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Kim J, Grün JT, Novakovic M, Kupce E, Rosenzweig R, Frydman L. Cross-Polarization Schemes for Improved Heteronuclear Transfers Involving Labile Protons in Biomolecular Solution NMR. Angew Chem Int Ed Engl 2023; 62:e202304900. [PMID: 37408374 DOI: 10.1002/anie.202304900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/16/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023]
Abstract
INEPT-based experiments are widely used for 1 H→15 N transfers, but often fail when involving labile protons due to solvent exchanges. J-based cross polarization (CP) strategies offer a more efficient alternative to perform such transfers, particularly when leveraging the Hwater ↔ ${ \leftrightarrow }$ HN exchange process to boost the 1 H→15 N transfer process. This leveraging, however, demands the simultaneous spin-locking of both Hwater and HN protons by a strong 1 H RF field, while fulfilling the γH B1,H =γN B1,N Hartmann-Hahn matching condition. Given the low value of γN /γH , however, these demands are often incompatible-particularly when experiments are executed by the power-limited cryogenic probes used in contemporary high field NMR. The present manuscript discusses CP alternatives that can alleviate this limitation, and evaluates their performance on urea, amino acids, and intrinsically disordered proteins. These alternatives include new CP variants based on frequency-swept and phase-modulated pulses, designed to simultaneously fulfill the aforementioned conflicting conditions. Their performances vis-à-vis current options are theoretically analyzed with Liouville-space simulations, and experimentally tested with double and triple resonance transfer experiments.
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Affiliation(s)
- Jihyun Kim
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - J Tassilo Grün
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Current address: BASF SE, RGA/AS-B 009, 67056, Ludwigshafen am Rhein, Germany
| | - Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Current address: Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093, Zürich, Switzerland
| | - Eriks Kupce
- Bruker Ltd., Banner Lane, Coventry, CV4 9GH, UK
| | - Rina Rosenzweig
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel
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2
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Lopez JM. Combined H-N Cross-Polarization and Carbonyl Detection NMR Spectroscopy Allow to Record High-Resolution, High-Sensitivity Spectra of Alpha-Synuclein in Bacterial Cells. Methods Mol Biol 2023; 2551:449-460. [PMID: 36310219 DOI: 10.1007/978-1-0716-2597-2_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Studies of intrinsically disordered proteins (IDPs) under physiological conditions by conventional NMR methods based on proton detection are severely limited by fast proton amide solvent exchange. Carbon detection has been proposed as a solution to the exchange problem but is hampered by low sensitivity. Here, we present a protocol combining proton-nitrogen cross-polarization and carbonyl detection to record high-resolution and high-sensitivity NMR spectra of IDPs under physiological conditions. The protocol describes a step-by-step method to register high-quality N-CO correlation spectrum of alpha-synuclein in E.coli bacterial cells at 37 °C.
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Affiliation(s)
- Juan M Lopez
- Pontificia Universidad Católica del Perú, Departamento de Ciencias - Química, CERMN, Lima, Perú.
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3
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Abstract
![]()
Thanks to recent
improvements in NMR spectrometer hardware and
pulse sequence design, modern 13C NMR has become a useful
tool for biomolecular applications. The complete assignment of a protein
can be accomplished by using 13C detected multinuclear
experiments and it can provide unique information relevant for the
study of a variety of different biomolecules including paramagnetic
proteins and intrinsically disordered proteins. A wide range of NMR
observables can be measured, concurring to the structural and dynamic
characterization of a protein in isolation, as part of a larger complex,
or even inside a living cell. We present the different properties
of 13C with respect to 1H, which provide the
rationale for the experiments developed and their application, the
technical aspects that need to be faced, and the many experimental
variants designed to address different cases. Application areas where
these experiments successfully complement proton NMR are also described.
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Affiliation(s)
- Isabella C Felli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
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4
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Novakovic M, Jayanthi S, Lupulescu A, Concilio MG, Kim J, Columbus D, Kuprov I, Frydman L. Heteronuclear transfers from labile protons in biomolecular NMR: Cross polarization, revisited. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 333:107083. [PMID: 34688177 DOI: 10.1016/j.jmr.2021.107083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/09/2021] [Accepted: 10/10/2021] [Indexed: 06/13/2023]
Abstract
INEPT- and HMQC-based pulse sequences are widely used to transfer polarization between heteronuclei, particularly in biomolecular spectroscopy: they are easy to setup and involve low power deposition. Still, these short-pulse polarization transfers schemes are challenged by fast solvent chemical exchange. An alternative to improve these heteronuclear transfers is J-driven cross polarization (J-CP), which transfers polarization by spin-locking the coupled spins under Hartmann-Hahn conditions. J-CP provides certain immunity against chemical exchange and other T2-like relaxation effects, a behavior that is here examined in depth by both Liouville-space numerical and analytical derivations describing the transfer efficiency. While superior to INEPT-based transfers, fast exchange may also slow down these J-CP transfers, hurting their efficiency. This study therefore explores the potential of repeated projective operations to improve 1H→15N and 1H→15N→13C J-CP transfers in the presence of fast solvent chemical exchanges. It is found that while repeating J-CP provides little 1H→15N transfer advantages over a prolonged CP, multiple contacts that keep both the water and the labile protons effectively spin-locked can improve 1H→15N→13C transfers in the presence of chemical exchange. The ensuing Looped, Concatenated Cross Polarization (L-CCP) compensates for single J-CP losses by relying on the 13C's longer lifetimes, leading to a kind of "algorithmic cooling" that can provide high polarization for the 15N as well as carbonyl and alpha 13Cs. This can facilitate certain experiments, as demonstrated with triple resonance experiments on intrinsically disordered proteins involving labile, chemically exchanging protons.
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Affiliation(s)
- Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sundaresan Jayanthi
- Department of Physics, Indian Institute of Space Science and Technology, Valiamala, Thiruvananthapuram 695 547, Kerala, India
| | | | - Maria Grazia Concilio
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jihyun Kim
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Columbus
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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5
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Felli IC, Bermel W, Pierattelli R. Exclusively heteronuclear NMR experiments for the investigation of intrinsically disordered proteins: focusing on proline residues. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:511-522. [PMID: 37904768 PMCID: PMC10539766 DOI: 10.5194/mr-2-511-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/02/2021] [Indexed: 11/01/2023]
Abstract
NMR represents a key spectroscopic technique that contributes to the emerging field of highly flexible, intrinsically disordered proteins (IDPs) or protein regions (IDRs) that lack a stable three-dimensional structure. A set of exclusively heteronuclear NMR experiments tailored for proline residues, highly abundant in IDPs/IDRs, are presented here. They provide a valuable complement to the widely used approach based on amide proton detection, filling the gap introduced by the lack of amide protons in proline residues within polypeptide chains. The novel experiments have very interesting properties for the investigations of IDPs/IDRs of increasing complexity.
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Affiliation(s)
- Isabella C. Felli
- CERM and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Roberta Pierattelli
- CERM and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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6
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Alik A, Bouguechtouli C, Julien M, Bermel W, Ghouil R, Zinn‐Justin S, Theillet F. Sensitivity‐Enhanced
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C‐NMR Spectroscopy for Monitoring Multisite Phosphorylation at Physiological Temperature and pH. Angew Chem Int Ed Engl 2020; 59:10411-10415. [DOI: 10.1002/anie.202002288] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/12/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Ania Alik
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Chafiaa Bouguechtouli
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Manon Julien
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Wolfgang Bermel
- Bruker BioSpin GmbH Silberstreifen 76287 Rheinstetten Germany
| | - Rania Ghouil
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Sophie Zinn‐Justin
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Francois‐Xavier Theillet
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
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7
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Alik A, Bouguechtouli C, Julien M, Bermel W, Ghouil R, Zinn‐Justin S, Theillet F. Sensitivity‐Enhanced
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C‐NMR Spectroscopy for Monitoring Multisite Phosphorylation at Physiological Temperature and pH. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002288] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ania Alik
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Chafiaa Bouguechtouli
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Manon Julien
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Wolfgang Bermel
- Bruker BioSpin GmbH Silberstreifen 76287 Rheinstetten Germany
| | - Rania Ghouil
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Sophie Zinn‐Justin
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Francois‐Xavier Theillet
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
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8
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Kumar A, Bellstedt P, Wiedemann C, Wißbrock A, Imhof D, Ramachandran R, Ohlenschläger O. NMR experiments on the transient interaction of the intrinsically disordered N-terminal peptide of cystathionine-β-synthase with heme. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 308:106561. [PMID: 31345774 DOI: 10.1016/j.jmr.2019.07.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
The N-terminal segment of human cystathionine-β-synthase (CBS(1-40)) constitutes an intrinsically disordered protein stretch that transiently interacts with heme. We illustrate that the HCBCACON experimental protocol provides an efficient alternative approach for probing transient interactions of intrinsically disordered proteins with heme in situations where the applicability of the conventional [1H, 15N]-HSQC experiment may be limited. This experiment starting with the excitation of protein side chain protons delivers information about the proline residues and thereby makes it possible to use these residues in interaction mapping experiments. Employing this approach in conjunction with site-specific mutation we show that transient heme binding is mediated by the Cys15-Pro16 motif of CBS(1-40).
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Affiliation(s)
- Amit Kumar
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany
| | - Peter Bellstedt
- Institute for Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University, Humboldtstr. 10, D-07743 Jena, Germany
| | - Christoph Wiedemann
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, D-06120 Halle, Germany
| | - Amelie Wißbrock
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Diana Imhof
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Ramadurai Ramachandran
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany
| | - Oliver Ohlenschläger
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
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9
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Schiavina M, Murrali MG, Pontoriero L, Sainati V, Kümmerle R, Bermel W, Pierattelli R, Felli IC. Taking Simultaneous Snapshots of Intrinsically Disordered Proteins in Action. Biophys J 2019; 117:46-55. [PMID: 31176511 PMCID: PMC6626832 DOI: 10.1016/j.bpj.2019.05.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/03/2019] [Accepted: 05/14/2019] [Indexed: 12/20/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) as well as intrinsically disordered regions (IDRs) of complex protein machineries have recently been recognized as key players in many cellular functions. NMR represents a unique tool to access atomic resolution structural and dynamic information on highly flexible IDPs/IDRs. Improvements in instrumental sensitivity made heteronuclear direct detection possible for biomolecular NMR applications. The CON experiment has become one of the most useful NMR experiments to get a snapshot of an IDP/IDR in conditions approaching physiological ones. The availability of NMR spectrometers equipped with multiple receivers now enables the acquisition of several experiments simultaneously instead of one after the other. Here, we propose several variants of the CON experiment in which, during the recovery delay, a second two-dimensional experiment is acquired, either based on 1H detection (CON//HN) or on 15N detection (CON//btNH, CON//(H)CAN). The possibility to collect simultaneous snapshots of an IDP/IDR through different two-dimensional spectra provides a novel tool to follow chemical reactions, such as the occurrence of posttranslational modifications, as well as to study samples of limited lifetime such as cell lysates or whole cells.
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Affiliation(s)
- Marco Schiavina
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff," University of Florence, Sesto Fiorentino, Florence, Italy
| | - Maria Grazia Murrali
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff," University of Florence, Sesto Fiorentino, Florence, Italy
| | - Letizia Pontoriero
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff," University of Florence, Sesto Fiorentino, Florence, Italy
| | - Valerio Sainati
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff," University of Florence, Sesto Fiorentino, Florence, Italy
| | | | | | - Roberta Pierattelli
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff," University of Florence, Sesto Fiorentino, Florence, Italy.
| | - Isabella C Felli
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff," University of Florence, Sesto Fiorentino, Florence, Italy.
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10
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Kumari P, Frey L, Sobol A, Lakomek NA, Riek R. 15N transverse relaxation measurements for the characterization of µs-ms dynamics are deteriorated by the deuterium isotope effect on 15N resulting from solvent exchange. JOURNAL OF BIOMOLECULAR NMR 2018; 72:125-137. [PMID: 30306288 DOI: 10.1007/s10858-018-0211-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/03/2018] [Indexed: 06/08/2023]
Abstract
15N R2 relaxation measurements are key for the elucidation of the dynamics of both folded and intrinsically disordered proteins (IDPs). Here we show, on the example of the intrinsically disordered protein α-synuclein and the folded domain PDZ2, that at physiological pH and near physiological temperatures amide-water exchange can severely skew Hahn-echo based 15N R2 relaxation measurements as well as low frequency data points in CPMG relaxation dispersion experiments. The nature thereof is the solvent exchange with deuterium in the sample buffer, which modulates the 15N chemical shift tensor via the deuterium isotope effect, adding to the apparent relaxation decay which leads to systematic errors in the relaxation data. This results in an artificial increase of the measured apparent 15N R2 rate constants-which should not be mistaken with protein inherent chemical exchange contributions, Rex, to 15N R2. For measurements of 15N R2 rate constants of IDPs and folded proteins at physiological temperatures and pH, we recommend therefore the use of a very low D2O molar fraction in the sample buffer, as low as 1%, or the use of an external D2O reference along with a modified 15N R2 Hahn-echo based experiment. This combination allows for the measurement of Rex contributions to 15N R2 originating from conformational exchange in a time window from µs to ms.
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Affiliation(s)
- Pratibha Kumari
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Lukas Frey
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Alexander Sobol
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Nils-Alexander Lakomek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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11
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Lippens G, Cahoreau E, Millard P, Charlier C, Lopez J, Hanoulle X, Portais JC. In-cell NMR: from metabolites to macromolecules. Analyst 2018; 143:620-629. [PMID: 29333554 DOI: 10.1039/c7an01635b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In-cell NMR of macromolecules has gained momentum over the last ten years as an approach that might bridge the branches of cell biology and structural biology. In this review, we put it in the context of earlier efforts that aimed to characterize by NMR the cellular environment of live cells and their intracellular metabolites. Although technical aspects distinguish these earlier in vivo NMR studies and the more recent in cell NMR efforts to characterize macromolecules in a cellular environment, we believe that both share major concerns ranging from sensitivity and line broadening to cell viability. Approaches to overcome the limitations in one subfield thereby can serve the other one and vice versa. The relevance in biomedical sciences might stretch from the direct following of drug metabolism in the cell to the observation of target binding, and thereby encompasses in-cell NMR both of metabolites and macromolecules. We underline the efforts of the field to move to novel biological insights by some selected examples.
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Affiliation(s)
- G Lippens
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - E Cahoreau
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - P Millard
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - C Charlier
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - J Lopez
- CERMN, Seccion Quimica, Departemento de Ciencias, Pontificia Universidad Catolica del Peru, Lima 32, Peru
| | - X Hanoulle
- Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), University of Lille, CNRS UMR8576, Lille, France
| | - J C Portais
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
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12
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Quinn CM, Wang M, Polenova T. NMR of Macromolecular Assemblies and Machines at 1 GHz and Beyond: New Transformative Opportunities for Molecular Structural Biology. Methods Mol Biol 2018; 1688:1-35. [PMID: 29151202 PMCID: PMC6217836 DOI: 10.1007/978-1-4939-7386-6_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
As a result of profound gains in sensitivity and resolution afforded by ultrahigh magnetic fields, transformative applications in the fields of structural biology and materials science are being realized. The development of dual low temperature superconducting (LTS)/high-temperature superconducting (HTS) magnets has enabled the achievement of magnetic fields above 1 GHz (23.5 T), which will open doors to an unprecedented new range of applications. In this contribution, we discuss the promise of ultrahigh field magnetic resonance. We highlight several methodological developments pertinent at high-magnetic fields including measurement of 1H-1H distances and 1H chemical shift anisotropy in the solid state as well as studies of quadrupolar nuclei such as 17O. Higher magnetic fields have advanced heteronuclear detection in solution NMR, valuable for applications including metabolomics and disordered proteins, as well as expanded use of proton detection in the solid state in conjunction with ultrafast magic angle spinning. We also present several recent applications to structural studies of the AP205 bacteriophage, the M2 channel from Influenza A, and biomaterials such as human bone. Gains in sensitivity and resolution from increased field strengths will enable advanced applications of NMR spectroscopy including in vivo studies of whole cells and intact virions.
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Affiliation(s)
- Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA.
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA.
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13
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Towards understanding cellular structure biology: In-cell NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:547-557. [PMID: 28257994 DOI: 10.1016/j.bbapap.2017.02.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/22/2017] [Accepted: 02/27/2017] [Indexed: 12/20/2022]
Abstract
To watch biological macromolecules perform their functions inside the living cells is the dream of any biologists. In-cell nuclear magnetic resonance is a branch of biomolecular NMR spectroscopy that can be used to observe the structures, interactions and dynamics of these molecules in the living cells at atomic level. In principle, in-cell NMR can be applied to different cellular systems to achieve biologically relevant structural and functional information. In this review, we summarize the existing approaches in this field and discuss its applications in protein interactions, folding, stability and post-translational modifications. We hope this review will emphasize the effectiveness of in-cell NMR for studies of intricate biological processes and for structural analysis in cellular environments.
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14
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Yoshimura Y, Oktaviani NA, Yonezawa K, Kamikubo H, Mulder FAA. Unambiguous Determination of Protein Arginine Ionization States in Solution by NMR Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yuichi Yoshimura
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry Aarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Nur Alia Oktaviani
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen The Netherlands
| | - Kento Yonezawa
- Graduate School of Materials Science Nara Institute of Science and Technology, Ikoma, Nara Japan
| | - Hironari Kamikubo
- Graduate School of Materials Science Nara Institute of Science and Technology, Ikoma, Nara Japan
| | - Frans A. A. Mulder
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry Aarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen The Netherlands
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15
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Yoshimura Y, Oktaviani NA, Yonezawa K, Kamikubo H, Mulder FAA. Unambiguous Determination of Protein Arginine Ionization States in Solution by NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 56:239-242. [PMID: 27897362 DOI: 10.1002/anie.201609605] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Indexed: 11/09/2022]
Abstract
Because arginine residues in proteins are expected to be in their protonated form almost without exception, reports demonstrating that a protein arginine residue is charge-neutral are rare and potentially controversial. Herein, we present a 13 C-detected NMR experiment for probing individual arginine residues in proteins notwithstanding the presence of chemical and conformational exchange effects. In the experiment, the 15 Nη and 15 Nϵ chemical shifts of an arginine head group are correlated with that of the directly attached 13 Cζ . In the resulting spectrum, the number of protons in the arginine head group can be obtained directly from the 15 N-1 H scalar coupling splitting pattern. We applied this method to unambiguously determine the ionization state of the R52 side chain in the photoactive yellow protein from Halorhodospira halophila. Although only three Hη atoms were previously identified by neutron crystallography, we show that R52 is predominantly protonated in solution.
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Affiliation(s)
- Yuichi Yoshimura
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Nur Alia Oktaviani
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Kento Yonezawa
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark.,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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