract
The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an 'RNA world', notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pK a values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.
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8
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Ren A, Micura R, Patel DJ. Structure-based mechanistic insights into catalysis by small self-cleaving ribozymes. Curr Opin Chem Biol 2017; 41:71-83. [PMID: 29107885 PMCID: PMC7955703 DOI: 10.1016/j.cbpa.2017.09.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/22/2017] [Accepted: 09/29/2017] [Indexed: 01/01/2023]
Abstract
Small self-cleaving ribozymes are widely distributed in nature and are essential for rolling-circle-based replication of satellite and pathogenic RNAs. Earlier structure-function studies on the hammerhead, hairpin, glmS, hepatitis delta virus and Varkud satellite ribozymes have provided insights into their overall architecture, their catalytic active site organization, and the role of nearby nucleobases and hydrated divalent cations in facilitating general acid-base and electrostatic-mediated catalysis. This review focuses on recent structure-function research on active site alignments and catalytic mechanisms of the Rzb hammerhead ribozyme, as well as newly-identified pistol, twister and twister-sister ribozymes. In contrast to an agreed upon mechanistic understanding of self-cleavage by Rzb hammerhead and pistol ribozymes, there exists a divergence of views as to the cleavage site alignments and catalytic mechanisms adopted by twister and twister-sister ribozymes. One approach to resolving this conundrum would be to extend the structural studies from currently available pre-catalytic conformations to their transition state mimic vanadate counterparts for both ribozymes.
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Affiliation(s)
- Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ronald Micura
- Institute of Organic Chemistry, Leopold Franzens University, Innsbruck A6020, Austria
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
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9
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Zheng L, Mairhofer E, Teplova M, Zhang Y, Ma J, Patel DJ, Micura R, Ren A. Structure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme. Nat Commun 2017; 8:1180. [PMID: 29081514 PMCID: PMC5660989 DOI: 10.1038/s41467-017-01276-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 09/01/2017] [Indexed: 11/13/2022] Open
Abstract
Here we report on the crystal structure and cleavage assays of a four-way junctional twister-sister self-cleaving ribozyme. Notably, 11 conserved spatially separated loop nucleotides are brought into close proximity at the ribozyme core through long-range interactions mediated by hydrated Mg2+ cations. The C62–A63 step at the cleavage site adopts a splayed-apart orientation, with flexible C62 directed outwards, whereas A63 is directed inwards and anchored by stacking and hydrogen-bonding interactions. Structure-guided studies of key base, sugar, and phosphate mutations in the twister-sister ribozyme, suggest contributions to the cleavage chemistry from interactions between a guanine at the active site and the non-bridging oxygen of the scissile phosphate, a feature found previously also for the related twister ribozyme. Our four-way junctional pre-catalytic structure differs significantly in the alignment at the cleavage step (splayed-apart vs. base-stacked) and surrounding residues and hydrated Mg2+ ions relative to a reported three-way junctional pre-catalytic structure of the twister-sister ribozyme. Twister-sister is a self-cleaving ribozyme. Here, the authors report the 2.0 Å crystal structure of the four-way junctional twister-sister ribozyme in the pre-catalytic state and discuss mechanistic implications based on their mutagenesis experiments and comparisons with other ribozyme structures.
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Affiliation(s)
- Luqian Zheng
- Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Elisabeth Mairhofer
- Institute of Organic Chemistry, Leopold Franzens University, A6020, Innsbruck, Austria
| | - Marianna Teplova
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Ye Zhang
- Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Jinbiao Ma
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China.,Collaborative Innovation Centre of Genetics and Development, Fudan University, 200438, Shanghai, China
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Ronald Micura
- Institute of Organic Chemistry, Leopold Franzens University, A6020, Innsbruck, Austria.
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China. .,Collaborative Innovation Centre of Genetics and Development, Fudan University, 200438, Shanghai, China.
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10
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Eggert F, Kulikov K, Domnick C, Leifels P, Kath-Schorr S. Iluminated by foreign letters - Strategies for site-specific cyclopropene modification of large functional RNAs via in vitro transcription. Methods 2017; 120:17-27. [PMID: 28454775 DOI: 10.1016/j.ymeth.2017.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/18/2017] [Accepted: 04/23/2017] [Indexed: 10/19/2022] Open
Abstract
The synthesis of sequence-specifically modified long RNA molecules, which cannot entirely be prepared via solid phase synthesis methods is experimentally challenging. We are using a new approach based on an expanded genetic alphabet preparing site-specifically modified RNA molecules via standard in vitro transcription. In this report, the site-specific labeling of functional RNAs, in particular ribozymes and a long non-coding RNA with cyclopropene moieties, is presented. We provide detailed instructions for RNA labeling via in vitro transcription and include required analytical methods to verify production and identity of the transcript. We further present post-transcriptional inverse electron demand Diels-Alder cycloaddition reactions on the cyclopropene-modified sequences and discuss applications of the genetic alphabet expansion transcription for in vitro preparation of labeled functional RNAs with complex foldings. In detail, the glmS and CPEB3 ribozymes were site-specifically decorated with methyl cyclopropene moieties using the unnatural TPT3CP triphosphate and were proven to be still functional. In addition, the structurally complex A region of the Xist lncRNA (401nt) was site-specifically modified with methyl cyclopropene and detected by fluorescence after cycloaddition reaction with a tetrazine-BODIPY conjugate.
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Affiliation(s)
- Frank Eggert
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Katharina Kulikov
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Christof Domnick
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Philipp Leifels
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Stephanie Kath-Schorr
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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11
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Dagenais P, Girard N, Bonneau E, Legault P. Insights into RNA structure and dynamics from recent NMR and X-ray studies of the Neurospora Varkud satellite ribozyme. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28382748 PMCID: PMC5573960 DOI: 10.1002/wrna.1421] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/21/2017] [Accepted: 03/08/2017] [Indexed: 12/31/2022]
Abstract
Despite the large number of noncoding RNAs and their importance in several biological processes, our understanding of RNA structure and dynamics at atomic resolution is still very limited. Like many other RNAs, the Neurospora Varkud satellite (VS) ribozyme performs its functions through dynamic exchange of multiple conformational states. More specifically, the VS ribozyme recognizes and cleaves its stem-loop substrate via a mechanism that involves several structural transitions within its stem-loop substrate. The recent publications of high-resolution structures of the VS ribozyme, obtained by NMR spectroscopy and X-ray crystallography, offer an opportunity to integrate the data and closely examine the structural and dynamic properties of this model RNA system. Notably, these investigations provide a valuable example of the divide-and-conquer strategy for structural and dynamic characterization of a large RNA, based on NMR structures of several individual subdomains. The success of this divide-and-conquer approach reflects the modularity of RNA architecture and the great care taken in identifying the independently-folding modules. Together with previous biochemical and biophysical characterizations, the recent NMR and X-ray studies provide a coherent picture into how the VS ribozyme recognizes its stem-loop substrate. Such in-depth characterization of this RNA enzyme will serve as a model for future structural and engineering studies of dynamic RNAs and may be particularly useful in planning divide-and-conquer investigations. WIREs RNA 2017, 8:e1421. doi: 10.1002/wrna.1421 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Pierre Dagenais
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Canada
| | - Nicolas Girard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Canada
| | - Eric Bonneau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Canada
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Canada
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12
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Chakraborty D, Ghosh S. The epsilon motif of hepatitis B virusRNAexhibits a potassium‐dependent ribonucleolytic activity. FEBS J 2017; 284:1184-1203. [DOI: 10.1111/febs.14050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/21/2017] [Accepted: 02/22/2017] [Indexed: 12/01/2022]
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13
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Crystal structure of Pistol, a class of self-cleaving ribozyme. Proc Natl Acad Sci U S A 2017; 114:1021-1026. [PMID: 28096403 DOI: 10.1073/pnas.1611191114] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Small self-cleaving ribozymes have been discovered in all evolutionary domains of life. They can catalyze site-specific RNA cleavage, and as a result, they have relevance in gene regulation. Comparative genomic analysis has led to the discovery of a new class of small self-cleaving ribozymes named Pistol. We report the crystal structure of Pistol at 2.97-Å resolution. Our results suggest that the Pistol ribozyme self-cleavage mechanism likely uses a guanine base in the active site pocket to carry out the phosphoester transfer reaction. The guanine G40 is in close proximity to serve as the general base for activating the nucleophile by deprotonating the 2'-hydroxyl to initiate the reaction (phosphoester transfer). Furthermore, G40 can also establish hydrogen bonding interactions with the nonbridging oxygen of the scissile phosphate. The proximity of G32 to the O5' leaving group suggests that G32 may putatively serve as the general acid. The RNA structure of Pistol also contains A-minor interactions, which seem to be important to maintain its tertiary structure and compact fold. Our findings expand the repertoire of ribozyme structures and highlight the conserved evolutionary mechanism used by ribozymes for catalysis.
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14
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Zhang S, Gu H, Chen H, Strong E, Ollie EW, Kellerman D, Liang D, Miyagi M, Anderson VE, Piccirilli JA, York DM, Harris ME. Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn(2+). Chem Commun (Camb) 2016; 52:4462-5. [PMID: 26859380 DOI: 10.1039/c5cc10212j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Solvent D2O and (18)O kinetic isotope effects on RNA 2'-O-transphosphorylation catalyzed by Zn(2+) demonstrate an altered transition state relative to specific base catalysis. A recent model from DFT calculations involving inner sphere coordination to the non-bridging and leaving group oxygens is consistent with the data.
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Affiliation(s)
- Shuming Zhang
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Hong Gu
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Haoyuan Chen
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University Piscataway, NJ 08854, USA
| | - Emily Strong
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Edward W Ollie
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Daniel Kellerman
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Danni Liang
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Masaru Miyagi
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Vernon E Anderson
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Joseph A Piccirilli
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Darrin M York
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University Piscataway, NJ 08854, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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15
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Ochieng PO, White NA, Feig M, Hoogstraten CG. Intrinsic Base-Pair Rearrangement in the Hairpin Ribozyme Directs RNA Conformational Sampling and Tertiary Interface Formation. J Phys Chem B 2016; 120:10885-10898. [PMID: 27701852 DOI: 10.1021/acs.jpcb.6b05606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Dynamic fluctuations in RNA structure enable conformational changes that are required for catalysis and recognition. In the hairpin ribozyme, the catalytically active structure is formed as an intricate tertiary interface between two RNA internal loops. Substantial alterations in the structure of each loop are observed upon interface formation, or docking. The very slow on-rate for this relatively tight interaction has led us to hypothesize a double conformational capture mechanism for RNA-RNA recognition. We used extensive molecular dynamics simulations to assess conformational sampling in the undocked form of the loop domain containing the scissile phosphate (loop A). We observed several major accessible conformations with distinctive patterns of hydrogen bonding and base stacking interactions in the active-site internal loop. Several important conformational features characteristic of the docked state were observed in well-populated substates, consistent with the kinetic sampling of docking-competent states by isolated loop A. Our observations suggest a hybrid or multistage binding mechanism, in which initial conformational selection of a docking-competent state is followed by induced-fit adjustment to an in-line, chemically reactive state only after formation of the initial complex with loop B.
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Affiliation(s)
- Patrick O Ochieng
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States
| | - Neil A White
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States
| | - Charles G Hoogstraten
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States
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16
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Gohara DW, Di Cera E. Molecular Mechanisms of Enzyme Activation by Monovalent Cations. J Biol Chem 2016; 291:20840-20848. [PMID: 27462078 DOI: 10.1074/jbc.r116.737833] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Regulation of enzymes through metal ion complexation is widespread in biology and underscores a physiological need for stability and high catalytic activity that likely predated proteins in the RNA world. In addition to divalent metals such as Ca2+, Mg2+, and Zn2+, monovalent cations often function as efficient and selective promoters of catalysis. Advances in structural biology unravel a rich repertoire of molecular mechanisms for enzyme activation by Na+ and K+ Strategies range from short-range effects mediated by direct participation in substrate binding, to more distributed effects that propagate long-range to catalytic residues. This review addresses general considerations and examples.
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Affiliation(s)
- David W Gohara
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Enrico Di Cera
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
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17
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Lacroix-Labonté J, Girard N, Dagenais P, Legault P. Rational engineering of the Neurospora VS ribozyme to allow substrate recognition via different kissing-loop interactions. Nucleic Acids Res 2016; 44:6924-34. [PMID: 27166370 PMCID: PMC5001590 DOI: 10.1093/nar/gkw401] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/30/2016] [Indexed: 12/24/2022] Open
Abstract
The Neurospora VS ribozyme is a catalytic RNA that has the unique ability to specifically recognize and cleave a stem-loop substrate through formation of a highly stable kissing-loop interaction (KLI). In order to explore the engineering potential of the VS ribozyme to cleave alternate substrates, we substituted the wild-type KLI by other known KLIs using an innovative engineering method that combines rational and combinatorial approaches. A bioinformatic search of the protein data bank was initially performed to identify KLIs that are structurally similar to the one found in the VS ribozyme. Next, substrate/ribozyme (S/R) pairs that incorporate these alternative KLIs were kinetically and structurally characterized. Interestingly, several of the resulting S/R pairs allowed substrate cleavage with substantial catalytic efficiency, although with reduced activity compared to the reference S/R pair. Overall, this study describes an innovative approach for RNA engineering and establishes that the KLI of the trans VS ribozyme can be adapted to cleave other folded RNA substrates.
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Affiliation(s)
- Julie Lacroix-Labonté
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Nicolas Girard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Pierre Dagenais
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
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18
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Harris ME, Piccirilli JA, York DM. Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1801-8. [PMID: 25936517 DOI: 10.1016/j.bbapap.2015.04.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 01/21/2023]
Abstract
The well-studied mechanism of ribonuclease A is believed to involve concerted general acid-base catalysis by two histidine residues, His12 and His119. The basic features of this mechanism are often cited to explain rate enhancement by both protein and RNA enzymes that catalyze RNA 2'-O-transphosphorylation. Recent kinetic isotope effect analyses and computational studies are providing a more chemically detailed description of the mechanism of RNase A and the rate limiting transition state. Overall, the results support an asynchronous mechanism for both solution and ribonuclease catalyzed reactions in which breakdown of a transient dianoinic phosphorane intermediate by 5'OP bond cleavage is rate limiting. Relative to non-enzymatic reactions catalyzed by specific base, a smaller KIE on the 5'O leaving group and a less negative βLG are observed for RNase A catalysis. Quantum mechanical calculations consistent with these data support a model in which electrostatic and H-bonding interactions with the non-bridging oxygens and proton transfer from His119 render departure of the 5'O less advanced and stabilize charge buildup in the transition state. Both experiment and computation indicate advanced 2'OP bond formation in the rate limiting transition state. However, this feature makes it difficult to resolve the chemical steps involved in 2'O activation. Thus, modeling the transition state for RNase A catalysis underscores those elements of its chemical mechanism that are well resolved, as well as highlighting those where ambiguity remains. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.
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Affiliation(s)
- Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44118, United States.
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, United States; Department of Chemistry, University of Chicago, Chicago, IL 60637, United States
| | - Darrin M York
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, United States; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States
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19
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Panteva MT, Dissanayake T, Chen H, Radak BK, Kuechler ER, Giambaşu GM, Lee TS, York DM. Multiscale methods for computational RNA enzymology. Methods Enzymol 2015; 553:335-74. [PMID: 25726472 PMCID: PMC4739856 DOI: 10.1016/bs.mie.2014.10.064] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNA catalysis is of fundamental importance to biology and yet remains ill-understood due to its complex nature. The multidimensional "problem space" of RNA catalysis includes both local and global conformational rearrangements, changes in the ion atmosphere around nucleic acids and metal ion binding, dependence on potentially correlated protonation states of key residues, and bond breaking/forming in the chemical steps of the reaction. The goal of this chapter is to summarize and apply multiscale modeling methods in an effort to target the different parts of the RNA catalysis problem space while also addressing the limitations and pitfalls of these methods. Classical molecular dynamics simulations, reference interaction site model calculations, constant pH molecular dynamics (CpHMD) simulations, Hamiltonian replica exchange molecular dynamics, and quantum mechanical/molecular mechanical simulations will be discussed in the context of the study of RNA backbone cleavage transesterification. This reaction is catalyzed by both RNA and protein enzymes, and here we examine the different mechanistic strategies taken by the hepatitis delta virus ribozyme and RNase A.
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Affiliation(s)
- Maria T Panteva
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Thakshila Dissanayake
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Haoyuan Chen
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Brian K Radak
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Erich R Kuechler
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - George M Giambaşu
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Tai-Sung Lee
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Darrin M York
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA.
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20
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Ramia NF, Spilman M, Tang L, Shao Y, Elmore J, Hale C, Cocozaki A, Bhattacharya N, Terns RM, Terns MP, Li H, Stagg SM. Essential structural and functional roles of the Cmr4 subunit in RNA cleavage by the Cmr CRISPR-Cas complex. Cell Rep 2014; 9:1610-1617. [PMID: 25482566 DOI: 10.1016/j.celrep.2014.11.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/14/2014] [Accepted: 11/05/2014] [Indexed: 10/24/2022] Open
Abstract
The Cmr complex is the multisubunit effector complex of the type III-B clustered regularly interspaced short palindromic repeats (CRISPR)-Cas immune system. The Cmr complex recognizes a target RNA through base pairing with the integral CRISPR RNA (crRNA) and cleaves the target at multiple regularly spaced locations within the complementary region. To understand the molecular basis of the function of this complex, we have assembled information from electron microscopic and X-ray crystallographic structural studies and mutagenesis of a complete Pyrococcus furiosus Cmr complex. Our findings reveal that four helically packed Cmr4 subunits, which make up the backbone of the Cmr complex, act as a platform to support crRNA binding and target RNA cleavage. Interestingly, we found a hook-like structural feature associated with Cmr4 that is likely the site of target RNA binding and cleavage. Our results also elucidate analogies in the mechanisms of crRNA and target molecule binding by the distinct Cmr type III-A and Cascade type I-E complexes.
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Affiliation(s)
- Nancy F Ramia
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Michael Spilman
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Li Tang
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Yaming Shao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Joshua Elmore
- Departments of Biochemistry and Molecular Biology, Genetics, and Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Caryn Hale
- Departments of Biochemistry and Molecular Biology, Genetics, and Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Alexis Cocozaki
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | | | - Rebecca M Terns
- Departments of Biochemistry and Molecular Biology, Genetics, and Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Michael P Terns
- Departments of Biochemistry and Molecular Biology, Genetics, and Microbiology, University of Georgia, Athens, GA 30602, USA.
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
| | - Scott M Stagg
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
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21
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Estarellas C, Otyepka M, Koča J, Banáš P, Krepl M, Šponer J. Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease. Biochim Biophys Acta Gen Subj 2014; 1850:1072-1090. [PMID: 25450173 DOI: 10.1016/j.bbagen.2014.10.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/15/2014] [Accepted: 10/20/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Many prokaryotic genomes comprise Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) offering defense against foreign nucleic acids. These immune systems are conditioned by the production of small CRISPR-derived RNAs matured from long RNA precursors. This often requires a Csy4 endoribonuclease cleaving the RNA 3'-end. METHODS We report extended explicit solvent molecular dynamic (MD) simulations of Csy4/RNA complex in precursor and product states, based on X-ray structures of product and inactivated precursor (55 simulations; ~3.7μs in total). RESULTS The simulations identify double-protonated His29 and deprotonated terminal phosphate as the likely dominant protonation states consistent with the product structure. We revealed potential substates consistent with Ser148 and His29 acting as the general base and acid, respectively. The Ser148 could be straightforwardly deprotonated through solvent and could without further structural rearrangements deprotonate the nucleophile, contrasting similar studies investigating the general base role of nucleobases in ribozymes. We could not locate geometries consistent with His29 acting as general base. However, we caution that the X-ray structures do not always capture the catalytically active geometries and then the reactive structures may be unreachable by the simulation technique. CONCLUSIONS We identified potential catalytic arrangement of the Csy4/RNA complex but we also report limitations of the simulation technique. Even for the dominant protonation state we could not achieve full agreement between the simulations and the structural data. GENERAL SIGNIFICANCE Potential catalytic arrangement of the Csy4/RNA complex is found. Further, we provide unique insights into limitations of simulations of protein/RNA complexes, namely, the influence of the starting experimental structures and force field limitations. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Affiliation(s)
- Carolina Estarellas
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic; Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic.
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22
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Henriksen NM, Hayatshahi HS, Davis D, Cheatham TE. Structural and energetic analysis of 2-aminobenzimidazole inhibitors in complex with the hepatitis C virus IRES RNA using molecular dynamics simulations. J Chem Inf Model 2014; 54:1758-72. [PMID: 24835734 PMCID: PMC4076022 DOI: 10.1021/ci500132c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Indexed: 12/15/2022]
Abstract
Despite the many biological functions of RNA, very few drugs have been designed or found to target RNA. Here we report the results of molecular dynamics (MD) simulations and binding energy analyses on hepatitis C virus internal ribosome entry site (IRES) RNA in complex with highly charged 2-aminobenzimidazole inhibitors. Initial coordinates were taken from NMR and crystallography studies that had yielded different binding modes. During MD simulations, the RNA-inhibitor complex is stable in the crystal conformation but not in the NMR conformation. Additionally, we found that existing and standard MD trajectory postprocessing free energy methods, such as the MM-GBSA and MM-PBSA approaches available in AMBER, seem unsuitable to properly rank the binding energies of complexes between highly charged molecules. A better correlation with the experimental data was found using a rather simple binding enthalpy calculation based on the explicitly solvated potential energies. In anticipation of further growth in the use of small molecules to target RNA, we include results addressing the impact of charge assignment on docking, the structural role of magnesium in the IRES-inhibitor complex, the entropic contribution to binding energy, and simulations of a plausible scaffold design for new inhibitors.
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Affiliation(s)
| | - Hamed S. Hayatshahi
- Department of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States
| | - Darrell
R. Davis
- Department of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States
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23
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Ganguly A, Thaplyal P, Rosta E, Bevilacqua PC, Hammes-Schiffer S. Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme. J Am Chem Soc 2014; 136:1483-96. [PMID: 24383543 PMCID: PMC3954522 DOI: 10.1021/ja4104217] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
The
hepatitis delta virus (HDV) ribozyme catalyzes a self-cleavage
reaction using a combination of nucleobase and metal ion catalysis.
Both divalent and monovalent ions can catalyze this reaction, although
the rate is slower with monovalent ions alone. Herein, we use quantum
mechanical/molecular mechanical (QM/MM) free energy simulations to
investigate the mechanism of this ribozyme and to elucidate the roles
of the catalytic metal ion. With Mg2+ at the catalytic
site, the self-cleavage mechanism is observed to be concerted with
a phosphorane-like transition state and a free energy barrier of ∼13
kcal/mol, consistent with free energy barrier values extrapolated
from experimental studies. With Na+ at the catalytic site,
the mechanism is observed to be sequential, passing through a phosphorane
intermediate, with free energy barriers of 2–4 kcal/mol for
both steps; moreover, proton transfer from the exocyclic amine of
protonated C75 to the nonbridging oxygen of the scissile phosphate
occurs to stabilize the phosphorane intermediate in the sequential
mechanism. To explain the slower rate observed experimentally with
monovalent ions, we hypothesize that the activation of the O2′
nucleophile by deprotonation and orientation is less favorable with
Na+ ions than with Mg2+ ions. To explore this
hypothesis, we experimentally measure the pKa of O2′ by kinetic and NMR methods and find it to be
lower in the presence of divalent ions rather than only monovalent
ions. The combined theoretical and experimental results indicate that
the catalytic Mg2+ ion may play three key roles: assisting
in the activation of the O2′ nucleophile, acidifying the general
acid C75, and stabilizing the nonbridging oxygen to prevent proton
transfer to it.
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Affiliation(s)
- Abir Ganguly
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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24
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Elsässer B, Fels G, Weare JH. QM/MM simulation (B3LYP) of the RNase A cleavage-transesterification reaction supports a triester A(N) + D(N) associative mechanism with an O2' H internal proton transfer. J Am Chem Soc 2014; 136:927-36. [PMID: 24372083 DOI: 10.1021/ja406122c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanism of the backbone cleavage-transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report quantum mechanics/molecule mechanics (QM/MM) free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2' oxygen on the neighboring diester phosphate bond, and both reach the same product state (PS) (a O3'-O2' cyclic phosphate and a O5' hydroxyl terminated fragment). Path 1, resembles the widely accepted dianionic transition-state (TS) general acid (His119)/base (His12) classical mechanism. However, this path has a barrier (25 kcal/mol) higher than that of the rate-limiting hydrolysis step and a very loose TS. In Path 2, the proton initially coordinating the O2' migrates to the nonbridging O1P in the initial reaction path rather than directly to the general base resulting in a triester (substrate as base) AN + DN mechanism with a monoanionic weakly stable intermediate. The structures in the transition region are associative with low barriers (TS1 10, TS2 7.5 kcal/mol). The Path 2 mechanism is consistent with the many results from enzyme and buffer catalyzed and uncatalyzed analog reactions and leads to a PS consistent with the reactive state for the following hydrolysis step. The differences between the consistently estimated barriers in Path 1 and 2 lead to a 10(11) difference in rate strongly supporting the less accepted triester mechanism.
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Affiliation(s)
- Brigitta Elsässer
- Department of Chemistry, University of Paderborn , Warburgerstr. 100, D-33098 Paderborn, Germany
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25
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Unraveling the Thermodynamics and Kinetics of RNA Assembly. Methods Enzymol 2014. [DOI: 10.1016/b978-0-12-801122-5.00017-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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26
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Structure of a dimeric crenarchaeal Cas6 enzyme with an atypical active site for CRISPR RNA processing. Biochem J 2013; 452:223-30. [PMID: 23527601 PMCID: PMC3652601 DOI: 10.1042/bj20130269] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The competition between viruses and hosts is played out in all branches of life. Many prokaryotes have an adaptive immune system termed ‘CRISPR’ (clustered regularly interspaced short palindromic repeats) which is based on the capture of short pieces of viral DNA. The captured DNA is integrated into the genomic DNA of the organism flanked by direct repeats, transcribed and processed to generate crRNA (CRISPR RNA) that is loaded into a variety of effector complexes. These complexes carry out sequence-specific detection and destruction of invading mobile genetic elements. In the present paper, we report the structure and activity of a Cas6 (CRISPR-associated 6) enzyme (Sso1437) from Sulfolobus solfataricus responsible for the generation of unit-length crRNA species. The crystal structure reveals an unusual dimeric organization that is important for the enzyme's activity. In addition, the active site lacks the canonical catalytic histidine residue that has been viewed as an essential feature of the Cas6 family. Although several residues contribute towards catalysis, none is absolutely essential. Coupled with the very low catalytic rate constants of the Cas6 family and the plasticity of the active site, this suggests that the crRNA recognition and chaperone-like activities of the Cas6 family should be considered as equal to or even more important than their role as traditional enzymes.
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27
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Petkovic S, Müller S. RNA self-processing: formation of cyclic species and concatemers from a small engineered RNA. FEBS Lett 2013; 587:2435-40. [PMID: 23796421 DOI: 10.1016/j.febslet.2013.06.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/05/2013] [Accepted: 06/05/2013] [Indexed: 01/08/2023]
Abstract
We have engineered a self-processing RNA, derived from the hairpin ribozyme that runs through a cascade of cleavage and ligation reactions thereby changing its topology. The first two cleavage events leave the resulting RNA with a 5'-OH group and a 2',3'-cyclic phosphate. Thus, upon refolding, intramolecular ligation delivers a cyclic species. In addition, we demonstrate formation of concatemers resulting from multiple intermolecular ligations. Our results demonstrate the potential of RNA for self-supported topology changes and support the suggestion of 2',3'-cyclic phosphates being suitable activated building blocks for reversible phosphodiester bond formation in the RNA world.
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Affiliation(s)
- Sonja Petkovic
- Ernst-Moritz-Arndt-Universität Greifswald, Institut für Biochemie, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
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28
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Sumita M, White NA, Julien KR, Hoogstraten CG. Intermolecular domain docking in the hairpin ribozyme: metal dependence, binding kinetics and catalysis. RNA Biol 2013; 10:425-35. [PMID: 23324606 PMCID: PMC3672286 DOI: 10.4161/rna.23609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The hairpin ribozyme is a prototype small, self-cleaving RNA motif. It exists naturally as a four-way RNA junction containing two internal loops on adjoining arms. These two loops interact in a cation-driven docking step prior to chemical catalysis to form a tightly integrated structure, with dramatic changes occurring in the conformation of each loop upon docking. We investigate the thermodynamics and kinetics of the docking process using constructs in which loop A and loop B reside on separate molecules. Using a novel CD difference assay to isolate the effects of metal ions linked to domain docking, we find the intermolecular docking process to be driven by sub-millimolar concentrations of the exchange-inert Co(NH3)63+. RNA self-cleavage requires binding of lower-affinity ions with greater apparent cooperativity than the docking process itself, implying that, even in the absence of direct coordination to RNA, metal ions play a catalytic role in hairpin ribozyme function beyond simply driving loop-loop docking. Surface plasmon resonance assays reveal remarkably slow molecular association, given the relatively tight loop-loop interaction. This observation is consistent with a “double conformational capture” model in which only collisions between loop A and loop B molecules that are simultaneously in minor, docking-competent conformations are productive for binding.
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Affiliation(s)
- Minako Sumita
- Department of Biochemistry and Molecular Biology; Michigan State University; East Lansing, MI USA
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29
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A New Toolkit for Modeling RNA from a Pseudo-Torsional Space. J Mol Biol 2012; 421:1-5. [DOI: 10.1016/j.jmb.2012.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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30
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RNA-Cleaving DNA Enzymes and Their Potential Therapeutic Applications as Antibacterial and Antiviral Agents. FROM NUCLEIC ACIDS SEQUENCES TO MOLECULAR MEDICINE 2012. [PMCID: PMC7119987 DOI: 10.1007/978-3-642-27426-8_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
DNA catalysts are synthetic single-stranded DNA molecules that have been identified by in vitro selection from random sequence DNA pools. The most prominent representatives of DNA catalysts (also known as DNA enzymes, deoxyribozymes, or DNAzymes) catalyze the site-specific cleavage of RNA substrates. Two distinct groups of RNA-cleaving DNA enzymes are the 10-23 and 8-17 enzymes. A typical RNA-cleaving DNA enzyme consists of a catalytic core and two short binding arms which form Watson–Crick base pairs with the RNA targets. RNA cleavage is usually achieved with the assistance of metal ions such as Mg2+, Ca2+, Mn2+, Pb2+, or Zn2+, but several chemically modified DNA enzymes can cleave RNA in the absence of divalent metal ions. A number of studies have shown the use of 10-23 DNA enzymes for modest downregulation of therapeutically relevant RNA targets in cultured cells and in whole mammals. Here we focus on mechanistic aspects of RNA-cleaving DNA enzymes and their potential to silence therapeutically appealing viral and bacterial gene targets. We also discuss delivery options and challenges involved in DNA enzyme-based therapeutic strategies.
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31
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Wachowius F, Höbartner C. Probing essential nucleobase functional groups in aptamers and deoxyribozymes by nucleotide analogue interference mapping of DNA. J Am Chem Soc 2011; 133:14888-91. [PMID: 21863810 DOI: 10.1021/ja205894w] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nucleotide analogue interference mapping of DNA (dNAIM) is here introduced as a new nonenzymatic interference-based approach that enables high-throughput identification of essential nucleobase functional groups in DNA aptamers and in the catalytic core of deoxyribozymes. Nucleobase-modified ribonucleotides are statistically incorporated into DNA by solid-phase synthesis, employing the 2'-OH group as a chemical tag for analysis of interference effects. This method is exemplified on an AMP-binding DNA aptamer and was further used to identify indispensable nucleobase functional groups for DNA-catalyzed RNA-ligation by the Mg(2+)-dependent deoxyribozymes 7S11 and 9DB1. dNAIM should prove broadly useful for facile structural probing of functional DNA for which active and inactive variants can be separated based on catalytic or ligand-binding activities.
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Affiliation(s)
- Falk Wachowius
- Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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