1
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Halder A, Kumar S, Valsson O, Reddy G. Mg 2+ Sensing by an RNA Fragment: Role of Mg 2+-Coordinated Water Molecules. J Chem Theory Comput 2020; 16:6702-6715. [PMID: 32941038 DOI: 10.1021/acs.jctc.0c00589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA molecules selectively bind to specific metal ions to populate their functional active states, making it important to understand their source of ion selectivity. In large RNA systems, metal ions interact with the RNA at multiple locations, making it difficult to decipher the precise role of ions in folding. To overcome this complexity, we studied the role of different metal ions (Mg2+, Ca2+, and K+) in the folding of a small RNA hairpin motif (5'-ucCAAAga-3') using unbiased all-atom molecular dynamics simulations. The advantage of studying this system is that it requires specific binding of a single metal ion to fold to its native state. We find that even for this small RNA, the folding free energy surface (FES) is multidimensional as different metal ions present in the solution can simultaneously facilitate folding. The FES shows that specific binding of a metal ion is indispensable for its folding. We further show that in addition to the negatively charged phosphate groups, the spatial organization of electronegative nucleobase atoms drives the site-specific binding of the metal ions. Even though the binding site cannot discriminate between different metal ions, RNA folds efficiently only in a Mg2+ solution. We show that the rigid network of Mg2+-coordinated water molecules facilitates the formation of important interactions in the transition state. The other metal ions such as K+ and Ca2+ cannot facilitate the formation of such interactions. These results allow us to hypothesize possible metal-sensing mechanisms in large metalloriboswitches and also provide useful insights into the design of appropriate collective variables for studying large RNA molecules using enhanced sampling methods.
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Affiliation(s)
- Antarip Halder
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Sunil Kumar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Omar Valsson
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
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2
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Zettl T, Shi X, Bonilla S, Sedlak SM, Lipfert J, Herschlag D. The structural ensemble of a Holliday junction determined by X-ray scattering interference. Nucleic Acids Res 2020; 48:8090-8098. [PMID: 32597986 PMCID: PMC7641307 DOI: 10.1093/nar/gkaa509] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 05/31/2020] [Accepted: 06/26/2020] [Indexed: 11/14/2022] Open
Abstract
The DNA four-way (Holliday) junction is the central intermediate of genetic recombination, yet key aspects of its conformational and thermodynamic properties remain unclear. While multiple experimental approaches have been used to characterize the canonical X-shape conformers under specific ionic conditions, the complete conformational ensemble of this motif, especially at low ionic conditions, remains largely undetermined. In line with previous studies, our single-molecule Förster resonance energy transfer (smFRET) measurements of junction dynamics revealed transitions between two states under high salt conditions, but smFRET could not determine whether there are fast and unresolvable transitions between distinct conformations or a broad ensemble of related states under low and intermediate salt conditions. We therefore used an emerging technique, X-ray scattering interferometry (XSI), to directly probe the conformational ensemble of the Holliday junction across a wide range of ionic conditions. Our results demonstrated that the four-way junction adopts an out-of-plane geometry under low ionic conditions and revealed a conformational state at intermediate ionic conditions previously undetected by other methods. Our results provide critical information to build toward a full description of the conformational landscape of the Holliday junction and underscore the utility of XSI for probing conformational ensembles under a wide range of solution conditions.
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Affiliation(s)
- Thomas Zettl
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, 80799 Munich, Germany
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Xuesong Shi
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Steve Bonilla
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Steffen M Sedlak
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, 80799 Munich, Germany
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, 80799 Munich, Germany
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
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3
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Kostenbader K, York DM. Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme. RNA (NEW YORK, N.Y.) 2019; 25:1439-1456. [PMID: 31363004 PMCID: PMC6795133 DOI: 10.1261/rna.071944.119] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/11/2019] [Indexed: 05/27/2023]
Abstract
The pistol ribozyme (Psr) is among the most recently discovered RNA enzymes and has been the subject of experiments aimed at elucidating the 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 the response of cleavage activity to mutations at G42 and P32 positions in the ribozyme, and thio substitutions of the substrate in the presence of different divalent metal ions. 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 three-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 interrelated but subtly different between the ribozymes.
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Affiliation(s)
- Ken Kostenbader
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8076, USA
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8076, USA
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4
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Hattab A, Dhaouadi Z, Malloum A, Fifen JJ, Lahmar S, Russo N, Sicilia E. Structures, binding energies and temperature effects in $$ \left[ {{\text{Mg}}\left( {{\text{NH}}_{3} } \right)_{n = 1 - 10} } \right]^{2 + } $$ clusters. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2454-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Arjmand F, Afsan Z, Sharma S, Parveen S, Yousuf I, Sartaj S, Siddique HR, Tabassum S. Recent advances in metallodrug-like molecules targeting non-coding RNAs in cancer chemotherapy. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.02.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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6
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Roh JH, Kilburn D, Behrouzi R, Sung W, Briber RM, Woodson SA. Effects of Preferential Counterion Interactions on the Specificity of RNA Folding. J Phys Chem Lett 2018; 9:5726-5732. [PMID: 30211556 PMCID: PMC6351067 DOI: 10.1021/acs.jpclett.8b02086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The real-time search for native RNA structure is essential for the operation of regulatory RNAs. We previously reported that a fraction of the Azoarcus ribozyme achieves a compact structure in less than a millisecond. To scrutinize the forces that drive initial folding steps, we used time-resolved SAXS to compare the folding dynamics of this ribozyme in thermodynamically isostable concentrations of different counterions. The results show that the size of the fast-folding population increases with the number of available counterions and correlates with the flexibility of initial RNA structures. Within 1 ms of folding, Mg2+ exhibits a smaller preferential interaction coefficient per charge, ΔΓ+/ Z, than Na+ or [Co(NH3)6]3+. The lower ΔΓ+/ Z corresponds to a smaller yield of folded RNA, although Mg2+ stabilizes native RNA more efficiently than other ions at equilibrium. These results suggest that strong Mg2+-RNA interactions impede the search for globally native structure during early folding stages.
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Affiliation(s)
- Joon Ho Roh
- Department of Materials Science and Engineering , University of Maryland , College Park , Maryland 20742 , United States
- T. C. Jenkins Department of Biophysics , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Duncan Kilburn
- T. C. Jenkins Department of Biophysics , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Reza Behrouzi
- Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Wokyung Sung
- Department of Physics , Pohang University of Science and Technology , Pohang 37673 , Republic of Korea
| | - R M Briber
- Department of Materials Science and Engineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Sarah A Woodson
- T. C. Jenkins Department of Biophysics , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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7
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Cepeda-Plaza M, McGhee CE, Lu Y. Evidence of a General Acid-Base Catalysis Mechanism in the 8-17 DNAzyme. Biochemistry 2018; 57:1517-1522. [PMID: 29389111 PMCID: PMC5879137 DOI: 10.1021/acs.biochem.7b01096] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
DNAzymes are catalytic DNA molecules that can perform a variety of reactions. Although advances have been made in obtaining DNAzymes via in vitro selection and many of them have been developed into sensors and imaging agents for metal ions, bacteria, and other molecules, the structural features responsible for these enzymatic reactions are still not well understood. Previous studies of the 8-17 DNAzyme have suggested conserved guanines close to the phosphodiester transfer site may play a role in the catalytic reaction. To identify the specific guanine and functional group of the guanine responsible for the reaction, we herein report the effects of replacing G1.1 and G14 (G; p Ka,N1 = 9.4) with analogues with a different p Ka at the N1 position, such as inosine (G14I; p Ka,N1 = 8.7), 2,6-diaminopurine (G14diAP; p Ka,N1 = 5.6), and 2-aminopurine (G14AP; p Ka,N1 = 3.8) on pH-dependent reaction rates. A comparison of the pH dependence of the reaction rates of these DNAzymes demonstrated that G14 in the bulge loop next to the cleavage site, is involved in proton transfer at the catalytic site. In contrast, we did not find any evidence of G1.1 being involved in acid-base catalysis. These results support general acid-base catalysis as a feasible strategy used in DNA catalysis, as in RNA and protein enzymes.
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Affiliation(s)
- Marjorie Cepeda-Plaza
- Department of Chemical Sciences, School of Exact Sciences, Universidad Andres Bello, República 275, Santiago, Chile
| | - Claire E. McGhee
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801
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8
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Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding. J Biol Inorg Chem 2017; 23:167-177. [DOI: 10.1007/s00775-017-1519-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/14/2017] [Indexed: 10/18/2022]
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9
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Liu X, Chen Y, Fierke CA. Inner-Sphere Coordination of Divalent Metal Ion with Nucleobase in Catalytic RNA. J Am Chem Soc 2017; 139:17457-17463. [PMID: 29116782 PMCID: PMC6020041 DOI: 10.1021/jacs.7b08755] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Identification of the function of metal ions and the RNA moieties, particularly nucleobases, that bind metal ions is important in RNA catalysis. Here we combine single-atom and abasic substitutions to probe functions of conserved nucleobases in ribonuclease P (RNase P). Structural and biophysical studies of bacterial RNase P propose direct coordination of metal ions by the nucleobases of conserved uridine and guanosine in helix P4 of the RNA subunit (P RNA). To biochemically probe the function of metal ion interactions, we substituted the universally conserved bulged uridine (U51) in the P4 helix of circularly permuted Bacillus subtilis P RNA with 4-thiouridine, 4-deoxyuridine, and abasic modifications and G378/379 with 2-aminopurine, N7-deazaguanosine, and 6-thioguanosine. The functional group modifications of U51 decrease RNase P-catalyzed phosphodiester bond cleavage 16- to 23-fold, as measured by the single-turnover cleavage rate constant. The activity of the 4-thiouridine RNase P is partially rescued by addition of Cd(II) or Mn(II) ions. This is the first time a metal-rescue experiment provides evidence for inner-sphere divalent metal ion coordination with a nucleobase. Modifications of G379 modestly decrease the cleavage activity of RNase P, suggesting outer-sphere coordination of O6 on G379 to a metal ion. These data provide biochemical evidence for catalytically important interactions of the P4 helix of P RNA with metal ions, demonstrating that the bulged uridine coordinates at least one catalytic metal ion through an inner-sphere interaction. The combination of single-atom and abasic nucleotide substitutions provides a powerful strategy to probe functions of conserved nucleobases in large RNAs.
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Affiliation(s)
- Xin Liu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yu Chen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Carol A. Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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10
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Kanazawa H, Kondo J. Crystal structure of a novel RNA motif that allows for precise positioning of a single metal ion. J Inorg Biochem 2017; 176:140-143. [PMID: 28898762 DOI: 10.1016/j.jinorgbio.2017.08.029] [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] [Received: 07/03/2017] [Revised: 08/15/2017] [Accepted: 08/30/2017] [Indexed: 11/18/2022]
Abstract
We have determined a crystal structure of an RNA duplex containing a novel metal-binding motif. The motif is composed of two sheared G○A base pairs, two unpaired A residues and four phosphate groups in close proximity. Four A residues make an A-A-A-A stacking column at the minor groove side and two G bases are highly inclined, thereby forming the pocket-shaped motif at the major groove side. In the present structure, a hydrated Sr2+ ion exists in the pocket and binds to the O6 and N7 atoms of the two G bases and four phosphate groups. According to the previously-reported metal-binding properties to RNA molecules, many of divalent cations, such as Mg2+, Mn2+, Co2+, Zn2+, Ba2+, Pb2+ and Cd2+, may bind to the motif. This metal-binding motif can be used as a modular building block that allows for precise positioning of a single metal ion in functional nucleic acid molecules.
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Affiliation(s)
- Hiroki Kanazawa
- Graduate School of Science and Technology, Sophia University, Tokyo 102-8554, Japan
| | - Jiro Kondo
- Graduate School of Science and Technology, Sophia University, Tokyo 102-8554, Japan; Department of Materials and Life Sciences, Sophia University, Tokyo 102-8554, Japan.
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11
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Karuppiah V, Ranaghan KE, Leferink NGH, Johannissen LO, Shanmugam M, Ní Cheallaigh A, Bennett NJ, Kearsey LJ, Takano E, Gardiner JM, van der Kamp MW, Hay S, Mulholland AJ, Leys D, Scrutton NS. Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase. ACS Catal 2017; 7:6268-6282. [PMID: 28966840 PMCID: PMC5617326 DOI: 10.1021/acscatal.7b01924] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/04/2017] [Indexed: 02/02/2023]
Abstract
Terpenoids form the largest and stereochemically most diverse class of natural products, and there is considerable interest in producing these by biocatalysis with whole cells or purified enzymes, and by metabolic engineering. The monoterpenes are an important class of terpenes and are industrially important as flavors and fragrances. We report here structures for the recently discovered Streptomyces clavuligerus monoterpene synthases linalool synthase (bLinS) and 1,8-cineole synthase (bCinS), and we show that these are active biocatalysts for monoterpene production using biocatalysis and metabolic engineering platforms. In metabolically engineered monoterpene-producing E. coli strains, use of bLinS leads to 300-fold higher linalool production compared with the corresponding plant monoterpene synthase. With bCinS, 1,8-cineole is produced with 96% purity compared to 67% from plant species. Structures of bLinS and bCinS, and their complexes with fluorinated substrate analogues, show that these bacterial monoterpene synthases are similar to previously characterized sesquiterpene synthases. Molecular dynamics simulations suggest that these monoterpene synthases do not undergo large-scale conformational changes during the reaction cycle, making them attractive targets for structured-based protein engineering to expand the catalytic scope of these enzymes toward alternative monoterpene scaffolds. Comparison of the bLinS and bCinS structures indicates how their active sites steer reactive carbocation intermediates to the desired acyclic linalool (bLinS) or bicyclic 1,8-cineole (bCinS) products. The work reported here provides the analysis of structures for this important class of monoterpene synthase. This should now guide exploitation of the bacterial enzymes as gateway biocatalysts for the production of other monoterpenes and monoterpenoids.
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Affiliation(s)
- Vijaykumar Karuppiah
- BBSRC/EPSRC
Manchester Synthetic Biology Research Centre for Fine and Specialty
Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School
of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Kara E. Ranaghan
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Nicole G. H. Leferink
- BBSRC/EPSRC
Manchester Synthetic Biology Research Centre for Fine and Specialty
Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School
of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Linus O. Johannissen
- BBSRC/EPSRC
Manchester Synthetic Biology Research Centre for Fine and Specialty
Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School
of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Muralidharan Shanmugam
- BBSRC/EPSRC
Manchester Synthetic Biology Research Centre for Fine and Specialty
Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School
of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Aisling Ní Cheallaigh
- BBSRC/EPSRC
Manchester Synthetic Biology Research Centre for Fine and Specialty
Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School
of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Nathan J. Bennett
- BBSRC/EPSRC
Manchester Synthetic Biology Research Centre for Fine and Specialty
Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School
of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Lewis J. Kearsey
- BBSRC/EPSRC
Manchester Synthetic Biology Research Centre for Fine and Specialty
Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School
of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Eriko Takano
- BBSRC/EPSRC
Manchester Synthetic Biology Research Centre for Fine and Specialty
Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School
of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - John M. Gardiner
- BBSRC/EPSRC
Manchester Synthetic Biology Research Centre for Fine and Specialty
Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School
of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Marc W. van der Kamp
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Sam Hay
- BBSRC/EPSRC
Manchester Synthetic Biology Research Centre for Fine and Specialty
Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School
of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - David Leys
- BBSRC/EPSRC
Manchester Synthetic Biology Research Centre for Fine and Specialty
Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School
of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Nigel S. Scrutton
- BBSRC/EPSRC
Manchester Synthetic Biology Research Centre for Fine and Specialty
Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School
of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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12
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Panja S, Hua B, Zegarra D, Ha T, Woodson SA. Metals induce transient folding and activation of the twister ribozyme. Nat Chem Biol 2017; 13:1109-1114. [PMID: 28825710 PMCID: PMC5605428 DOI: 10.1038/nchembio.2459] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 07/18/2017] [Indexed: 11/15/2022]
Abstract
Twister is a small ribozyme present in almost all kingdoms of life that rapidly self-cleaves in variety of divalent metal ions. We used activity assays, bulk FRET and single-molecule FRET (smFRET) to understand how different metal ions promote folding and self-cleavage of the Oryza sativa Twister ribozyme. Although most ribozymes require additional Mg2+ for catalysis, Twister inverts this expectation, requiring 20–30 times less Mg2+ to self-cleave than to fold. Transition metals such as Co2+, Ni2+ and Zn2+ activate Twister more efficiently than Mg2+ ions. Although Twister is fully active in ≤ 0.5 mM MgCl2, smFRET experiments showed that the ribozyme visits the folded state infrequently under these conditions. Comparison of folding and self-cleavage rates indicates that most folding events lead to catalysis, which correlates with metal bond strength. Thus, the robust activity of Twister reports on transient metal ion binding under physiological conditions.
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Affiliation(s)
- Subrata Panja
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Boyang Hua
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Diego Zegarra
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Taekjip Ha
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
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13
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Characterization of tRNALeu binding interactions with Cu2+ and Pb2+ and their biological implications. J Inorg Biochem 2017; 171:90-99. [DOI: 10.1016/j.jinorgbio.2017.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/12/2017] [Accepted: 03/19/2017] [Indexed: 11/17/2022]
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14
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Bingaman JL, Zhang S, Stevens DR, Yennawar NH, Hammes-Schiffer S, Bevilacqua PC. The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme. Nat Chem Biol 2017; 13:439-445. [PMID: 28192411 PMCID: PMC5362308 DOI: 10.1038/nchembio.2300] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 12/09/2016] [Indexed: 01/06/2023]
Abstract
RNA enzymes (ribozymes) have remarkably diverse biological roles despite having limited chemical diversity. Protein enzymes enhance their reactivity through recruitment of cofactors; likewise, the naturally occurring glmS ribozyme uses the glucosamine-6-phosphate (GlcN6P) organic cofactor for phosphodiester bond cleavage. Prior structural and biochemical studies have implicated GlcN6P as the general acid. Here we describe new catalytic roles of GlcN6P through experiments and calculations. Large stereospecific normal thio effects and a lack of metal-ion rescue in the holoribozyme indicate that nucleobases and the cofactor play direct chemical roles and align the active site for self-cleavage. Large stereospecific inverse thio effects in the aporibozyme suggest that the GlcN6P cofactor disrupts an inhibitory interaction of the nucleophile. Strong metal-ion rescue in the aporibozyme reveals that this cofactor also provides electrostatic stabilization. Ribozyme organic cofactors thus perform myriad catalytic roles, thereby allowing RNA to compensate for its limited functional diversity.
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Affiliation(s)
- Jamie L. Bingaman
- Department of Chemistry and Center for RNA Molecular
Biology, The Pennsylvania State University, University Park, Pennsylvania 16802,
United States
| | - Sixue Zhang
- Department of Chemistry, University of Illinois at
Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - David R. Stevens
- Department of Chemistry, University of Illinois at
Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Neela H. Yennawar
- X-ray Crystallography Facility, Huck Institutes of the Life
Sciences, The Pennsylvania State University, 8 Althouse Laboratory, University Park,
Pennsylvania 16802, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at
Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Philip C. Bevilacqua
- Department of Chemistry and Center for RNA Molecular
Biology, The Pennsylvania State University, University Park, Pennsylvania 16802,
United States
- Department of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, Pennsylvania 16802, United
States
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15
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Luo YL, Zhang XY, Wang Y, Han FJ, Xu F, Chen YS. Mediating physicochemical properties and paclitaxel release of pH-responsive H-type multiblock copolymer self-assembly nanomicelles through epoxidation. J Mater Chem B 2017; 5:3111-3121. [DOI: 10.1039/c7tb00073a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We focused on modulation of the physicochemical and biomedical properties of copolymer nanomicellesviaepoxidation, which provided significant improvements.
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Affiliation(s)
- Yan-Ling Luo
- Key Laboratory of Macromolecular Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- P. R. China
| | - Xue-Yin Zhang
- Key Laboratory of Macromolecular Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- P. R. China
| | - Yuan Wang
- Key Laboratory of Macromolecular Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- P. R. China
| | - Fang-Jie Han
- Key Laboratory of Macromolecular Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- P. R. China
| | - Feng Xu
- Key Laboratory of Macromolecular Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- P. R. China
| | - Ya-Shao Chen
- Key Laboratory of Macromolecular Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- P. R. China
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16
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Börner R, Kowerko D, Miserachs HG, Schaffer MF, Sigel RK. Metal ion induced heterogeneity in RNA folding studied by smFRET. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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17
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The X-ray Structures of Six Octameric RNA Duplexes in the Presence of Different Di- and Trivalent Cations. Int J Mol Sci 2016; 17:ijms17070988. [PMID: 27355942 PMCID: PMC4964368 DOI: 10.3390/ijms17070988] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/10/2016] [Accepted: 06/15/2016] [Indexed: 12/15/2022] Open
Abstract
Due to the polyanionic nature of RNA, the principles of charge neutralization and electrostatic condensation require that cations help to overcome the repulsive forces in order for RNA to adopt a three-dimensional structure. A precise structural knowledge of RNA-metal ion interactions is crucial to understand the mechanism of metal ions in the catalytic or regulatory activity of RNA. We solved the crystal structure of an octameric RNA duplex in the presence of the di- and trivalent metal ions Ca(2+), Mn(2+), Co(2+), Cu(2+), Sr(2+), and Tb(3+). The detailed investigation reveals a unique innersphere interaction to uracil and extends the knowledge of the influence of metal ions for conformational changes in RNA structure. Furthermore, we could demonstrate that an accurate localization of the metal ions in the X-ray structures require the consideration of several crystallographic and geometrical parameters as well as the anomalous difference map.
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18
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Ito K, Schramm MP, Kanaura M, Ide M, Endo N, Iwasawa T. Synthesis of tri-arylated cyclotriveratrilenes with ortho - and meta -extended functionality. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2015.12.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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19
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Schramm MP, Kanaura M, Ito K, Ide M, Iwasawa T. Introverted Phosphorus-Au Cavitands for Catalytic Use. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501426] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Qi X, Xia T. Structure, dynamics, and mechanism of the lead-dependent ribozyme. Biomol Concepts 2015; 2:305-14. [PMID: 25962038 DOI: 10.1515/bmc.2011.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 06/06/2011] [Indexed: 12/24/2022] Open
Abstract
Leadzyme is a small catalytic RNA that was identified by in vitro selection for Pb2+-dependent cleavage from a tRNA library. Leadzyme employs a unique two-step Pb2+-specific mechanism to cleave within its active site. NMR and crystal structures of the active site revealed different folding patterns, but neither features the in-line alignment for attack by the 2'-OH nucleophilic group. These experimentally determined structures most likely represent ground states and are catalytically inactive. There are significant dynamics of the active site and the motif samples multiple conformations at the ground states. Various metal ion binding sites have been identified, including one that may be occupied by a catalytic Pb2+. Based on functional group analysis, a computational model of the transition state has been proposed. This model features a unique base triple that is consistent with sequence and functional group requirements for catalysis. This structure is likely only populated transiently, but imposing appropriate conformational constraints may significantly stabilize this state thereby promoting catalysis. Other ions may inhibit the cleavage by competing for the Pb2+ binding site, or by stabilizing the ground state thereby suppressing its transition to the catalytically active conformation. Some rare earth ions can enhance the reaction via an unknown mechanism. Because of its unique chemistry and dynamic behavior, leadzyme can continue to serve as an excellent model system for teaching us RNA biology and chemistry.
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21
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Kanaura M, Ito K, Schramm MP, Ajami D, Iwasawa T. Cavitands with inwardly and outwardly directed functional groups. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.06.072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Panteva MT, GiambaȈsu GM, York DM. Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations. J Comput Chem 2015; 36:970-82. [PMID: 25736394 PMCID: PMC4409555 DOI: 10.1002/jcc.23881] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 01/17/2015] [Accepted: 02/08/2015] [Indexed: 01/09/2023]
Abstract
The prevalence of Mg(2+) ions in biology and their essential role in nucleic acid structure and function has motivated the development of various Mg(2+) ion models for use in molecular simulations. Currently, the most widely used models in biomolecular simulations represent a nonbonded metal ion as an ion-centered point charge surrounded by a nonelectrostatic pairwise potential that takes into account dispersion interactions and exchange effects that give rise to the ion's excluded volume. One strategy toward developing improved models for biomolecular simulations is to first identify a Mg(2+) model that is consistent with the simulation force fields that closely reproduces a range of properties in aqueous solution, and then, in a second step, balance the ion-water and ion-solute interactions by tuning parameters in a pairwise fashion where necessary. The present work addresses the first step in which we compare 17 different nonbonded single-site Mg(2+) ion models with respect to their ability to simultaneously reproduce structural, thermodynamic, kinetic and mass transport properties in aqueous solution. None of the models based on a 12-6 nonelectrostatic nonbonded potential was able to reproduce the experimental radial distribution function, solvation free energy, exchange barrier and diffusion constant. The models based on a 12-6-4 potential offered improvement, and one model in particular, in conjunction with the SPC/E water model, performed exceptionally well for all properties. The results reported here establish useful benchmark calculations for Mg(2+) ion models that provide insight into the origin of the behavior in aqueous solution, and may aid in the development of next-generation models that target specific binding sites in biomolecules.
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Affiliation(s)
- Maria T. Panteva
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry & Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8076, USA
| | - George M. GiambaȈsu
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry & Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8076, USA
| | - Darrin M. York
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry & Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8076, USA
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23
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Chen H, Piccirilli JA, Harris ME, York DM. Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1795-800. [PMID: 25812974 DOI: 10.1016/j.bbapap.2015.02.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/26/2015] [Accepted: 02/27/2015] [Indexed: 12/19/2022]
Abstract
Divalent metal ions, due to their ability to stabilize high concentrations of negative charge, are important for RNA folding and catalysis. Detailed models derived from the structures and kinetics of enzymes and from computational simulations have been developed. However, in most cases the specific catalytic modes involving metal ions and their mechanistic roles and effects on transition state structures remain controversial. Valuable information about the nature of the transition state is provided by measurement of kinetic isotope effects (KIEs). However, KIEs reflect changes in all bond vibrational modes that differ between the ground state and transition state. QM calculations are therefore essential for developing structural models of the transition state and evaluating mechanistic alternatives. Herein, we present computational models for Zn2+ binding to RNA 2'O-transphosphorylation reaction models that aid in the interpretation of KIE experiments. Different Zn2+ binding modes produce distinct KIE signatures, and one binding mode involving two zinc ions is in close agreement with KIEs measured for non-enzymatic catalysis by Zn2+ aquo ions alone. Interestingly, the KIE signatures in this specific model are also very close to those in RNase A catalysis. These results allow a quantitative connection to be made between experimental KIE measurements and transition state structure and bonding, and provide insight into RNA 2'O-ransphosphorylation reactions catalyzed by metal ions and enzymes. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.
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Affiliation(s)
- Haoyuan Chen
- 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
| | - Joseph A Piccirilli
- Department of Chemistry, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, United States
| | - Michael E Harris
- Department of Biochemistry, Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, United States
| | - Darrin M York
- Department of Biochemistry, Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, United States.
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24
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Kaminker I, Bye M, Mendelman N, Gislason K, Sigurdsson ST, Goldfarb D. Distance measurements between manganese(ii) and nitroxide spin-labels by DEER determine a binding site of Mn2+ in the HP92 loop of ribosomal RNA. Phys Chem Chem Phys 2015; 17:15098-102. [DOI: 10.1039/c5cp01624j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
W-band (95 GHz) double electron–electron resonance (DEER) distance measurements between Mn2+ and nitroxide spin labels were used to determine the location of a Mn2+ binding site within an RNA molecule.
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Affiliation(s)
- Ilia Kaminker
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Morgan Bye
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Natanel Mendelman
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Kristmann Gislason
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Snorri Th. Sigurdsson
- University of Iceland
- Department of Chemistry
- Science Institute Dunhaga 3
- 107 Reykjavik
- Iceland
| | - Daniella Goldfarb
- University of Iceland
- Department of Chemistry
- Science Institute Dunhaga 3
- 107 Reykjavik
- Iceland
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25
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Marcia M, Pyle AM. Principles of ion recognition in RNA: insights from the group II intron structures. RNA (NEW YORK, N.Y.) 2014; 20:516-27. [PMID: 24570483 PMCID: PMC3964913 DOI: 10.1261/rna.043414.113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/29/2014] [Indexed: 05/20/2023]
Abstract
Metal ions promote both RNA folding and catalysis, thus being essential in stabilizing the structure and determining the function of large RNA molecules, including group II introns. The latter are self-splicing metalloribozymes, containing a heteronuclear four-metal-ion center within the active site. In addition to these catalytic ions, group II introns bind many other structural ions, including delocalized ions that bind the RNA diffusively and well-ordered ions that bind the RNA tightly with high occupancy. The latter ions, which can be studied by biophysical methods, have not yet been analyzed systematically. Here, we compare crystal structures of the group IIC intron from Oceanobacillus iheyensis and classify numerous site-bound ions, which are primarily localized in the intron core and near long-range tertiary contacts. Certain ion-binding sites resemble motifs observed in known RNA structures, while others are idiosyncratic to the group II intron. Particularly interesting are (1) ions proximal to the active site, which may participate in splicing together with the catalytic four-metal-ion center, (2) organic ions that bind regions predicted to interact with intron-encoded proteins, and (3) unusual monovalent ions bound to GU wobble pairs, GA mismatches, the S-turn, the tetraloop-receptor, and the T-loop. Our analysis extends the general principles by which ions participate in RNA structural organization and it will aid in the determination and interpretation of future RNA structures.
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Affiliation(s)
- Marco Marcia
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
- Corresponding authorE-mail
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26
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Abstract
Ions surround nucleic acids in what is referred to as an ion atmosphere. As a result, the folding and dynamics of RNA and DNA and their complexes with proteins and with each other cannot be understood without a reasonably sophisticated appreciation of these ions' electrostatic interactions. However, the underlying behavior of the ion atmosphere follows physical rules that are distinct from the rules of site binding that biochemists are most familiar and comfortable with. The main goal of this review is to familiarize nucleic acid experimentalists with the physical concepts that underlie nucleic acid-ion interactions. Throughout, we provide practical strategies for interpreting and analyzing nucleic acid experiments that avoid pitfalls from oversimplified or incorrect models. We briefly review the status of theories that predict or simulate nucleic acid-ion interactions and experiments that test these theories. Finally, we describe opportunities for going beyond phenomenological fits to a next-generation, truly predictive understanding of nucleic acid-ion interactions.
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Affiliation(s)
- Jan Lipfert
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands;
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27
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Ohashi K, Ito K, Iwasawa T. Self-Folded Silyl Cavitands with In- and Outwardly Directed Allyl Groups. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301843] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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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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29
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Abstract
RNA and DNA carry out diverse functions in biology including catalysis, splicing, gene regulation, and storage of genetic information. Interest has grown in understanding how nucleic acids perform such sophisticated functions given their limited molecular repertoire. RNA can fold into diverse shapes that often perturb pKa values and allow it to ionize appreciably under biological conditions, thereby extending its molecular diversity. The goal of this chapter is to enable experimental measurement of pKa's in RNA and DNA. A number of experimental methods for measuring pKa values in RNA and DNA have been developed over the last 10 years, including RNA cleavage kinetics; UV-, fluorescence-, and NMR-detected pH titrations; and Raman crystallography. We begin with general considerations for choosing a pKa assay and then describe experimental conditions, advantages, and disadvantages for these assays. Potential pitfalls in measuring a pKa are provided including the presence of apparent pKa's due to a kinetic pKa or coupled acid- and alkali-promoted RNA unfolding, as well as degradation of RNA, precipitation of metal hydroxides and poor baselines. Use of multiple data fitting procedures and the study of appropriate mutants are described as ways to avoid some of these pitfalls. Application of these experimental methods to RNA and DNA will increase the number of available nucleic acid pKa values in the literature, which should deepen insight into biology and provide benchmarks for pKa calculations. Future directions for measuring pKa's in nucleic acids are discussed.
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Affiliation(s)
- Pallavi Thaplyal
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Philip C Bevilacqua
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA.
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30
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Enhanced group II intron retrohoming in magnesium-deficient Escherichia coli via selection of mutations in the ribozyme core. Proc Natl Acad Sci U S A 2013; 110:E3800-9. [PMID: 24043808 DOI: 10.1073/pnas.1315742110] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mobile group II introns are bacterial retrotransposons thought to be evolutionary ancestors of spliceosomal introns and retroelements in eukaryotes. They consist of a catalytically active intron RNA ("ribozyme") and an intron-encoded reverse transcriptase, which function together to promote RNA splicing and intron mobility via reverse splicing of the intron RNA into new DNA sites ("retrohoming"). Although group II introns are active in bacteria, their natural hosts, they function inefficiently in eukaryotes, where lower free Mg(2+) concentrations decrease their ribozyme activity and constitute a natural barrier to group II intron proliferation within nuclear genomes. Here, we show that retrohoming of the Ll.LtrB group II intron is strongly inhibited in an Escherichia coli mutant lacking the Mg(2+) transporter MgtA, and we use this system to select mutations in catalytic core domain V (DV) that partially rescue retrohoming at low Mg(2+) concentrations. We thus identified mutations in the distal stem of DV that increase retrohoming efficiency in the MgtA mutant up to 22-fold. Biochemical assays of splicing and reverse splicing indicate that the mutations increase the fraction of intron RNA that folds into an active conformation at low Mg(2+) concentrations, and terbium-cleavage assays suggest that this increase is due to enhanced Mg(2+) binding to the distal stem of DV. Our findings indicate that DV is involved in a critical Mg(2+)-dependent RNA folding step in group II introns and demonstrate the feasibility of selecting intron variants that function more efficiently at low Mg(2+) concentrations, with implications for evolution and potential applications in gene targeting.
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31
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Cepeda-Plaza M, Null EL, Lu Y. Metal ion as both a cofactor and a probe of metal-binding sites in a uranyl-specific DNAzyme: a uranyl photocleavage study. Nucleic Acids Res 2013; 41:9361-70. [PMID: 23939617 PMCID: PMC3814387 DOI: 10.1093/nar/gkt694] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
DNAzymes are known to bind metal ions specifically to carry out catalytic functions. Despite many studies since DNAzymes were discovered nearly two decades ago, the metal-binding sites in DNAzymes are not fully understood. Herein, we adopt uranyl photocleavage to probe specific uranyl-binding sites in the 39E DNAzyme with catalytically relevant concentrations of uranyl. The results indicate that uranyl binds between T23 and C25 in the bulge loop, G11 and T12 in the stem loop of the enzyme strand, as well as between T2.4 and G3 close to the cleavage site in the substrate strand. Control experiments using two 39E DNAzyme mutants revealed a different cleavage pattern of the mutated region. Another DNAzyme, the 8–17 DNAzyme, which has a similar secondary structure but shows no activity in the presence of uranyl, indicated a different uranyl-dependent photocleavage as well. In addition, a close correlation between the concentration-dependent photocleavage and enzymatic activities is also demonstrated. Together, these experiments suggest that uranyl photocleavage has been successfully used to probe catalytically relevant uranyl-binding sites in the 39E DNAzyme. As uranyl is the cofactor of the 39E DNAzyme as well as the probe, specific uranyl binding has now been identified without disruption of the structure.
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Affiliation(s)
- Marjorie Cepeda-Plaza
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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32
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Chatterjee A, Dixit MK, Tembe BL. Solvation Structures and Dynamics of the Magnesium Chloride (Mg2+–Cl–) Ion Pair in Water–Ethanol Mixtures. J Phys Chem A 2013; 117:8703-9. [PMID: 23829688 DOI: 10.1021/jp4031706] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anupam Chatterjee
- Department of Chemistry, Indian Institute of Technology, Bombay, Powai, Mumbai
400076, India
| | - Mayank Kumar Dixit
- Department of Chemistry, Indian Institute of Technology, Bombay, Powai, Mumbai
400076, India
| | - B. L. Tembe
- Department of Chemistry, Indian Institute of Technology, Bombay, Powai, Mumbai
400076, India
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33
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Li PTX. Analysis of diffuse K+ and Mg2+ ion binding to a two-base-pair kissing complex by single-molecule mechanical unfolding. Biochemistry 2013; 52:4991-5001. [PMID: 23842027 DOI: 10.1021/bi400646x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The folding and stability of RNA tertiary interactions depend critically on cationic conditions. It is usually difficult, however, to isolate such effects on tertiary interactions from those on the entire RNA. By manipulating conformations of single RNA molecules using optical tweezers, we distinguished individual steps of breaking and forming of a two-base-pair kissing interaction from those of secondary folding. The binding of metal ions to the small tertiary structure appeared to be saturable with an apparent Kd of 160 mM for K(+) and 1.5 mM for Mg(2+). The kissing formation was estimated to be associated with binding of ~2-3 diffuse K(+) or Mg(2+) ions. At their saturated binding, Mg(2+) provided ~3 kcal/mol more stabilizing energy to the structure than K(+). Furthermore, the cations change the unkissing forces significantly more than the kissing ones. For example, the presence of Mg(2+) ions increased the average unkissing force from 21 pN to 44 pN, surprisingly high for breaking merely two base pairs; in contrast, the mean kissing force was changed by only 4.5 pN. Interestingly, the differential salt effects on the transition forces were not caused by different changes in the height of the kinetic barriers but were instead attributed to how different molecular structures respond to the applied force. Our results showed the importance of diffuse cation binding to the stability of tertiary interaction and demonstrated the utility of mechanical unfolding in studying tertiary interactions.
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Affiliation(s)
- Pan T X Li
- Department of Biological Sciences and The RNA Institute, University at Albany, SUNY , Albany, New York 12222, United States
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34
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Tanpure AA, Pawar MG, Srivatsan SG. Fluorescent Nucleoside Analogs: Probes for Investigating Nucleic Acid Structure and Function. Isr J Chem 2013. [DOI: 10.1002/ijch.201300010] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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35
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Chen J, Ganguly A, Miswan Z, Hammes-Schiffer S, Bevilacqua PC, Golden BL. Identification of the catalytic Mg²⁺ ion in the hepatitis delta virus ribozyme. Biochemistry 2013; 52:557-67. [PMID: 23311293 DOI: 10.1021/bi3013092] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The hepatitis delta virus ribozyme catalyzes an RNA cleavage reaction using a catalytic nucleobase and a divalent metal ion. The catalytic base, C75, serves as a general acid and has a pK(a) shifted toward neutrality. Less is known about the role of metal ions in the mechanism. A recent crystal structure of the precleavage ribozyme identified a Mg²⁺ ion that interacts through its partial hydration sphere with the G25·U20 reverse wobble. In addition, this Mg²⁺ ion is in position to directly coordinate the nucleophile, the 2'-hydroxyl of U(-1), suggesting it can serve as a Lewis acid to facilitate deprotonation of the 2'-hydroxyl. To test the role of the active site Mg²⁺ ion, we replaced the G25·U20 reverse wobble with an isosteric A25·C20 reverse wobble. This change was found to significantly reduce the negative potential at the active site, as supported by electrostatics calculations, suggesting that active site Mg²⁺ binding could be adversely affected by the mutation. The kinetic analysis and molecular dynamics of the A25·C20 double mutant suggest that this variant stably folds into an active structure. However, pH-rate profiles of the double mutant in the presence of Mg²⁺ are inverted relative to the profiles for the wild-type ribozyme, suggesting that the A25·C20 double mutant has lost the active site metal ion. Overall, these studies support a model in which the partially hydrated Mg²⁺ positioned at the G25·U20 reverse wobble is catalytic and could serve as a Lewis acid, a Brønsted base, or both to facilitate deprotonation of the nucleophile.
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Affiliation(s)
- Ji Chen
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN 47907, USA
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36
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Donghi D, Pechlaner M, Finazzo C, Knobloch B, Sigel RKO. The structural stabilization of the κ three-way junction by Mg(II) represents the first step in the folding of a group II intron. Nucleic Acids Res 2012; 41:2489-504. [PMID: 23275550 PMCID: PMC3575829 DOI: 10.1093/nar/gks1179] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Folding of group II introns is characterized by a first slow compaction of domain 1 (D1) followed by the rapid docking of other domains to this scaffold. D1 compaction initiates in a small subregion encompassing the κ and ζ elements. These two tertiary elements are also the major interaction sites with domain 5 to form the catalytic core. Here, we provide the first characterization of the structure adopted at an early folding step and show that the folding control element can be narrowed down to the three-way junction with the κ motif. In our nuclear magnetic resonance studies of this substructure derived from the yeast mitochondrial group II intron Sc.ai5γ, we show that a high affinity Mg(II) ion stabilizes the κ element and enables coaxial stacking between helices d′ and d′′, favoring a rigid duplex across the three-way junction. The κ-element folds into a stable GAAA-tetraloop motif and engages in A-minor interactions with helix d′. The addition of cobalt(III)hexammine reveals three distinct binding sites. The Mg(II)-promoted structural rearrangement and rigidification of the D1 core can be identified as the first micro-step of D1 folding.
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Affiliation(s)
- Daniela Donghi
- Institute of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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37
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Analyzing coordination preferences of Mg2+ complexes: insights from computational and database study. Struct Chem 2012. [DOI: 10.1007/s11224-012-0113-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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38
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Nelson KE, Ihms HE, Mazumdar D, Bruesehoff PJ, Lu Y. The importance of peripheral sequences in determining the metal selectivity of an in vitro-selected Co(2+) -dependent DNAzyme. Chembiochem 2012; 13:381-91. [PMID: 22250000 PMCID: PMC3299816 DOI: 10.1002/cbic.201100724] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Indexed: 11/12/2022]
Abstract
DNAzymes are catalytically active DNA molecules that use metal cofactors for their enzymatic functions. While a growing number of DNAzymes with diverse functions and metal selectivities have been reported, the relationships between metal ion selectivity, conserved sequences and structures responsible for selectivity remain to be elucidated. To address this issue, we report biochemical assays of a family of previously reported in vitro selected DNAzymes. This family includes the clone 11 DNAzyme, which was isolated by positive and negative selection, and the clone 18 DNAzyme, which was isolated by positive selection alone. The clone 11 DNAzyme has a higher selectivity for Co(2+) over Pb(2+) compared with clone 18. The reasons for this difference are explored here through phylogenetic comparison, mutational analysis and stepwise truncation. A novel DNAzyme truncation method incorporated a nick in the middle of the DNAzyme to allow for truncation close to the nicked site while preserving peripheral sequences at both ends of the DNAzyme. The results demonstrate that peripheral sequences within the substrate binding arms, most notably the stem loop, loop II, are sufficient to restore its selectivity for Co(2+) over Pb(2+) to levels observed in clone 11. A comparison of these sequences' secondary structures and Co(2+) selectivities suggested that metastable structures affect metal ion selectivity. The Co(2+) selectivity of the clone 11 DNAzyme showed that the metal ion binding and selectivities of small, in vitro selected DNAzymes may be more complex than previously appreciated, and that clone 11 may be more similar to larger ribozymes than to other small DNAzymes in its structural complexity and behavior. These factors should be taken into account when metal-ion selectivity is required in rationally designed DNAzymes and DNAzyme-based biosensors.
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Affiliation(s)
- Kevin E. Nelson
- Department of Biochemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
- Department of Pediatrics, Primary Children’s Medical Center, University of Utah, 100 North Mario Capecchi Drive, Salt Lake City, UT 84113 (USA)
| | - Hannah E. Ihms
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Debapriya Mazumdar
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Peter J. Bruesehoff
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Yi Lu
- Department of Biochemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
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Ward WL, DeRose VJ. Ground-state coordination of a catalytic metal to the scissile phosphate of a tertiary-stabilized Hammerhead ribozyme. RNA (NEW YORK, N.Y.) 2012; 18:16-23. [PMID: 22124015 PMCID: PMC3261738 DOI: 10.1261/rna.030239.111] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 10/11/2011] [Indexed: 05/24/2023]
Abstract
Although the Hammerhead ribozyme (HHRz) has long been used as a model system in the field of ribozyme enzymology, several details of its mechanism are still not well understood. In particular, significant questions remain concerning the disposition and role of catalytic metals in the HHRz. Previous metal-rescue experiments using a "minimal" HHRz resulted in prediction of a catalytic metal that is bound in the A9/G10.1 site in the ground state of the reaction and that bridges to the scissile phosphate further along the reaction pathway. "Native" or extended HHRz constructs contain tertiary contacts that stabilize a more compact structure at moderate ionic strength. We performed Cd(2+) rescue experiments on an extended HHRz from Schistosoma mansoni using stereo-pure scissile phosphorothioate-substituted substrates in order to determine whether a metal ion makes contact with the scissile phosphate in the ground state or further along the reaction coordinate. Inhibition in Ca(2+)/Mg(2+) and rescue by thiophilic Cd(2+) was specific for the R(p)-S stereoisomer of the scissile phosphate. The affinity of the rescuing Cd(2+), measured in two different ionic strength backgrounds, increased fourfold to 17-fold when the pro-R(p) oxygen is replaced by sulfur. These data support a model in which the rescuing metal ion makes a ground-state interaction with the scissile phosphate in the native HHRz. The resulting model for Mg(2+) activation in the HHRz places a metal ion in contact with the scissile phosphate, where it may provide ground-state electrostatic activation of the substrate.
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Affiliation(s)
- W. Luke Ward
- Department of Chemistry, University of Oregon, Eugene, Oregon 97403-1253, USA
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1253, USA
| | - Victoria J. DeRose
- Department of Chemistry, University of Oregon, Eugene, Oregon 97403-1253, USA
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1253, USA
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40
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Erat MC, Coles J, Finazzo C, Knobloch B, Sigel RK. Accurate analysis of Mg2+ binding to RNA: From classical methods to a novel iterative calculation procedure. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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41
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Kiy MM, Jacobi ZE, Liu J. Metal-induced specific and nonspecific oligonucleotide folding studied by FRET and related biophysical and bioanalytical implications. Chemistry 2011; 18:1202-8. [PMID: 22180064 DOI: 10.1002/chem.201102515] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Indexed: 01/12/2023]
Abstract
Metal induced nucleic acid folding has been extensively studied with ribozymes, DNAzymes, tRNA and riboswitches. These RNA/DNA molecules usually have a high content of double-stranded regions to support a rigid scaffold. On the other hand, such rigid structural features are not available for many in vitro selected or rationally designed DNA aptamers; they adopt flexible random coil structures in the absence of target molecules. Upon target binding, these aptamers adaptively fold into a compact structure with a reduced end-to-end distance, making fluorescence resonance energy transfer (FRET) a popular signaling mechanism. However, nonspecific folding induced by mono- or divalent metal ions can also reduce the end-to-end distance and thus lead to false positive results. In this study we used a FRET pair labeled Hg(II) binding DNA and monitored metal-induced folding in the presence of various cations. While nonspecific electrostatically mediated folding can be very significant, at each tested salt condition, Hg(II) induced folding was still observed with a similar sensitivity. We also studied the biophysical meaning of the acceptor/donor fluorescence ratio that allowed us to explain the experimental observations. Potential solutions for this ionic strength problem have been discussed. For example, probes designed to signal the formation of double-stranded DNA showed a lower dependency on ionic strength.
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Affiliation(s)
- Mehmet Murat Kiy
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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42
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He Y, Lu Y. Metal-ion-dependent folding of a uranyl-specific DNAzyme: insight into function from fluorescence resonance energy transfer studies. Chemistry 2011; 17:13732-42. [PMID: 22052817 DOI: 10.1002/chem.201100352] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 07/25/2011] [Indexed: 01/28/2023]
Abstract
Fluorescence resonance energy transfer (FRET) has been used to study the global folding of an uranyl (UO(2)(2+))-specific 39E DNAzyme in the presence of Mg(2+), Zn(2+), Pb(2+), or UO(2)(2+). At pH 5.5 and physiological ionic strength (100 mM Na(+)), two of the three stems in this DNAzyme folded into a compact structure in the presence of Mg(2+) or Zn(2+). However, no folding occurred in the presence of Pb(2+) or UO(2)(2+); this is analogous to the "lock-and-key" catalysis mode first observed in the Pb(2+)-specific 8-17 DNAzyme. However, Mg(2+) and Zn(2+) exert different effects on the 8-17 and 39E DNAzymes. Whereas Mg(2+) or Zn(2+)-dependent folding promoted 8-17 DNAzyme activity, the 39E DNAzyme folding induced by Mg(2+) or Zn(2+) inhibited UO(2)(2+)-specific activity. Group IIA series of metal ions (Mg(2+), Ca(2+), Sr(2+)) also caused global folding of the 39E DNAzyme, for which the apparent binding affinity between these metal ions and the DNAzyme decreases as the ionic radius of the metal ions increases. Because the ionic radius of Sr(2+) (1.12 Å) is comparable to that of Pb(2+) (1.20 Å), but contrary to Pb(2+), Sr(2+) induces the DNAzyme to fold under identical conditions, ionic size alone cannot account for the unique folding behaviors induced by Pb(2+) and UO(2)(2+). Under low ionic strength (30 mM Na(+)), all four metal ions (Mg(2+), Zn(2+), Pb(2+), and UO(2)(2+)), caused 39E DNAzyme folding, suggesting that metal ions can neutralize the negative charge of DNA-backbone phosphates in addition to playing specific catalytic roles. Mg(2+) at low (<2 mM) concentration promoted UO(2)(2+)-specific activity, whereas Mg(2+) at high (>2 mM) concentration inhibited the UO(2)(2+)-specific activity. Therefore, the lock-and-key mode of DNAzymes depends on ionic strength, and the 39E DNAzyme is in the lock-and-key mode only at ionic strengths of 100 mM or greater.
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Affiliation(s)
- Ying He
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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43
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Golden BL. Two distinct catalytic strategies in the hepatitis δ virus ribozyme cleavage reaction. Biochemistry 2011; 50:9424-33. [PMID: 22003985 DOI: 10.1021/bi201157t] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The hepatitis delta virus (HDV) ribozyme and related RNAs are widely dispersed in nature. This RNA is a small nucleolytic ribozyme that self-cleaves to generate products with a 2',3'-cyclic phosphate and a free 5'-hydroxyl. Although small ribozymes are dependent on divalent metal ions under biologically relevant buffer conditions, they function in the absence of divalent metal ions at high ionic strengths. This characteristic suggests that a functional group within the covalent structure of small ribozymes is facilitating catalysis. Structural and mechanistic analyses have demonstrated that the HDV ribozyme active site contains a cytosine with a perturbed pK(a) that serves as a general acid to protonate the leaving group. The reaction of the HDV ribozyme in monovalent cations alone never approaches the velocity of the Mg(2+)-dependent reaction, and there is significant biochemical evidence that a Mg(2+) ion participates directly in catalysis. A recent crystal structure of the HDV ribozyme revealed that there is a metal binding pocket in the HDV ribozyme active site. Modeling of the cleavage site into the structure suggested that this metal ion can interact directly with the scissile phosphate and the nucleophile. In this manner, the Mg(2+) ion can serve as a Lewis acid, facilitating deprotonation of the nucleophile and stabilizing the conformation of the cleavage site for in-line attack of the nucleophile at the scissile phosphate. This catalytic strategy had previously been observed only in much larger ribozymes. Thus, in contrast to most large and small ribozymes, the HDV ribozyme uses two distinct catalytic strategies in its cleavage reaction.
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Affiliation(s)
- Barbara L Golden
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-2063, United States.
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Kong RM, Zhang XB, Chen Z, Meng HM, Song ZL, Tan W, Shen GL, Yu RQ. Unimolecular Catalytic DNA Biosensor for Amplified Detection of l-Histidine via an Enzymatic Recycling Cleavage Strategy. Anal Chem 2011; 83:7603-7. [DOI: 10.1021/ac2018926] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Rong-Mei Kong
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Zhuo Chen
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Hong-Min Meng
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Zhi-Ling Song
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Weihong Tan
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Department of Chemistry and Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Guo-Li Shen
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Ru-Qin Yu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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45
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Długosz M, Huber GA, McCammon JA, Trylska J. Brownian dynamics study of the association between the 70S ribosome and elongation factor G. Biopolymers 2011; 95:616-27. [PMID: 21394717 PMCID: PMC3125448 DOI: 10.1002/bip.21619] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 02/28/2011] [Accepted: 02/28/2011] [Indexed: 02/01/2023]
Abstract
Protein synthesis on the ribosome involves a number of external protein factors that bind at its functional sites. One key factor is the elongation factor G (EF-G) that facilitates the translocation of transfer RNAs between their binding sites, as well as advancement of the messenger RNA by one codon. The details of the EF-G/ribosome diffusional encounter and EF-G association pathway still remain unanswered. Here, we applied Brownian dynamics methodology to study bimolecular association in the bacterial EF-G/70S ribosome system. We estimated the EF-G association rate constants at 150 and 300 mM monovalent ionic strengths and obtained reasonable agreement with kinetic experiments. We have also elucidated the details of EF-G/ribosome association paths and found that positioning of the L11 protein of the large ribosomal subunit is likely crucial for EF-G entry to its binding site.
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Affiliation(s)
- Maciej Długosz
- Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Warsaw, Poland.
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46
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Veeraraghavan N, Ganguly A, Golden BL, Bevilacqua PC, Hammes-Schiffer S. Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation. J Phys Chem B 2011; 115:8346-57. [PMID: 21644800 PMCID: PMC3144556 DOI: 10.1021/jp203202e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The crystal structure of the precleaved form of the hepatitis delta virus (HDV) ribozyme reveals two G•U wobbles near the active site: a rare reverse G•U wobble involving a syn G base, and a standard G•U wobble at the cleavage site. The catalytic mechanism for this ribozyme has been proposed to involve a Mg(2+) ion bound to the reverse G•U wobble, as well as a protonated C75 base. We carried out molecular dynamics simulations to analyze metal ion interaction with the reverse and standard G•U wobbles and to investigate the impact of C75 protonation on the structure and motions of the ribozyme. We identified two types of Mg(2+) ions associated with the ribozyme, chelated and diffuse, at the reverse and standard G•U wobbles, respectively, which appear to contribute to catalysis and stability, respectively. These two metal ion sites exhibit relatively independent behavior. Protonation of C75 was observed to locally organize the active site in a manner that facilitates the catalytic mechanism, in which C75(+) acts as a general acid and Mg(2+) as a Lewis acid. The simulations also indicated that the overall structure and thermal motions of the ribozyme are not significantly influenced by the catalytic Mg(2+) interaction or C75 protonation. This analysis suggests that the reaction pathway of the ribozyme is dominated by small local motions at the active site rather than large-scale global conformational changes. These results are consistent with a wealth of experimental data.
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Affiliation(s)
- Narayanan Veeraraghavan
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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47
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Veeraraghavan N, Ganguly A, Chen JH, Bevilacqua PC, Hammes-Schiffer S, Golden BL. Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions. Biochemistry 2011; 50:2672-82. [PMID: 21348498 PMCID: PMC3068245 DOI: 10.1021/bi2000164] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The hepatitis delta virus (HDV) ribozyme uses both metal ion and nucleobase catalysis in its cleavage mechanism. A reverse G·U wobble was observed in a recent crystal structure of the precleaved state. This unusual base pair positions a Mg(2+) ion to participate in catalysis. Herein, we used molecular dynamics (MD) and X-ray crystallography to characterize the conformation and metal binding characteristics of this base pair in product and precleaved forms. Beginning with a crystal structure of the product form, we observed formation of the reverse G·U wobble during MD trajectories. We also demonstrated that this base pair is compatible with the diffraction data for the product-bound state. During MD trajectories of the product form, Na(+) ions interacted with the reverse G·U wobble in the RNA active site, and a Mg(2+) ion, introduced in certain trajectories, remained bound at this site. Beginning with a crystal structure of the precleaved form, the reverse G·U wobble with bound Mg(2+) remained intact during MD simulations. When we removed Mg(2+) from the starting precleaved structure, Na(+) ions interacted with the reverse G·U wobble. In support of the computational results, we observed competition between Na(+) and Mg(2+) in the precleaved ribozyme crystallographically. Nonlinear Poisson-Boltzmann calculations revealed a negatively charged patch near the reverse G·U wobble. This anionic pocket likely serves to bind metal ions and to help shift the pK(a) of the catalytic nucleobase, C75. Thus, the reverse G·U wobble motif serves to organize two catalytic elements, a metal ion and catalytic nucleobase, within the active site of the HDV ribozyme.
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Affiliation(s)
- Narayanan Veeraraghavan
- Huck Institutes of Life Sciences, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Abir Ganguly
- Department of Chemistry, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Jui-Hui Chen
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, Indiana 47907
| | - Philip C. Bevilacqua
- Huck Institutes of Life Sciences, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802,Department of Chemistry, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802,To whom correspondence should be addressed. B.L.G.: telephone (765) 496-6165; fax (765) 494-7897; . S.H.-S. telephone (814) 865-6442; fax (814) 865-2927; . P.C.B. telephone (814) 863-3812; fax (814) 865-2927.
| | - Sharon Hammes-Schiffer
- Department of Chemistry, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802,To whom correspondence should be addressed. B.L.G.: telephone (765) 496-6165; fax (765) 494-7897; . S.H.-S. telephone (814) 865-6442; fax (814) 865-2927; . P.C.B. telephone (814) 863-3812; fax (814) 865-2927.
| | - Barbara L. Golden
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, Indiana 47907,To whom correspondence should be addressed. B.L.G.: telephone (765) 496-6165; fax (765) 494-7897; . S.H.-S. telephone (814) 865-6442; fax (814) 865-2927; . P.C.B. telephone (814) 863-3812; fax (814) 865-2927.
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48
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Brooks KM, Hampel KJ. Rapid steps in the glmS ribozyme catalytic pathway: cation and ligand requirements. Biochemistry 2011; 50:2424-33. [PMID: 21395279 DOI: 10.1021/bi101842u] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The glmS ribozyme is a conserved riboswitch found in numerous Gram-positive bacteria and responds to the cellular concentrations of glucosamine 6-phosphate (GlcN6P). GlcN6P binding promotes site-specific self-cleavage in the 5' UTR of the glmS mRNA, resulting in downregulation of gene expression. The glmS ribozyme has previously been shown to lack strong cation specificity when the rate-limiting folding step of the cleavage reaction pathway is measured. This does not provide data regarding cation and ligand specificities of the glmS ribozyme during the rapid ligand binding chemical catalysis events. Prefolding of the ribozyme in Mg(2+)-containing buffers effectively isolates the rapid ligand binding and catalytic events (k(obs) > 60 min(-1)) from rate-limiting folding (k(obs) < 4 min(-1)). Here we employ this experimental design to assay the cations and ligand requirements for rapid ligand binding and catalysis. We show that molar concentrations of monovalent cations are also capable of inducing the formation of the native GlcN6P binding structure but are unable to promote ligand binding and catalysis rates of >4 min(-1). Our data show that the sole obligatory role for divalent cations, for which there is crystallographic evidence, is coordination of the phosphate moiety of GlcN6P in the ligand-binding pocket. In further support of this hypothesis, our data show that a nonphosphorylated analogue of GlcN6P, glucosamine, is unable to promote rapid ligand binding and catalysis in the presence of divalent cations. Folding of the ribozyme is, therefore, relatively independent of cation identity, but the rapid initiation of catalysis upon the addition of ligand is stricter.
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Affiliation(s)
- Krista M Brooks
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, Stafford Hall, 95 Carrigan Drive, University of Vermont, Burlington, Vermont 05401, United States
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49
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Mazumdar D, Nagraj N, Kim HK, Meng X, Brown AK, Sun Q, Li W, Lu Y. Activity, folding and Z-DNA formation of the 8-17 DNAzyme in the presence of monovalent ions. J Am Chem Soc 2010; 131:5506-15. [PMID: 19326878 DOI: 10.1021/ja8082939] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The effect of monovalent ions on both the reactivity and global folding of the 8-17 DNAzyme is investigated, and the results are compared with those of the hammerhead ribozyme, which has similar size and secondary structure. In contrast to the hammerhead ribozyme, the 8-17 DNAzyme activity is not detectable in the presence of 4 M K(+), Rb(+), or Cs(+) or in the presence of 80 mM, [Co(NH(3))(6)](3+). Only 4 M Li(+), NH(4)(+) and, to a lesser extent, Na(+) conferred detectable activity. The observed rate constants (k(obs) approximately 10(-3) min(-1) for Li(+) and NH(4)(+)) are approximately 1000-fold lower than that in the presence of 10 mM Mg(2+), and approximately 200,000-fold slower than that in the presence of 100 microM Pb(2+). Since the hammerhead ribozyme displays monovalent ion-dependent activity that is often within approximately 10-fold of divalent metal ion-dependent activity, these results suggest that the 8-17 DNAzyme, obtained by in vitro selections, has evolved to have a more stringent divalent metal ion requirement for high activity as compared to the naturally occurring ribozymes, making the 8-17 DNAzyme an excellent choice as a Pb(2+) sensor with high selectivity. In contrast to the activity data, folding was observed in the presence of all the monovalent ions investigated, although those monovalent ions that do not support DNAzyme activity have weaker binding affinity (K(d) approximately 0.35 M for Rb(+) and Cs(+)), while those that confer DNAzyme activity possess stronger affinity (K(d) approximately 0.22 M for Li(+), Na(+) and NH(4)(+)). In addition, a correlation between metal ion charge density, binding affinity and enzyme activity was found among mono- and divalent metal ions except Pb(2+); higher charge density resulted in stronger affinity and higher activity, suggesting that the observed folding and activity is at least partially due to electrostatic interactions between ions and the DNAzyme. Finally, circular dichroism (CD) study has revealed Z-DNA formation with the monovalent metal ions, Zn(2+) and Mg(2+); the K(d) values obtained using CD were in the same range as those obtained from folding studies using FRET. However, Z-DNA formation was not observed with Pb(2+). These results indicate that Pb(2+)-dependent function follows a different mechanism from the monovalent metal ions and other divalent metal ions; in the presence of latter metal ions, metal-ion dependent folding and structural changes, including formation of Z-DNA, play an important role in the catalytic function of the 8-17 DNAzyme.
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Affiliation(s)
- Debapriya Mazumdar
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Kirmizialtin S, Elber R. Computational exploration of mobile ion distributions around RNA duplex. J Phys Chem B 2010; 114:8207-20. [PMID: 20518549 DOI: 10.1021/jp911992t] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Atomically detailed distributions of ions around an A-form RNA are computed. Different mixtures of monovalent and divalent ions are considered explicitly. Studies of tightly bound and of diffusive (but bound) ions around 25 base pairs RNA are conducted in explicit solvent. Replica exchange simulations provide detailed equilibrium distributions with moderate computing resources (20 ns of simulation using 64 replicas). The simulations show distinct behavior of single and double charged cations. Binding of Mg(2+) ion includes tight binding to specific sites while Na(+) binds only diffusively. The tight binding of Mg(2+) is with a solvation shell while Na(+) can bind directly to RNA. Negative mobile ions can be found near the RNA but must be assisted by proximate and mobile cations. At distances larger than 16 A from the RNA center, a model of RNA as charged rod in a continuum of ionic solution provides quantitative description of the ion density (the same as in atomically detailed simulation). At shorter distances, the structure of RNA (and ions) has a significant impact on the pair correlation functions. Predicted binding sites of Mg(2+) at the RNA surface are in accord with structures from crystallography. Electric field relaxation is investigated. The relaxation due to solution rearrangements is completed in tens of picoseconds, while the contribution of RNA tumbling continues to a few nanoseconds.
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Affiliation(s)
- Serdal Kirmizialtin
- Department of Chemistry and Biochemistry and Institute of Computational Engineering and Sciences (ICES), 1 University Station, ICES, C0200, The University of Texas at Austin, Austin, Texas 78712, USA
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