1
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Aguion PI, Marchanka A, Carlomagno T. Nucleic acid-protein interfaces studied by MAS solid-state NMR spectroscopy. J Struct Biol X 2022; 6:100072. [PMID: 36090770 PMCID: PMC9449856 DOI: 10.1016/j.yjsbx.2022.100072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Solid-state NMR (ssNMR) has become a well-established technique to study large and insoluble protein assemblies. However, its application to nucleic acid-protein complexes has remained scarce, mainly due to the challenges presented by overlapping nucleic acid signals. In the past decade, several efforts have led to the first structure determination of an RNA molecule by ssNMR. With the establishment of these tools, it has become possible to address the problem of structure determination of nucleic acid-protein complexes by ssNMR. Here we review first and more recent ssNMR methodologies that study nucleic acid-protein interfaces by means of chemical shift and peak intensity perturbations, direct distance measurements and paramagnetic effects. At the end, we review the first structure of an RNA-protein complex that has been determined from ssNMR-derived intermolecular restraints.
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Affiliation(s)
- Philipp Innig Aguion
- Institute for Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Alexander Marchanka
- Institute for Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Teresa Carlomagno
- School of Biosciences/College of Life and Enviromental Sciences, Institute of Cancer and Genomic Sciences/College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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2
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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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3
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Liang L, Ji Y, Chen K, Gao P, Zhao Z, Hou G. Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems. Chem Rev 2022; 122:9880-9942. [PMID: 35006680 DOI: 10.1021/acs.chemrev.1c00779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.
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Affiliation(s)
- Lixin Liang
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Ji
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuizhi Chen
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Pan Gao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Zhenchao Zhao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
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4
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Separovic F, Hofferek V, Duff AP, McConville MJ, Sani MA. In-cell DNP NMR reveals multiple targeting effect of antimicrobial peptide. J Struct Biol X 2022; 6:100074. [PMID: 36147732 PMCID: PMC9486116 DOI: 10.1016/j.yjsbx.2022.100074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/25/2022] [Accepted: 08/29/2022] [Indexed: 11/28/2022] Open
Abstract
DNP NMR allowed simultaneous monitoring of lipids, proteins and nucleic acids of E. coli cells. The bacterial stress response against an antimicrobial peptide was measured in situ. The antimicrobial peptide maculatin 1.1 significantly compacted nucleic acids in bacteria. Maculatin 1.1 prevented salt bridges forming between membrane lipids.
Dynamic nuclear polarization NMR spectroscopy was used to investigate the effect of the antimicrobial peptide (AMP) maculatin 1.1 on E. coli cells. The enhanced 15N NMR signals from nucleic acids, proteins and lipids identified a number of unanticipated physiological responses to peptide stress, revealing that membrane-active AMPs can have a multi-target impact on E. coli cells. DNP-enhanced 15N-observed 31P-dephased REDOR NMR allowed monitoring how Mac1 induced DNA condensation and prevented intermolecular salt bridges between the main E. coli lipid phosphatidylethanolamine (PE) molecules. The latter was supported by similar results obtained using E. coli PE lipid systems. Overall, the ability to monitor the action of antimicrobial peptides in situ will provide greater insight into their mode of action.
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Affiliation(s)
- Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Vinzenz Hofferek
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Anthony P. Duff
- National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Kirrawee DC, NSW 2232, Australia
| | - Malcom J. McConville
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Marc-Antoine Sani
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
- Corresponding author.
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5
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Aguion PI, Kirkpatrick J, Carlomagno T, Marchanka A. Identifizierung von RNA‐Basenpaaren und vollständige Zuordnung von Nukleobasen‐Resonanzen durch Protonen‐detektierte Festkörper‐NMR‐Spektroskopie bei MAS Geschwindigkeiten von 100 kHz. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Philipp Innig Aguion
- Institut für organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ) Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Deutschland
| | - John Kirkpatrick
- Institut für organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ) Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Deutschland
- NMR-basierte strukturelle Chemie Helmholtz-Zentrum für Infektionsforschung Inhoffenstrasse 7 38124 Braunschweig Deutschland
| | - Teresa Carlomagno
- Institut für organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ) Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Deutschland
- NMR-basierte strukturelle Chemie Helmholtz-Zentrum für Infektionsforschung Inhoffenstrasse 7 38124 Braunschweig Deutschland
| | - Alexander Marchanka
- Institut für organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ) Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Deutschland
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6
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Malär AA, Wili N, Völker LA, Kozlova MI, Cadalbert R, Däpp A, Weber ME, Zehnder J, Jeschke G, Eckert H, Böckmann A, Klose D, Mulkidjanian AY, Meier BH, Wiegand T. Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase. Nat Commun 2021; 12:5293. [PMID: 34489448 PMCID: PMC8421360 DOI: 10.1038/s41467-021-25599-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023] Open
Abstract
The ATP hydrolysis transition state of motor proteins is a weakly populated protein state that can be stabilized and investigated by replacing ATP with chemical mimics. We present atomic-level structural and dynamic insights on a state created by ADP aluminum fluoride binding to the bacterial DnaB helicase from Helicobacter pylori. We determined the positioning of the metal ion cofactor within the active site using electron paramagnetic resonance, and identified the protein protons coordinating to the phosphate groups of ADP and DNA using proton-detected 31P,1H solid-state nuclear magnetic resonance spectroscopy at fast magic-angle spinning > 100 kHz, as well as temperature-dependent proton chemical-shift values to prove their engagements in hydrogen bonds. 19F and 27Al MAS NMR spectra reveal a highly mobile, fast-rotating aluminum fluoride unit pointing to the capture of a late ATP hydrolysis transition state in which the phosphoryl unit is already detached from the arginine and lysine fingers.
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Affiliation(s)
| | - Nino Wili
- Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | | | - Maria I Kozlova
- Department of Physics, Osnabrück University, Osnabrück, Germany
| | | | | | | | | | | | - Hellmut Eckert
- Institut für Physikalische Chemie, WWU Münster, Münster, Germany
- Instituto de Física de Sao Carlos, Universidade de Sao Paulo, Sao Carlos, SP, Brazil
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Daniel Klose
- Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Armen Y Mulkidjanian
- Department of Physics, Osnabrück University, Osnabrück, Germany.
- School of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Thomas Wiegand
- Physical Chemistry, ETH Zürich, Zürich, Switzerland.
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany.
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen, Aachen, Germany.
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7
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Carlomagno T, Aguion P, Kirkpatrick J, Marchanka A. Identification of RNA base pairs and complete assignment of nucleobase resonances by 1H-detected solid-state NMR spectroscopy at 100 kHz MAS. Angew Chem Int Ed Engl 2021; 60:23903-23910. [PMID: 34379871 PMCID: PMC8597087 DOI: 10.1002/anie.202107263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Indexed: 12/02/2022]
Abstract
Knowledge of RNA structure, either in isolation or in complex, is fundamental to understand the mechanism of cellular processes. Solid‐state NMR (ssNMR) is applicable to high molecular‐weight complexes and does not require crystallization; thus, it is well‐suited to study RNA as part of large multicomponent assemblies. Recently, we solved the first structures of both RNA and an RNA‐protein complex by ssNMR using conventional 13C‐ and 15N‐detection. This approach is limited by the severe overlap of the RNA peaks together with the low sensitivity of multidimensional experiments. Here, we overcome the limitations in sensitivity and resolution by using 1H‐detection at fast MAS rates. We develop experiments that allow the identification of complete nucleobase spin‐systems together with their site‐specific base pair pattern using sub‐milligram quantities of one uniformly labelled RNA sample. These experiments provide rapid access to RNA secondary structure by ssNMR in protein‐RNA complexes of any size.
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Affiliation(s)
- Teresa Carlomagno
- Leibniz Universität Hannover, BMWZ Institute of Organic Chemistry, Schneiderberg 38, 30167, Hannover, GERMANY
| | - Philipp Aguion
- Leibniz Universität Hannover: Leibniz Universitat Hannover, Institute of Organic Chemistry, Hannover, GERMANY
| | - John Kirkpatrick
- Leibniz Universität Hannover: Leibniz Universitat Hannover, Institute of Organic Chemistry, GERMANY
| | - Alexander Marchanka
- Leibniz Universität Hannover: Leibniz Universitat Hannover, Institute of Organic Chemistry, GERMANY
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8
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Lacabanne D, Boudet J, Malär AA, Wu P, Cadalbert R, Salmon L, Allain FHT, Meier BH, Wiegand T. Protein Side-Chain-DNA Contacts Probed by Fast Magic-Angle Spinning NMR. J Phys Chem B 2020; 124:11089-11097. [PMID: 33238710 PMCID: PMC7734624 DOI: 10.1021/acs.jpcb.0c08150] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Protein–nucleic
acid interactions are essential in a variety
of biological events ranging from the replication of genomic DNA to
the synthesis of proteins. Noncovalent interactions guide such molecular
recognition events, and protons are often at the center of them, particularly
due to their capability of forming hydrogen bonds to the nucleic acid
phosphate groups. Fast magic-angle spinning experiments (100 kHz)
reduce the proton NMR line width in solid-state NMR of fully protonated
protein–DNA complexes to such an extent that resolved proton
signals from side-chains coordinating the DNA can be detected. We
describe a set of NMR experiments focusing on the detection of protein
side-chains from lysine, arginine, and aromatic amino acids and discuss
the conclusions that can be obtained on their role in DNA coordination.
We studied the 39 kDa enzyme of the archaeal pRN1 primase complexed
with DNA and characterize protein–DNA contacts in the presence
and absence of bound ATP molecules.
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Affiliation(s)
| | - Julien Boudet
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Pengzhi Wu
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.,Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Loic Salmon
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.,Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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9
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Solid-state NMR spectroscopy for characterization of RNA and RNP complexes. Biochem Soc Trans 2020; 48:1077-1087. [PMID: 32573690 DOI: 10.1042/bst20191080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/24/2020] [Accepted: 05/27/2020] [Indexed: 12/15/2022]
Abstract
Ribonucleic acids are driving a multitude of biological processes where they act alone or in complex with proteins (ribonucleoproteins, RNP). To understand these processes both structural and mechanistic information about RNA is necessary. Due to their conformational plasticity RNA pose a challenge for mainstream structural biology methods. Solid-state NMR (ssNMR) spectroscopy is an emerging technique that can be applied to biomolecular complexes of any size in close-to-native conditions. This review outlines recent methodological developments in ssNMR for structural characterization of RNA and protein-RNA complexes and provides relevant examples.
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10
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Wiegand T. A solid-state NMR tool box for the investigation of ATP-fueled protein engines. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 117:1-32. [PMID: 32471533 DOI: 10.1016/j.pnmrs.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 06/11/2023]
Abstract
Motor proteins are involved in a variety of cellular processes. Their main purpose is to convert the chemical energy released during adenosine triphosphate (ATP) hydrolysis into mechanical work. In this review, solid-state Nuclear Magnetic Resonance (NMR) approaches are discussed allowing studies of structures, conformational events and dynamic features of motor proteins during a variety of enzymatic reactions. Solid-state NMR benefits from straightforward sample preparation based on sedimentation of the proteins directly into the Magic-Angle Spinning (MAS) rotor. Protein resonance assignment is the crucial and often time-limiting step in interpreting the wealth of information encoded in the NMR spectra. Herein, potentials, challenges and limitations in resonance assignment for large motor proteins are presented, focussing on both biochemical and spectroscopic approaches. This work highlights NMR tools available to study the action of the motor domain and its coupling to functional processes, as well as to identify protein-nucleotide interactions during events such as DNA replication. Arrested protein states of reaction coordinates such as ATP hydrolysis can be trapped for NMR studies by using stable, non-hydrolysable ATP analogues that mimic the physiological relevant states as accurately as possible. Recent advances in solid-state NMR techniques ranging from Dynamic Nuclear Polarization (DNP), 31P-based heteronuclear correlation experiments, 1H-detected spectra at fast MAS frequencies >100 kHz to paramagnetic NMR are summarized and their applications to the bacterial DnaB helicase from Helicobacter pylori are discussed.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
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11
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Wiegand T, Schledorn M, Malär AA, Cadalbert R, Däpp A, Terradot L, Meier BH, Böckmann A. Nucleotide Binding Modes in a Motor Protein Revealed by 31 P- and 1 H-Detected MAS Solid-State NMR Spectroscopy. Chembiochem 2020; 21:324-330. [PMID: 31310428 PMCID: PMC7318265 DOI: 10.1002/cbic.201900439] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Indexed: 12/16/2022]
Abstract
Protein-nucleic acid interactions play important roles not only in energy-providing reactions, such as ATP hydrolysis, but also in reading, extending, packaging, or repairing genomes. Although they can often be analyzed in detail with X-ray crystallography, complementary methods are needed to visualize them in complexes, which are not crystalline. Here, we show how solid-state NMR spectroscopy can detect and classify protein-nucleic interactions through site-specific 1 H- and 31 P-detected spectroscopic methods. The sensitivity of 1 H chemical-shift values on noncovalent interactions involved in these molecular recognition processes is exploited allowing us to probe directly the chemical bonding state, an information, which is not directly accessible from an X-ray structure. We show that these methods can characterize interactions in easy-to-prepare sediments of the 708 kDa dodecameric DnaB helicase in complex with ADP:AlF4- :DNA, and this despite the very challenging size of the complex.
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Affiliation(s)
- Thomas Wiegand
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Maarten Schledorn
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Alexander A. Malär
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Riccardo Cadalbert
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Alexander Däpp
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Laurent Terradot
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Beat H. Meier
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural BiochemistryLabex EcofectUMR 5086 CNRS/Université de Lyon7 Passage du vercors69367LyonFrance
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12
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Schnieders R, Keyhani S, Schwalbe H, Fürtig B. More than Proton Detection-New Avenues for NMR Spectroscopy of RNA. Chemistry 2020; 26:102-113. [PMID: 31454110 PMCID: PMC6973061 DOI: 10.1002/chem.201903355] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Indexed: 12/16/2022]
Abstract
Ribonucleic acid oligonucleotides (RNAs) play pivotal roles in cellular function (riboswitches), chemical biology applications (SELEX-derived aptamers), cell biology and biomedical applications (transcriptomics). Furthermore, a growing number of RNA forms (long non-coding RNAs, circular RNAs) but also RNA modifications are identified, showing the ever increasing functional diversity of RNAs. To describe and understand this functional diversity, structural studies of RNA are increasingly important. However, they are often more challenging than protein structural studies as RNAs are substantially more dynamic and their function is often linked to their structural transitions between alternative conformations. NMR is a prime technique to characterize these structural dynamics with atomic resolution. To extend the NMR size limitation and to characterize large RNAs and their complexes above 200 nucleotides, new NMR techniques have been developed. This Minireview reports on the development of NMR methods that utilize detection on low-γ nuclei (heteronuclei like 13 C or 15 N with lower gyromagnetic ratio than 1 H) to obtain unique structural and dynamic information for large RNA molecules in solution. Experiments involve through-bond correlations of nucleobases and the phosphodiester backbone of RNA for chemical shift assignment and make information on hydrogen bonding uniquely accessible. Previously unobservable NMR resonances of amino groups in RNA nucleobases are now detected in experiments involving conformational exchange-resistant double-quantum 1 H coherences, detected by 13 C NMR spectroscopy. Furthermore, 13 C and 15 N chemical shifts provide valuable information on conformations. All the covered aspects point to the advantages of low-γ nuclei detection experiments in RNA.
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Affiliation(s)
- Robbin Schnieders
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Sara Keyhani
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
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13
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14
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Marchanka A, Kreutz C, Carlomagno T. Isotope labeling for studying RNA by solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2018; 71:151-164. [PMID: 29651587 DOI: 10.1007/s10858-018-0180-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/07/2018] [Indexed: 06/08/2023]
Abstract
Nucleic acids play key roles in most biological processes, either in isolation or in complex with proteins. Often they are difficult targets for structural studies, due to their dynamic behavior and high molecular weight. Solid-state nuclear magnetic resonance spectroscopy (ssNMR) provides a unique opportunity to study large biomolecules in a non-crystalline state at atomic resolution. Application of ssNMR to RNA, however, is still at an early stage of development and presents considerable challenges due to broad resonances and poor dispersion. Isotope labeling, either as nucleotide-specific, atom-specific or segmental labeling, can resolve resonance overlaps and reduce the line width, thus allowing ssNMR studies of RNA domains as part of large biomolecules or complexes. In this review we discuss the methods for RNA production and purification as well as numerous approaches for isotope labeling of RNA. Furthermore, we give a few examples that emphasize the instrumental role of isotope labeling and ssNMR for studying RNA as part of large ribonucleoprotein complexes.
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Affiliation(s)
- Alexander Marchanka
- Centre for Biomolecular Drug Research (BMWZ) and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hanover, Germany
| | - Christoph Kreutz
- Organic Chemistry, University of Innsbruck (CCB), Innrain 80/82, 6020, Innsbruck, Austria
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research (BMWZ) and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hanover, Germany.
- Helmholtz Centre for Infection Research, Group of NMR-based Structural Chemistry, Inhoffenstraße 7, 38124, Brunswick, Germany.
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15
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Abstract
Various recent developments in solid-state nuclear magnetic resonance (ssNMR) spectroscopy have enabled an array of new insights regarding the structure, dynamics, and interactions of biomolecules. In the ever more integrated world of structural biology, ssNMR studies provide structural and dynamic information that is complementary to the data accessible by other means. ssNMR enables the study of samples lacking a crystalline lattice, featuring static as well as dynamic disorder, and does so independent of higher-order symmetry. The present study surveys recent applications of biomolecular ssNMR and examines how this technique is increasingly integrated with other structural biology techniques, such as (cryo) electron microscopy, solution-state NMR, and X-ray crystallography. Traditional ssNMR targets include lipid bilayer membranes and membrane proteins in a lipid bilayer environment. Another classic application has been in the area of protein misfolding and aggregation disorders, where ssNMR has provided essential structural data on oligomers and amyloid fibril aggregates. More recently, the application of ssNMR has expanded to a growing array of biological assemblies, ranging from non-amyloid protein aggregates, protein–protein complexes, viral capsids, and many others. Across these areas, multidimensional magic angle spinning (MAS) ssNMR has, in the last decade, revealed three-dimensional structures, including many that had been inaccessible by other structural biology techniques. Equally important insights in structural and molecular biology derive from the ability of MAS ssNMR to probe information beyond comprehensive protein structures, such as dynamics, solvent exposure, protein–protein interfaces, and substrate–enzyme interactions.
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16
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Yang Y, Wang S. RNA Characterization by Solid-State NMR Spectroscopy. Chemistry 2018; 24:8698-8707. [DOI: 10.1002/chem.201705583] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Yufei Yang
- College of Chemistry and Molecular Engineering and Beijing NMR Center; Peking University; No.5 Yiheyuan Road, Haidian District Beijing 100871 P. R. China
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering and Beijing NMR Center; Peking University; No.5 Yiheyuan Road, Haidian District Beijing 100871 P. R. China
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Marchanka A, Simon B, Althoff-Ospelt G, Carlomagno T. RNA structure determination by solid-state NMR spectroscopy. Nat Commun 2015; 6:7024. [PMID: 25960310 PMCID: PMC4432599 DOI: 10.1038/ncomms8024] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/25/2015] [Indexed: 01/29/2023] Open
Abstract
Knowledge of the RNA three-dimensional structure, either in isolation or as part of RNP complexes, is fundamental to understand the mechanism of numerous cellular processes. Because of its flexibility, RNA represents a challenge for crystallization, while the large size of cellular complexes brings solution-state NMR to its limits. Here, we demonstrate an alternative approach on the basis of solid-state NMR spectroscopy. We develop a suite of experiments and RNA labeling schemes and demonstrate for the first time that ssNMR can yield a RNA structure at high-resolution. This methodology allows structural analysis of segmentally labelled RNA stretches in high-molecular weight cellular machines—independent of their ability to crystallize— and opens the way to mechanistic studies of currently difficult-to-access RNA-protein assemblies. The determination of RNA structures within high-molecular weight protein-RNA complexes in non-crystalline state is technically challenging. Here, the authors describe a solid-state NMR protocol for the determination of RNA structures at high resolution.
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Affiliation(s)
- Alexander Marchanka
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Teresa Carlomagno
- 1] Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany [2] Helmholtz Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124 Braunschweig, Germany
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18
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Abramov G, Goldbourt A. Nucleotide-type chemical shift assignment of the encapsulated 40 kbp dsDNA in intact bacteriophage T7 by MAS solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2014; 59:219-230. [PMID: 24875850 DOI: 10.1007/s10858-014-9840-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 05/20/2014] [Indexed: 06/03/2023]
Abstract
The icosahedral bacteriophage T7 is a 50 MDa double-stranded DNA (dsDNA) virus that infects Escherichia coli. Although there is substantial information on the physical and morphological properties of T7, structural information, based mostly on Raman spectroscopy and cryo-electron microscopy, is limited. Here, we apply the magic-angle spinning (MAS) solid-state NMR (SSNMR) technique to study a uniformly (13)C and (15)N labeled wild-type T7 phage. We describe the details of the large-scale preparation and purification of an isotopically enriched phage sample under fully hydrated conditions, and show a complete (13)C and a near-complete (15)N nucleotide-type specific assignment of the sugar and base moieties in the 40 kbp dsDNA of T7 using two-dimensional (13)C-(13)C and (15)N-(13)C correlation experiments. The chemical shifts are interpreted as reporters of a B-form conformation of the encapsulated dsDNA. While MAS SSNMR was found to be extremely useful in determining the structures of proteins in native-like environments, its application to nucleic acids has lagged behind, leaving a missing (13)C and (15)N chemical shift database. This work therefore expands the (13)C and (15)N database of real B-form DNA systems, and opens routes to characterize more complex nucleic acid systems by SSNMR.
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Affiliation(s)
- Gili Abramov
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 69978, Ramat Aviv, Tel Aviv, Israel
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19
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Carlomagno T. Present and future of NMR for RNA-protein complexes: a perspective of integrated structural biology. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:126-136. [PMID: 24656085 DOI: 10.1016/j.jmr.2013.10.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 10/14/2013] [Accepted: 10/16/2013] [Indexed: 06/03/2023]
Abstract
Nucleic acids are gaining enormous importance as key molecules in almost all biological processes. Most nucleic acids do not act in isolation but are generally associated with proteins to form high-molecular-weight nucleoprotein complexes. In this perspective article I focus on the structural studies of supra-molecular ribonucleoprotein (RNP) assemblies in solution by a combination of state-of-the-art TROSY-based NMR experiments and other structural biology techniques. I discuss ways how to combine sparse NMR data with low-resolution structural information from small-angle scattering, fluorescence and electron paramagnetic resonance spectroscopy to obtain the structure of large RNP particles by an integrated structural biology approach. In the last section I give a perspective for the study of RNP complexes by solid-state NMR.
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Affiliation(s)
- Teresa Carlomagno
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
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20
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Morag O, Abramov G, Goldbourt A. Complete chemical shift assignment of the ssDNA in the filamentous bacteriophage fd reports on its conformation and on its interface with the capsid shell. J Am Chem Soc 2014; 136:2292-301. [PMID: 24447194 DOI: 10.1021/ja412178n] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fd bacteriophage is a filamentous virus consisting of a circular single-stranded DNA (ssDNA) wrapped by thousands of copies of a major coat protein subunit (the capsid). The coat protein subunits are mostly α-helical and curved, and are arranged in the capsid in consecutive pentamers related by a translation along the main viral axis and a rotation of ~36° (C5S2 symmetry). The DNA is right-handed and helical, but information on its structure and on its interface with the capsid is incomplete. We present here an approach for assigning the DNA nucleotides and studying its interactions with the capsid by magic-angle spinning solid-state NMR. Capsid contacts with the ssDNA are obtained using a two-dimensional (13)C-(13)C correlation experiment and a proton-mediated (31)P-(13)C polarization transfer experiment, both acquired on an aromatic-unlabeled phage sample. Our results allow us to map the residues that face the interior of the capsid and to show that the ssDNA-capsid interactions are sustained mainly by electrostatic interactions between the positively charged lysine side chains and the phosphate backbone. The use of natural abundance aromatic amino acids in the growth media facilitated the complete assignment of the four nucleotides and the observation of internucleotide contacts. Using chemical shift analysis, our study shows that structural features of the deoxyribose carbons reporting on the sugar pucker are strikingly similar to those observed recently for the Pf1 phage. However, the ssDNA-protein interface is different, and chemical shift markers of base pairing are different. This experimental approach can be utilized in other filamentous and icosahedral bacteriophages, and also in other biomolecular complexes involving structurally and functionally important DNA-protein interactions.
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Affiliation(s)
- Omry Morag
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Ramat Aviv 69978, Tel Aviv, Israel
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21
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Weingarth M, Baldus M. Solid-state NMR-based approaches for supramolecular structure elucidation. Acc Chem Res 2013; 46:2037-46. [PMID: 23586937 DOI: 10.1021/ar300316e] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Supramolecular chemistry provides structural and conformational information about complexes formed from multiple molecules. While the molecule is held together by strong intramolecular contacts like covalent bonds, supramolecular structures can be further stabilized by weaker or transient intermolecular interactions. These interactions can confer a great diversity and sensitivity to exogenous factors like temperature, pressure, or ionic strength to multimolecular arrangements. Solid-state nuclear magnetic resonance (ssNMR) can provide atomic-scale structural and dynamical information in highly disordered or heterogeneous biological systems, even in complex environments such as cellular membranes or whole cells. In these systems, the molecule of interest no longer exists as a separate unit, but it entangles with its surroundings in a dynamic interplay. Researchers have long accounted for the complexity of these intermolecular arrangements through a rather phenomenological description. But now the focus is shifting toward a detailed understanding of supramolecular structure at atomic resolution, constantly expanding our understanding of the stunning influence of the environment. In this Account, we discuss how ssNMR can help to dissect the remarkable interplay between intra- and intermolecular interactions. We describe biochemical and spectroscopic strategies that tailor ssNMR spectroscopic methods to the challenge of supramolecular structure investigation. In particular, we consider protein-protein interactions or the protein-membrane topology, and we review recent applications of these techniques. Furthermore, we summarize methods for integrating ssNMR information with other experimental techniques or computational methods, and we offer perspectives on how this overall information allows us to target increasingly large and intricate supramolecular structures of biomolecules. Advancements in ssNMR methodology and instrumentation, including the incorporation of signal enhancement methods such as dynamic nuclear polarization will further increase the potential of ssNMR spectroscopy, and together with additional developments in the field of NMR-hybrid strategies, ssNMR may become an ideal tool to study the heterogeneous, dynamic, and often transient nature of molecular interactions in complex biological systems.
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Affiliation(s)
- Markus Weingarth
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Marc Baldus
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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22
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Marchanka A, Simon B, Carlomagno T. A Suite of Solid-State NMR Experiments for RNA Intranucleotide Resonance Assignment in a 21 kDa Protein-RNA Complex. Angew Chem Int Ed Engl 2013; 52:9996-10001. [DOI: 10.1002/anie.201304779] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Indexed: 02/06/2023]
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23
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Marchanka A, Simon B, Carlomagno T. A Suite of Solid-State NMR Experiments for RNA Intranucleotide Resonance Assignment in a 21 kDa Protein-RNA Complex. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304779] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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24
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Asami S, Rakwalska-Bange M, Carlomagno T, Reif B. Untersuchung von Protein-RNA-Interaktionsstellen mithilfe 1H-detektierter MAS-Festkörper-NMR-Spektroskopie. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Asami S, Rakwalska-Bange M, Carlomagno T, Reif B. Protein-RNA Interfaces Probed by1H-Detected MAS Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2013; 52:2345-9. [DOI: 10.1002/anie.201208024] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Indexed: 11/08/2022]
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26
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Li S, Su Y, Hong M. Intramolecular 1H-13C distance measurement in uniformly 13C, 15N labeled peptides by solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2012; 45-46:51-58. [PMID: 22749432 PMCID: PMC3414644 DOI: 10.1016/j.ssnmr.2012.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 04/29/2012] [Accepted: 06/05/2012] [Indexed: 06/01/2023]
Abstract
A (1)H-(13)C frequency-selective REDOR (FS-REDOR) experiment is developed for measuring intramolecular (1)H-(13)C distances in uniformly (13)C, (15)N-labeled molecules. Theory and simulations show that the experiment removes the interfering homonuclear (1)H-(1)H, (13)C-(13)C and heteronuclear (1)H-(15)N, (13)C-(15)N dipolar interactions while retaining the desired heteronuclear (1)H-(13)C dipolar interaction. Our results indicate that this technique, combined with the numerical fitting, can be used to measure a (1)H-(13)C distance up to 5Å. We also demonstrate that the measured intramolecular (1)H-(13)C distances are useful to determine dihedral angles in proteins.
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Affiliation(s)
- Shenhui Li
- Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Yongchao Su
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Mei Hong
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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27
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Gardiennet C, Schütz AK, Hunkeler A, Kunert B, Terradot L, Böckmann A, Meier BH. Hochaufgelöste Festkörper-NMR-Spektren einer sedimentierten, nichtkristallinen dodekameren Helicase (59 kDa). Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200779] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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28
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Gardiennet C, Schütz AK, Hunkeler A, Kunert B, Terradot L, Böckmann A, Meier BH. A Sedimented Sample of a 59 kDa Dodecameric Helicase Yields High-Resolution Solid-State NMR Spectra. Angew Chem Int Ed Engl 2012; 51:7855-8. [DOI: 10.1002/anie.201200779] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 04/10/2012] [Indexed: 11/10/2022]
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29
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Bertini I, Engelke F, Luchinat C, Parigi G, Ravera E, Rosa C, Turano P. NMR properties of sedimented solutes. Phys Chem Chem Phys 2012; 14:439-47. [DOI: 10.1039/c1cp22978h] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Huang W, Varani G, Drobny GP. Interactions of protein side chains with RNA defined with REDOR solid state NMR. JOURNAL OF BIOMOLECULAR NMR 2011; 51:347-356. [PMID: 21947838 DOI: 10.1007/s10858-011-9573-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 08/11/2011] [Indexed: 05/31/2023]
Abstract
Formation of the complex between human immunodeficiency virus type-1 Tat protein and the transactivation response region (TAR) RNA is vital for transcriptional elongation, yet the structure of the Tat-TAR complex remains to be established. The NMR structures of free TAR, and TAR bound to Tat-derived peptides have been obtained by solution NMR, but only a small number of intermolecular NOEs could be identified unambiguously, preventing the determination of a complete structure. Here we show that a combination of multiple solid state NMR REDOR experiments can be used to obtain multiple distance constraints from (15)N to (13)C spins within the backbone and side chain guanidinium groups of arginine in a Tat-derived peptide, using (19)F spins incorporated into the base of U23 in TAR and (31)P spins in the P22 and P23 phosphate groups. Distances between the side chain of Arg52 and the base and phosphodiester backbone near U23 measured by REDOR NMR are comparable to distances observed in solution NMR-derived structural models, indicating that interactions of TAR RNA with key amino acid side chains in Tat are the same in the amorphous solid state as in solution. This method is generally applicable to other protein-RNA complexes where crystallization or solution NMR has failed to provide high resolution structural information.
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Affiliation(s)
- Wei Huang
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington, DC 98195, USA
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31
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Akiva-Tal A, Kababya S, Balazs YS, Glazer L, Berman A, Sagi A, Schmidt A. In situ molecular NMR picture of bioavailable calcium stabilized as amorphous CaCO₃ biomineral in crayfish gastroliths. Proc Natl Acad Sci U S A 2011; 108:14763-8. [PMID: 21873244 PMCID: PMC3169114 DOI: 10.1073/pnas.1102608108] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bioavailable calcium is maintained by some crustaceans, in particular freshwater crayfish, by stabilizing amorphous calcium carbonate (ACC) within reservoir organs--gastroliths, readily providing the Ca(2+) needed to build a new exoskeleton. Despite the key scientific and biomedical importance of the in situ molecular-level picture of biogenic ACC and its stabilization in a bioavailable form, its description has eluded efforts to date. Herein, using multinuclear NMR, we accomplish in situ molecular-level characterization of ACC within intact gastroliths of the crayfish Cherax quadricarinatus. In addition to the known CaCO(3), chitin scaffold and inorganic phosphate (Pi), we identify within the gastrolith two primary metabolites, citrate and phosphoenolpyruvate (PEP) and quantify their abundance by applying solution NMR techniques to the gastrolith "soluble matrix." The long-standing question on the physico-chemical state of ACC stabilizing, P-bearing moieties within the gastrolith is answered directly by the application of solid state rotational-echo double-resonance (REDOR) and transferred-echo double-resonance (TEDOR) NMR to the intact gastroliths: Pi and PEP are found molecularly dispersed throughout the ACC as a solid solution. Citrate carboxylates are found < 5 Å from a phosphate (intermolecular CP distance), an interaction that must be mediated by Ca(2+). The high abundance and extensive interactions of these molecules with the ACC matrix identify them as the central constituents stabilizing the bioavailable form of calcium. This study further emphasizes that it is imperative to characterize the intact biogenic CaCO(3). Solid state NMR spectroscopy is shown to be a robust and accessible means of determining composition, internal structure, and molecular functionality in situ.
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Affiliation(s)
- Anat Akiva-Tal
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 32000 Israel
| | - Shifi Kababya
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 32000 Israel
| | - Yael S. Balazs
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 32000 Israel
| | - Lilah Glazer
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel; and
| | - Amir Berman
- The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel; and
- Department of Biotechnology Engineering and Ilse Katz Institute for NanoScience and Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Amir Sagi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel; and
| | - Asher Schmidt
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 32000 Israel
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Huang W, Varani G, Drobny GP. 13C/15N-19F intermolecular REDOR NMR study of the interaction of TAR RNA with Tat peptides. J Am Chem Soc 2010; 132:17643-5. [PMID: 21105680 PMCID: PMC3238802 DOI: 10.1021/ja1051439] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complex of the HIV TAR RNA with the viral regulatory protein Tat is of considerable interest, but the plasticity of this interaction has made it impossible so far to establish the structure of that complex. In order to explore a new approach to obtain structural information on protein-RNA complexes, we performed (13)C/(15)N-(19)F REDOR NMR experiments in the solid state on TAR bound to a peptide comprising the RNA-binding section of Tat. A critical arginine in the peptide was uniformly (13)C and (15)N labeled, and 5-fluorouridine was incorporated at the U23 position of TAR. REDOR irradiation resulted in dephasing of the (13)C and (15)N resonances, indicating the proximity of the U23(5F)-C and U23(5F)-N spin pairs. Best fits to the REDOR data show the U23(5F)-C distances and the U23(5F)-N distances are in good agreement with the distances obtained from solution NMR structures of partial complexes of Tat with TAR. These results demonstrate that it is possible to study protein-RNA complexes using solid-state REDOR NMR measurements, adding to a growing list of solid state techniques for studying protein-nucleic acid complexes.
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Affiliation(s)
- Wei Huang
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
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