51
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Chemo-enzymatic labeling for rapid assignment of RNA molecules. Methods 2016; 103:11-7. [PMID: 27090003 DOI: 10.1016/j.ymeth.2016.03.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 03/17/2016] [Accepted: 03/22/2016] [Indexed: 11/22/2022] Open
Abstract
Even though Nuclear Magnetic Resonance (NMR) spectroscopy is one of the few techniques capable of determining atomic resolution structures of RNA, it is constrained by two major problems of chemical shift overlap of resonances and rapid signal loss due to line broadening. Emerging tools to tackle these problems include synthesis of atom specifically labeled or chemically modified nucleotides. Herein we review the synthesis of these nucleotides, the design and production of appropriate RNA samples, and the application and analysis of the NMR experiments that take advantage of these labels.
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52
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Soomro RA, Hallam KR, Ibupoto ZH, Tahira A, Sherazi STH, Juddin S, Jawaid S, Willander M. Glutaric Acid Assisted Fabrication of CuO Nanostructures and their Application in Development of Highly Sensitive Electrochemical Sensor System for Carbamates. ELECTROANAL 2016. [DOI: 10.1002/elan.201501095] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Razium Ali Soomro
- Interface Analysis Centre; School of Physics; University of Bristol; Bristol BS8 1TL UK
- National Centre of Excellence in Analytical Chemistry; University of Sindh; Jamshoro 76080 Pakistan
| | - Keith Richard Hallam
- Interface Analysis Centre; School of Physics; University of Bristol; Bristol BS8 1TL UK
| | | | - Aneela Tahira
- Dr M. A. Kazi Institute of Chemistry; University of Sindh; Jamshoro 76080 Pakistan
| | | | - Siraj Juddin
- National Centre of Excellence in Analytical Chemistry; University of Sindh; Jamshoro 76080 Pakistan
| | - Sana Jawaid
- National Centre of Excellence in Analytical Chemistry; University of Sindh; Jamshoro 76080 Pakistan
| | - Magnus Willander
- Department of Science and Technology; Campus Norrkoping; Linkoping University; SE-60174 Norrkoping Sweden
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53
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Gu Y, Hansen AL, Peng Y, Brüschweiler R. Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yina Gu
- Department of Chemistry and Biochemistry The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
| | - Alexandar L. Hansen
- Campus Chemical Instrument Center The Ohio State University 460 W. 12th Avenue Columbus OH 43210 USA
| | - Yu Peng
- Department of Chemistry and Biochemistry The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
- Campus Chemical Instrument Center The Ohio State University 460 W. 12th Avenue Columbus OH 43210 USA
- Department of Biological Chemistry and Pharmacology The Ohio State University 1645 Neil Avenue Columbus OH 43210 USA
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54
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Gu Y, Hansen AL, Peng Y, Brüschweiler R. Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data. Angew Chem Int Ed Engl 2016; 55:3117-9. [PMID: 26821600 DOI: 10.1002/anie.201511711] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Indexed: 01/03/2023]
Abstract
Functional motions of (15)N-labeled proteins can be monitored by solution NMR spin relaxation experiments over a broad range of timescales. These experiments however typically take of the order of several days to a week per protein. Recently, NMR chemical exchange saturation transfer (CEST) experiments have emerged to probe slow millisecond motions complementing R1ρ and CPMG-type experiments. CEST also simultaneously reports on site-specific R1 and R2 parameters. It is shown here how CEST-derived R1 and R2 relaxation parameters can be measured within a few hours at an accuracy comparable to traditional relaxation experiments. Using a "lean" version of the model-free approach S(2) order parameters can be determined that match those from the standard model-free approach applied to (15)N R1, R2 , and {(1)H}-(15)N NOE data. The new methodology, which is demonstrated for ubiquitin and arginine kinase (42 kDa), should serve as an effective screening tool of protein dynamics from picosecond-to-millisecond timescales.
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Affiliation(s)
- Yina Gu
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Yu Peng
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA. .,Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA. .,Department of Biological Chemistry and Pharmacology, The Ohio State University, 1645 Neil Avenue, Columbus, OH, 43210, USA.
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55
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Chen B, LeBlanc R, Dayie TK. SAM-II Riboswitch Samples at least Two Conformations in Solution in the Absence of Ligand: Implications for Recognition. Angew Chem Int Ed Engl 2016; 55:2724-7. [PMID: 26800479 DOI: 10.1002/anie.201509997] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/18/2015] [Indexed: 11/10/2022]
Abstract
Conformational equilibria are increasingly recognized as pivotal for biological function. Traditional structural analyses provide a static image of conformers in solution that sometimes present conflicting views. From (13) C and (1) H chemical exchange saturation transfer experiments, in concert with ligation and selective labeling strategies, we show that in the absence of metabolite, a Mg(2+) (0-0.5 mm)-bound apo SAM-II riboswitch RNA exists in a minor (≈10 %) partially closed state that rapidly exchanges with a predominantly (≈90 %) open form with a lifetime of ≈32 ms. The base and sugar (H6,C6, H1',C1') chemical shifts of C43 for the dominant conformer are similar to those of a free CMP, but those of the minor apo species are comparable to shifts of CMPs in helical RNA regions. Our results suggest that these transient, low populated states stabilized by Mg(2+) will likely enhance rapid ligand recognition and, we anticipate, will play potentially ubiquitous roles in RNA signaling.
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Affiliation(s)
- Bin Chen
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sciences Building (296), 8314 Paint Branch Dr., College Park, MD, 20782, USA
| | - Regan LeBlanc
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sciences Building (296), 8314 Paint Branch Dr., College Park, MD, 20782, USA
| | - T Kwaku Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sciences Building (296), 8314 Paint Branch Dr., College Park, MD, 20782, USA.
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56
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Chen B, LeBlanc R, Dayie TK. SAM‐II Riboswitch Samples at least Two Conformations in Solution in the Absence of Ligand: Implications for Recognition. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509997] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Bin Chen
- Center for Biomolecular Structure and Organization Department of Chemistry and Biochemistry University of Maryland Biomolecular Sciences Building (296), 8314 Paint Branch Dr. College Park MD 20782 USA
| | - Regan LeBlanc
- Center for Biomolecular Structure and Organization Department of Chemistry and Biochemistry University of Maryland Biomolecular Sciences Building (296), 8314 Paint Branch Dr. College Park MD 20782 USA
| | - T. Kwaku Dayie
- Center for Biomolecular Structure and Organization Department of Chemistry and Biochemistry University of Maryland Biomolecular Sciences Building (296), 8314 Paint Branch Dr. College Park MD 20782 USA
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57
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Longhini AP, LeBlanc RM, Becette O, Salguero C, Wunderlich CH, Johnson BA, D'Souza VM, Kreutz C, Dayie TK. Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations. Nucleic Acids Res 2015; 44:e52. [PMID: 26657632 PMCID: PMC4824079 DOI: 10.1093/nar/gkv1333] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 11/16/2015] [Indexed: 11/12/2022] Open
Abstract
Stable isotope labeling is central to NMR studies of nucleic acids. Development of methods that incorporate labels at specific atomic positions within each nucleotide promises to expand the size range of RNAs that can be studied by NMR. Using recombinantly expressed enzymes and chemically synthesized ribose and nucleobase, we have developed an inexpensive, rapid chemo-enzymatic method to label ATP and GTP site specifically and in high yields of up to 90%. We incorporated these nucleotides into RNAs with sizes ranging from 27 to 59 nucleotides using in vitro transcription: A-Site (27 nt), the iron responsive elements (29 nt), a fluoride riboswitch from Bacillus anthracis (48 nt), and a frame-shifting element from a human corona virus (59 nt). Finally, we showcase the improvement in spectral quality arising from reduced crowding and narrowed linewidths, and accurate analysis of NMR relaxation dispersion (CPMG) and TROSY-based CEST experiments to measure μs-ms time scale motions, and an improved NOESY strategy for resonance assignment. Applications of this selective labeling technology promises to reduce difficulties associated with chemical shift overlap and rapid signal decay that have made it challenging to study the structure and dynamics of large RNAs beyond the 50 nt median size found in the PDB.
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Affiliation(s)
- Andrew P Longhini
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USAfi
| | - Regan M LeBlanc
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USAfi
| | - Owen Becette
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USAfi
| | - Carolina Salguero
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christoph H Wunderlich
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Bruce A Johnson
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY 10031, USA One Moon Scientific, Inc., 839 Grant Avenue, Westfield, NJ 07090-2322, USA
| | - Victoria M D'Souza
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - T Kwaku Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USAfi
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58
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Carneiro MG, Reddy JG, Griesinger C, Lee D. Speeding-up exchange-mediated saturation transfer experiments by Fourier transform. JOURNAL OF BIOMOLECULAR NMR 2015; 63:237-244. [PMID: 26350257 DOI: 10.1007/s10858-015-9985-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/02/2015] [Indexed: 06/05/2023]
Abstract
Protein motions over various time scales are crucial for protein function. NMR relaxation dispersion experiments play a key role in explaining these motions. However, the study of slow conformational changes with lowly populated states remained elusive. The recently developed exchange-mediated saturation transfer experiments allow the detection and characterization of such motions, but require extensive measurement time. Here we show that, by making use of Fourier transform, the total acquisition time required to measure an exchange-mediated saturation transfer profile can be reduced by twofold in case that one applies linear prediction. In addition, we demonstrate that the analytical solution for R1ρ experiments can be used for fitting the exchange-mediated saturation transfer profile. Furthermore, we show that simultaneous analysis of exchange-mediated saturation transfer profiles with two different radio-frequency field strengths is required for accurate and precise characterization of the exchange process and the exchanging states.
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Affiliation(s)
- Marta G Carneiro
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical chemistry, Am Fassberg 11, 37077, Goettingen, Germany
| | - Jithender G Reddy
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical chemistry, Am Fassberg 11, 37077, Goettingen, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical chemistry, Am Fassberg 11, 37077, Goettingen, Germany
| | - Donghan Lee
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical chemistry, Am Fassberg 11, 37077, Goettingen, Germany.
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 529 South Jackson Street, Louisville, KY, 40202, USA.
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59
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Zhao B, Zhang Q. Measuring Residual Dipolar Couplings in Excited Conformational States of Nucleic Acids by CEST NMR Spectroscopy. J Am Chem Soc 2015; 137:13480-3. [PMID: 26462068 DOI: 10.1021/jacs.5b09014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Nucleic acids undergo structural transitions to access sparsely populated and transiently lived conformational states--or excited conformational states--that play important roles in diverse biological processes. Despite ever-increasing detection of these functionally essential states, 3D structure determination of excited states (ESs) of RNA remains elusive. This is largely due to challenges in obtaining high-resolution structural constraints in these ESs by conventional structural biology approaches. Here, we present nucleic-acid-optimized chemical exchange saturation transfer (CEST) NMR spectroscopy for measuring residual dipolar couplings (RDCs), which provide unique long-range angular constraints in ESs of nucleic acids. We demonstrate these approaches on a fluoride riboswitch, where one-bond (13)C-(1)H RDCs from both base and sugar moieties provide direct structural probes into an ES of the ligand-free riboswitch.
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Affiliation(s)
- Bo Zhao
- Department of Biochemistry and Biophysics and ‡Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Qi Zhang
- Department of Biochemistry and Biophysics and ‡Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
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60
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Wunderlich CH, Juen MA, LeBlanc RM, Longhini AP, Dayie TK, Kreutz C. Stable isotope-labeled RNA phosphoramidites to facilitate dynamics by NMR. Methods Enzymol 2015; 565:461-94. [PMID: 26577742 DOI: 10.1016/bs.mie.2015.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Given that Ribonucleic acids (RNAs) are a central hub of various cellular processes, methods to synthesize these RNAs for biophysical studies are much needed. Here, we showcase the applicability of 6-(13)C-pyrimidine phosphoramidites to introduce isolated (13)C-(1)H spin pairs into RNAs up to 40 nucleotides long. The method allows the incorporation of 6-(13)C-uridine and -cytidine residues at any desired position within a target RNA. By site-specific positioning of the (13)C-label using RNA solid phase synthesis, these stable isotope-labeling patterns are especially well suited to resolve resonance assignment ambiguities. Of even greater importance, the labeling pattern affords accurate quantification of important functional transitions of biologically relevant RNAs (e.g., riboswitch aptamer domains, viral RNAs, or ribozymes) in the μs- to ms time regime and beyond without complications of one bond carbon scalar couplings. We outline the chemical synthesis of the 6-(13)C-pyrimidine building blocks and their use in RNA solid phase synthesis and demonstrate their utility in Carr Purcell Meiboom Gill relaxation dispersion, ZZ exchange, and chemical exchange saturation transfer NMR experiments.
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Affiliation(s)
- Christoph H Wunderlich
- Institute of Organic Chemistry and Center for Biomolecular Sciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Michael A Juen
- Institute of Organic Chemistry and Center for Biomolecular Sciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Regan M LeBlanc
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, USA
| | - Andrew P Longhini
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, USA
| | - T Kwaku Dayie
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, USA.
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Biomolecular Sciences Innsbruck, University of Innsbruck, Innsbruck, Austria.
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61
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Xue Y, Kellogg D, Kimsey IJ, Sathyamoorthy B, Stein ZW, McBrairty M, Al-Hashimi HM. Characterizing RNA Excited States Using NMR Relaxation Dispersion. Methods Enzymol 2015; 558:39-73. [PMID: 26068737 DOI: 10.1016/bs.mie.2015.02.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Changes in RNA secondary structure play fundamental roles in the cellular functions of a growing number of noncoding RNAs. This chapter describes NMR-based approaches for characterizing microsecond-to-millisecond changes in RNA secondary structure that are directed toward short-lived and low-populated species often referred to as "excited states." Compared to larger scale changes in RNA secondary structure, transitions toward excited states do not require assistance from chaperones, are often orders of magnitude faster, and are localized to a small number of nearby base pairs in and around noncanonical motifs. Here, we describe a procedure for characterizing RNA excited states using off-resonance R1ρ NMR relaxation dispersion utilizing low-to-high spin-lock fields (25-3000 Hz). R1ρ NMR relaxation dispersion experiments are used to measure carbon and nitrogen chemical shifts in base and sugar moieties of the excited state. The chemical shift data are then interpreted with the aid of secondary structure prediction to infer potential excited states that feature alternative secondary structures. Candidate structures are then tested by using mutations, single-atom substitutions, or by changing physiochemical conditions, such as pH and temperature, to either stabilize or destabilize the candidate excited state. The resulting chemical shifts of the mutants or under different physiochemical conditions are then compared to those of the ground and excited states. Application is illustrated with a focus on the transactivation response element from the human immune deficiency virus type 1, which exists in dynamic equilibrium with at least two distinct excited states.
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Affiliation(s)
- Yi Xue
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA
| | - Dawn Kellogg
- Department of Chemistry, Duke University, Durham, North Carolina, USA
| | - Isaac J Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Zachary W Stein
- Biophysics Enhanced Program, University of Michigan Ann Arbor, Michigan, USA
| | - Mitchell McBrairty
- Biophysics Enhanced Program, University of Michigan Ann Arbor, Michigan, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA; Department of Chemistry, Duke University, Durham, North Carolina, USA.
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62
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Zhao B, Zhang Q. Characterizing excited conformational states of RNA by NMR spectroscopy. Curr Opin Struct Biol 2015; 30:134-146. [PMID: 25765780 DOI: 10.1016/j.sbi.2015.02.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 02/14/2015] [Accepted: 02/18/2015] [Indexed: 11/25/2022]
Abstract
Conformational dynamics is a hallmark of diverse non-coding RNA functions. During these functional processes, RNA molecules almost ubiquitously undergo conformational transitions that are tuned to meet distinct structural and kinetic requirements for proper function. A complete mechanistic understanding of RNA function requires comprehensive structural and dynamic knowledge of these complex transitions, which often involve alternative higher-energy conformational states that pose a major challenge for high-resolution structural study by conventional methods. In this review, we describe recent progress in RNA NMR that has started to unveil detailed structural, thermodynamic and kinetic insights into some of these excited conformational states of RNA and their functional roles in biology.
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Affiliation(s)
- Bo Zhao
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
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63
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Zhou Y, Yang D. 13Cα CEST experiment on uniformly 13C-labeled proteins. JOURNAL OF BIOMOLECULAR NMR 2015; 61:89-94. [PMID: 25465387 DOI: 10.1007/s10858-014-9888-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 11/26/2014] [Indexed: 06/04/2023]
Abstract
A new HSQC-based (13)Cα CEST pulse scheme is proposed, which is suitable for uniformly (13)C- or (13)C, (15)N-labeled samples in either water or heavy water. Except for Thr and Ser residues, the sensitivity of this scheme for uniformly labeled samples is similar to that of the previous scheme for selectively (13)Cα-labeled samples with 100% isotope enrichment. The experiment is demonstrated on an acyl carrier protein domain. Our (13)Cα CEST data reveal that the minor state of the acyl carrier protein has high helical propensity. The new scheme will facilitate structural characterization of invisible minor states.
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Affiliation(s)
- Yang Zhou
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
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64
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Moschen T, Wunderlich CH, Spitzer R, Levic J, Micura R, Tollinger M, Kreutz C. Ligand-detected relaxation dispersion NMR spectroscopy: dynamics of preQ1-RNA binding. Angew Chem Int Ed Engl 2015; 54:560-3. [PMID: 25403518 PMCID: PMC4353840 DOI: 10.1002/anie.201409779] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 12/21/2022]
Abstract
An NMR-based approach to characterizing the binding kinetics of ligand molecules to biomolecules, like RNA or proteins, by ligand-detected Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments is described. A (15)N-modified preQ1 ligand is used to acquire relaxation dispersion experiments in the presence of low amounts of the Fsu class I preQ1 aptamer RNA, and increasing ligand concentrations to probe the RNA small molecule interaction. Our experimental data strongly support the conformational selection mechanism postulated. The approach gives direct access to two parameters of a ligand-receptor interaction: the off rate and the population of the small molecule-receptor complex. A detailed description of the kinetics underlying the ligand binding process is of crucial importance to fully understanding a riboswitch's function and to evaluate potential new antibiotics candidates targeting the noncoding RNA species. Ligand-detected NMR relaxation dispersion experiments represent a valuable diagnostic tool for the characterization of binding mechanisms.
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Affiliation(s)
- Thomas Moschen
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Christoph Hermann Wunderlich
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Romana Spitzer
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Jasmin Levic
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Ronald Micura
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Martin Tollinger
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Christoph Kreutz
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
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65
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Zhou Y, Yang D. Effects of J couplings and unobservable minor states on kinetics parameters extracted from CEST data. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 249:118-125. [PMID: 25462955 DOI: 10.1016/j.jmr.2014.10.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 10/16/2014] [Accepted: 10/18/2014] [Indexed: 06/04/2023]
Abstract
Chemical exchange saturation transfer (CEST) experiments have emerged as a powerful tool for characterizing dynamics and sparse populated conformers of protein in slow exchanging systems. We show that J couplings and 'invisible' minor states can cause systematic errors in kinetics parameters and chemical shifts extracted from CEST data. For weakly coupled spin systems, the J coupling effect can be removed using an approximation method. This method is warranted through detailed theoretical derivation, supported by results from simulations and experiments on an acyl carrier protein domain. Simulations demonstrate that the effect of 'invisible' minor states on the extracted kinetics parameters depends on the chemical shifts, populations, exchange rates of the 'invisible' states to the observed major or minor state and exchange models. Moreover, the extracted chemical shifts of the observed minor state can also be influenced by the "invisible" minor states. The presence of an off-pathway folding intermediate in the acyl carrier protein domain explains why the exchange rates obtained with a two-state model from individual residues that displayed only two obvious CEST dips varied significantly and the extracted exchange rates for 15N and 13CO spins located in the same peptide bond could be very different. The approximation method described here simplifies CEST data analysis in many situations where the coupling effect cannot be ignored and decoupling techniques are not desirable. In addition, this study also raises alerts for 'invisible' minor states which can cause errors in not only kinetics parameters but also chemical shifts of the observed minor state.
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Affiliation(s)
- Yang Zhou
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
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66
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Bothe JR, Stein ZW, Al-Hashimi HM. Evaluating the uncertainty in exchange parameters determined from off-resonance R1ρ relaxation dispersion for systems in fast exchange. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 244:18-29. [PMID: 24819426 PMCID: PMC4222517 DOI: 10.1016/j.jmr.2014.04.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 05/25/2023]
Abstract
Spin relaxation in the rotating frame (R1ρ) is a powerful NMR technique for characterizing fast microsecond timescale exchange processes directed toward short-lived excited states in biomolecules. At the limit of fast exchange, only k(ex)=k(1)+k(-1) and Φex=p(G)p(E)(Δω)(2) can be determined from R1ρ data limiting the ability to characterize the structure and energetics of the excited state conformation. Here, we use simulations to examine the uncertainty with which exchange parameters can be determined for two state systems in intermediate-to-fast exchange using off-resonance R1ρ relaxation dispersion. R1ρ data computed by solving the Bloch-McConnell equations reveals small but significant asymmetry with respect to offset (R1ρ (ΔΩ)≠R1ρ (-ΔΩ)), which is a hallmark of slow-to-intermediate exchange, even under conditions of fast exchange for free precession chemical exchange line broadening (k(ex)/Δω>10). A grid search analysis combined with bootstrap and Monte-Carlo based statistical approaches for estimating uncertainty in exchange parameters reveals that both the sign and magnitude of Δω can be determined at a useful level of uncertainty for systems in fast exchange (k(ex)/Δω<10) but that this depends on the uncertainty in the R1ρ data and requires a thorough examination of the multidimensional variation of χ(2) as a function of exchange parameters. Results from simulations are complemented by analysis of experimental R1ρ data measured in three nucleic acid systems with exchange processes occurring on the slow (k(ex)/Δω=0.2; pE=∼0.7%), fast (k(ex)/Δω=∼10-16; p(E)=∼13%) and very fast (k(ex)=39,000 s(-1)) chemical shift timescales.
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Affiliation(s)
- Jameson R Bothe
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Zachary W Stein
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Chemistry, Duke University School of Medicine, Durham, NC 27710, United States.
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