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Bolik-Coulon N, Zachrdla M, Bouvignies G, Pelupessy P, Ferrage F. Comprehensive analysis of relaxation decays from high-resolution relaxometry. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 355:107555. [PMID: 37797558 DOI: 10.1016/j.jmr.2023.107555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
Relaxometry consists in measuring relaxation rates over orders of magnitude of magnetic fields to probe motions of complex systems. High-resolution relaxometry (HRR) experiments can be performed on conventional high-field NMR magnets equipped with a sample shuttle. During the experiment, the sample shuttle transfers the sample between the high-field magnetic center and a chosen position in the stray field for relaxation during a variable delay, thus using the stray field as a variable field. As the relaxation delay occurs outside of the probe, HRR experiments cannot rely on the control of cross-relaxation pathways, which is standard in high-field relaxation pulse sequences. Thus, decay rates are not pure relaxation rates, which may impair a reliable description of the dynamics. Previously, we took into account cross-relaxation effects in the analysis of high-resolution relaxometry data by applying a correction factor to relaxometry decay rates in order to estimate relaxation rates. These correction factors were obtained from the iterative simulation of the relaxation decay while the sample lies outside of the probe and a preceding analysis of relaxation rates which relies on the approximation of a priori multi-exponential decays by mono-exponential functions. However, an analysis protocol matching directly experimental and simulated relaxometry decays should be more self consistent and more generally applicable as it can accommodate deviations from mono-exponential decays. Here, we introduce Matching INtensities for the Optimization of Timescales and Amplitudes of motions Under Relaxometry (MINOTAUR), a framework for the analysis of high-resolution relaxometry that takes as input the intensity decays at all fields. This approach uses the full relaxation matrix to calculate intensity decays, allowing complex relaxation pathways to be taken into account. Therefore, it eliminates the need for a correction of decay rates and for fitting multi-exponential decays with mono-exponential functions. The MINOTAUR software is designed as a flexible framework where relaxation matrices and spectral density functions corresponding to various models of motions can be defined on a case-by-case basis. The agreement with our previous analyses of protein side-chain dynamics from carbon-13 relaxation is excellent, while providing a more robust analysis tool. We expect MINOTAUR to become the tool of choice for the analysis of high-resolution relaxometry.
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Affiliation(s)
- Nicolas Bolik-Coulon
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France.
| | - Milan Zachrdla
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - Guillaume Bouvignies
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - Philippe Pelupessy
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France.
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2
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Korn SM, Dhamotharan K, Jeffries CM, Schlundt A. The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements. Nat Commun 2023; 14:3331. [PMID: 37286558 DOI: 10.1038/s41467-023-38882-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 05/17/2023] [Indexed: 06/09/2023] Open
Abstract
The nucleocapsid protein (N) of SARS-CoV-2 plays a pivotal role during the viral life cycle. It is involved in RNA transcription and accounts for packaging of the large genome into virus particles. N manages the enigmatic balance of bulk RNA-coating versus precise RNA-binding to designated cis-regulatory elements. Numerous studies report the involvement of its disordered segments in non-selective RNA-recognition, but how N organizes the inevitable recognition of specific motifs remains unanswered. We here use NMR spectroscopy to systematically analyze the interactions of N's N-terminal RNA-binding domain (NTD) with individual cis RNA elements clustering in the SARS-CoV-2 regulatory 5'-genomic end. Supported by broad solution-based biophysical data, we unravel the NTD RNA-binding preferences in the natural genome context. We show that the domain's flexible regions read the intrinsic signature of preferred RNA elements for selective and stable complex formation within the large pool of available motifs.
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Affiliation(s)
- Sophie Marianne Korn
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Karthikeyan Dhamotharan
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL) Hamburg Site, c/o Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607, Hamburg, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany.
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3
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How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation. Curr Opin Struct Biol 2022; 77:102459. [PMID: 36148743 DOI: 10.1016/j.sbi.2022.102459] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022]
Abstract
Nuclear magnetic resonance (NMR) spin relaxation experiments currently probe molecular motions on timescales from picoseconds to nanoseconds. The detailed interpretation of these motions in atomic detail benefits from complementarity with the results from molecular dynamics (MD) simulations. In this mini-review, we describe the recent developments in experimental techniques to study the backbone dynamics from 15N relaxation and side-chain dynamics from 13C relaxation, discuss the different analysis approaches from model-free to dynamics detectors, and highlight the many ways that NMR relaxation experiments and MD simulations can be used together to improve the interpretation and gain insights into protein dynamics.
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4
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Salvi N, Zapletal V, Jaseňáková Z, Zachrdla M, Padrta P, Narasimhan S, Marquardsen T, Tyburn JM, Žídek L, Blackledge M, Ferrage F, Kadeřávek P. Convergent views on disordered protein dynamics from NMR and computational approaches. Biophys J 2022; 121:3785-3794. [PMID: 36131545 PMCID: PMC9674986 DOI: 10.1016/j.bpj.2022.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/07/2022] [Accepted: 09/15/2022] [Indexed: 11/02/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) is a class of biologically important proteins exhibiting specific biophysical characteristics. They lack a hydrophobic core, and their conformational behavior is strongly influenced by electrostatic interactions. IDPs and IDRs are highly dynamic, and a characterization of the motions of IDPs and IDRs is essential for their physically correct description. NMR together with molecular dynamics simulations are the methods best suited to such a task because they provide information about dynamics of proteins with atomistic resolution. Here, we present a study of motions of a disordered C-terminal domain of the delta subunit of RNA polymerase from Bacillus subtilis. Positively and negatively charged residues in the studied domain form transient electrostatic contacts critical for the biological function. Our study is focused on investigation of ps-ns dynamics of backbone of the delta subunit based on analysis of amide 15N NMR relaxation data and molecular dynamics simulations. In order to extend an informational content of NMR data to lower frequencies, which are more sensitive to slower motions, we combined standard (high-field) NMR relaxation experiments with high-resolution relaxometry. Altogether, we collected data reporting the relaxation at 12 different magnetic fields, resulting in an unprecedented data set. Our results document that the analysis of such data provides a consistent description of dynamics and confirms the validity of so far used protocols of the analysis of dynamics of IDPs also for a partially folded protein. In addition, the potential to access detailed description of motions at the timescale of tens of ns with the help of relaxometry data is discussed. Interestingly, in our case, it appears to be mostly relevant for a region involved in the formation of temporary contacts within the disordered region, which was previously proven to be biologically important.
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Affiliation(s)
- Nicola Salvi
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France
| | - Vojtěch Zapletal
- National Centre for Biomolecular Research, Faculty of Science and Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zuzana Jaseňáková
- National Centre for Biomolecular Research, Faculty of Science and Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Milan Zachrdla
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Petr Padrta
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Subhash Narasimhan
- National Centre for Biomolecular Research, Faculty of Science and Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | | | - Lukáš Žídek
- National Centre for Biomolecular Research, Faculty of Science and Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Martin Blackledge
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France.
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris, France.
| | - Pavel Kadeřávek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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The Role of Disordered Regions in Orchestrating the Properties of Multidomain Proteins: The SARS-CoV-2 Nucleocapsid Protein and Its Interaction with Enoxaparin. Biomolecules 2022; 12:biom12091302. [PMID: 36139141 PMCID: PMC9496478 DOI: 10.3390/biom12091302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
Novel and efficient strategies need to be developed to interfere with the SARS-CoV-2 virus. One of the most promising pharmaceutical targets is the nucleocapsid protein (N), responsible for genomic RNA packaging. N is composed of two folded domains and three intrinsically disordered regions (IDRs). The globular RNA binding domain (NTD) and the tethered IDRs are rich in positively charged residues. The study of the interaction of N with polyanions can thus help to elucidate one of the key driving forces responsible for its function, i.e., electrostatics. Heparin, one of the most negatively charged natural polyanions, has been used to contrast serious cases of COVID-19 infection, and we decided to study its interaction with N at the molecular level. We focused on the NTR construct, which comprises the NTD and two flanking IDRs, and on the NTD construct in isolation. We characterized this interaction using different nuclear magnetic resonance approaches and isothermal titration calorimetry. With these tools, we were able to identify an extended surface of NTD involved in the interaction. Moreover, we assessed the importance of the IDRs in increasing the affinity for heparin, highlighting how different tracts of these flexible regions modulate the interaction.
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Pontoriero L, Schiavina M, Korn SM, Schlundt A, Pierattelli R, Felli IC. NMR Reveals Specific Tracts within the Intrinsically Disordered Regions of the SARS-CoV-2 Nucleocapsid Protein Involved in RNA Encountering. Biomolecules 2022; 12:biom12070929. [PMID: 35883485 PMCID: PMC9312987 DOI: 10.3390/biom12070929] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is crucial for the highly organized packaging and transcription of the genomic RNA. Studying atomic details of the role of its intrinsically disordered regions (IDRs) in RNA recognition is challenging due to the absence of structure and to the repetitive nature of their primary sequence. IDRs are known to act in concert with the folded domains of N and here we use NMR spectroscopy to identify the priming events of N interacting with a regulatory SARS-CoV-2 RNA element. 13C-detected NMR experiments, acquired simultaneously to 1H detected ones, provide information on the two IDRs flanking the N-terminal RNA binding domain (NTD) within the N-terminal region of the protein (NTR, 1–248). We identify specific tracts of the IDRs that most rapidly sense and engage with RNA, and thus provide an atom-resolved picture of the interplay between the folded and disordered regions of N during RNA interaction.
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Affiliation(s)
- Letizia Pontoriero
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (L.P.); (M.S.)
| | - Marco Schiavina
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (L.P.); (M.S.)
| | - Sophie M. Korn
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Molecular Biosciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany;
| | - Andreas Schlundt
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Molecular Biosciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany;
- Correspondence: (A.S.); (R.P.); (I.C.F.)
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (L.P.); (M.S.)
- Correspondence: (A.S.); (R.P.); (I.C.F.)
| | - Isabella C. Felli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (L.P.); (M.S.)
- Correspondence: (A.S.); (R.P.); (I.C.F.)
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7
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Roberts MF, Cai J, V Natarajan S, Khan HM, Reuter N, Gershenson A, Redfield AG. Phospholipids in Motion: High-Resolution 31P NMR Field Cycling Studies. J Phys Chem B 2021; 125:8827-8838. [PMID: 34320805 DOI: 10.1021/acs.jpcb.1c02105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Diverse phospholipid motions are key to membrane function but can be quite difficult to untangle and quantify. High-resolution field cycling 31P NMR spin-lattice relaxometry, where the sample is excited at high field, shuttled in the magnet bore for low-field relaxation, then shuttled back to high field for readout of the residual magnetization, provides data on phospholipid dynamics and structure. This information is encoded in the field dependence of the 31P spin-lattice relaxation rate (R1). In the field range from 11.74 down to 0.003 T, three dipolar nuclear magnetic relaxation dispersions (NMRDs) and one due to 31P chemical shift anisotropy contribute to R1 of phospholipids. Extraction of correlation times and maximum relaxation amplitudes for these NMRDs provides (1) lateral diffusion constants for different phospholipids in the same bilayer, (2) estimates of how additives alter the motion of the phospholipid about its long axis, and (3) an average 31P-1H angle with respect to the bilayer normal, which reveals that polar headgroup motion is not restricted on a microsecond timescale. Relative motions within a phospholipid are also provided by comparing 31P NMRD profiles for specifically deuterated molecules as well as 13C and 1H field dependence profiles to that of 31P. Although this work has dealt exclusively with phospholipids in small unilamellar vesicles, these same NMRDs can be measured for phospholipids in micelles and nanodisks, making this technique useful for monitoring lipid behavior in a variety of structures and assessing how additives alter specific lipid motions.
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Affiliation(s)
- Mary F Roberts
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Jingfei Cai
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Sivanandam V Natarajan
- Department of Biochemistry and the Rosenstiel Basic Medical Sciences Research Institute, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Hanif M Khan
- Department of Molecular Biology and Computational Biology Unit, Department of Informatics, University of Bergen, 5020 Bergen, Norway
| | - Nathalie Reuter
- Department of Molecular Biology and Computational Biology Unit, Department of Informatics, University of Bergen, 5020 Bergen, Norway
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Alfred G Redfield
- Department of Biochemistry and the Rosenstiel Basic Medical Sciences Research Institute, Brandeis University, Waltham, Massachusetts 02454, United States
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Redzic JS, Lee E, Born A, Issaian A, Henen MA, Nichols PJ, Blue A, Hansen KC, D'Alessandro A, Vögeli B, Eisenmesser EZ. The Inherent Dynamics and Interaction Sites of the SARS-CoV-2 Nucleocapsid N-Terminal Region. J Mol Biol 2021; 433:167108. [PMID: 34161778 PMCID: PMC8214912 DOI: 10.1016/j.jmb.2021.167108] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/16/2022]
Abstract
The nucleocapsid protein is one of four structural proteins encoded by SARS-CoV-2 and plays a central role in packaging viral RNA and manipulating the host cell machinery, yet its dynamic behavior and promiscuity in nucleotide binding has made standard structural methods to address its atomic-resolution details difficult. To begin addressing the SARS-CoV-2 nucleocapsid protein interactions with both RNA and the host cell along with its dynamic behavior, we have specifically focused on the folded N-terminal domain (NTD) and its flanking regions using nuclear magnetic resonance solution studies. Studies performed here reveal a large repertoire of interactions, which includes a temperature-dependent self-association mediated by the disordered flanking regions that also serve as binding sites for host cell cyclophilin-A while nucleotide binding is largely mediated by the central NTD core. NMR studies that include relaxation experiments have revealed the complicated dynamic nature of this viral protein. Specifically, while much of the N-terminal core domain exhibits micro-millisecond motions, a central β-hairpin shows elevated inherent flexibility on the pico-nanosecond timescale and the serine/arginine-rich region of residues 176-209 undergoes multiple exchange phenomena. Collectively, these studies have begun to reveal the complexities of the nucleocapsid protein dynamics and its preferred interaction sites with its biological targets.
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Affiliation(s)
- Jasmina S Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Eunjeong Lee
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Alexandra Born
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Aaron Issaian
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States; Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Ashley Blue
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, United States
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States.
| | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States.
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9
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Smith AA, Bolik-Coulon N, Ernst M, Meier BH, Ferrage F. How wide is the window opened by high-resolution relaxometry on the internal dynamics of proteins in solution? JOURNAL OF BIOMOLECULAR NMR 2021; 75:119-131. [PMID: 33759077 PMCID: PMC8018934 DOI: 10.1007/s10858-021-00361-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
The dynamics of molecules in solution is usually quantified by the determination of timescale-specific amplitudes of motions. High-resolution nuclear magnetic resonance (NMR) relaxometry experiments-where the sample is transferred to low fields for longitudinal (T1) relaxation, and back to high field for detection with residue-specific resolution-seeks to increase the ability to distinguish the contributions from motion on timescales slower than a few nanoseconds. However, tumbling of a molecule in solution masks some of these motions. Therefore, we investigate to what extent relaxometry improves timescale resolution, using the "detector" analysis of dynamics. Here, we demonstrate improvements in the characterization of internal dynamics of methyl-bearing side chains by carbon-13 relaxometry in the small protein ubiquitin. We show that relaxometry data leads to better information about nanosecond motions as compared to high-field relaxation data only. Our calculations show that gains from relaxometry are greater with increasing correlation time of rotational diffusion.
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Affiliation(s)
- Albert A Smith
- Institut für Medizinische Physik und Biophysik, Universität Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.
- Physical Chemistry ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Nicolas Bolik-Coulon
- Laboratoire des biomolécules, LBM, Département de Chimie, École normale superieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Matthias Ernst
- Physical Chemistry ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Fabien Ferrage
- Laboratoire des biomolécules, LBM, Département de Chimie, École normale superieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
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10
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Bolik-Coulon N, Kadeřávek P, Pelupessy P, Dumez JN, Ferrage F, Cousin SF. Theoretical and computational framework for the analysis of the relaxation properties of arbitrary spin systems. Application to high-resolution relaxometry. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 313:106718. [PMID: 32234674 DOI: 10.1016/j.jmr.2020.106718] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 06/11/2023]
Abstract
A wide variety of nuclear magnetic resonance experiments rely on the prediction and analysis of relaxation processes. Recently, innovative approaches have been introduced where the sample travels through a broad range of magnetic fields in the course of the experiment, such as dissolution dynamic nuclear polarization or high-resolution relaxometry. Understanding the relaxation properties of nuclear spin systems over orders of magnitude of magnetic fields is essential to rationalize the results of these experiments. For example, during a high-resolution relaxometry experiment, the absence of control of nuclear spin relaxation pathways during the sample transfers and relaxation delays leads to systematic deviations of polarization decays from an ideal mono-exponential decay with the pure longitudinal relaxation rate. These deviations have to be taken into account to describe quantitatively the dynamics of the system. Here, we present computational tools to (1) calculate analytical expressions of relaxation rates for a broad variety of spin systems and (2) use these analytical expressions to correct the deviations arising in high-resolution relaxometry experiments. These tools lead to a better understanding of nuclear spin relaxation, which is required to improve the sensitivity of many pulse sequences, and to better characterize motions in macromolecules.
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Affiliation(s)
- Nicolas Bolik-Coulon
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Pavel Kadeřávek
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Philippe Pelupessy
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | | | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Samuel F Cousin
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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11
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Jaseňáková Z, Zapletal V, Padrta P, Zachrdla M, Bolik-Coulon N, Marquardsen T, Tyburn JM, Žídek L, Ferrage F, Kadeřávek P. Boosting the resolution of low-field [Formula: see text] relaxation experiments on intrinsically disordered proteins with triple-resonance NMR. JOURNAL OF BIOMOLECULAR NMR 2020; 74:139-145. [PMID: 31960224 DOI: 10.1007/s10858-019-00298-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/31/2019] [Indexed: 06/10/2023]
Abstract
Improving our understanding of nanosecond motions in disordered proteins requires the enhanced sampling of the spectral density function obtained from relaxation at low magnetic fields. High-resolution relaxometry and two-field NMR measurements of relaxation have, so far, only been based on the recording of one- or two-dimensional spectra, which provide insufficient resolution for challenging disordered proteins. Here, we introduce a 3D-HNCO-based two-field NMR experiment for measurements of protein backbone [Formula: see text] amide longitudinal relaxation rates. The experiment provides accurate longitudinal relaxation rates at low field (0.33 T in our case) preserving the resolution and sensitivity typical for high-field NMR spectroscopy. Radiofrequency pulses applied on six different radiofrequency channels are used to manipulate the spin system at both fields. The experiment was demonstrated on the C-terminal domain of [Formula: see text] subunit of RNA polymerase from Bacillus subtilis, a protein with highly repetitive amino-acid sequence and very low dispersion of backbone chemical shifts.
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Affiliation(s)
- Zuzana Jaseňáková
- National Centre for Biomolecular Research, Faculty of Science and Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Vojtěch Zapletal
- National Centre for Biomolecular Research, Faculty of Science and Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Petr Padrta
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Milan Zachrdla
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Nicolas Bolik-Coulon
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | | | - Jean-Max Tyburn
- Bruker BioSpin, 34 rue de l'Industrie BP 10002, 67166, Wissembourg Cedex, France
| | - Lukáš Žídek
- National Centre for Biomolecular Research, Faculty of Science and Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
| | - Pavel Kadeřávek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
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12
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Kadeřávek P, Bolik-Coulon N, Cousin SF, Marquardsen T, Tyburn JM, Dumez JN, Ferrage F. Protein Dynamics from Accurate Low-Field Site-Specific Longitudinal and Transverse Nuclear Spin Relaxation. J Phys Chem Lett 2019; 10:5917-5922. [PMID: 31509419 DOI: 10.1021/acs.jpclett.9b02233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nuclear magnetic relaxation provides invaluable quantitative site-specific information on the dynamics of complex systems. Determining dynamics on nanosecond time scales requires relaxation measurements at low magnetic fields incompatible with high-resolution NMR. Here, we use a two-field NMR spectrometer to measure carbon-13 transverse and longitudinal relaxation rates at a field as low as 0.33 T (proton Larmor frequency 14 MHz) in specifically labeled side chains of the protein ubiquitin. The use of radiofrequency pulses enhances the accuracy of measurements as compared to high-resolution relaxometry approaches, where the sample is moved in the stray field of the superconducting magnet. Importantly, we demonstrate that accurate measurements at a single low magnetic field provide enough information to characterize complex motions on low nanosecond time scales, which opens a new window for the determination of site-specific nanosecond motions in complex systems such as proteins.
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Affiliation(s)
- Pavel Kadeřávek
- Laboratoire des Biomolécules, LBM, Département de chimie , École normale supérieure , PSL University, Sorbonne Université, CNRS, 75005 Paris , France
| | - Nicolas Bolik-Coulon
- Laboratoire des Biomolécules, LBM, Département de chimie , École normale supérieure , PSL University, Sorbonne Université, CNRS, 75005 Paris , France
| | - Samuel F Cousin
- Laboratoire des Biomolécules, LBM, Département de chimie , École normale supérieure , PSL University, Sorbonne Université, CNRS, 75005 Paris , France
| | | | - Jean-Max Tyburn
- Bruker BioSpin , 34 rue de l'Industrie BP 10002, 67166 Wissembourg Cedex, France
| | | | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie , École normale supérieure , PSL University, Sorbonne Université, CNRS, 75005 Paris , France
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13
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Cousin SF, Kadeřávek P, Bolik-Coulon N, Gu Y, Charlier C, Carlier L, Bruschweiler-Li L, Marquardsen T, Tyburn JM, Brüschweiler R, Ferrage F. Time-Resolved Protein Side-Chain Motions Unraveled by High-Resolution Relaxometry and Molecular Dynamics Simulations. J Am Chem Soc 2018; 140:13456-13465. [DOI: 10.1021/jacs.8b09107] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samuel F. Cousin
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Pavel Kadeřávek
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Nicolas Bolik-Coulon
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Yina Gu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Cyril Charlier
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Ludovic Carlier
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Jean-Max Tyburn
- Bruker BioSpin, 34 rue de l’Industrie BP 10002, 67166 Wissembourg Cedex, France
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Fabien Ferrage
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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14
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Kadeřávek P, Strouk L, Cousin SF, Charlier C, Bodenhausen G, Marquardsen T, Tyburn J, Bovier P, Engelke F, Maas W, Ferrage F. Full Correlations across Broad NMR Spectra by Two‐Field Total Correlation Spectroscopy. Chemphyschem 2017; 18:2772-2776. [DOI: 10.1002/cphc.201700369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 04/28/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Pavel Kadeřávek
- Département de Chimie, Laboratoire des Biomolécules (LBM), École Normale Supérieure—PSL Research University, UPMC Univ Paris 06, CNRS 24 rue Lhomond 75005 Paris France
- Laboratoire des Biomolécules (LBM)Sorbonne Universités, UPMC, Univ Paris 06, Ecole Normale Supérieure, CNRS France
| | - Léonard Strouk
- Département de Chimie, Laboratoire des Biomolécules (LBM), École Normale Supérieure—PSL Research University, UPMC Univ Paris 06, CNRS 24 rue Lhomond 75005 Paris France
- Laboratoire des Biomolécules (LBM)Sorbonne Universités, UPMC, Univ Paris 06, Ecole Normale Supérieure, CNRS France
| | - Samuel F. Cousin
- Département de Chimie, Laboratoire des Biomolécules (LBM), École Normale Supérieure—PSL Research University, UPMC Univ Paris 06, CNRS 24 rue Lhomond 75005 Paris France
- Laboratoire des Biomolécules (LBM)Sorbonne Universités, UPMC, Univ Paris 06, Ecole Normale Supérieure, CNRS France
- Current address: Department of Chemical PhysicsWeizmann Institute of Science Rehovot Israel
| | - Cyril Charlier
- Département de Chimie, Laboratoire des Biomolécules (LBM), École Normale Supérieure—PSL Research University, UPMC Univ Paris 06, CNRS 24 rue Lhomond 75005 Paris France
- Laboratoire des Biomolécules (LBM)Sorbonne Universités, UPMC, Univ Paris 06, Ecole Normale Supérieure, CNRS France
- Current address: Laboratory of Chemical PhysicsNIDDK, NIH Bethesda MD 20892 USA
| | - Geoffrey Bodenhausen
- Département de Chimie, Laboratoire des Biomolécules (LBM), École Normale Supérieure—PSL Research University, UPMC Univ Paris 06, CNRS 24 rue Lhomond 75005 Paris France
- Laboratoire des Biomolécules (LBM)Sorbonne Universités, UPMC, Univ Paris 06, Ecole Normale Supérieure, CNRS France
| | | | - Jean‐Max Tyburn
- Bruker BioSpin 34 rue de l'Industrie BP 10002 67166 Wissembourg Cedex France
| | | | - Frank Engelke
- Bruker BioSpin GmbH Silberstreifen 4 76287 Rheinstetten Germany
| | - Werner Maas
- Bruker BioSpin Billerica Massachusetts 01821 USA
| | - Fabien Ferrage
- Département de Chimie, Laboratoire des Biomolécules (LBM), École Normale Supérieure—PSL Research University, UPMC Univ Paris 06, CNRS 24 rue Lhomond 75005 Paris France
- Laboratoire des Biomolécules (LBM)Sorbonne Universités, UPMC, Univ Paris 06, Ecole Normale Supérieure, CNRS France
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15
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Chou CY, Chu M, Chang CF, Yu T, Huang TH, Sakellariou D. High sensitivity high-resolution full range relaxometry using a fast mechanical sample shuttling device and a cryo-probe. JOURNAL OF BIOMOLECULAR NMR 2016; 66:187-194. [PMID: 27744623 DOI: 10.1007/s10858-016-0066-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
Field-dependent NMR studies of bio-molecular systems using a sample shuttling hardware operating on a high-field NMR apparatus have provided valuable structural and dynamic information. We have recently published a design of a compact sample transportation device, called "field-cycler", which was installed in a commercial spectrometer and which provided highly precise positioning and stability during high speed shuttling. In this communication, we demonstrate the first use of a sample shuttling device on a commercial high field standard bore NMR spectrometer, equipped with a commercial triple resonance cryogenically cooled NMR probe. The performance and robustness of the hardware operating in 1D and 2D field cycling experiments, as well as the impact of the sample shuttling time on the signal intensity are discussed.
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Affiliation(s)
- Ching-Yu Chou
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191, Gif-Sur-Yvette, France
- Laboratoire des Biomolécules, Département de Chimie, UMR7203 CNRS-UPMC-ENS, Ecole Normale Supérieure, 24 Rue Lhomond, 75005, Paris Cedex 05, France
- Field Cycling Technology Ltd., 10F., No.136, Chaiqiao Rd., Xiangshan, Hsinchu, 300, Taiwan, ROC
| | - Minglee Chu
- Institute of Physics, Academia Sinica, Taipei, Taiwan, ROC
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, ROC
| | - Tsunai Yu
- Institute of Biomedical Science, Academia Sinica, Taipei, Taiwan, ROC
| | - Tai-Huang Huang
- Institute of Biomedical Science, Academia Sinica, Taipei, Taiwan, ROC.
| | - Dimitris Sakellariou
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191, Gif-Sur-Yvette, France
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16
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Rosenberg MM, Redfield AG, Roberts MF, Hedstrom L. Substrate and Cofactor Dynamics on Guanosine Monophosphate Reductase Probed by High Resolution Field Cycling 31P NMR Relaxometry. J Biol Chem 2016; 291:22988-22998. [PMID: 27613871 PMCID: PMC5087720 DOI: 10.1074/jbc.m116.739516] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 08/31/2016] [Indexed: 12/31/2022] Open
Abstract
Guanosine-5'-monophosphate reductase (GMPR) catalyzes the reduction of GMP to IMP and ammonia with concomitant oxidation of NADPH. Here we investigated the structure and dynamics of enzyme-bound substrates and cofactors by measuring 31P relaxation rates over a large magnetic field range using high resolution field cycling NMR relaxometry. Surprisingly, these experiments reveal differences in the low field relaxation profiles for the monophosphate of GMP compared with IMP in their respective NADP+ complexes. These complexes undergo partial reactions that mimic different steps in the overall catalytic cycle. The relaxation profiles indicate that the substrate monophosphates have distinct interactions in E·IMP·NADP+ and E·GMP·NADP+ complexes. These findings were not anticipated by x-ray crystal structures, which show identical interactions for the monophosphates of GMP and IMP in several inert complexes. In addition, the motion of the cofactor is enhanced in the E·GMP·NADP+ complex. Last, the motions of the substrate and cofactor are coordinately regulated; the cofactor has faster local motions than GMP in the deamination complex but is more constrained than IMP in that complex, leading to hydride transfer. These results show that field cycling can be used to investigate the dynamics of protein-bound ligands and provide new insights into how portions of the substrate remote from the site of chemical transformation promote catalysis.
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Affiliation(s)
| | | | - Mary F Roberts
- the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467-3860
| | - Lizbeth Hedstrom
- From the Departments of Biology,
- Chemistry, Brandeis University, Waltham, Massachusetts 02453 and
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17
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Cousin SF, Kadeřávek P, Haddou B, Charlier C, Marquardsen T, Tyburn JM, Bovier PA, Engelke F, Maas W, Bodenhausen G, Pelupessy P, Ferrage F. Recovering Invisible Signals by Two-Field NMR Spectroscopy. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Samuel F. Cousin
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Pavel Kadeřávek
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Baptiste Haddou
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR, 8640 Pasteur; 75005 Paris France
| | - Cyril Charlier
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
- Laboratory of Chemical Physics, NIDDK, NIH; Bethesda MD 20892 USA
| | | | - Jean-Max Tyburn
- Bruker BioSpin; 34 rue de l'Industrie BP 10002 67166 Wissembourg Cedex France
| | | | - Frank Engelke
- Bruker BioSpin GmbH; Silberstreifen 4 76287 Rheinstetten Germany
| | | | - Geoffrey Bodenhausen
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Philippe Pelupessy
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Fabien Ferrage
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
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18
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Cousin SF, Kadeřávek P, Haddou B, Charlier C, Marquardsen T, Tyburn JM, Bovier PA, Engelke F, Maas W, Bodenhausen G, Pelupessy P, Ferrage F. Recovering Invisible Signals by Two-Field NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:9886-9. [DOI: 10.1002/anie.201602978] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Samuel F. Cousin
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Pavel Kadeřávek
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Baptiste Haddou
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR, 8640 Pasteur; 75005 Paris France
| | - Cyril Charlier
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
- Laboratory of Chemical Physics, NIDDK, NIH; Bethesda MD 20892 USA
| | | | - Jean-Max Tyburn
- Bruker BioSpin; 34 rue de l'Industrie BP 10002 67166 Wissembourg Cedex France
| | | | - Frank Engelke
- Bruker BioSpin GmbH; Silberstreifen 4 76287 Rheinstetten Germany
| | | | - Geoffrey Bodenhausen
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Philippe Pelupessy
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Fabien Ferrage
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
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19
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Papageorgiou N, Lichière J, Baklouti A, Ferron F, Sévajol M, Canard B, Coutard B. Structural characterization of the N-terminal part of the MERS-CoV nucleocapsid by X-ray diffraction and small-angle X-ray scattering. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:192-202. [PMID: 26894667 PMCID: PMC7159594 DOI: 10.1107/s2059798315024328] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/17/2015] [Indexed: 02/07/2023]
Abstract
The N protein of coronaviruses is a multifunctional protein that is organized into several domains. The N‐terminal part is composed of an intrinsically disordered region (IDR) followed by a structured domain called the N‐terminal domain (NTD). In this study, the structure determination of the N‐terminal region of the MERS‐CoV N protein via X‐ray diffraction measurements is reported at a resolution of 2.4 Å. Since the first 30 amino acids were not resolved by X‐ray diffraction, the structural study was completed by a SAXS experiment to propose a structural model including the IDR. This model presents the N‐terminal region of the MERS‐CoV as a monomer that displays structural features in common with other coronavirus NTDs.
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20
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Charlier C, Cousin SF, Ferrage F. Protein dynamics from nuclear magnetic relaxation. Chem Soc Rev 2016; 45:2410-22. [DOI: 10.1039/c5cs00832h] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein dynamics are explored by a variety of methods designed to measure nuclear magnetic relaxation rates.
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Affiliation(s)
- Cyril Charlier
- École Normale Supérieure-PSL Research University
- Département de Chimie
- 75005 Paris
- France
- Sorbonne Universités
| | - Samuel F. Cousin
- École Normale Supérieure-PSL Research University
- Département de Chimie
- 75005 Paris
- France
- Sorbonne Universités
| | - Fabien Ferrage
- École Normale Supérieure-PSL Research University
- Département de Chimie
- 75005 Paris
- France
- Sorbonne Universités
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21
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Cousin SF, Charlier C, Kadeřávek P, Marquardsen T, Tyburn JM, Bovier PA, Ulzega S, Speck T, Wilhelm D, Engelke F, Maas W, Sakellariou D, Bodenhausen G, Pelupessy P, Ferrage F. High-resolution two-field nuclear magnetic resonance spectroscopy. Phys Chem Chem Phys 2016; 18:33187-33194. [DOI: 10.1039/c6cp05422f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two-field NMR provides correlations of nuclear spins at the most favourable magnetic fields in a single experiment.
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Affiliation(s)
- Samuel F. Cousin
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - Cyril Charlier
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - Pavel Kadeřávek
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | | | | | | | | | | | | | | | | | | | - Geoffrey Bodenhausen
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - Philippe Pelupessy
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - Fabien Ferrage
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
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22
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Chang CK, Hou MH, Chang CF, Hsiao CD, Huang TH. The SARS coronavirus nucleocapsid protein--forms and functions. Antiviral Res 2014; 103:39-50. [PMID: 24418573 PMCID: PMC7113676 DOI: 10.1016/j.antiviral.2013.12.009] [Citation(s) in RCA: 338] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/08/2013] [Accepted: 12/20/2013] [Indexed: 12/14/2022]
Abstract
Coronavirus N proteins share the same modular organization. Structures of SARS-CoV N protein provide insight into nucleocapsid formation. N protein binds to nucleic acid at multiple sites in a coupled-allostery manner. A RNP packaging model highlighting the importance of disorder and modularity is proposed.
The nucleocapsid phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV N protein) packages the viral genome into a helical ribonucleocapsid (RNP) and plays a fundamental role during viral self-assembly. It is a protein with multifarious activities. In this article we will review our current understanding of the N protein structure and its interaction with nucleic acid. Highlights of the progresses include uncovering the modular organization, determining the structures of the structural domains, realizing the roles of protein disorder in protein–protein and protein–nucleic acid interactions, and visualizing the ribonucleoprotein (RNP) structure inside the virions. It was also demonstrated that N-protein binds to nucleic acid at multiple sites with a coupled-allostery manner. We propose a SARS-CoV RNP model that conforms to existing data and bears resemblance to the existing RNP structures of RNA viruses. The model highlights the critical role of modular organization and intrinsic disorder of the N protein in the formation and functions of the dynamic RNP capsid in RNA viruses. This paper forms part of a symposium in Antiviral Research on “From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses.”
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Affiliation(s)
- Chung-ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, ROC
| | - Ming-Hon Hou
- Department of Life Science, National Chung Hsing University, Taichung 40254, Taiwan, ROC
| | - Chi-Fon Chang
- The Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan, ROC
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan, ROC
| | - Tai-huang Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, ROC; The Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan, ROC; Department of Physics, National Taiwan Normal University, Taipei 11677, Taiwan, ROC.
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23
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Gradziel CS, Wang Y, Stec B, Redfield AG, Roberts MF. Cytotoxic amphiphiles and phosphoinositides bind to two discrete sites on the Akt1 PH domain. Biochemistry 2014; 53:462-72. [PMID: 24383815 DOI: 10.1021/bi401720v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The mechanism of binding of two promising anticancer agents (the cytotoxic alkylphospholipids perifosine and miltefosine) to the Akt PH domain is investigated by high-resolution field-cycling (31)P nuclear magnetic resonance (NMR) spectroscopy using a spin-labeled recombinant PH domain. These results strongly indicate that there are two discrete amphiphile binding sites on the domain: (i) the cationic site that binds phosphoinositides and some alkylphospholipids and (ii) a second site that is occupied by only the alkylphospholipids. The identification of this second site for amphiphiles on the Akt1 PH domain provides a new target for drug development as well as insights into the regulation of the activity of the intact Akt1 protein. The field-cycling NMR methodology could be used to define discrete phospholipid or amphiphile binding sites on a wide variety of peripheral membrane proteins.
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Affiliation(s)
- Cheryl S Gradziel
- Department of Chemistry, Boston College , Chestnut Hill, Massachusetts 02467, United States
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Charlier C, Khan SN, Marquardsen T, Pelupessy P, Reiss V, Sakellariou D, Bodenhausen G, Engelke F, Ferrage F. Nanosecond time scale motions in proteins revealed by high-resolution NMR relaxometry. J Am Chem Soc 2013; 135:18665-72. [PMID: 24228712 PMCID: PMC3865798 DOI: 10.1021/ja409820g] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Understanding
the molecular determinants underlying protein function
requires the characterization of both structure and dynamics at atomic
resolution. Nuclear relaxation rates allow a precise characterization
of protein dynamics at the Larmor frequencies of spins. This usually
limits the sampling of motions to a narrow range of frequencies corresponding
to high magnetic fields. At lower fields one cannot achieve sufficient
sensitivity and resolution in NMR. Here, we use a fast shuttle device
where the polarization builds up and the signals are detected at high
field, while longitudinal relaxation takes place at low fields 0.5
< B0 < 14.1 T. The sample is propelled
over a distance up to 50 cm by a blowgun-like system in about 50 ms.
The analysis of nitrogen-15 relaxation in the protein ubiquitin over
such a wide range of magnetic fields offers unprecedented insights
into molecular dynamics. Some key regions of the protein feature structural
fluctuations on nanosecond time scales, which have so far been overlooked
in high-field relaxation studies. Nanosecond motions in proteins may
have been underestimated by traditional high-field approaches, and
slower supra-τc motions that have no effect on relaxation
may have been overestimated. High-resolution relaxometry thus opens
the way to a quantitative characterization of nanosecond motions in
proteins.
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Affiliation(s)
- Cyril Charlier
- Laboratoire des Biomolécules, Département de Chimie, UMR 7203 CNRS-UPMC-ENS, Ecole Normale Supérieure , 24 Rue Lhomond, 75231 Paris Cedex 05, France
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25
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NMR spectroscopy on domain dynamics in biomacromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:58-117. [DOI: 10.1016/j.pbiomolbio.2013.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 12/22/2022]
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26
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Redfield AG. High-resolution NMR field-cycling device for full-range relaxation and structural studies of biopolymers on a shared commercial instrument. JOURNAL OF BIOMOLECULAR NMR 2012; 52:159-177. [PMID: 22200887 DOI: 10.1007/s10858-011-9594-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 12/05/2011] [Indexed: 05/31/2023]
Abstract
Improvements are described in a shuttling field-cycling device (Redfield in Magn Reson Chem 41:753-768, 2003), designed to allow widespread access to this useful technique by configuring it as a removable module to a commercial 500 MHz NMR instrument. The main improvements described here, leading to greater versatility, high reliability and simple construction, include: shuttling provided by a linear motor driven by an integrated-control servomotor; provision of automated bucking magnets to allow fast two-stage cycling to nearly zero field; and overall control by a microprocessor. A brief review of history and publications that have used the system is followed by a discussion of topics related to such a device including discussion of some future applications. A description of new aspects of the shuttling device follows. The minimum round trip time to 1T and above is less than 0.25 s and to 0.002 T is 0.36 s. Commercial probes are used and sensitivity is that of the host spectrometer reduced only by relaxation during travel. A key element is development of a linkage that prevents vibration of the linear motor from reaching the probe.
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Affiliation(s)
- Alfred G Redfield
- Biochemistry Department, Brandeis University, Mail stop 009, Waltham, MA 02154, USA.
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Keane SC, Liu P, Leibowitz JL, Giedroc DP. Functional transcriptional regulatory sequence (TRS) RNA binding and helix destabilizing determinants of murine hepatitis virus (MHV) nucleocapsid (N) protein. J Biol Chem 2012; 287:7063-73. [PMID: 22241479 DOI: 10.1074/jbc.m111.287763] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Coronavirus (CoV) nucleocapsid (N) protein contains two structurally independent RNA binding domains. These are denoted N-terminal domain (NTD) and C-terminal domain and are joined by a charged linker region rich in serine and arginine residues (SR linker). In mouse hepatitis virus (MHV), the NTD binds the transcriptional regulatory sequence (TRS) RNA, a conserved hexanucleotide sequence required for subgenomic RNA synthesis. The NTD is also capable of disrupting a short RNA duplex. We show here that three residues on the β3 (Arg-125 and Tyr-127) and β5 (Tyr-190) strands play key roles in TRS RNA binding and helix destabilization with Ala substitutions of these residues lethal to the virus. NMR studies of the MHV NTD·TRS complex revealed that this region defines a major RNA binding interface in MHV with site-directed spin labeling studies consistent with a model in which the adenosine-rich 3'-region of TRS is anchored by Arg-125, Tyr-127, and Tyr-190 in a way that is critical for efficient subgenomic RNA synthesis in MHV. Characterization of CoV N NTDs from infectious bronchitis virus and from severe acute respiratory syndrome CoV revealed that, although detailed NTD-TRS determinants are distinct from those of MHV NTD, rapid helix destabilization activity of CoV N NTDs is most strongly correlated with CoV function and virus viability.
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Affiliation(s)
- Sarah C Keane
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, USA
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28
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Chou CY, Chu M, Chang CF, Huang TH. A compact high-speed mechanical sample shuttle for field-dependent high-resolution solution NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 214:302-8. [PMID: 22200566 DOI: 10.1016/j.jmr.2011.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2011] [Revised: 11/16/2011] [Accepted: 12/02/2011] [Indexed: 05/22/2023]
Abstract
Analysis of NMR relaxation data has provided significant insight on molecular dynamic, leading to a more comprehensive understanding of macromolecular functions. However, traditional methodology allows relaxation measurements performed only at a few fixed high fields, thus severely restricting their potential for extracting more complete dynamic information. Here we report the design and performance of a compact high-speed servo-mechanical shuttle assembly adapted to a commercial 600 MHz high-field superconducting magnet. The assembly is capable of shuttling the sample in a regular NMR tube from the center of the magnet to the top (fringe field ∼0.01 T) in 100 ms with no loss of sensitivity other than that due to intrinsic relaxation. The shuttle device can be installed by a single experienced user in 30 min. Excellent 2D-(15)N-HSQC spectra of (u-(13)C, (15)N)-ubiquitin with relaxation at low fields (3.77 T) and detection at 14.1T were obtained to illustrate its utility in R(1) measurements of macromolecules at low fields. Field-dependent (13)C-R(1) data of (3,3,3-d)-alanine at various field strengths were determined and analyzed to assess CSA and (1)H-(13)C dipolar contributions to the carboxyl (13)C-R(1).
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Affiliation(s)
- Ching-Yu Chou
- Department of Physics, National Taiwan Normal University, Taipei 116, Taiwan, ROC
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29
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Torchia DA. Dynamics of biomolecules from picoseconds to seconds at atomic resolution. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 212:1-10. [PMID: 21840740 DOI: 10.1016/j.jmr.2011.07.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 07/14/2011] [Indexed: 05/31/2023]
Abstract
Although biomolecular dynamics has been investigated using NMR for at least 40 years, only in the past 20 years have internal motions been characterized at atomic resolution throughout proteins and nucleic acids. This development was made possible by multidimensional heteronuclear NMR approaches that provide near complete sequential signal assignments of uniformly labeled biomolecules. Recent methodological advances have enabled characterization of internal dynamics on timescales ranging from picoseconds to seconds, both in solution and in the solid state. The size, complexity and functional significance of biomolecules investigated by NMR continue to grow, as do the insights that have been obtained about function. In this article I review a number of recent advances that have made such studies possible, and provide a few examples of where NMR either by itself or in combination with other approaches has paved the way to a better understanding of the complex relationship between dynamics and biomolecular function. Finally, I discuss prospects for further advances in this field.
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Shapira B, Prestegard JH. Electron-nuclear interactions as probes of domain motion in proteins. J Chem Phys 2010; 132:115102. [PMID: 20331317 DOI: 10.1063/1.3328644] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Long range interactions between nuclear spins and paramagnetic ions can serve as a sensitive monitor of internal motion of various parts of proteins, including functional loops and separate domains. In the case of interdomain motion, the interactions between the ion and NMR-observable nuclei are modulated in direction and magnitude mainly by a combination of overall and interdomain motions. The effects on observable parameters such as paramagnetic relaxation enhancement (PRE) and pseudocontact shift (PCS) can, in principle, be used to characterize motion. These parameters are frequently used for the purpose of structural refinements. However, their use to probe actual domain motions is less common and is lacking a proper theoretical treatment from a motional perspective. In this work, a suitable spin Hamiltonian is incorporated in a two body diffusion model to produce the time correlation function for the nuclear spin-paramagnetic ion interactions. Simulated observables for nuclei in different positions with respect to the paramagnetic ion are produced. Based on these simulations, it demonstrated that both the PRE and the PCS can be very sensitive probes of domain motion. Results for different nuclei within the protein sense different aspects of the motions. Some are more sensitive to the amplitude of the internal motion, others are more sensitive to overall diffusion rates, allowing separation of these contributions. Experimentally, the interaction strength can also be tuned by substitution of different paramagnetic ions or by varying magnetic field strength (in the case of lanthanides) to allow the use of more detailed diffusion models without reducing the reliability of data fitting.
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Affiliation(s)
- Boaz Shapira
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
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31
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Palmer AG. A topical issue: NMR investigations of molecular dynamics. JOURNAL OF BIOMOLECULAR NMR 2009; 45:1-4. [PMID: 19669621 PMCID: PMC7087731 DOI: 10.1007/s10858-009-9345-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
- Arthur G. Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032 USA
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