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Schiavina M, Bracaglia L, Rodella MA, Kümmerle R, Konrat R, Felli IC, Pierattelli R. Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz. Nat Protoc 2024; 19:406-440. [PMID: 38087081 DOI: 10.1038/s41596-023-00921-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/20/2023] [Indexed: 02/12/2024]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for characterizing biomolecules such as proteins and nucleic acids at atomic resolution. Increased magnetic field strengths drive progress in biomolecular NMR applications, leading to improved performance, e.g., higher resolution. A new class of NMR spectrometers with a 28.2 T magnetic field (1.2 GHz 1H frequency) has been commercially available since the end of 2019. The availability of ultra-high-field NMR instrumentation makes it possible to investigate more complex systems using NMR. This is especially true for highly flexible intrinsically disordered proteins (IDPs) and highly flexible regions (IDRs) of complex multidomain proteins. Indeed, the investigation of these proteins is frequently hampered by the crowding of NMR spectra. The advantages, however, are accompanied by challenges that the user must overcome when conducting experiments at such a high field (e.g., large spectral widths, radio frequency bandwidth, performance of decoupling schemes). This protocol presents strategies and tricks for optimising high-field NMR experiments for IDPs/IDRs based on the analysis of the relaxation properties of the investigated protein. The protocol, tested on three IDPs of different molecular weight and structural complexity, focuses on 13C-detected NMR at 1.2 GHz. A set of experiments, including some multiple receiver experiments, and tips to implement versions tailored for IDPs/IDRs are described. However, the general approach and most considerations can also be applied to experiments that acquire 1H or 15N nuclei and to experiments performed at lower field strengths.
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Affiliation(s)
- Marco Schiavina
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy.
| | - Lorenzo Bracaglia
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy
| | - Maria Anna Rodella
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy
| | | | - Robert Konrat
- Department of Computational and Structural Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Isabella C Felli
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy.
| | - Roberta Pierattelli
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy.
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Schiavina M, Konrat R, Ceccolini I, Mateos B, Konrat R, Felli IC, Pierattelli R. Studies of proline conformational dynamics in IDPs by 13C-detected cross-correlated NMR relaxation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 354:107539. [PMID: 37632987 DOI: 10.1016/j.jmr.2023.107539] [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: 07/04/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/28/2023]
Abstract
Intrinsically disordered proteins (IDPs) are significantly enriched in proline residues, which can populate specific local secondary structural elements called PPII helices, characterized by small packing densities. Proline is often thought to promote disorder, but it can participate in specific π·CH interactions with aromatic side chains resulting in reduced conformational flexibilities of the polypeptide. Differential local motional dynamics are relevant for the stabilization of preformed structural elements and can serve as nucleation sites for the establishment of long-range interactions. NMR experiments to probe the dynamics of proline ring systems would thus be highly desirable. Here we present a pulse scheme based on 13C detection to quantify dipole-dipole cross-correlated relaxation (CCR) rates at methylene CH2 groups in proline residues. Applying 13C-CON detection strategy provides exquisite spectral resolution allowing applications also to high molecular weight IDPs even in conditions approaching the physiological ones. The pulse scheme is illustrated with an application to the 220 amino acids long protein Osteopontin, an extracellular cytokine involved in inflammation and cancer progression, and a construct in which three proline-aromatic sequence patches have been mutated.
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Affiliation(s)
- Marco Schiavina
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Ruth Konrat
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Irene Ceccolini
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Borja Mateos
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria.
| | - 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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3
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Tibble RW, Gross JD. A call to order: Examining structured domains in biomolecular condensates. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 346:107318. [PMID: 36657879 PMCID: PMC10878105 DOI: 10.1016/j.jmr.2022.107318] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/20/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Diverse cellular processes have been observed or predicted to occur in biomolecular condensates, which are comprised of proteins and nucleic acids that undergo liquid-liquid phase separation (LLPS). Protein-driven LLPS often involves weak, multivalent interactions between intrinsically disordered regions (IDRs). Due to their inherent lack of defined tertiary structures, NMR has been a powerful resource for studying the behavior and interactions of IDRs in condensates. While IDRs in proteins are necessary for phase separation, core proteins enriched in condensates often contain structured domains that are essential for their function and contribute to phase separation. How phase separation can affect the structure and conformational dynamics of structured domains is critical for understanding how biochemical reactions can be effectively regulated in cellular condensates. In this perspective, we discuss the consequences phase separation can have on structured domains and outline NMR observables we believe are useful for assessing protein structure and dynamics in condensates.
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Affiliation(s)
- Ryan W Tibble
- Program in Chemistry and Chemical Biology, University of California, San Francisco, United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, United States
| | - John D Gross
- Program in Chemistry and Chemical Biology, University of California, San Francisco, United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, United States.
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4
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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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5
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Wong LE, Kim TH, Muhandiram DR, Forman-Kay JD, Kay LE. NMR Experiments for Studies of Dilute and Condensed Protein Phases: Application to the Phase-Separating Protein CAPRIN1. J Am Chem Soc 2020; 142:2471-2489. [DOI: 10.1021/jacs.9b12208] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Leo E. Wong
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Tae Hun Kim
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Hospital for Sick Children, Program in Molecular Medicine, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
| | - D. Ranjith Muhandiram
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Julie D. Forman-Kay
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Hospital for Sick Children, Program in Molecular Medicine, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
| | - Lewis E. Kay
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Hospital for Sick Children, Program in Molecular Medicine, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
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6
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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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7
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Batchelor M, Wolny M, Baker EG, Paci E, Kalverda AP, Peckham M. Dynamic ion pair behavior stabilizes single α-helices in proteins. J Biol Chem 2019; 294:3219-3234. [PMID: 30593502 PMCID: PMC6398138 DOI: 10.1074/jbc.ra118.006752] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/17/2018] [Indexed: 11/06/2022] Open
Abstract
Ion pairs are key stabilizing interactions between oppositely charged amino acid side chains in proteins. They are often depicted as single conformer salt bridges (hydrogen-bonded ion pairs) in crystal structures, but it is unclear how dynamic they are in solution. Ion pairs are thought to be particularly important in stabilizing single α-helix (SAH) domains in solution. These highly stable domains are rich in charged residues (such as Arg, Lys, and Glu) with potential ion pairs across adjacent turns of the helix. They provide a good model system to investigate how ion pairs can contribute to protein stability. Using NMR spectroscopy, small-angle X-ray light scattering (SAXS), and molecular dynamics simulations, we provide here experimental evidence that ion pairs exist in a SAH in murine myosin 7a (residues 858-935), but that they are not fixed or long lasting. In silico modeling revealed that the ion pairs within this α-helix exhibit dynamic behavior, rapidly forming and breaking and alternating between different partner residues. The low-energy helical state was compatible with a great variety of ion pair combinations. Flexible ion pair formation utilizing a subset of those available at any one time avoided the entropic penalty of fixing side chain conformations, which likely contributed to helix stability overall. These results indicate the dynamic nature of ion pairs in SAHs. More broadly, thermodynamic stability in other proteins is likely to benefit from the dynamic behavior of multi-option solvent-exposed ion pairs.
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Affiliation(s)
- Matthew Batchelor
- From the School of Molecular and Cellular Biology and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Marcin Wolny
- From the School of Molecular and Cellular Biology and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Emily G Baker
- the School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Emanuele Paci
- From the School of Molecular and Cellular Biology and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Arnout P Kalverda
- From the School of Molecular and Cellular Biology and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Michelle Peckham
- From the School of Molecular and Cellular Biology and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
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8
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Murrali MG, Schiavina M, Sainati V, Bermel W, Pierattelli R, Felli IC. 13C APSY-NMR for sequential assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2018; 70:167-175. [PMID: 29492731 DOI: 10.1007/s10858-018-0167-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/09/2018] [Indexed: 06/08/2023]
Abstract
The increasingly recognized biological relevance of intrinsically disordered proteins requires a continuous expansion of the tools for their characterization via NMR spectroscopy, the only technique so far able to provide atomic-resolution information on these highly mobile macromolecules. Here we present the implementation of projection spectroscopy in 13C-direct detected NMR experiments to achieve the sequence specific assignment of IDPs. The approach was used to obtain the complete backbone assignment at high temperature of α-synuclein, a paradigmatic intrinsically disordered protein.
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Affiliation(s)
- Maria Grazia Murrali
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Marco Schiavina
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Valerio Sainati
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen, 76287, Rheinstetten, Germany
| | - Roberta Pierattelli
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy.
- Department of Chemistry "Ugo Schiff", University of Florence, 50019, Sesto Fiorentino, Florence, Italy.
| | - Isabella C Felli
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy.
- Department of Chemistry "Ugo Schiff", University of Florence, 50019, Sesto Fiorentino, Florence, Italy.
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9
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Göbl C, Resch M, Strickland M, Hartlmüller C, Viertler M, Tjandra N, Madl T. Verbesserung der Dispersion der chemischen Verschiebungen von unstrukturierten Proteinen durch einen kovalent gebundenen Lanthanoidkomplex. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Christoph Göbl
- Center for Integrated Protein Science Munich; Technische Universität München; Fakultät für Chemie; Lichtenbergstraße 4 85748 Garching Deutschland
- Institut für Strukturbiologie; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Deutschland
| | - Moritz Resch
- Center for Integrated Protein Science Munich; Technische Universität München; Fakultät für Chemie; Lichtenbergstraße 4 85748 Garching Deutschland
- Institut für Strukturbiologie; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Deutschland
| | - Madeleine Strickland
- Laboratory of Structural Biophysics Biochemistry and Biophysics Center; National Heart, Lung, and Blood Institute; National Institutes of Health; Building 50 Bethesda MD 20814 USA
| | - Christoph Hartlmüller
- Center for Integrated Protein Science Munich; Technische Universität München; Fakultät für Chemie; Lichtenbergstraße 4 85748 Garching Deutschland
- Institut für Strukturbiologie; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Deutschland
| | - Martin Viertler
- Institut für Strukturbiologie; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Deutschland
| | - Nico Tjandra
- Laboratory of Structural Biophysics Biochemistry and Biophysics Center; National Heart, Lung, and Blood Institute; National Institutes of Health; Building 50 Bethesda MD 20814 USA
| | - Tobias Madl
- Center for Integrated Protein Science Munich; Technische Universität München; Fakultät für Chemie; Lichtenbergstraße 4 85748 Garching Deutschland
- Institut für Strukturbiologie; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Deutschland
- Institut für Molekularbiologie & Biochemie; Zentrum für Medizinische Forschung; Medizinische Universität Graz; 8010 Graz Österreich
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10
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Piai A, Calçada EO, Tarenzi T, Grande AD, Varadi M, Tompa P, Felli IC, Pierattelli R. Just a Flexible Linker? The Structural and Dynamic Properties of CBP-ID4 Revealed by NMR Spectroscopy. Biophys J 2016; 110:372-381. [PMID: 26789760 DOI: 10.1016/j.bpj.2015.11.3516] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/12/2015] [Accepted: 11/25/2015] [Indexed: 01/01/2023] Open
Abstract
Here, we present a structural and dynamic description of CBP-ID4 at atomic resolution. ID4 is the fourth intrinsically disordered linker of CREB-binding protein (CBP). In spite of the largely disordered nature of CBP-ID4, NMR chemical shifts and relaxation measurements show a significant degree of α-helix sampling in the protein regions encompassing residues 2-25 and 101-128 (1852-1875 and 1951-1978 in full-length CBP). Proline residues are uniformly distributed along the polypeptide, except for the two α-helical regions, indicating that they play an active role in modulating the structural features of this CBP fragment. The two helical regions are lacking known functional motifs, suggesting that they represent thus-far uncharacterized functional modules of CBP. This work provides insights into the functions of this protein linker that may exploit its plasticity to modulate the relative orientations of neighboring folded domains of CBP and fine-tune its interactions with a multitude of partners.
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Affiliation(s)
- Alessandro Piai
- Magnetic Resonance Center, University of Florence, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy
| | - Eduardo O Calçada
- Magnetic Resonance Center, University of Florence, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy
| | - Thomas Tarenzi
- Magnetic Resonance Center, University of Florence, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy
| | - Alessandro Del Grande
- Magnetic Resonance Center, University of Florence, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy
| | - Mihaly Varadi
- VIB Structural Biology Research Center, Vlaams Instituut voor Biotechnologie at Vrije Universiteit Brussel, Brussel, Belgium
| | - Peter Tompa
- VIB Structural Biology Research Center, Vlaams Instituut voor Biotechnologie at Vrije Universiteit Brussel, Brussel, Belgium; Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Isabella C Felli
- Magnetic Resonance Center, University of Florence, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy.
| | - Roberta Pierattelli
- Magnetic Resonance Center, University of Florence, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy.
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11
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Göbl C, Resch M, Strickland M, Hartlmüller C, Viertler M, Tjandra N, Madl T. Increasing the Chemical-Shift Dispersion of Unstructured Proteins with a Covalent Lanthanide Shift Reagent. Angew Chem Int Ed Engl 2016; 55:14847-14851. [PMID: 27763708 PMCID: PMC5146990 DOI: 10.1002/anie.201607261] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/16/2016] [Indexed: 01/19/2023]
Abstract
The study of intrinsically disordered proteins (IDPs) by NMR often suffers from highly overlapped resonances that prevent unambiguous chemical-shift assignments, and data analysis that relies on well-separated resonances. We present a covalent paramagnetic lanthanide-binding tag (LBT) for increasing the chemical-shift dispersion and facilitating the chemical-shift assignment of challenging, repeat-containing IDPs. Linkage of the DOTA-based LBT to a cysteine residue induces pseudo-contact shifts (PCS) for resonances more than 20 residues from the spin-labeling site. This leads to increased chemical-shift dispersion and decreased signal overlap, thereby greatly facilitating chemical-shift assignment. This approach is applicable to IDPs of varying sizes and complexity, and is particularly helpful for repeat-containing IDPs and low-complexity regions. This results in improved efficiency for IDP analysis and binding studies.
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Affiliation(s)
- Christoph Göbl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Moritz Resch
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Madeleine Strickland
- Laboratory of Structural Biophysics Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 50, Bethesda, MD, 20814, USA
| | - Christoph Hartlmüller
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Martin Viertler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Nico Tjandra
- Laboratory of Structural Biophysics Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 50, Bethesda, MD, 20814, USA
| | - Tobias Madl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010, Graz, Austria
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12
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Lopez J, Schneider R, Cantrelle FX, Huvent I, Lippens G. Studying Intrinsically Disordered Proteins under True In Vivo Conditions by Combined Cross-Polarization and Carbonyl-Detection NMR Spectroscopy. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601850] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Juan Lopez
- Université de Lille; CNRS; UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle; 59000 Lille France
- Departamento de Ciencias-Quimica; Pontificia Universidad Catolica del Peru; Av. Universitaria 1801 Lima 32 Peru
| | - Robert Schneider
- Université de Lille; CNRS; UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle; 59000 Lille France
| | - Francois-Xavier Cantrelle
- Université de Lille; CNRS; UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle; 59000 Lille France
| | - Isabelle Huvent
- Université de Lille; CNRS; UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle; 59000 Lille France
| | - Guy Lippens
- Université de Lille; CNRS; UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle; 59000 Lille France
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés; Université de Toulouse; CNRS; INRA; INSA Toulouse; 135 Avenue de Rangueil 31077 Toulouse France
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13
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Lopez J, Schneider R, Cantrelle FX, Huvent I, Lippens G. Studying Intrinsically Disordered Proteins under True In Vivo Conditions by Combined Cross-Polarization and Carbonyl-Detection NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:7418-22. [DOI: 10.1002/anie.201601850] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 03/28/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Juan Lopez
- Université de Lille; CNRS; UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle; 59000 Lille France
- Departamento de Ciencias-Quimica; Pontificia Universidad Catolica del Peru; Av. Universitaria 1801 Lima 32 Peru
| | - Robert Schneider
- Université de Lille; CNRS; UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle; 59000 Lille France
| | - Francois-Xavier Cantrelle
- Université de Lille; CNRS; UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle; 59000 Lille France
| | - Isabelle Huvent
- Université de Lille; CNRS; UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle; 59000 Lille France
| | - Guy Lippens
- Université de Lille; CNRS; UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle; 59000 Lille France
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés; Université de Toulouse; CNRS; INRA; INSA Toulouse; 135 Avenue de Rangueil 31077 Toulouse France
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14
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Wiedemann C, Bellstedt P, Häfner S, Herbst C, Bordusa F, Görlach M, Ohlenschläger O, Ramachandran R. A Set of Efficient nD NMR Protocols for Resonance Assignments of Intrinsically Disordered Proteins. Chemphyschem 2016; 17:1961-8. [PMID: 27061973 DOI: 10.1002/cphc.201600155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 11/07/2022]
Abstract
The RF pulse scheme RN[N-CA HEHAHA]NH, which provides a convenient approach to the acquisition of different multidimensional chemical shift correlation NMR spectra leading to backbone resonance assignments, including those of the proline residues of intrinsically disordered proteins (IDPs), is experimentally demonstrated. Depending on the type of correlation data required, the method involves the generation of in-phase ((15) N)(x) magnetisation via different magnetisation transfer pathways such as H→N→CO→N, HA→CA→CO→N, H→N→CA→N and H→CA→N, the subsequent application of (15) N-(13) C(α) heteronuclear Hartmann-Hahn mixing over a period of ≈100 ms, chemical-shift labelling of relevant nuclei before and after the heteronuclear mixing step and amide proton detection in the acquisition dimension. It makes use of the favourable relaxation properties of IDPs and the presence of (1) JCαN and (2) JCαN couplings to achieve efficient correlation of the backbone resonances of each amino acid residue "i" with the backbone amide resonances of residues "i-1" and "i+1". It can be implemented in a straightforward way through simple modifications of the RF pulse schemes commonly employed in protein NMR studies. The efficacy of the approach is demonstrated using a uniformly ((15) N,(13) C) labelled sample of α-synuclein. The different possibilities for obtaining the amino-acid-type information, simultaneously with the connectivity data between the backbone resonances of sequentially neighbouring residues, have also been outlined.
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Affiliation(s)
- Christoph Wiedemann
- Institute of Biochemistry/Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Peter Bellstedt
- Faculty of Chemistry and Earth Sciences, Friedrich Schiller University Jena, Humboldstr. 10, 07743, Jena, Germany
| | - Sabine Häfner
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Christian Herbst
- Department of Physics, Faculty of Science, Ubon Ratchathani University, 34190, Ubon Ratchathani, Thailand
| | - Frank Bordusa
- Institute of Biochemistry/Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Matthias Görlach
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Oliver Ohlenschläger
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Ramadurai Ramachandran
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
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15
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Nowakowski M, Saxena S, Stanek J, Żerko S, Koźmiński W. Applications of high dimensionality experiments to biomolecular NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 90-91:49-73. [PMID: 26592945 DOI: 10.1016/j.pnmrs.2015.07.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 07/03/2015] [Accepted: 07/03/2015] [Indexed: 05/23/2023]
Abstract
High dimensionality NMR experiments facilitate resonance assignment and precise determination of spectral parameters such as coupling constants. Sparse non-uniform sampling enables acquisition of experiments of high dimensionality with high resolution in acceptable time. In this review we present and compare some significant applications of NMR experiments of dimensionality higher than three in the field of biomolecular studies in solution.
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Affiliation(s)
- Michał Nowakowski
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Saurabh Saxena
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Jan Stanek
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Szymon Żerko
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Wiktor Koźmiński
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland.
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16
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Saxena S, Stanek J, Cevec M, Plavec J, Koźmiński W. High resolution 4D HPCH experiment for sequential assignment of (13)C-labeled RNAs via phosphodiester backbone. JOURNAL OF BIOMOLECULAR NMR 2015; 63:291-298. [PMID: 26409925 PMCID: PMC4642592 DOI: 10.1007/s10858-015-9989-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 09/20/2015] [Indexed: 06/05/2023]
Abstract
The three-dimensional structure determination of RNAs by NMR spectroscopy requires sequential resonance assignment, often hampered by assignment ambiguities and limited dispersion of (1)H and (13)C chemical shifts, especially of C4'/H4'. Here we present a novel through-bond 4D HPCH NMR experiment involving phosphate backbone where C4'-H4' correlations are resolved along the (1)H3'-(31)P spectral planes. The experiment provides high peak resolution and effectively removes ambiguities encountered during assignments. Enhanced peak dispersion is provided by the inclusion of additional (31)P and (1)H3' dimensions and constant-time evolution of chemical shifts. High spectral resolution is obtained by using non-uniform sampling in three indirect dimensions. The experiment fully utilizes the isotopic (13)C-labeling with evolution of C4' carbons. Band selective (13)C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the C4'-C3' and C4'-C5' homonuclear couplings. Multiple quantum line narrowing is employed to minimize sensitivity loses. The 4D HPCH experiment is verified and successfully applied to a non-coding 34-nt RNA consisting typical structure elements and a 14-nt RNA hairpin capped by cUUCGg tetraloop.
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Affiliation(s)
- Saurabh Saxena
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02089, Warsaw, Poland
| | - Jan Stanek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02089, Warsaw, Poland
| | - Mirko Cevec
- Slovenian NMR Centre, National Institute of Chemistry, 1000, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, 1000, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, 1000, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02089, Warsaw, Poland.
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17
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Wiedemann C, Goradia N, Häfner S, Herbst C, Görlach M, Ohlenschläger O, Ramachandran R. HN-NCA heteronuclear TOCSY-NH experiment for (1)H(N) and (15)N sequential correlations in ((13)C, (15)N) labelled intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2015; 63:201-212. [PMID: 26282620 DOI: 10.1007/s10858-015-9976-x] [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: 05/20/2015] [Accepted: 08/08/2015] [Indexed: 06/04/2023]
Abstract
A simple triple resonance NMR experiment that leads to the correlation of the backbone amide resonances of each amino acid residue 'i' with that of residues 'i-1' and 'i+1' in ((13)C, (15)N) labelled intrinsically disordered proteins (IDPs) is presented. The experimental scheme, {HN-NCA heteronuclear TOCSY-NH}, exploits the favourable relaxation properties of IDPs and the presence of (1) J CαN and (2) J CαN couplings to transfer the (15)N x magnetisation from amino acid residue 'i' to adjacent residues via the application of a band-selective (15)N-(13)C(α) heteronuclear cross-polarisation sequence of ~100 ms duration. Employing non-uniform sampling in the indirect dimensions, the efficacy of the approach has been demonstrated by the acquisition of 3D HNN chemical shift correlation spectra of α-synuclein. The experimental performance of the RF pulse sequence has been compared with that of the conventional INEPT-based HN(CA)NH pulse scheme. As the availability of data from both the HCCNH and HNN experiments will make it possible to use the information extracted from one experiment to simplify the analysis of the data of the other and lead to a robust approach for unambiguous backbone and side-chain resonance assignments, a time-saving strategy for the simultaneous collection of HCCNH and HNN data is also described.
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Affiliation(s)
- Christoph Wiedemann
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
- Institute of Biochemistry/Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle/Salle, Germany
| | - Nishit Goradia
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Sabine Häfner
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Christian Herbst
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
- Department of Physics, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Matthias Görlach
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Oliver Ohlenschläger
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Ramadurai Ramachandran
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
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18
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Felli IC, Pierattelli R. Spin-state-selective methods in solution- and solid-state biomolecular 13C NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 84-85:1-13. [PMID: 25669738 DOI: 10.1016/j.pnmrs.2014.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 10/26/2014] [Indexed: 06/04/2023]
Abstract
Spin-state-selective methods to achieve homonuclear decoupling in the direct acquisition dimension of (13)C detected NMR experiments have been one of the key contributors to converting (13)C detected NMR experiments into really useful tools for studying biomolecules. We discuss here in detail the various methods that have been proposed, summarize the large array of new experiments that have been developed and present applications to different kinds of proteins in different aggregation states.
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Affiliation(s)
- Isabella C Felli
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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19
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Goradia N, Wiedemann C, Herbst C, Görlach M, Heinemann SH, Ohlenschläger O, Ramachandran R. An Approach to NMR Assignment of Intrinsically Disordered Proteins. Chemphyschem 2015; 16:739-46. [DOI: 10.1002/cphc.201402872] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Indexed: 01/06/2023]
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20
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Piai A, Hošek T, Gonnelli L, Zawadzka-Kazimierczuk A, Koźmiński W, Brutscher B, Bermel W, Pierattelli R, Felli IC. "CON-CON" assignment strategy for highly flexible intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2014; 60:209-18. [PMID: 25326659 DOI: 10.1007/s10858-014-9867-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/10/2014] [Indexed: 05/21/2023]
Abstract
Intrinsically disordered proteins (IDPs) are a class of highly flexible proteins whose characterization by NMR spectroscopy is complicated by severe spectral overlaps. The development of experiments designed to facilitate the sequence-specific assignment procedure is thus very important to improve the tools for the characterization of IDPs and thus to be able to focus on IDPs of increasing size and complexity. Here, we present and describe the implementation of a set of novel ¹H-detected 5D experiments, (HACA)CON(CACO)NCO(CA)HA, BT-(H)NCO(CAN)CONNH and BT-HN(COCAN)CONNH, optimized for the study of highly flexible IDPs that exploit the best resolved correlations, those involving the carbonyl and nitrogen nuclei of neighboring amino acids, to achieve sequence-specific resonance assignment. Together with the analogous recently proposed pulse schemes based on ¹³C detection, they form a complete set of experiments for sequence-specific assignment of highly flexible IDPs. Depending on the particular sample conditions (concentration, lifetime, pH, temperature, etc.), these experiments present certain advantages and disadvantages that will be discussed. Needless to say, that the availability of a variety of complementary experiments will be important for accurate determination of resonance frequencies in complex IDPs.
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Affiliation(s)
- Alessandro Piai
- CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
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21
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Felli IC, Gonnelli L, Pierattelli R. In-cell ¹³C NMR spectroscopy for the study of intrinsically disordered proteins. Nat Protoc 2014; 9:2005-16. [PMID: 25079425 DOI: 10.1038/nprot.2014.124] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A large number of proteins carry out their function in highly flexible and disordered states, lacking a well-defined 3D structure. These proteins, referred to as intrinsically disordered proteins (IDPs), are now in the spotlight of modern structural biology. Nuclear magnetic resonance (NMR) spectroscopy represents a unique tool for accessing atomic resolution information on IDPs in complex environments as whole cells, provided that the methods are optimized to their peculiar properties and to the characteristics of in-cell experiments. We describe procedures for the preparation of in-cell NMR samples, as well as for the setup of NMR experiments and their application to in-cell studies, using human α-synuclein overexpressed in Escherichia coli as an example. The expressed protein is labeled with (13)C and (15)N stable isotopes to enable the direct recording of (13)C-detected NMR experiments optimized for the properties of IDPs. The entire procedure covers 24 h, including cell transformation, cell growth overnight, setup of the spectrometer and NMR experiment recording.
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Affiliation(s)
- Isabella C Felli
- Magnetic Resonance Center (CERM), Department of Chemistry 'Ugo Schiff', University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Gonnelli
- Magnetic Resonance Center (CERM), Department of Chemistry 'Ugo Schiff', University of Florence, Sesto Fiorentino, Italy
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM), Department of Chemistry 'Ugo Schiff', University of Florence, Sesto Fiorentino, Italy
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22
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Reddy JG, Hosur RV. A reduced dimensionality NMR pulse sequence and an efficient protocol for unambiguous assignment in intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2014; 59:199-210. [PMID: 24854885 DOI: 10.1007/s10858-014-9839-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 05/08/2014] [Indexed: 05/21/2023]
Abstract
Resonance assignment in intrinsically disordered proteins poses a great challenge because of poor chemical shift dispersion in most of the nuclei that are commonly monitored. Reduced dimensionality (RD) experiments where more than one nuclei are co-evolved simultaneously along one of the time axes of a multi-dimensional NMR experiment help to resolve this problem partially, and one can conceive of different combinations of nuclei for co-evolution depending upon the magnetization transfer pathways and the desired information content in the spectrum. Here, we present a RD experiment, (4,3)D-hNCOCAnH, which uses a combination of CO and CA chemical shifts along one of the axes of the 3-dimensional spectrum, to improve spectral dispersion on one hand, and provide information on four backbone atoms of every residue-HN, N, CA and CO chemical shifts-from a single experiment, on the other. The experiment provides multiple unidirectional sequential (i → i - 1) amide (1)H correlations along different planes of the spectrum enabling easy assignment of most nuclei along the protein backbone. Occasional ambiguities that may arise due to degeneracy of amide proton chemical shifts are proposed to be resolved using the HNN experiment described previously (Panchal et al. in J Biomol NMR 20:135-147, 2001). Applications of the experiment and the assignment protocol have been demonstrated using intrinsically disordered α-synuclein (140 aa) protein.
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Affiliation(s)
- Jithender G Reddy
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), 1, Homi Bhabha Road, Colaba, 400005, Mumbai, India
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23
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Felli IC, Pierattelli R. Novel methods based on (13)C detection to study intrinsically disordered proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:115-25. [PMID: 24656084 DOI: 10.1016/j.jmr.2013.10.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 05/23/2023]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by highly flexible solvent exposed backbones and can sample many different conformations. These properties confer them functional advantages, complementary to those of folded proteins, which need to be characterized to expand our view of how protein structural and dynamic features affect function beyond the static picture of a single well defined 3D structure that has influenced so much our way of thinking. NMR spectroscopy provides a unique tool for the atomic resolution characterization of highly flexible macromolecules in general and of IDPs in particular. The peculiar properties of IDPs however have profound effects on spectroscopic parameters. It is thus worth thinking about these aspects to make the best use of the great potential of NMR spectroscopy to contribute to this fascinating field of research. In particular, after many years of dealing with exclusively heteronuclear NMR experiments based on (13)C direct detection, we would like here to address their relevance when studying IDPs.
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Affiliation(s)
- Isabella C Felli
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Roberta Pierattelli
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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24
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Nováček J, Žídek L, Sklenář V. Toward optimal-resolution NMR of intrinsically disordered proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:41-52. [PMID: 24656079 DOI: 10.1016/j.jmr.2013.12.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 12/04/2013] [Accepted: 12/11/2013] [Indexed: 06/03/2023]
Abstract
Proteins, which, in their native conditions, sample a multitude of distinct conformational states characterized by high spatiotemporal heterogeneity, most often termed as intrinsically disordered proteins (IDPs), have become a target of broad interest over the past 15years. With the growing evidence of their important roles in fundamental cellular processes, there is an urgent need to characterize the conformational behavior of IDPs at the highest possible level. The unique feature of NMR spectroscopy in the context of IDPs is its ability to supply details of their structural and temporal alterations at atomic-level resolution. Here, we briefly review recently proposed NMR-based strategies to characterize transient states populated by IDPs and summarize the latest achievements and future prospects in methodological development. Because low chemical shift dispersion represents the major obstacle encountered when studying IDPs by nuclear magnetic resonance, particular attention is paid to techniques allowing one to approach the physical limits of attainable resolution.
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Affiliation(s)
- Jiří Nováček
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Lukáš Žídek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Vladimír Sklenář
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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25
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The crowd you're in with: Effects of different types of crowding agents on protein aggregation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:346-57. [DOI: 10.1016/j.bbapap.2013.11.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 11/01/2013] [Accepted: 11/11/2013] [Indexed: 11/21/2022]
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26
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Bermel W, Felli IC, Gonnelli L, Koźmiński W, Piai A, Pierattelli R, Zawadzka-Kazimierczuk A. High-dimensionality 13C direct-detected NMR experiments for the automatic assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 57:353-61. [PMID: 24203099 DOI: 10.1007/s10858-013-9793-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/23/2013] [Indexed: 05/13/2023]
Abstract
We present three novel exclusively heteronuclear 5D (13)C direct-detected NMR experiments, namely (H(N-flip)N)CONCACON, (HCA)CONCACON and (H)CACON(CA)CON, designed for easy sequence-specific resonance assignment of intrinsically disordered proteins (IDPs). The experiments proposed have been optimized to overcome the drawbacks which may dramatically complicate the characterization of IDPs by NMR, namely the small dispersion of chemical shifts and the fast exchange of the amide protons with the solvent. A fast and reliable automatic assignment of α-synuclein chemical shifts was obtained with the Tool for SMFT-based Assignment of Resonances (TSAR) program based on the information provided by these experiments.
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Affiliation(s)
- Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen, 76287, Rheinstetten, Germany
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27
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Kosol S, Contreras-Martos S, Cedeño C, Tompa P. Structural characterization of intrinsically disordered proteins by NMR spectroscopy. Molecules 2013; 18:10802-28. [PMID: 24008243 PMCID: PMC6269831 DOI: 10.3390/molecules180910802] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/19/2013] [Accepted: 08/30/2013] [Indexed: 01/25/2023] Open
Abstract
Recent advances in NMR methodology and techniques allow the structural investigation of biomolecules of increasing size with atomic resolution. NMR spectroscopy is especially well-suited for the study of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) which are in general highly flexible and do not have a well-defined secondary or tertiary structure under functional conditions. In the last decade, the important role of IDPs in many essential cellular processes has become more evident as the lack of a stable tertiary structure of many protagonists in signal transduction, transcription regulation and cell-cycle regulation has been discovered. The growing demand for structural data of IDPs required the development and adaption of methods such as 13C-direct detected experiments, paramagnetic relaxation enhancements (PREs) or residual dipolar couplings (RDCs) for the study of ‘unstructured’ molecules in vitro and in-cell. The information obtained by NMR can be processed with novel computational tools to generate conformational ensembles that visualize the conformations IDPs sample under functional conditions. Here, we address NMR experiments and strategies that enable the generation of detailed structural models of IDPs.
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Affiliation(s)
- Simone Kosol
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels 1050, Belgium; E-Mails: (S.C.M.); (C.C.)
- Authors to whom correspondence should be addressed; E-Mails: (S.K.); (P.T.)
| | - Sara Contreras-Martos
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels 1050, Belgium; E-Mails: (S.C.M.); (C.C.)
| | - Cesyen Cedeño
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels 1050, Belgium; E-Mails: (S.C.M.); (C.C.)
| | - Peter Tompa
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels 1050, Belgium; E-Mails: (S.C.M.); (C.C.)
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest 1518, Hungary
- Authors to whom correspondence should be addressed; E-Mails: (S.K.); (P.T.)
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28
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Kragelj J, Ozenne V, Blackledge M, Jensen MR. Conformational Propensities of Intrinsically Disordered Proteins from NMR Chemical Shifts. Chemphyschem 2013; 14:3034-45. [DOI: 10.1002/cphc.201300387] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Indexed: 12/22/2022]
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Kazimierczuk K, Stanek J, Zawadzka-Kazimierczuk A, Koźmiński W. High-Dimensional NMR Spectra for Structural Studies of Biomolecules. Chemphyschem 2013; 14:3015-25. [DOI: 10.1002/cphc.201300277] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Indexed: 11/06/2022]
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Uversky VN. Digested disorder: Quarterly intrinsic disorder digest (January/February/March, 2013). INTRINSICALLY DISORDERED PROTEINS 2013; 1:e25496. [PMID: 28516015 PMCID: PMC5424799 DOI: 10.4161/idp.25496] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 01/13/2023]
Abstract
The current literature on intrinsically disordered proteins is blooming. A simple PubMed search for “intrinsically disordered protein OR natively unfolded protein” returns about 1,800 hits (as of June 17, 2013), with many papers published quite recently. To keep interested readers up to speed with this literature, we are starting a “Digested Disorder” project, which will encompass a series of reader’s digest type of publications aiming at the objective representation of the research papers and reviews on intrinsically disordered proteins. The only two criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest covers papers published during the period of January, February and March of 2013. The papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; College of Medicince; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
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