1
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Sinzger-D'Angelo M, Hanst M, Reinhardt F, Koeppl H. Effects of mRNA conformational switching on translational noise in gene circuits. J Chem Phys 2024; 160:134108. [PMID: 38573847 DOI: 10.1063/5.0186927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/08/2024] [Indexed: 04/06/2024] Open
Abstract
Intragenic translational heterogeneity describes the variation in translation at the level of transcripts for an individual gene. A factor that contributes to this source of variation is the mRNA structure. Both the composition of the thermodynamic ensemble, i.e., the stationary distribution of mRNA structures, and the switching dynamics between those play a role. The effect of the switching dynamics on intragenic translational heterogeneity remains poorly understood. We present a stochastic translation model that accounts for mRNA structure switching and is derived from a Markov model via approximate stochastic filtering. We assess the approximation on various timescales and provide a method to quantify how mRNA structure dynamics contributes to translational heterogeneity. With our approach, we allow quantitative information on mRNA switching from biophysical experiments or coarse-grain molecular dynamics simulations of mRNA structures to be included in gene regulatory chemical reaction network models without an increase in the number of species. Thereby, our model bridges a gap between mRNA structure kinetics and gene expression models, which we hope will further improve our understanding of gene regulatory networks and facilitate genetic circuit design.
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Affiliation(s)
| | - Maleen Hanst
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Felix Reinhardt
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Heinz Koeppl
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
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2
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Xu Z, Gu S, Li Y, Wu J, Zhao Y. Recognition-Enabled Automated Analyte Identification via 19F NMR. Anal Chem 2022; 94:8285-8292. [PMID: 35622989 DOI: 10.1021/acs.analchem.2c00642] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nuclear magnetic resonance (NMR) is an indispensable tool for structural elucidation and noninvasive analysis. Automated identification of analytes with NMR is highly pursued in metabolism research and disease diagnosis; however, this process is often complicated by the signal overlap and the sample matrix. We herein report a detection scheme based on 19F NMR spectroscopy and dynamic recognition, which effectively simplifies the detection signal and mitigates the influence of the matrix on the detection. It is demonstrated that this approach can not only detect and differentiate capsaicin and dihydrocapsaicin in complex real-world samples but also quantify the ibuprofen content in sustained-release capsules. Based on the 19F signals obtained in the detection using a set of three 19F probes, automated analyte identification is achieved, effectively reducing the odds of misrecognition caused by structural similarity.
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Affiliation(s)
- Zhenchuang Xu
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Siyi Gu
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Yipeng Li
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Jian Wu
- Instrumental Analysis Center, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Yanchuan Zhao
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China.,Key Laboratory of Energy Regulation Materials, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
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3
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Hohmann KF, Blümler A, Heckel A, Fürtig B. The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements. Nucleic Acids Res 2021; 49:11337-11349. [PMID: 34614185 PMCID: PMC8565331 DOI: 10.1093/nar/gkab876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 11/14/2022] Open
Abstract
In bacteria RNA gene regulatory elements refold dependent on environmental clues between two or more long-lived conformational states each associated with a distinct regulatory state. The refolding kinetics are strongly temperature-dependent and especially at lower temperatures they reach timescales that are biologically not accessible. To overcome this problem, RNA chaperones have evolved. However, the precise molecular mechanism of how these proteins accelerate RNA refolding reactions remains enigmatic. Here we show how the RNA chaperone StpA of Escherichia coli leads to an acceleration of a bistable RNA's refolding kinetics through the selective destabilization of key base pairing interactions. We find in laser assisted real-time NMR experiments on photocaged bistable RNAs that the RNA chaperone leads to a two-fold increase in refolding rates at low temperatures due to reduced stability of ground state conformations. Further, we can show that upon interaction with StpA, base pairing interactions in the bistable RNA are modulated to favor refolding through the dominant pseudoknotted transition pathway. Our results shed light on the molecular mechanism of the interaction between RNA chaperones and bistable RNAs and are the first step into a functional classification of chaperones dependent on their biophysical mode of operation.
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Affiliation(s)
- Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance BMRZ, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main, Germany
| | - Anja Blümler
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance BMRZ, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main, Germany
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4
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Grün JT, Schwalbe H. Folding dynamics of polymorphic G-quadruplex structures. Biopolymers 2021; 113:e23477. [PMID: 34664713 DOI: 10.1002/bip.23477] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/14/2022]
Abstract
G-quadruplexes (G4), found in numerous places within the human genome, are involved in essential processes of cell regulation. Chromosomal DNA G4s are involved for example, in replication and transcription as first steps of gene expression. Hence, they influence a plethora of downstream processes. G4s possess an intricate structure that differs from canonical B-form DNA. Identical DNA G4 sequences can adopt multiple long-lived conformations, a phenomenon known as G4 polymorphism. A detailed understanding of the molecular mechanisms that drive G4 folding is essential to understand their ambivalent regulatory roles. Disentangling the inherent dynamic and polymorphic nature of G4 structures thus is key to unravel their biological functions and make them amenable as molecular targets in novel therapeutic approaches. We here review recent experimental approaches to monitor G4 folding and discuss structural aspects for possible folding pathways. Substantial progress in the understanding of G4 folding within the recent years now allows drawing comprehensive models of the complex folding energy landscape of G4s that we herein evaluate based on computational and experimental evidence.
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Affiliation(s)
- J Tassilo Grün
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Frankfurt/M, Germany.,Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Frankfurt/M, Germany
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5
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Pintér G, Hohmann K, Grün J, Wirmer-Bartoschek J, Glaubitz C, Fürtig B, Schwalbe H. Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:291-320. [PMID: 37904763 PMCID: PMC10539803 DOI: 10.5194/mr-2-291-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/07/2021] [Indexed: 11/01/2023]
Abstract
The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.
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Affiliation(s)
- György Pintér
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - J. Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
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6
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Hett T, Zbik T, Mukherjee S, Matsuoka H, Bönigk W, Klose D, Rouillon C, Brenner N, Peuker S, Klement R, Steinhoff HJ, Grubmüller H, Seifert R, Schiemann O, Kaupp UB. Spatiotemporal Resolution of Conformational Changes in Biomolecules by Combining Pulsed Electron-Electron Double Resonance Spectroscopy with Microsecond Freeze-Hyperquenching. J Am Chem Soc 2021; 143:6981-6989. [PMID: 33905249 DOI: 10.1021/jacs.1c01081] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The function of proteins is linked to their conformations that can be resolved with several high-resolution methods. However, only a few methods can provide the temporal order of intermediates and conformational changes, with each having its limitations. Here, we combine pulsed electron-electron double resonance spectroscopy with a microsecond freeze-hyperquenching setup to achieve spatiotemporal resolution in the angstrom range and lower microsecond time scale. We show that the conformational change of the Cα-helix in the cyclic nucleotide-binding domain of the Mesorhizobium loti potassium channel occurs within about 150 μs and can be resolved with angstrom precision. Thus, this approach holds great promise for obtaining 4D landscapes of conformational changes in biomolecules.
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Affiliation(s)
- Tobias Hett
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Tobias Zbik
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Shatanik Mukherjee
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Hideto Matsuoka
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Wolfgang Bönigk
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Daniel Klose
- Fachbereich Physik, Universität Osnabrück, Barbarastraße 7, 49076 Osnabrück, Germany
| | - Christophe Rouillon
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Norbert Brenner
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Sebastian Peuker
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Reinhard Klement
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Reinhard Seifert
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - U Benjamin Kaupp
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.,Life & Medical Sciences Institute (LIMES), University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
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7
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Qiu T, Wang Z, Liu H, Guo D, Qu X. Review and prospect: NMR spectroscopy denoising and reconstruction with low-rank Hankel matrices and tensors. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:324-345. [PMID: 32797694 DOI: 10.1002/mrc.5082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 05/16/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is an important analytical tool in chemistry, biology, and life science, but it suffers from relatively low sensitivity and long acquisition time. Thus, improving the apparent signal-to-noise ratio and accelerating data acquisition became indispensable. In this review, we summarize the recent progress on low-rank Hankel matrix and tensor methods, which exploit the exponential property of free-induction decay signals, to enable effective denoising and spectra reconstruction. We also outline future developments that are likely to make NMR spectroscopy a far more powerful technique.
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Affiliation(s)
- Tianyu Qiu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Zi Wang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Huiting Liu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Di Guo
- School of Computer and Information Engineering, Xiamen University of Technology, Xiamen, China
| | - Xiaobo Qu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
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8
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Fürtig B, Oberhauser EM, Zetzsche H, Klötzner DP, Heckel A, Schwalbe H. Refolding through a Linear Transition State Enables Fast Temperature Adaptation of a Translational Riboswitch. Biochemistry 2020; 59:1081-1086. [PMID: 32134253 DOI: 10.1021/acs.biochem.9b01044] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The adenine-sensing riboswitch from the Gram-negative bacterium Vibrio vulnificus is an RNA-based gene regulatory element that acts in response to both its cognate low-molecular weight ligand and temperature. The combined sensitivity to environmental temperature and ligand concentration is maintained by an equilibrium of three distinct conformations involving two ligand-free states and one ligand-bound state. The key structural element that undergoes refolding in the ligand-free states comprises a 35-nucleotide temperature response module. Here, we present the structural characterization of this temperature response module. We employ high-resolution NMR spectroscopy and photocaged RNAs as molecular probes to decipher the kinetic and thermodynamic framework of the secondary structure transition in the apo state of the riboswitch. We propose a model for the transition state adopted during the thermal refolding of the temperature response module that connects two mutually exclusive long-lived and stable conformational states. This transition state is characterized by a comparatively low free activation enthalpy. A pseudoknot conformation in the transition state, as commonly seen in RNA refolding, is therefore unlikely. More likely, the transition state of the adenine-sensing riboswitch temperature response module features a linear conformation.
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Affiliation(s)
- Boris Fürtig
- Johann Wolfgang Goethe University, Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Max von Laue Strasse 7, 60438 Frankfurt/Main, Germany
| | - Eva Marie Oberhauser
- Institute of Organic Chemistry and Chemical Biology, Max von Laue Strasse 7, 60438 Frankfurt/Main, Germany
| | - Heidi Zetzsche
- Johann Wolfgang Goethe University, Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Max von Laue Strasse 7, 60438 Frankfurt/Main, Germany
| | - Dean-Paulos Klötzner
- Institute of Organic Chemistry and Chemical Biology, Max von Laue Strasse 7, 60438 Frankfurt/Main, Germany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology, Max von Laue Strasse 7, 60438 Frankfurt/Main, Germany
| | - Harald Schwalbe
- Johann Wolfgang Goethe University, Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Max von Laue Strasse 7, 60438 Frankfurt/Main, Germany
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9
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Site-Specific Spin Labeling of RNA for NMR and EPR Structural Studies. Methods Mol Biol 2020. [PMID: 32006317 DOI: 10.1007/978-1-0716-0278-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Many RNA architectures were discovered to be involved in essential biological pathways acting as catalysts and/or regulators of gene expression, transcription, translation, splicing, or viral infection. The key to understand their diverse biological functions is to investigate their structure and dynamic. Nuclear Magnetic Resonance (NMR) is a powerful method to gain insight into these properties. However, the study of high-molecular-weight RNAs by NMR remains challenging. Advances in biochemical and NMR methods over the recent years allow to overcome the limitation of NMR. In particular, the incorporation of paramagnetic probes, coupled to the measurement of the induced effects on nuclear spins, has become an efficient tool providing long-range distance restraints and information on dynamic in solution. At the same time, the use of spin label enabled the application of Electron Paramagnetic Resonance (EPR) to study biological macromolecules. Combining NMR and EPR is emerging as a new approach to investigate the architecture of biological systems.Here, we describe an efficient protocol to introduce a paramagnetic probe into a RNA at a specific position. This method enables various combinations of isotopic labeling for NMR and is also of interest for EPR studies.
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10
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A 300-fold enhancement of imino nucleic acid resonances by hyperpolarized water provides a new window for probing RNA refolding by 1D and 2D NMR. Proc Natl Acad Sci U S A 2020; 117:2449-2455. [PMID: 31949004 DOI: 10.1073/pnas.1916956117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
NMR sensitivity-enhancement methods involving hyperpolarized water could be of importance for solution-state biophysical investigations. Hyperpolarized water (HyperW) can enhance the 1H NMR signals of exchangeable sites by orders of magnitude over their thermal counterparts, while providing insight into chemical exchange and solvent accessibility at a site-resolved level. As HyperW's enhancements are achieved by exploiting fast solvent exchanges associated with minimal interscan delays, possibilities for the rapid monitoring of chemical reactions and biomolecular (re)folding are opened. HyperW NMR can also accommodate heteronuclear transfers, facilitating the rapid acquisition of 2-dimensional (2D) 15N-1H NMR correlations, and thereby combining an enhanced spectral resolution with speed and sensitivity. This work demonstrates how these qualities can come together for the study of nucleic acids. HyperW injections were used to target the guanine-sensing riboswitch aptamer domain (GSRapt) of the xpt-pbuX operon in Bacillus subtilis Unlike what had been observed in proteins, where residues benefited of HyperW NMR only if/when sufficiently exposed to water, these enhancements applied to every imino resonance throughout the RNA. The >300-fold enhancements observed in the resulting 1H NMR spectra allowed us to monitor in real time the changes that GSRapt undergoes upon binding hypoxanthine, a high-affinity interaction leading to conformational refolding on a ∼1-s timescale at 36 °C. Structural responses could be identified for several nucleotides by 1-dimensional (1D) imino 1H NMR as well as by 2D HyperW NMR spectra acquired upon simultaneous injection of hyperpolarized water and hypoxanthine. The folding landscape revealed by this HyperW strategy for GSRapt, is briefly discussed.
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11
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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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12
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Wang F, Sun LZ, Sun T, Chang S, Xu X. Helix-Based RNA Landscape Partition and Alternative Secondary Structure Determination. ACS OMEGA 2019; 4:15407-15413. [PMID: 31572840 PMCID: PMC6761681 DOI: 10.1021/acsomega.9b01430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
RNA is a versatile macromolecule with the ability to fold into and interconvert between multiple functional conformations. The elucidation of the RNA folding landscape, especially the knowledge of alternative structures, is critical to uncover the physical mechanism of RNA functions. Here, we introduce a helix-based strategy for RNA folding landscape partition and alternative secondary structure determination. The benchmark test of 27 RNAs involving alternative stable structures shows that the model has the ability to divide the whole landscape into distinct partitions at the secondary structure level and predict the representative structures for each partition. Furthermore, the predicted structures and equilibrium populations of metastable conformations for the 2'dG-sensing riboswitch reveal the allosteric conformational switch on transcript length, which is consistent with the experimental study, indicating the importance of metastable states for RNA-based gene regulation. The model delivers a starting point for the landscape-based strategy toward the RNA folding mechanism and functions.
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Affiliation(s)
- Fengfei Wang
- Institute
of Bioinformatics and Medical Engineering, School of Mathematics and
Physics, Jiangsu University of Technology, Changzhou, Jiangsu 213001, China
| | - Li-Zhen Sun
- Department
of Applied Physics, Zhejiang University
of Technology, Hangzhou, Zhejiang 310023, China
| | - Tingting Sun
- Department
of Physics, Zhejiang University of Science
and Technology, Hangzhou, Zhejiang 310023, China
| | - Shan Chang
- Institute
of Bioinformatics and Medical Engineering, School of Mathematics and
Physics, Jiangsu University of Technology, Changzhou, Jiangsu 213001, China
| | - Xiaojun Xu
- Institute
of Bioinformatics and Medical Engineering, School of Mathematics and
Physics, Jiangsu University of Technology, Changzhou, Jiangsu 213001, China
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13
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Kinetic Mechanism of RNA Helix-Terminal Basepairing-A Kinetic Minima Network Analysis. Biophys J 2019; 117:1674-1683. [PMID: 31590890 DOI: 10.1016/j.bpj.2019.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 11/22/2022] Open
Abstract
RNA functions are often kinetically controlled. The folding kinetics of RNAs involves global structural changes and local nucleotide movement, such as base flipping. The most elementary step in RNA folding is the closing and opening of a basepair. By integrating molecular dynamics simulation, master equation, and kinetic Monte Carlo simulation, we investigate the kinetics mechanism of RNA helix-terminal basepairing. The study reveals a six-state folding scheme with three dominant folding pathways of tens, hundreds, and thousands of nanoseconds of folding timescales, respectively. The overall kinetics is rate limited by the detrapping of a misfolded state with the overall folding time of 10-5 s. Moreover, the analysis examines the different roles of the various driving forces, such as the basepairing and stacking interactions and the ion binding/dissociation effects on structural changes. The results may provide useful insights for developing a basepair opening/closing rate model and further kinetics models of large RNAs.
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14
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Thompson RD, Baisden JT, Zhang Q. NMR characterization of RNA small molecule interactions. Methods 2019; 167:66-77. [PMID: 31128236 DOI: 10.1016/j.ymeth.2019.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 01/25/2023] Open
Abstract
Exciting discoveries of naturally occurring ligand-sensing and disease-linked noncoding RNAs have promoted significant interests in understanding RNA-small molecule interactions. NMR spectroscopy is a powerful tool for characterizing intermolecular interactions. In this review, we describe protocols and approaches for applying NMR spectroscopy to investigate interactions between RNA and small molecules. We review protocols for RNA sample preparation, methods for identifying RNA-binding small molecules, approaches for mapping RNA-small molecule interactions, determining complex structures, and characterizing binding kinetics. We hope this review will provide a guideline to streamline NMR applications in studying RNA-small molecule interactions, facilitating both basic mechanistic understandings of RNA functions and translational efforts in developing RNA-targeted therapeutics.
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Affiliation(s)
- Rhese D Thompson
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jared T Baisden
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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15
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Combined smFRET and NMR analysis of riboswitch structural dynamics. Methods 2019; 153:22-34. [DOI: 10.1016/j.ymeth.2018.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 12/13/2022] Open
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16
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Abstract
The phenomenon of chemical or conformational exchange in NMR spectroscopy has enabled detailed characterization of time-dependent aspects of biomolecular function, including folding, molecular recognition, allostery, and catalysis, on timescales from microsecond to second. Importantly, NMR methods based on a variety of spin relaxation parameters have been developed that provide quantitative information on interconversion kinetics, thermodynamic properties, and structural features of molecular states populated to a fraction of a percent at equilibrium and otherwise unobservable by other NMR approaches. The ongoing development of more sophisticated experimental techniques and the necessity to apply these methods to larger and more complex molecular systems engenders a corresponding need for theoretical advances describing such techniques and facilitating data analysis in applications. This review surveys current aspects of the theory of chemical exchange, as utilized in ZZ-exchange; Hahn and Carr-Purcell-Meiboom-Gill (CPMG) spin-echo; and R1ρ, chemical exchange saturation transfer (CEST), and dark state saturation transfer (DEST) spin-locking experiments. The review emphasizes theoretical results for kinetic topologies with more than two interconverting states, both to obtain compact analytical forms suitable for data analysis and to establish conditions for distinguishability between alternative kinetic schemes.
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Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States.
| | - Hans Koss
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
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17
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Szekely O, Armony G, Olsen GL, Bigman LS, Levy Y, Fass D, Frydman L. Identification and Rationalization of Kinetic Folding Intermediates for a Low-Density Lipoprotein Receptor Ligand-Binding Module. Biochemistry 2018; 57:4776-4787. [PMID: 29979586 DOI: 10.1021/acs.biochem.8b00466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many mutations that cause familial hypercholesterolemia localize to ligand-binding domain 5 (LA5) of the low-density lipoprotein receptor, motivating investigation of the folding and misfolding of this small, disulfide-rich, calcium-binding domain. LA5 folding is known to involve non-native disulfide isomers, yet these folding intermediates have not been structurally characterized. To provide insight into these intermediates, we used nuclear magnetic resonance (NMR) to follow LA5 folding in real time. We demonstrate that misfolded or partially folded disulfide intermediates are indistinguishable from the unfolded state when focusing on the backbone NMR signals, which provide information on the formation of only the final, native state. However, 13C labeling of cysteine side chains differentiated transient intermediates from the unfolded and native states and reported on disulfide bond formation in real time. The cysteine pairings in a dominant intermediate were identified using 13C-edited three-dimensional NMR, and coarse-grained molecular dynamics simulations were used to investigate the preference of this disulfide set over other non-native arrangements. The transient population of LA5 species with particular non-native cysteine connectitivies during folding supports the conclusion that cysteine pairing is not random and that there is a bias toward certain structural ensembles during the folding process, even prior to the binding of calcium.
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Affiliation(s)
- Or Szekely
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Gad Armony
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Gregory Lars Olsen
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Lavi S Bigman
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Yaakov Levy
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Deborah Fass
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Lucio Frydman
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 7610001 , Israel
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18
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Schlagnitweit J, Steiner E, Karlsson H, Petzold K. Efficient Detection of Structure and Dynamics in Unlabeled RNAs: The SELOPE Approach. Chemistry 2018; 24:6067-6070. [PMID: 29504639 PMCID: PMC5947647 DOI: 10.1002/chem.201800992] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 01/10/2023]
Abstract
The knowledge of structure and dynamics is crucial to explain the function of RNAs. While nuclear magnetic resonance (NMR) is well suited to probe these for complex biomolecules, it requires expensive, isotopically labeled samples, and long measurement times. Here we present SELOPE, a new robust, proton-only NMR method that allows us to obtain site-specific overview of structure and dynamics in an entire RNA molecule using an unlabeled sample. SELOPE simplifies assignment and allows for cost-effective screening of the response of nucleic acids to physiological changes (e.g. ion concentration) or screening of drugs in a high throughput fashion. This single technique allows us to probe an unprecedented range of exchange time scales (the whole μs to ms motion range) with increased sensitivity, surpassing all current experiments to detect chemical exchange. For the first time we could describe an RNA excited state using an unlabeled RNA.
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Affiliation(s)
- Judith Schlagnitweit
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
| | - Emilie Steiner
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
| | - Hampus Karlsson
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
| | - Katja Petzold
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
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19
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Helmling C, Klötzner DP, Sochor F, Mooney RA, Wacker A, Landick R, Fürtig B, Heckel A, Schwalbe H. Life times of metastable states guide regulatory signaling in transcriptional riboswitches. Nat Commun 2018; 9:944. [PMID: 29507289 PMCID: PMC5838219 DOI: 10.1038/s41467-018-03375-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 02/06/2018] [Indexed: 11/26/2022] Open
Abstract
Transcriptional riboswitches modulate downstream gene expression by a tight coupling of ligand-dependent RNA folding kinetics with the rate of transcription. RNA folding pathways leading to functional ON and OFF regulation involve the formation of metastable states within well-defined sequence intervals during transcription. The kinetic requirements for the formation and preservation of these metastable states in the context of transcription remain unresolved. Here, we reversibly trap the previously defined regulatory relevant metastable intermediate of the Mesoplasma florum 2′-deoxyguanosine (2′dG)-sensing riboswitch using a photocaging-ligation approach, and monitor folding to its native state by real-time NMR in both presence and absence of ligand. We further determine transcription rates for two different bacterial RNA polymerases. Our results reveal that the riboswitch functions only at transcription rates typical for bacterial polymerases (10–50 nt s−1) and that gene expression is modulated by 40–50% only, while subtle differences in folding rates guide population ratios within the structural ensemble to a specific regulatory outcome. Riboswitches are RNA-based regulatory elements, which regulate downstream gene expression by binding of small molecular weight ligands. Here the authors demonstrate the molecular mechanism of a transcriptional riboswitch that integrates changes in transcription rates, metabolite concentration, and kinetic on- and off-rates of ligand binding.
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Affiliation(s)
- Christina Helmling
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Dean-Paulos Klötzner
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Florian Sochor
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Rachel Anne Mooney
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany.
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany.
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20
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Adrian M, Winnerdy FR, Heddi B, Phan AT. Rotation of Guanine Amino Groups in G-Quadruplexes: A Probe for Local Structure and Ligand Binding. Biophys J 2017; 113:775-784. [PMID: 28834714 DOI: 10.1016/j.bpj.2017.05.053] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/22/2017] [Accepted: 05/25/2017] [Indexed: 12/25/2022] Open
Abstract
Nucleic acids are dynamic molecules whose functions may depend on their conformational fluctuations and local motions. In particular, amino groups are dynamic components of nucleic acids that participate in the formation of various secondary structures such as G-quadruplexes. Here, we present a cost-efficient NMR method to quantify the rotational dynamics of guanine amino groups in G-quadruplex nucleic acids. An isolated spectrum of amino protons from a specific tetrad-bound guanine can be extracted from the nuclear Overhauser effect spectroscopy spectrum based on the close proximity between the intra-residue imino and amino protons. We apply the method in different structural contexts of G-quadruplexes and their complexes. Our results highlight the role of stacking and hydrogen-bond interactions in restraining amino-group rotation. The measurement of the rotation rate of individual amino groups could give insight into the dynamic processes occurring at specific locations within G-quadruplex nucleic acids, providing valuable probes for local structure, dynamics, and ligand binding.
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Affiliation(s)
- Michael Adrian
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Fernaldo Richtia Winnerdy
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Brahim Heddi
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Anh Tuân Phan
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
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21
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Clay MC, Ganser LR, Merriman DK, Al-Hashimi HM. Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics. Nucleic Acids Res 2017; 45:e134. [PMID: 28609788 PMCID: PMC5737546 DOI: 10.1093/nar/gkx525] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/01/2017] [Accepted: 06/05/2017] [Indexed: 11/15/2022] Open
Abstract
Recent studies have shown that RNAs exist in dynamic equilibrium with short-lived low-abundance 'excited states' that form by reshuffling base pairs in and around non-canonical motifs. These conformational states are proposed to be rich in non-canonical motifs and to play roles in the folding and regulatory functions of non-coding RNAs but their structure proves difficult to characterize given their transient nature. Here, we describe an approach for determining sugar pucker conformation in RNA excited states through nuclear magnetic resonance measurements of C1΄ and C4΄ rotating frame spin relaxation (R1ρ) in uniformly 13C/15N labeled RNA samples. Application to HIV-1 TAR exposed slow modes of sugar repuckering dynamics at the μs and ms timescale accompanying transitions between non-helical (C2΄-endo) to helical (C3΄-endo) conformations during formation of two distinct excited states. In contrast, we did not obtain any evidence for slow sugar repuckering dynamics for nucleotides in a variety of structural contexts that do not undergo non-helical to helical transitions. Our results outline a route for significantly improving the conformational characterization of RNA excited states and suggest that slow modes of repuckering dynamics gated by transient changes in secondary structure are quite common in RNA.
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Affiliation(s)
- Mary C. Clay
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Laura R. Ganser
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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22
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Franco R, Favier A, Schanda P, Brutscher B. Optimized fast mixing device for real-time NMR applications. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 281:125-129. [PMID: 28595119 PMCID: PMC5542027 DOI: 10.1016/j.jmr.2017.05.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 05/29/2017] [Indexed: 05/03/2023]
Abstract
We present an improved fast mixing device based on the rapid mixing of two solutions inside the NMR probe, as originally proposed by Hore and coworkers (J. Am. Chem. Soc. 125 (2003) 12484-12492). Such a device is important for off-equilibrium studies of molecular kinetics by multidimensional real-time NMR spectrsocopy. The novelty of this device is that it allows removing the injector from the NMR detection volume after mixing, and thus provides good magnetic field homogeneity independently of the initial sample volume placed in the NMR probe. The apparatus is simple to build, inexpensive, and can be used without any hardware modification on any type of liquid-state NMR spectrometer. We demonstrate the performance of our fast mixing device in terms of improved magnetic field homogeneity, and show an application to the study of protein folding and the structural characterization of transiently populated folding intermediates.
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Affiliation(s)
- Rémi Franco
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France
| | - Adrien Favier
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France
| | - Paul Schanda
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France
| | - Bernhard Brutscher
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.
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23
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Schanda P, Ernst M. Studying Dynamics by Magic-Angle Spinning Solid-State NMR Spectroscopy: Principles and Applications to Biomolecules. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:1-46. [PMID: 27110043 PMCID: PMC4836562 DOI: 10.1016/j.pnmrs.2016.02.001] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Magic-angle spinning solid-state NMR spectroscopy is an important technique to study molecular structure, dynamics and interactions, and is rapidly gaining importance in biomolecular sciences. Here we provide an overview of experimental approaches to study molecular dynamics by MAS solid-state NMR, with an emphasis on the underlying theoretical concepts and differences of MAS solid-state NMR compared to solution-state NMR. The theoretical foundations of nuclear spin relaxation are revisited, focusing on the particularities of spin relaxation in solid samples under magic-angle spinning. We discuss the range of validity of Redfield theory, as well as the inherent multi-exponential behavior of relaxation in solids. Experimental challenges for measuring relaxation parameters in MAS solid-state NMR and a few recently proposed relaxation approaches are discussed, which provide information about time scales and amplitudes of motions ranging from picoseconds to milliseconds. We also discuss the theoretical basis and experimental measurements of anisotropic interactions (chemical-shift anisotropies, dipolar and quadrupolar couplings), which give direct information about the amplitude of motions. The potential of combining relaxation data with such measurements of dynamically-averaged anisotropic interactions is discussed. Although the focus of this review is on the theoretical foundations of dynamics studies rather than their application, we close by discussing a small number of recent dynamics studies, where the dynamic properties of proteins in crystals are compared to those in solution.
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Affiliation(s)
- Paul Schanda
- CEA, Institut de Biologie Structurale (IBS), 38027 Grenoble, France ; CNRS, Institut de Biologie Structurale (IBS), 38027 Grenoble, France ; Université Grenoble Alpes, IBS, 38027 Grenoble, France
| | - Matthias Ernst
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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24
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Nowakowski M, Saxena S, Stanek J, Żerko S, Koźmiński W. Applications of high dimensionality experiments to biomolecular NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 90-91:49-73. [PMID: 26592945 DOI: 10.1016/j.pnmrs.2015.07.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 07/03/2015] [Accepted: 07/03/2015] [Indexed: 05/23/2023]
Abstract
High dimensionality NMR experiments facilitate resonance assignment and precise determination of spectral parameters such as coupling constants. Sparse non-uniform sampling enables acquisition of experiments of high dimensionality with high resolution in acceptable time. In this review we present and compare some significant applications of NMR experiments of dimensionality higher than three in the field of biomolecular studies in solution.
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Affiliation(s)
- Michał Nowakowski
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Saurabh Saxena
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Jan Stanek
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Szymon Żerko
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Wiktor Koźmiński
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland.
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25
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Helmling C, Keyhani S, Sochor F, Fürtig B, Hengesbach M, Schwalbe H. Rapid NMR screening of RNA secondary structure and binding. JOURNAL OF BIOMOLECULAR NMR 2015; 63:67-76. [PMID: 26188386 DOI: 10.1007/s10858-015-9967-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/13/2015] [Indexed: 05/10/2023]
Abstract
Determination of RNA secondary structures by NMR spectroscopy is a useful tool e.g. to elucidate RNA folding space or functional aspects of regulatory RNA elements. However, current approaches of RNA synthesis and preparation are usually time-consuming and do not provide analysis with single nucleotide precision when applied for a large number of different RNA sequences. Here, we significantly improve the yield and 3' end homogeneity of RNA preparation by in vitro transcription. Further, by establishing a native purification procedure with increased throughput, we provide a shortcut to study several RNA constructs simultaneously. We show that this approach yields μmol quantities of RNA with purities comparable to PAGE purification, while avoiding denaturation of the RNA.
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Affiliation(s)
- Christina Helmling
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany
| | - Sara Keyhani
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany
| | - Florian Sochor
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany
| | - Boris Fürtig
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany.
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26
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Yang S, Al-Hashimi HM. Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs. J Phys Chem B 2015; 119:9614-26. [PMID: 26131693 DOI: 10.1021/acs.jpcb.5b03859] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A growing number of studies employ time-averaged experimental data to determine dynamic ensembles of biomolecules. While it is well-known that different ensembles can satisfy experimental data to within error, the extent and nature of these degeneracies, and their impact on the accuracy of the ensemble determination remains poorly understood. Here, we use simulations and a recently introduced metric for assessing ensemble similarity to explore degeneracies in determining ensembles using NMR residual dipolar couplings (RDCs) with specific application to A-form helices in RNA. Various target ensembles were constructed representing different domain-domain orientational distributions that are confined to a topologically restricted (<10%) conformational space. Five independent sets of ensemble averaged RDCs were then computed for each target ensemble and a "sample and select" scheme used to identify degenerate ensembles that satisfy RDCs to within experimental uncertainty. We find that ensembles with different ensemble sizes and that can differ significantly from the target ensemble (by as much as ∑Ω ∼ 0.4 where ∑Ω varies between 0 and 1 for maximum and minimum ensemble similarity, respectively) can satisfy the ensemble averaged RDCs. These deviations increase with the number of unique conformers and breadth of the target distribution, and result in significant uncertainty in determining conformational entropy (as large as 5 kcal/mol at T = 298 K). Nevertheless, the RDC-degenerate ensembles are biased toward populated regions of the target ensemble, and capture other essential features of the distribution, including the shape. Our results identify ensemble size as a major source of uncertainty in determining ensembles and suggest that NMR interactions such as RDCs and spin relaxation, on their own, do not carry the necessary information needed to determine conformational entropy at a useful level of precision. The framework introduced here provides a general approach for exploring degeneracies in ensemble determination for different types of experimental data.
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Affiliation(s)
- Shan Yang
- †Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, United States
| | - Hashim M Al-Hashimi
- ‡Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, North Carolina 27705, United States
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27
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Giambaşu GM, York DM, Case DA. Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin. RNA (NEW YORK, N.Y.) 2015; 21:963-74. [PMID: 25805858 PMCID: PMC4408802 DOI: 10.1261/rna.047357.114] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 01/17/2015] [Indexed: 05/16/2023]
Abstract
RNA hairpins are widespread and very stable motifs that contribute decisively to RNA folding and biological function. The GTP1G2C3A4C5U6U7C8G9G10U11G12C13C14 construct (with a central UUCG tetraloop) has been extensively studied by solution NMR, and offers and excellent opportunity to evaluate the structure and dynamical description afforded by molecular dynamics (MD) simulations. Here, we compare average structural parameters and NMR relaxation rates estimated from a series of multiple independent explicit solvent MD simulations using the two most recent RNA AMBER force fields (ff99 and ff10). Predicted overall tumbling times are ∼20% faster than those inferred from analysis of NMR data and follow the same trend when temperature and ionic strength is varied. The Watson-Crick stem and the "canonical" UUCG loop structure are maintained in most simulations including the characteristic syn conformation along the glycosidic bond of G9, although some key hydrogen bonds in the loop are partially disrupted. Our analysis pinpoints G9-G10 backbone conformations as a locus of discrepancies between experiment and simulation. In general the results for the more recent force-field parameters (ff10) are closer to experiment than those for the older ones (ff99). This work provides a comprehensive and detailed comparison of state of the art MD simulations against a wide variety of solution NMR measurements.
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Affiliation(s)
- George M Giambaşu
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Darrin M York
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - David A Case
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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28
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RNA folding: structure prediction, folding kinetics and ion electrostatics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 827:143-83. [PMID: 25387965 DOI: 10.1007/978-94-017-9245-5_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.
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29
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Fürtig B, Reining A, Sochor F, Oberhauser EM, Heckel A, Schwalbe H. Characterization of conformational dynamics of bistable RNA by equilibrium and non-equilibrium NMR. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2014; 55:11.13.1-16. [PMID: 25631532 DOI: 10.1002/0471142700.nc1113s55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Unlike proteins, a given RNA sequence can adopt more than a single conformation. The two (or more) conformations are long-lived and have similar stabilities, but interconvert only slowly. Such bi- or multistability is often linked to the biological functions of the RNA. This unit describes how nuclear magnetic resonance (NMR) spectroscopy can be used to characterize the conformational dynamics of bistable RNAs.
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Affiliation(s)
- Boris Fürtig
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University, Frankfurt, Germany; Institute of Organic Chemistry and Chemical Biology, Cluster of Excellence Macromolecular Complexes, Johann Wolfgang Goethe University, Frankfurt, Germany
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30
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Kumar A, Balbach J. Real-time protein NMR spectroscopy and investigation of assisted protein folding. Biochim Biophys Acta Gen Subj 2014; 1850:1965-72. [PMID: 25497212 DOI: 10.1016/j.bbagen.2014.12.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/26/2014] [Accepted: 12/02/2014] [Indexed: 12/23/2022]
Abstract
BACKGROUND During protein-folding reactions toward the native structure, short-lived intermediate states can be populated. Such intermediates expose hydrophobic patches and can self-associate leading to non-productive protein misfolding. A major focus of current research is the characterization of short-lived intermediates and how molecular chaperones enable productive folding. Real-time NMR spectroscopy, together with the development of advanced methods, is reviewed here and the potential these methods have to characterize intermediate states as well as interactions with molecular chaperone proteins at single-residue resolution is highlighted. SCOPE OF REVIEW Various chaperone interactions can guide the protein-folding reaction and thus are important for protein structure formation, stability, and activity of their substrates. Chaperone-assisted protein folding, characterization of intermediates, and their molecular interactions using real-time NMR spectroscopy will be discussed. Additionally, recent advances in NMR methods employed for characterization of high-energy intermediates will be discussed. MAJOR CONCLUSIONS Real-time NMR combines high resolution with kinetic information of protein reactions, which can be employed not only for protein-folding studies and the characterization of folding intermediates but also to investigate the molecular mechanisms of assisted protein folding. GENERAL SIGNIFICANCE Real-time NMR spectroscopy remains an effective tool to reveal structural details about the interaction between chaperones and transient intermediates. Methodologically, it provides in-depth understanding of how kinetic intermediates and their thermodynamics contribute to the protein-folding reaction. This review summarizes the most recent advances in this field. This article is part of a Special Issue titled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Affiliation(s)
- Amit Kumar
- Institut für Physik, Biophysik, und Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther Universität Halle-Wittenberg, Halle D-06120, Germany
| | - Jochen Balbach
- Institut für Physik, Biophysik, und Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther Universität Halle-Wittenberg, Halle D-06120, Germany.
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Mann M, Kucharík M, Flamm C, Wolfinger MT. Memory-efficient RNA energy landscape exploration. Bioinformatics 2014; 30:2584-91. [PMID: 24833804 PMCID: PMC4155248 DOI: 10.1093/bioinformatics/btu337] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 04/25/2014] [Accepted: 05/08/2014] [Indexed: 02/01/2023] Open
Abstract
MOTIVATION Energy landscapes provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions. Higher abstraction levels based on a macro-state decomposition of the landscape enable the study of larger systems; however, they are still restricted by huge memory requirements of exact approaches. RESULTS We present a highly parallelizable local enumeration scheme that enables the computation of exact macro-state transition models with highly reduced memory requirements. The approach is evaluated on RNA secondary structure landscapes using a gradient basin definition for macro-states. Furthermore, we demonstrate the need for exact transition models by comparing two barrier-based approaches, and perform a detailed investigation of gradient basins in RNA energy landscapes. AVAILABILITY AND IMPLEMENTATION Source code is part of the C++ Energy Landscape Library available at http://www.bioinf.uni-freiburg.de/Software/.
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Affiliation(s)
- Martin Mann
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Marcel Kucharík
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Christoph Flamm
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Michael T Wolfinger
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
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32
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Lebars I, Vileno B, Bourbigot S, Turek P, Wolff P, Kieffer B. A fully enzymatic method for site-directed spin labeling of long RNA. Nucleic Acids Res 2014; 42:e117. [PMID: 24981512 PMCID: PMC4150755 DOI: 10.1093/nar/gku553] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Site-directed spin labeling is emerging as an essential tool to investigate the structural and dynamical features of RNA. We propose here an enzymatic method, which allows the insertion of a paramagnetic center at a specific position in an RNA molecule. The technique is based on a segmental approach using a ligation protocol with T4 RNA ligase 2. One transcribed acceptor RNA is ligated to a donor RNA in which a thio-modified nucleotide is introduced at its 5′-end by in vitro transcription with T7 RNA polymerase. The paramagnetic thiol-specific reagent is subsequently attached to the RNA ligation product. This novel strategy is demonstrated by introducing a paramagnetic probe into the 55 nucleotides long RNA corresponding to K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-Box leader RNA. The efficiency of the coupling reaction and the quality of the resulting spin-labeled RNA were assessed by Mass Spectrometry, Electron Paramagnetic Resonance (EPR) and Nuclear Magnetic Resonance (NMR). This method enables various combinations of isotopic segmental labeling and spin labeling schemes, a strategy that will be of particular interest to investigate the structural and dynamical properties of large RNA complexes by NMR and EPR spectroscopies.
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Affiliation(s)
- Isabelle Lebars
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Biologie Structurale, Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé et de la Recherche Médicale (INSERM) U964/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, 67404 Illkirch cedex, France
| | - Bertrand Vileno
- Institut de Chimie, Laboratoire Propriétés Optiques & Magnétiques des Architectures Moléculaires, Université de Strasbourg, UMR 7177 CNRS, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg Cedex, France
| | - Sarah Bourbigot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Biologie Structurale, Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé et de la Recherche Médicale (INSERM) U964/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, 67404 Illkirch cedex, France
| | - Philippe Turek
- Institut de Chimie, Laboratoire Propriétés Optiques & Magnétiques des Architectures Moléculaires, Université de Strasbourg, UMR 7177 CNRS, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg Cedex, France
| | - Philippe Wolff
- Institut de Biologie Moléculaire et Cellulaire, Plateforme Protéomique Strasbourg Esplanade, FRC 1589 CNRS, 15 rue René Descartes, 67084 Strasbourg Cedex, France Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité des ARN, Université de Strasbourg, UPR 9002 CNRS, 15 rue René Descartes, 67084 Strasbourg Cedex, France
| | - Bruno Kieffer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Biologie Structurale, Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé et de la Recherche Médicale (INSERM) U964/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, 67404 Illkirch cedex, France
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Nozinovic S, Reining A, Kim YB, Noeske J, Schlepckow K, Wöhnert J, Schwalbe H. The importance of helix P1 stability for structural pre-organization and ligand binding affinity of the adenine riboswitch aptamer domain. RNA Biol 2014; 11:655-6. [PMID: 24921630 PMCID: PMC4152369 DOI: 10.4161/rna.29439] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We report here an in-depth characterization of the aptamer domain of the transcriptional adenine-sensing riboswitch (pbuE) by NMR and fluorescence spectroscopy. By NMR studies, the structure of two aptamer sequences with different lengths of the helix P1, the central element involved in riboswitch conformational switching, was characterized. Hydrogen-bond interactions could be mapped at nucleotide resolution providing information about secondary and tertiary structure, structure homogeneity and dynamics. Our study reveals that the elongation of helix P1 has pronounced effects not only on the local but on the global structure of the apo aptamer domain. The structural differences induced by stabilizing helix P1 were found to be linked to changes of the ligand binding affinity as revealed from analysis of kinetic and thermodynamic data obtained from stopped-flow fluorescence studies. The results provide new insight into the sequence-dependent fine tuning of the structure and function of purine-sensing riboswitches.
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Affiliation(s)
- Senada Nozinovic
- Johann Wolfgang Goethe-University Frankfurt; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 7; Frankfurt, Germany; Institute of Organic Chemistry and Chemical Biology
| | - Anke Reining
- Johann Wolfgang Goethe-University Frankfurt; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 7; Frankfurt, Germany; Institute of Organic Chemistry and Chemical Biology
| | - Yong-Boum Kim
- Johann Wolfgang Goethe-University Frankfurt; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 7; Frankfurt, Germany; Institute of Organic Chemistry and Chemical Biology
| | - Jonas Noeske
- Department of Molecular and Cell Biology; University of California at Berkeley; Berkeley, CA USA
| | - Kai Schlepckow
- Johann Wolfgang Goethe-University Frankfurt; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 7; Frankfurt, Germany; Institute of Organic Chemistry and Chemical Biology
| | - Jens Wöhnert
- Johann Wolfgang Goethe-University Frankfurt; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 7; Frankfurt, Germany; Institute for Molecular Biosciences; Max-von-Laue-Strasse 9; Frankfurt, Germany
| | - Harald Schwalbe
- Johann Wolfgang Goethe-University Frankfurt; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 7; Frankfurt, Germany; Institute of Organic Chemistry and Chemical Biology
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34
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Mayzel M, Rosenlöw J, Isaksson L, Orekhov VY. Time-resolved multidimensional NMR with non-uniform sampling. JOURNAL OF BIOMOLECULAR NMR 2014; 58:129-39. [PMID: 24435565 PMCID: PMC3929766 DOI: 10.1007/s10858-013-9811-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 12/30/2013] [Indexed: 05/11/2023]
Abstract
Time-resolved experiments demand high resolution both in spectral dimensions and in time of the studied kinetic process. The latter requirement traditionally prohibits applications of the multidimensional experiments, which, although capable of providing invaluable information about structure and dynamics and almost unlimited spectral resolution, require too lengthy data collection. Our work shows that the problem has a solution in using modern methods of NMR data collection and signal processing. A continuous fast pulsing three-dimensional experiment is acquired using non-uniform sampling during full time of the studied reaction. High sensitivity and time-resolution of a few minutes is achieved by simultaneous processing of the full data set with the multi-dimensional decomposition. The method is verified and illustrated in realistic simulations and by measuring deuterium exchange rates of amide protons in ubiquitin. We applied the method for characterizing kinetics of in vitro phosphorylation of two tyrosine residues in an intrinsically disordered cytosolic domain of the B cell receptor protein CD79b. Signals of many residues including tyrosines in both phosphorylated and unmodified forms of CD79b are found in a heavily crowded region of 2D ¹H-¹⁵N correlation spectrum and the significantly enhanced spectral resolution provided by the 3D time-resolved approach was essential for the quantitative site-specific analysis.
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Affiliation(s)
- Maxim Mayzel
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
| | - Joakim Rosenlöw
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
| | - Linnéa Isaksson
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
| | - Vladislav Y. Orekhov
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
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35
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Borkar AN, De Simone A, Montalvao RW, Vendruscolo M. A method of determining RNA conformational ensembles using structure-based calculations of residual dipolar couplings. J Chem Phys 2014; 138:215103. [PMID: 23758399 DOI: 10.1063/1.4804301] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We describe a method of determining the conformational fluctuations of RNA based on the incorporation of nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) as replica-averaged structural restraints in molecular dynamics simulations. In this approach, the alignment tensor required to calculate the RDCs corresponding to a given conformation is estimated from its shape, and multiple replicas of the RNA molecule are simulated simultaneously to reproduce in silico the ensemble-averaging procedure performed in the NMR measurements. We provide initial evidence that with this approach it is possible to determine accurately structural ensembles representing the conformational fluctuations of RNA by applying the reference ensemble test to the trans-activation response element of the human immunodeficiency virus type 1.
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Affiliation(s)
- Aditi N Borkar
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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36
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Mehta A, Sonam S, Gouri I, Loharch S, Sharma DK, Parkesh R. SMMRNA: a database of small molecule modulators of RNA. Nucleic Acids Res 2014; 42:D132-41. [PMID: 24163098 PMCID: PMC3965028 DOI: 10.1093/nar/gkt976] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 09/13/2013] [Accepted: 10/01/2013] [Indexed: 02/05/2023] Open
Abstract
We have developed SMMRNA, an interactive database, available at http://www.smmrna.org, with special focus on small molecule ligands targeting RNA. Currently, SMMRNA consists of ∼770 unique ligands along with structural images of RNA molecules. Each ligand in the SMMRNA contains information such as Kd, Ki, IC50, ΔTm, molecular weight (MW), hydrogen donor and acceptor count, XlogP, number of rotatable bonds, number of aromatic rings and 2D and 3D structures. These parameters can be explored using text search, advanced search, substructure and similarity-based analysis tools that are embedded in SMMRNA. A structure editor is provided for 3D visualization of ligands. Advance analysis can be performed using substructure and OpenBabel-based chemical similarity fingerprints. Upload facility for both RNA and ligands is also provided. The physicochemical properties of the ligands were further examined using OpenBabel descriptors, hierarchical clustering, binning partition and multidimensional scaling. We have also generated a 3D conformation database of ligands to support the structure and ligand-based screening. SMMRNA provides comprehensive resource for further design, development and refinement of small molecule modulators for selective targeting of RNA molecules.
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Affiliation(s)
- Ankita Mehta
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| | - Surabhi Sonam
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| | - Isha Gouri
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| | - Saurabh Loharch
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| | - Deepak K. Sharma
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| | - Raman Parkesh
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
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37
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Zhao B, Hansen AL, Zhang Q. Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R(1ρ) NMR spectroscopy. J Am Chem Soc 2013; 136:20-3. [PMID: 24299272 DOI: 10.1021/ja409835y] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantitative characterization of dynamic exchange between various conformational states provides essential insights into the molecular basis of many regulatory RNA functions. Here, we present an application of nucleic-acid-optimized carbon chemical exchange saturation transfer (CEST) and low spin-lock field R(1ρ) relaxation dispersion (RD) NMR experiments in characterizing slow chemical exchange in nucleic acids that is otherwise difficult if not impossible to be quantified by the ZZ-exchange NMR experiment. We demonstrated the application on a 47-nucleotide fluoride riboswitch in the ligand-free state, for which CEST and R(1ρ) RD profiles of base and sugar carbons revealed slow exchange dynamics involving a sparsely populated (p ~ 10%) and shortly lived (τ ~ 10 ms) NMR "invisible" state. The utility of CEST and low spin-lock field R(1ρ) RD experiments in studying slow exchange was further validated in characterizing an exchange as slow as ~60 s(-1).
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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
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38
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Probing high-affinity 11-mer DNA aptamer against Lup an 1 (β-conglutin). Anal Bioanal Chem 2013; 405:9343-9. [PMID: 24126837 DOI: 10.1007/s00216-013-7385-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/12/2013] [Accepted: 09/16/2013] [Indexed: 12/22/2022]
Abstract
Aptamers are synthetic nucleic acids with great potential as analytical tools. However, the length of selected aptamers (typically 60-100 bases) can affect affinity, due to the presence of bases not required for interaction with the target, and therefore, the truncation of these selected sequences and identification of binding domains is a critical step to produce potent aptamers with higher affinities and specificities and lowered production costs. In this paper we report the truncation of an aptamer that specifically binds to β-conglutin (Lup an 1), an anaphylactic allergen. Through comparing the predicted secondary structures of the aptamers, a hairpin structure with a G-rich loop was determined to be the binding motif. The highest affinity was observed with a truncation resulting in an 11-mer sequence that had an apparent equilibrium dissociation constant (K D) of 1.7 × 10(-9) M. This 11-mer sequence was demonstrated to have high specificity for β-conglutin and showed no cross-reactivity to other lupin conglutins (α-, δ-, γ-conglutins) and closely related proteins such as gliadin. Finally, the structure of the truncated 11-mer aptamer was preliminarily elucidated, and the GQRS Mapper strongly predicted the presence of a G-quadruplex, which was subsequently corroborated using one-dimensional NMR, thus highlighting the stability of the truncated structure.
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39
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Rennella E, Brutscher B. Fast Real-Time NMR Methods for Characterizing Short-Lived Molecular States. Chemphyschem 2013; 14:3059-70. [DOI: 10.1002/cphc.201300339] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Indexed: 12/22/2022]
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40
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Abstract
Photo-chemically induced dynamic nuclear polarization (CIDNP) is a nuclear magnetic resonance (NMR) phenomenon which, among other things, is exploited to extract information on biomolecular structure via probing solvent-accessibilities of tryptophan (Trp), tyrosine (Tyr), and histidine (His) amino acid side chains both in polypeptides and proteins in solution. The effect, normally triggered by a (laser) light-induced photochemical reaction in situ, yields both positive and/or negative signal enhancements in the resulting NMR spectra which reflect the solvent exposure of these residues both in equilibrium and during structural transformations in "real time". As such, the method can offer - qualitatively and, to a certain extent, quantitatively - residue-specific structural and kinetic information on both the native and, in particular, the non-native states of proteins which, often, is not readily available from more routine NMR techniques. In this review, basic experimental procedures of the photo-CIDNP technique as applied to amino acids and proteins are discussed, recent improvements to the method highlighted, and future perspectives presented. First, the basic principles of the phenomenon based on the theory of the radical pair mechanism (RPM) are outlined. Second, a description of standard photo-CIDNP applications is given and it is shown how the effect can be exploited to extract residue-specific structural information on the conformational space sampled by unfolded or partially folded proteins on their "path" to the natively folded form. Last, recent methodological advances in the field are highlighted, modern applications of photo-CIDNP in the context of biological NMR evaluated, and an outlook into future perspectives of the method is given.
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Affiliation(s)
- Lars T Kuhn
- DFG Research Center Molecular Physiology of the Brain (CMPB), European Neuroscience Institute Göttingen (ENI-G) and EXC 171 Microscopy at the Nanometer Range, Göttingen, Germany,
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41
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Abstract
Transitions between the different conformational states play a critical role in many RNA catalytic and regulatory functions. In this study, we use the Kinetic Monte Carlo method to investigate the kinetic mechanism for the conformational switches between bistable RNA hairpins. We find three types of conformational switch pathways for RNA hairpins: refolding after complete unfolding, folding through basepair-exchange pathways and through pseudoknot-assisted pathways, respectively. The result of the competition between the three types of pathways depends mainly on the location of the rate-limiting base stacks (such as the GC base stacks) in the structures. Depending on the structural relationships between the two bistable hairpins, the conformational switch can follow single or multiple dominant pathways. The predicted folding pathways are supported by the activation energy results derived from the Arrhenius plot as well as the NMR spectroscopy data.
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Affiliation(s)
- Xiaojun XU
- Department of Physics and Department of Biochemistry University of Missouri, Columbia, MO 65211
| | - Shi-Jie CHEN
- Department of Physics and Department of Biochemistry University of Missouri, Columbia, MO 65211
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42
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Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Light-controlled tools. Angew Chem Int Ed Engl 2012; 51:8446-76. [PMID: 22829531 DOI: 10.1002/anie.201202134] [Citation(s) in RCA: 738] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Indexed: 12/21/2022]
Abstract
Spatial and temporal control over chemical and biological processes plays a key role in life, where the whole is often much more than the sum of its parts. Quite trivially, the molecules of a cell do not form a living system if they are only arranged in a random fashion. If we want to understand these relationships and especially the problems arising from malfunction, tools are necessary that allow us to design sophisticated experiments that address these questions. Highly valuable in this respect are external triggers that enable us to precisely determine where, when, and to what extent a process is started or stopped. Light is an ideal external trigger: It is highly selective and if applied correctly also harmless. It can be generated and manipulated with well-established techniques, and many ways exist to apply light to living systems--from cells to higher organisms. This Review will focus on developments over the last six years and includes discussions on the underlying technologies as well as their applications.
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Affiliation(s)
- Clara Brieke
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, 60438 Frankfurt/Main, Germany
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43
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Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Lichtgesteuerte Werkzeuge. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202134] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Clara Brieke
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
| | - Falk Rohrbach
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Gottschalk
- Buchmann‐Institut für Molekulare Lebenswissenschaften, Institut für Biochemie, Max‐von‐Laue‐Straße 15, 60438 Frankfurt/Main (Deutschland)
| | - Günter Mayer
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Heckel
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
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44
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Nakamura Y, Ishiguro A, Miyakawa S. RNA plasticity and selectivity applicable to therapeutics and novel biosensor development. Genes Cells 2012; 17:344-64. [PMID: 22487172 PMCID: PMC3444689 DOI: 10.1111/j.1365-2443.2012.01596.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 02/03/2012] [Indexed: 12/25/2022]
Abstract
Aptamers are short, single-stranded nucleic acid sequences that are selected in vitro from large oligonucleotide libraries based on their high affinity to a target molecule. Hence, aptamers can be thought of as a nucleic acid analog to antibodies. However, several viewpoints hold that the potential of aptamers arises from interesting characteristics that are distinct from, or in some cases, superior to those of antibodies. This review summarizes the recent achievements in aptamer programs developed in our laboratory against basic and therapeutic protein targets. Through these studies, we became aware of the remarkable conformational plasticity and selectivity of RNA, on which the published report has not shed much light even though this is evidently a crucial feature for the strong specificity and affinity of RNA aptamers.
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Affiliation(s)
- Yoshikazu Nakamura
- Department of Basic Medical Sciences, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
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45
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Rinnenthal J, Buck J, Ferner J, Wacker A, FÜrtig B, Schwalbe H. Mapping the landscape of RNA dynamics with NMR spectroscopy. Acc Chem Res 2011; 44:1292-301. [PMID: 21894962 DOI: 10.1021/ar200137d] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Among the three major classes of biomacromolecules (DNA, RNA, and proteins) RNA's pronounced dynamics are the most explicitly linked to its wide variety of functions, which include catalysis and the regulation of transcription, translation, and splicing. These functions are mediated by a range of RNA biomachinery, including such varied examples as macromolecular noncoding RNAs, microRNAs, small interfering RNAs, riboswitch RNAs, and RNA thermometers. In each case, the functional dynamics of an interconversion is characterized by an associated rate constant. In this Account, we provide an introduction to NMR spectroscopic characterization of the landscape of RNA dynamics. We introduce strategies for measuring NMR parameters at various time scales as well as the underlying models for describing the corresponding rate constants. RNA exhibits significant dynamic motion, which can be modulated by (i) intermolecular interactions, including specific and nonspecific binding of ions (such as Mg(2+) and tertiary amines), (ii) metabolites in riboswitches or RNA aptamers, and (iii) macromolecular interactions within ribonucleic protein particles, including the ribosome and the spliceosome. Our understanding of the nature of these dynamic changes in RNA targets is now being incorporated into RNA-specific approaches in the design of RNA inhibitors. Interactions of RNA with proteins, other RNAs, or small molecules often occur through binding mechanisms that follow an induced fit mechanism or a conformational selection mechanism, in which one of several populated RNA conformations is selected through ligand binding. The extent of functional dynamics, including the kinetic formation of a specific RNA tertiary fold, is dependent on the messenger RNA (mRNA) chain length. Thus, during de novo synthesis of mRNA, both in prokaryotes and eukaryotes, nascent mRNA of various lengths will adopt different secondary and tertiary structures. The speed of transcription has a critical influence on the functional dynamics of the RNA being synthesized. In addition to modulating the local dynamics of a conformational RNA ensemble, a given RNA sequence may adopt more than one global, three-dimensional structure. RNA modification is one way to select among these alternative structures, which are often characterized by nearly equal stability, but with high energy barriers for conformational interconversion. The refolding of different secondary and tertiary structures has been found to be a major regulatory mechanism for transcription and translation. These conformational transitions can be characterized with NMR spectroscopy, for any given RNA sequence, in response to external stimuli.
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Affiliation(s)
- Jörg Rinnenthal
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany
| | - Janina Buck
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany
| | - Boris FÜrtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany
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46
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Bothe JR, Nikolova EN, Eichhorn CD, Chugh J, Hansen AL, Al-Hashimi HM. Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy. Nat Methods 2011; 8:919-31. [PMID: 22036746 PMCID: PMC3320163 DOI: 10.1038/nmeth.1735] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many recently discovered noncoding RNAs do not fold into a single native conformation but sample many different conformations along their free-energy landscape to carry out their biological function. Here we review solution-state NMR techniques that measure the structural, kinetic and thermodynamic characteristics of RNA motions spanning picosecond to second timescales at atomic resolution, allowing unprecedented insights into the RNA dynamic structure landscape. From these studies a basic description of the RNA dynamic structure landscape is emerging, bringing new insights into how RNA structures change to carry out their function as well as applications in RNA-targeted drug discovery and RNA bioengineering.
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Affiliation(s)
- Jameson R. Bothe
- Department of Chemistry, The University of Michigan, Ann Arbor, Michigan, USA
| | - Evgenia N. Nikolova
- Chemical Biology Doctoral Program, The University of Michigan, Ann Arbor, Michigan, USA
| | - Catherine D. Eichhorn
- Chemical Biology Doctoral Program, The University of Michigan, Ann Arbor, Michigan, USA
| | - Jeetender Chugh
- Department of Biophysics, The University of Michigan, Ann Arbor, Michigan, USA
| | - Alexandar L. Hansen
- Department of Chemistry, The University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, The University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario, Canada
| | - Hashim M. Al-Hashimi
- Department of Chemistry, The University of Michigan, Ann Arbor, Michigan, USA
- Department of Biophysics, The University of Michigan, Ann Arbor, Michigan, USA
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47
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Spitzer R, Kloiber K, Tollinger M, Kreutz C. Kinetics of DNA refolding from longitudinal exchange NMR spectroscopy. Chembiochem 2011; 12:2007-10. [PMID: 21739562 DOI: 10.1002/cbic.201100318] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Indexed: 12/22/2022]
Affiliation(s)
- Romana Spitzer
- Institute of Organic Chemistry, University of Innsbruck, Innrain 52a, 6020 Innsbruck, Austria
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48
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Abstract
The RNA folding trajectory features numerous off-pathway folding traps, which represent conformations that are often equally as stable as the native functional ones. Therefore, the conversion between these off-pathway structures and the native correctly folded ones is the critical step in RNA folding. This process, referred to as RNA refolding, is slow, and is represented by a transition state that has a characteristic high free energy. Because this kinetically limiting process occurs in vivo, proteins (called RNA chaperones) have evolved that facilitate the (re)folding of RNA molecules. Here, we present an overview of how proteins interact with RNA molecules in order to achieve properly folded states. In this respect, the discrimination between static and transient interactions is crucial, as different proteins have evolved a multitude of mechanisms for RNA remodeling. For RNA chaperones that act in a sequence-unspecific manner and without the use of external sources of energy, such as ATP, transient RNA–protein interactions represent the basis of the mode of action. By presenting stretches of positively charged amino acids that are positioned in defined spatial configurations, RNA chaperones enable the RNA backbone, via transient electrostatic interactions, to sample a wider conformational space that opens the route for efficient refolding reactions.
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Affiliation(s)
- Martina Doetsch
- Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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49
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Kloiber K, Spitzer R, Tollinger M, Konrat R, Kreutz C. Probing RNA dynamics via longitudinal exchange and CPMG relaxation dispersion NMR spectroscopy using a sensitive 13C-methyl label. Nucleic Acids Res 2011; 39:4340-51. [PMID: 21252295 PMCID: PMC3105391 DOI: 10.1093/nar/gkq1361] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The refolding kinetics of bistable RNA sequences were studied in unperturbed equilibrium via 13C exchange NMR spectroscopy. For this purpose a straightforward labeling technique was elaborated using a 2′-13C-methoxy uridine modification, which was prepared by a two-step synthesis and introduced into RNA using standard protocols. Using 13C longitudinal exchange NMR spectroscopy the refolding kinetics of a 20 nt bistable RNA were characterized at temperatures between 298 and 310 K, yielding the enthalpy and entropy differences between the conformers at equilibrium and the activation energy of the refolding process. The kinetics of a more stable 32 nt bistable RNA could be analyzed by the same approach at elevated temperatures, i.e. at 314 and 316 K. Finally, the dynamics of a multi-stable RNA able to fold into two hairpin- and a pseudo-knotted conformation was studied by 13C relaxation dispersion NMR spectroscopy.
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Affiliation(s)
- Karin Kloiber
- Institute of Organic Chemistry, Leopold Franzens University, Innrain 52a, 6020 Innsbruck, Austria
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50
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Stelzer AC, Kratz JD, Zhang Q, Al-Hashimi HM. RNA dynamics by design: biasing ensembles towards the ligand-bound state. Angew Chem Int Ed Engl 2011; 49:5731-3. [PMID: 20583015 DOI: 10.1002/anie.201000814] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Andrew C Stelzer
- Department of Chemistry and Biophysics, University of Michigan, 930 North University, Ann Arbor, MI 48109, USA
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