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Schnieders R, Keyhani S, Schwalbe H, Fürtig B. More than Proton Detection-New Avenues for NMR Spectroscopy of RNA. Chemistry 2020; 26:102-113. [PMID: 31454110 PMCID: PMC6973061 DOI: 10.1002/chem.201903355] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Indexed: 12/16/2022]
Abstract
Ribonucleic acid oligonucleotides (RNAs) play pivotal roles in cellular function (riboswitches), chemical biology applications (SELEX-derived aptamers), cell biology and biomedical applications (transcriptomics). Furthermore, a growing number of RNA forms (long non-coding RNAs, circular RNAs) but also RNA modifications are identified, showing the ever increasing functional diversity of RNAs. To describe and understand this functional diversity, structural studies of RNA are increasingly important. However, they are often more challenging than protein structural studies as RNAs are substantially more dynamic and their function is often linked to their structural transitions between alternative conformations. NMR is a prime technique to characterize these structural dynamics with atomic resolution. To extend the NMR size limitation and to characterize large RNAs and their complexes above 200 nucleotides, new NMR techniques have been developed. This Minireview reports on the development of NMR methods that utilize detection on low-γ nuclei (heteronuclei like 13 C or 15 N with lower gyromagnetic ratio than 1 H) to obtain unique structural and dynamic information for large RNA molecules in solution. Experiments involve through-bond correlations of nucleobases and the phosphodiester backbone of RNA for chemical shift assignment and make information on hydrogen bonding uniquely accessible. Previously unobservable NMR resonances of amino groups in RNA nucleobases are now detected in experiments involving conformational exchange-resistant double-quantum 1 H coherences, detected by 13 C NMR spectroscopy. Furthermore, 13 C and 15 N chemical shifts provide valuable information on conformations. All the covered aspects point to the advantages of low-γ nuclei detection experiments in RNA.
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Affiliation(s)
- Robbin Schnieders
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Sara Keyhani
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
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2
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Marušič M, Schlagnitweit J, Petzold K. RNA Dynamics by NMR Spectroscopy. Chembiochem 2019; 20:2685-2710. [PMID: 30997719 PMCID: PMC6899578 DOI: 10.1002/cbic.201900072] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/12/2019] [Indexed: 12/22/2022]
Abstract
An ever-increasing number of functional RNAs require a mechanistic understanding. RNA function relies on changes in its structure, so-called dynamics. To reveal dynamic processes and higher energy structures, new NMR methods have been developed to elucidate these dynamics in RNA with atomic resolution. In this Review, we provide an introduction to dynamics novices and an overview of methods that access most dynamic timescales, from picoseconds to hours. Examples are provided as well as insight into theory, data acquisition and analysis for these different methods. Using this broad spectrum of methodology, unprecedented detail and invisible structures have been obtained and are reviewed here. RNA, though often more complicated and therefore neglected, also provides a great system to study structural changes, as these RNA structural changes are more easily defined-Lego like-than in proteins, hence the numerous revelations of RNA excited states.
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Affiliation(s)
- Maja Marušič
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetSolnavägen 917177StockholmSweden
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetSolnavägen 917177StockholmSweden
| | - Katja Petzold
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetSolnavägen 917177StockholmSweden
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3
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Applications of NMR to structure determination of RNAs large and small. Arch Biochem Biophys 2017; 628:42-56. [PMID: 28600200 DOI: 10.1016/j.abb.2017.06.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 05/31/2017] [Accepted: 06/04/2017] [Indexed: 02/07/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool to investigate the structure and dynamics of RNA, because many biologically important RNAs have conformationally flexible structures, which makes them difficult to crystallize. Functional, independently folded RNA domains, range in size between simple stem-loops of as few as 10-20 nucleotides, to 50-70 nucleotides, the size of tRNA and many small ribozymes, to a few hundred nucleotides, the size of more complex RNA enzymes and of the functional domains of non-coding transcripts. In this review, we discuss new methods for sample preparation, assignment strategies and structure determination for independently folded RNA domains of up to 100 kDa in molecular weight.
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Borkar AN, Bardaro MF, Camilloni C, Aprile FA, Varani G, Vendruscolo M. Structure of a low-population binding intermediate in protein-RNA recognition. Proc Natl Acad Sci U S A 2016; 113:7171-6. [PMID: 27286828 PMCID: PMC4932932 DOI: 10.1073/pnas.1521349113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The interaction of the HIV-1 protein transactivator of transcription (Tat) and its cognate transactivation response element (TAR) RNA transactivates viral transcription and represents a paradigm for the widespread occurrence of conformational rearrangements in protein-RNA recognition. Although the structures of free and bound forms of TAR are well characterized, the conformations of the intermediates in the binding process are still unknown. By determining the free energy landscape of the complex using NMR residual dipolar couplings in replica-averaged metadynamics simulations, we observe two low-population intermediates. We then rationally design two mutants, one in the protein and another in the RNA, that weaken specific nonnative interactions that stabilize one of the intermediates. By using surface plasmon resonance, we show that these mutations lower the release rate of Tat, as predicted. These results identify the structure of an intermediate for RNA-protein binding and illustrate a general strategy to achieve this goal with high resolution.
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Affiliation(s)
- Aditi N Borkar
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michael F Bardaro
- Department of Chemistry, University of Washington, Seattle, WA 98197-1700
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Francesco A Aprile
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98197-1700
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
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5
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Cornilescu G, Didychuk AL, Rodgers ML, Michael LA, Burke JE, Montemayor EJ, Hoskins AA, Butcher SE. Structural Analysis of Multi-Helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA. J Mol Biol 2016; 428:777-789. [PMID: 26655855 PMCID: PMC4790120 DOI: 10.1016/j.jmb.2015.11.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/25/2015] [Accepted: 11/30/2015] [Indexed: 01/17/2023]
Abstract
NMR and SAXS (small-angle X-ray scattering)/WAXS (wide-angle X-ray scattering) are highly complementary approaches for the analysis of RNA structure in solution. Here we describe an efficient NMR-SAXS/WAXS approach for structural investigation of multi-helical RNAs. We illustrate this approach by determining the overall fold of a 92-nt 3-helix junction from the U4/U6 di-snRNA. The U4/U6 di-snRNA is conserved in eukaryotes and is part of the U4/U6.U5 tri-snRNP, a large ribonucleoprotein complex that comprises a major subunit of the assembled spliceosome. Helical orientations can be determined by X-ray scattering data alone, but the addition of NMR RDC (residual dipolar coupling) restraints improves the structure models. RDCs were measured in two different external alignment media and also by magnetic susceptibility anisotropy. The resulting alignment tensors are collinear, which is a previously noted problem for nucleic acids. Including WAXS data in the calculations produces models with significantly better fits to the scattering data. In solution, the U4/U6 di-snRNA forms a 3-helix junction with a planar Y-shaped structure and has no detectable tertiary interactions. Single-molecule Förster resonance energy transfer data support the observed topology. A comparison with the recently determined cryo-electron microscopy structure of the U4/U6.U5 tri-snRNP illustrates how proteins scaffold the RNA and dramatically alter the geometry of the U4/U6 3-helix junction.
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Affiliation(s)
- Gabriel Cornilescu
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Allison L Didychuk
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Margaret L Rodgers
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Lauren A Michael
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Jordan E Burke
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Eric J Montemayor
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
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Salmon L, Giambaşu GM, Nikolova EN, Petzold K, Bhattacharya A, Case DA, Al-Hashimi HM. Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings. J Am Chem Soc 2015; 137:12954-65. [PMID: 26306428 PMCID: PMC4748170 DOI: 10.1021/jacs.5b07229] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Approaches that combine experimental data and computational molecular dynamics (MD) to determine atomic resolution ensembles of biomolecules require the measurement of abundant experimental data. NMR residual dipolar couplings (RDCs) carry rich dynamics information, however, difficulties in modulating overall alignment of nucleic acids have limited the ability to fully extract this information. We present a strategy for modulating RNA alignment that is based on introducing variable dynamic kinks in terminal helices. With this strategy, we measured seven sets of RDCs in a cUUCGg apical loop and used this rich data set to test the accuracy of an 0.8 μs MD simulation computed using the Amber ff10 force field as well as to determine an atomic resolution ensemble. The MD-generated ensemble quantitatively reproduces the measured RDCs, but selection of a sub-ensemble was required to satisfy the RDCs within error. The largest discrepancies between the RDC-selected and MD-generated ensembles are observed for the most flexible loop residues and backbone angles connecting the loop to the helix, with the RDC-selected ensemble resulting in more uniform dynamics. Comparison of the RDC-selected ensemble with NMR spin relaxation data suggests that the dynamics occurs on the ps-ns time scales as verified by measurements of R(1ρ) relaxation-dispersion data. The RDC-satisfying ensemble samples many conformations adopted by the hairpin in crystal structures indicating that intrinsic plasticity may play important roles in conformational adaptation. The approach presented here can be applied to test nucleic acid force fields and to characterize dynamics in diverse RNA motifs at atomic resolution.
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Affiliation(s)
- Loïc Salmon
- Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - George M. Giambaşu
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Evgenia N. Nikolova
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | | | - David A. Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Hashim M. Al-Hashimi
- Department of Biochemistry and Chemistry, Duke University School of Medicine, Durham, North Carolina, USA
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Ravera E, Salmon L, Fragai M, Parigi G, Al-Hashimi H, Luchinat C. Insights into domain-domain motions in proteins and RNA from solution NMR. Acc Chem Res 2014; 47:3118-26. [PMID: 25148413 PMCID: PMC4204921 DOI: 10.1021/ar5002318] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Many multidomain proteins and ribonucleic acids consist of domains
that autonomously fold and that are linked together by flexible junctions.
This architectural design allows domains to sample a wide range of
positions with respect to one another, yet do so in a way that retains
structural specificity, since the number of sampled conformations
remains extremely small compared to the total conformations that would
be sampled if the domains were connected by an infinitely long linker.
This “tuned” flexibility in interdomain conformation
is in turn used in many biochemical processes. There is great
interest in characterizing the dynamic properties
of multidomain systems, and moving beyond conventional descriptions
in terms of static structures, toward the characterization of population-weighted
ensembles describing a distribution of many conformations sampled
in solution. There is also great interest in understanding the design
principles and underlying physical and chemical interactions that
specify the nature of interdomain flexibility. NMR spectroscopy is
one of the most powerful techniques for characterizing motions in
complex biomolecules and has contributed greatly toward our basic
understanding of dynamics in proteins and nucleic acids and its role
in folding, recognition, and signaling. Here, we review methods
that have been developed in our laboratories
to address these challenges. Our approaches are based on the ability
of one domain of the molecule to self-align in a magnetic field, or
to dominate the overall orientation of the molecule, so that the conformational
freedom of other domains can be assessed by their degree of alignment
induced by the aligned part. In turn, this self-alignment ability
can be intrinsic or can be caused by tagging appropriate constructs
to the molecule of interest. In general, self-alignment is due to
magnetic susceptibility anisotropy. Nucleic acids with elongated helices
have this feature, as well as several paramagnetic metal centers that
can be found in, or attached to, a protein domain.
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Affiliation(s)
- Enrico Ravera
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Loïc Salmon
- Department
of Biophysics, University of Michigan, 830 N. University, Ann Arbor, Michigan 48109, United States
| | - Marco Fragai
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Hashim Al-Hashimi
- Department
of Biochemistry and Department of Chemistry, Duke University School of Medicine, 307 Research Drive, Durham, North Carolina 27710, United States
| | - Claudio Luchinat
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
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8
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Emani PS, Bardaro MF, Huang W, Aragon S, Varani G, Drobny GP. Elucidating molecular motion through structural and dynamic filters of energy-minimized conformer ensembles. J Phys Chem B 2014; 118:1726-42. [PMID: 24479561 PMCID: PMC3983377 DOI: 10.1021/jp409386t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Complex RNA structures are constructed
from helical segments connected
by flexible loops that move spontaneously and in response to binding
of small molecule ligands and proteins. Understanding the conformational
variability of RNA requires the characterization of the coupled time
evolution of interconnected flexible domains. To elucidate the collective
molecular motions and explore the conformational landscape of the
HIV-1 TAR RNA, we describe a new methodology that utilizes energy-minimized
structures generated by the program “Fragment Assembly of RNA
with Full-Atom Refinement (FARFAR)”. We apply structural filters
in the form of experimental residual dipolar couplings (RDCs) to select
a subset of discrete energy-minimized conformers and carry out principal
component analyses (PCA) to corroborate the choice of the filtered
subset. We use this subset of structures to calculate solution T1 and T1ρ relaxation times for 13C spins in multiple residues in different domains of the molecule
using two simulation protocols that we previously published. We match
the experimental T1 times to within 2% and the T1ρ times to within less than 10% for helical residues. These results
introduce a protocol to construct viable dynamic trajectories for
RNA molecules that accord well with experimental NMR data and support
the notion that the motions of the helical portions of this small
RNA can be described by a relatively small number of discrete conformations
exchanging over time scales longer than 1 μs.
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Affiliation(s)
- Prashant S Emani
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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9
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Abstract
Conformational changes in nucleic acids play a key role in the way genetic information is stored, transferred, and processed in living cells. Here, we describe new approaches that employ a broad range of experimental data, including NMR-derived chemical shifts and residual dipolar couplings, small-angle X-ray scattering, and computational approaches such as molecular dynamics simulations to determine ensembles of DNA and RNA at atomic resolution. We review the complementary information that can be obtained from diverse sets of data and the various methods that have been developed to combine these data with computational methods to construct ensembles and assess their uncertainty. We conclude by surveying RNA and DNA ensembles determined using these methods, highlighting the unique physical and functional insights obtained so far.
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Affiliation(s)
- Loïc Salmon
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109;
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10
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Al-Hashimi HM. NMR studies of nucleic acid dynamics. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 237:191-204. [PMID: 24149218 PMCID: PMC3984477 DOI: 10.1016/j.jmr.2013.08.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 08/23/2013] [Indexed: 05/12/2023]
Abstract
Nucleic acid structures have to satisfy two diametrically opposite requirements; on one hand they have to adopt well-defined 3D structures that can be specifically recognized by proteins; on the other hand, their structures must be sufficiently flexible to undergo very large conformational changes that are required during key biochemical processes, including replication, transcription, and translation. How do nucleic acids introduce flexibility into their 3D structure without losing biological specificity? Here, I describe the development and application of NMR spectroscopic techniques in my laboratory for characterizing the dynamic properties of nucleic acids that tightly integrate a broad set of NMR measurements, including residual dipolar couplings, spin relaxation, and relaxation dispersion with sample engineering and computational approaches. This approach allowed us to obtain fundamental new insights into directional flexibility in nucleic acids that enable their structures to change in a very specific functional manner.
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Affiliation(s)
- Hashim M Al-Hashimi
- Department of Chemistry & Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA.
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