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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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2
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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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Bernardo-Seisdedos G, Schedlbauer A, Pereira-Ortuzar T, Mato JM, Millet O. Protoporphyrin IX Binds to Iron(II)-Loaded and to Zinc-Loaded Human Frataxin. LIFE (BASEL, SWITZERLAND) 2023; 13:life13010222. [PMID: 36676171 PMCID: PMC9866752 DOI: 10.3390/life13010222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/14/2023]
Abstract
(1) Background: Human frataxin is an iron binding protein that participates in the biogenesis of iron sulfur clusters and enhances ferrochelatase activity. While frataxin association to other proteins has been extensively characterized up to the structural level, much less is known about the putative capacity of frataxin to interact with functionally related metabolites. In turn, current knowledge about frataxin's capacity to coordinate metal ions is limited to iron (II and III); (2) Methods: here, we used NMR spectroscopy, Molecular Dynamics, and Docking approaches to demonstrate new roles of frataxin; (3) Results: We demonstrate that frataxin also binds Zn2+ in a structurally similar way to Fe2+, but with lower affinity. In turn, both Fe2+-loaded and Zn2+-loaded frataxins specifically associate to protoporphyrin IX with micromolar affinity, while apo-frataxin does not bind to the porphyrin. Protoporphyrin IX association to metal-loaded frataxin shares the binding epitope with ferrochelatase; and (4) Conclusions: these findings expand the plethora of relevant molecular targets for frataxin and may help to elucidate the yet unknown different roles that this protein exerts in iron regulation and metabolism.
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Affiliation(s)
- Ganeko Bernardo-Seisdedos
- ATLAS Molecular Pharma, Bizkaia Science and Technology Park, 48160 Derio, Spain
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Andreas Schedlbauer
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Tania Pereira-Ortuzar
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - José M. Mato
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain
- Biomedical Research Network on Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Oscar Millet
- ATLAS Molecular Pharma, Bizkaia Science and Technology Park, 48160 Derio, Spain
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain
- Biomedical Research Network on Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence:
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4
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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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5
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Dubey A, Viennet T, Chhabra S, Takeuchi K, Seo HC, Bermel W, Frueh DP, Arthanari H. 15N-Detected TROSY NMR experiments to study large disordered proteins in high-field magnets. Chem Commun (Camb) 2022; 58:9512-9515. [PMID: 35920752 PMCID: PMC9578535 DOI: 10.1039/d2cc02005j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intrinsically disordered regions (IDRs) of proteins are critical in the regulation of biological processes but difficult to study structurally. Nuclear magnetic resonance (NMR) is uniquely equipped to provide structural information on IDRs at atomic resolution; however, existing NMR methods often pose a challenge for large molecular weight IDRs. Resonance assignment of IDRs using 15ND-detection was previously demonstrated and shown to overcome some of these limitations. Here, we improve the methodology by overcoming the need for deuterated buffers and provide better sensitivity and resolution at higher magnetic fields and physiological salt concentrations using transverse relaxation optimized spectroscopy (TROSY). Finally, large disordered regions with low sequence complexity can be assigned efficiently using these new methods as demonstrated by achieving near complete assignment of the 398-residue N-terminal IDR of the transcription factor NFAT1 harboring 18% prolines.
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Affiliation(s)
- Abhinav Dubey
- Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Thibault Viennet
- Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sandeep Chhabra
- Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Koh Takeuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hee-Chan Seo
- Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Molecular Biology, University of Bergen, Bergen 5020, Norway
| | - Wolfgang Bermel
- Magnetic Resonance Spectroscopy NMR Application, Bruker BioSpin GmbH, 76287, Rheinstetten, Germany
| | - Dominique P Frueh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Haribabu Arthanari
- Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
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6
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Fucci IJ, Byrd RA. nightshift: A Python program for plotting simulated NMR spectra from assigned chemical shifts from the Biological Magnetic Resonance Data Bank. Protein Sci 2022; 31:63-74. [PMID: 34516045 PMCID: PMC8740831 DOI: 10.1002/pro.4181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 01/03/2023]
Abstract
Nuclear magnetic resonance (NMR) provides site specific information on local environments through chemical shifts. NMR is widely used in the study of proteins, ranging from determination of three-dimensional (3D) structures to characterizing dynamics and binding of small molecules and other proteins or ligands. Assigned chemical shift data for the atoms within proteins is a treasure trove of information that can facilitate a broad range of biochemical and biophysical studies. The Biological Magnetic Resonance Data Bank (BMRB) is a publicly accessible database that contains a large number of assigned chemical shifts; however, translating this wealth of knowledge into a practical application is not straightforward. Herein we present nightshift: a Python command line utility and library for plotting simulated two-dimensional (2D) and 3D NMR spectra from assigned chemical shifts in the BMRB. This tool allows users to simulate routinely collected amide and methyl fingerprint spectra, backbone triple-resonance assignment spectra, and user-defined custom correlations, including ones that do not necessarily correspond to published experiments. This tool enables experienced NMR spectroscopists, those learning the craft, and interested scientists seeking to utilize NMR the ability to preview or examine a wide range of spectra for proteins whose assignments are deposited in the BMRB, irrespective of whether those experiments have been executed or reported. The tool applies equally to folded and intrinsically disordered proteins, limited only by the existence of a BMRB deposition. The features of nightshift are described along with applications that illustrate the ease with which complicated correlation spectra and binding events can be simulated.
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Affiliation(s)
- Ian J. Fucci
- Center for Structural Biology, Center for Cancer Research, National Cancer InstituteFrederickMarylandUSA
| | - R. Andrew Byrd
- Center for Structural Biology, Center for Cancer Research, National Cancer InstituteFrederickMarylandUSA
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7
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Probing Surfaces in Dynamic Protein Interactions. J Mol Biol 2020; 432:2949-2972. [DOI: 10.1016/j.jmb.2020.02.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 01/09/2023]
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8
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Munari F, D'Onofrio M, Assfalg M. Solution NMR insights into dynamic supramolecular assemblies of disordered amyloidogenic proteins. Arch Biochem Biophys 2020; 683:108304. [PMID: 32097611 DOI: 10.1016/j.abb.2020.108304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 12/29/2022]
Abstract
The extraordinary flexibility and structural heterogeneity of intrinsically disordered proteins (IDP) make them functionally versatile molecules. We have now begun to better understand their fundamental role in biology, however many aspects of their behaviour remain difficult to grasp experimentally. This is especially true for the intermolecular interactions which lead to the formation of transient or highly dynamic supramolecular self-assemblies, such as oligomers, aggregation intermediates and biomolecular condensates. Both the emerging functions and pathogenicity of these structures have stimulated great efforts to develop methodologies capable of providing useful insights. Significant progress in solution NMR spectroscopy has made this technique one of the most powerful to describe structural and dynamic features of IDPs within such assemblies at atomic resolution. Here, we review the most recent works that have illuminated key aspects of IDP assemblies and contributed significant advancements towards our understanding of the complex conformational landscape of prototypical disease-associated proteins. We also include a primer on some of the fundamental and innovative NMR methods being used in the discussed studies.
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Affiliation(s)
- Francesca Munari
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
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9
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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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10
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Mateos B, Conrad-Billroth C, Schiavina M, Beier A, Kontaxis G, Konrat R, Felli IC, Pierattelli R. The Ambivalent Role of Proline Residues in an Intrinsically Disordered Protein: From Disorder Promoters to Compaction Facilitators. J Mol Biol 2019; 432:3093-3111. [PMID: 31794728 DOI: 10.1016/j.jmb.2019.11.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/23/2019] [Accepted: 11/14/2019] [Indexed: 12/31/2022]
Abstract
Intrinsically disordered proteins (IDPs) carry out many biological functions. They lack a stable three-dimensional structure, but rather adopt many different conformations in dynamic equilibrium. The interplay between local dynamics and global rearrangements is key for their function. In IDPs, proline residues are significantly enriched. Given their unique physicochemical and structural properties, a more detailed understanding of their potential role in stabilizing partially folded states in IDPs is highly desirable. Nuclear magnetic resonance (NMR) spectroscopy, and in particular 13C-detected NMR, is especially suitable to address these questions. We applied a 13C-detected strategy to study Osteopontin, a largely disordered IDP with a central compact region. By using the exquisite sensitivity and spectral resolution of these novel techniques, we gained unprecedented insight into cis-Pro populations, their local structural dynamics, and their role in mediating long-range contacts. Our findings clearly call for a reassessment of the structural and functional role of proline residues in IDPs. The emerging picture shows that proline residues have ambivalent structural roles. They are not simply disorder promoters but rather can, depending on the primary sequence context, act as nucleation sites for structural compaction in IDPs. These unexpected features provide a versatile mechanistic toolbox to enrich the conformational ensembles of IDPs with specific features for adapting to changing molecular and cellular environments.
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Affiliation(s)
- Borja Mateos
- Department of Structural and Computational Biology, University of Vienna, Max Perutz Labs, Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Clara Conrad-Billroth
- Department of Structural and Computational Biology, University of Vienna, Max Perutz Labs, Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Marco Schiavina
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Andreas Beier
- Department of Structural and Computational Biology, University of Vienna, Max Perutz Labs, Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Georg Kontaxis
- Department of Structural and Computational Biology, University of Vienna, Max Perutz Labs, Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, University of Vienna, Max Perutz Labs, Vienna Biocenter Campus 5, 1030 Vienna, Austria.
| | - Isabella C Felli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - 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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11
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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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12
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Isotopic Labeling of Eukaryotic Membrane Proteins for NMR Studies of Interactions and Dynamics. Methods Enzymol 2018; 614:37-65. [PMID: 30611431 DOI: 10.1016/bs.mie.2018.08.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Membrane proteins, and especially G-protein coupled receptors (GPCRs), are increasingly important targets of structural biology studies due to their involvement in many biomedically critical pathways in humans. These proteins are often highly dynamic and thus benefit from studies by NMR spectroscopy in parallel with complementary crystallographic and cryo-EM analyses. However, such studies are often complicated by a range of practical concerns, including challenges in preparing suitably isotopically labeled membrane protein samples, large sizes of protein/detergent or protein/lipid complexes, and limitations on sample concentrations and stabilities. Here we describe our approach to addressing these challenges via the use of simple eukaryotic expression systems and modified NMR experiments, using the human adenosine A2A receptor as an example. Protocols are provided for the preparation of U-2H (13C,1H-Ile δ1)-labeled membrane proteins from overexpression in the methylotrophic yeast Pichia pastoris, as well as techniques for studying the fast ns-ps sidechain dynamics of the methyl groups of such samples. We believe that, with the proper optimization, these protocols should be generalizable to other GPCRs and human membrane proteins.
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13
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Cancer Mutations of the Tumor Suppressor SPOP Disrupt the Formation of Active, Phase-Separated Compartments. Mol Cell 2018; 72:19-36.e8. [PMID: 30244836 DOI: 10.1016/j.molcel.2018.08.027] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 05/29/2018] [Accepted: 08/03/2018] [Indexed: 12/30/2022]
Abstract
Mutations in the tumor suppressor SPOP (speckle-type POZ protein) cause prostate, breast, and other solid tumors. SPOP is a substrate adaptor of the cullin3-RING ubiquitin ligase and localizes to nuclear speckles. Although cancer-associated mutations in SPOP interfere with substrate recruitment to the ligase, mechanisms underlying assembly of SPOP with its substrates in liquid nuclear bodies and effects of SPOP mutations on assembly are poorly understood. Here, we show that substrates trigger phase separation of SPOP in vitro and co-localization in membraneless organelles in cells. Enzymatic activity correlates with cellular co-localization and in vitro mesoscale assembly formation. Disease-associated SPOP mutations that lead to the accumulation of proto-oncogenic proteins interfere with phase separation and co-localization in membraneless organelles, suggesting that substrate-directed phase separation of this E3 ligase underlies the regulation of ubiquitin-dependent proteostasis.
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14
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15N detection harnesses the slow relaxation property of nitrogen: Delivering enhanced resolution for intrinsically disordered proteins. Proc Natl Acad Sci U S A 2018; 115:E1710-E1719. [PMID: 29432148 DOI: 10.1073/pnas.1717560115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Studies over the past decade have highlighted the functional significance of intrinsically disordered proteins (IDPs). Due to conformational heterogeneity and inherent dynamics, structural studies of IDPs have relied mostly on NMR spectroscopy, despite IDPs having characteristics that make them challenging to study using traditional 1H-detected biomolecular NMR techniques. Here, we develop a suite of 3D 15N-detected experiments that take advantage of the slower transverse relaxation property of 15N nuclei, the associated narrower linewidth, and the greater chemical shift dispersion compared with those of 1H and 13C resonances. The six 3D experiments described here start with aliphatic 1H magnetization to take advantage of its higher initial polarization, and are broadly applicable for backbone assignment of proteins that are disordered, dynamic, or have unfavorable amide proton exchange rates. Using these experiments, backbone resonance assignments were completed for the unstructured regulatory domain (residues 131-294) of the human transcription factor nuclear factor of activated T cells (NFATC2), which includes 28 proline residues located in functionally important serine-proline (SP) repeats. The complete assignment of the NFATC2 regulatory domain enabled us to study phosphorylation of NFAT by kinase PKA and phosphorylation-dependent binding of chaperone protein 14-3-3 to NFAT, providing mechanistic insight on how 14-3-3 regulates NFAT nuclear translocation.
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15
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Kougentakis CM, Grasso EM, Robinson AC, Caro JA, Schlessman JL, Majumdar A, García-Moreno E B. Anomalous Properties of Lys Residues Buried in the Hydrophobic Interior of a Protein Revealed with 15N-Detect NMR Spectroscopy. J Phys Chem Lett 2018; 9:383-387. [PMID: 29266956 DOI: 10.1021/acs.jpclett.7b02668] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ionizable residues buried in hydrophobic environments in proteins are essential for many fundamental biochemical processes. These residues titrate with anomalous pKa values that are challenging to reproduce with structure-based calculations owing to the conformational reorganization coupled to their ionization. Detailed characterization of this conformational reorganization is of interest; unfortunately, the properties of buried Lys residues are difficult to study experimentally. Here we demonstrate the utility of 15N NMR spectroscopy to gain insight into the protonation state, state of hydration and conformational dynamics of the Nζ amino group of buried Lys residues. The experiments were applied to five variants of staphylococcal nuclease, with internal Lys residues that titrate with pKa values ranging from 6.2 to 8.1. Direct detection of buried Lys residues with these NMR spectroscopy methods will enable correlation between thermodynamic and structural data as well as unprecedented examination of how conformational transitions coupled to their ionization affect their pKa values.
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Affiliation(s)
| | | | | | | | - Jamie L Schlessman
- Chemistry Department, United States Naval Academy , 572M Holloway Rd MS 9B, Annapolis, Maryland 21402, United States
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16
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Direct detection of carbon and nitrogen nuclei for high-resolution analysis of intrinsically disordered proteins using NMR spectroscopy. Methods 2018; 138-139:39-46. [PMID: 29341926 DOI: 10.1016/j.ymeth.2018.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 01/18/2023] Open
Abstract
Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique for characterizing the structural and dynamic properties of intrinsically disordered proteins and protein regions (IDPs & IDRs). However, the application of NMR to IDPs has been limited by poor chemical shift dispersion in two-dimensional (2D) 1H-15N heteronuclear correlation spectra. Among the various detection schemes available for heteronuclear correlation spectroscopy, 13C direct-detection has become a mainstay for investigations of IDPs owing to the favorable chemical shift dispersion in 2D 13C'-15N correlation spectra. Recent advances in cryoprobe technology have enhanced the sensitivity for direct detection of both 13C and 15N resonances at high magnetic field strengths, thus prompting the development of 15N direct-detect experiments to complement established 13C-detection experiments. However, the application of 15N-detection has not been widely explored for IDPs. Here we compare 1H, 13C, and 15N detection schemes for a variety of 2D heteronuclear correlation spectra and evaluate their performance on the basis of resolution, chemical shift dispersion, and sensitivity. We performed experiments with a variety of disordered systems ranging in size and complexity; from a small IDR (99 amino acids), to a large low complexity IDR (185 amino acids), and finally a ∼73 kDa folded homopentameric protein that also contains disordered regions (133 amino acids/monomer). We conclude that, while requiring high sample concentration and long acquisition times, 15N-detection often offers enhanced resolution over other detection schemes in studies of disordered protein regions with low complexity sequences.
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17
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Current Solution NMR Techniques for Structure-Function Studies of Proteins and RNA Molecules. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:43-58. [DOI: 10.1007/978-981-13-2200-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Voehler M, Ashoka MA, Meiler J, Bock PE. Carbon and amide detect backbone assignment methods of a novel repeat protein from the staphylocoagulase in S. aureus. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:243-249. [PMID: 28819722 PMCID: PMC6057470 DOI: 10.1007/s12104-017-9757-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 08/05/2017] [Indexed: 06/07/2023]
Abstract
The C-terminal repeat domain of staphylocoagulase that is secreted by the S. aureus is believed to play an important role interacting with fibrinogen and promotes blood clotting. To study this interaction by NMR, full assignment of each amide residue in the HSQC spectrum was required. Despite of the short sequence of the repeat construct, the HSQC spectrum contained a substantial amount of overlapped and exchange broadened resonances, indicating little secondary or tertiary structure. This caused severe problems while using the conventional, amide based NMR method for the backbone assignment. With the growing interest in small apparently disordered proteins, these issues are being faced more frequently. An alternative strategy to improve the backbone assignment capability involved carbon direct detection methods. Circumventing the amide proton detection offers a larger signal dispersion and more uniform signal intensity. For peptides with higher concentrations and in combination with the cold carbon channels of new cryoprobes, higher fields, and sufficiently long relaxation times, the disadvantage of the lower sensitivity of the 13C nucleus can be overcome. Another advantage of this method is the assignment of the proline backbone residues. Complete assignment with the carbon-detected strategy was achieved with a set of only two 3D, one 2D, and a HNCO measurement, which was necessary to translate the information to the HSQC spectrum.
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Affiliation(s)
- Markus Voehler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232-8725, USA.
| | - Maddur Appajaiah Ashoka
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232-8725, USA
| | - Paul E Bock
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
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19
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Schnieders R, Richter C, Warhaut S, de Jesus V, Keyhani S, Duchardt-Ferner E, Keller H, Wöhnert J, Kuhn LT, Breeze AL, Bermel W, Schwalbe H, Fürtig B. Evaluation of 15N-detected H-N correlation experiments on increasingly large RNAs. JOURNAL OF BIOMOLECULAR NMR 2017; 69:31-44. [PMID: 28879611 DOI: 10.1007/s10858-017-0132-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/30/2017] [Indexed: 06/07/2023]
Abstract
Recently, 15N-detected multidimensional NMR experiments have been introduced for the investigation of proteins. Utilization of the slow transverse relaxation of nitrogen nuclei in a 15N-TROSY experiment allowed recording of high quality spectra for high molecular weight proteins, even in the absence of deuteration. Here, we demonstrate the applicability of three 15N-detected H-N correlation experiments (TROSY, BEST-TROSY and HSQC) to RNA. With the newly established 15N-detected BEST-TROSY experiment, which proves to be the most sensitive 15N-detected H-N correlation experiment, spectra for five RNA molecules ranging in size from 5 to 100 kDa were recorded. These spectra yielded high resolution in the 15N-dimension even for larger RNAs since the increase in line width with molecular weight is more pronounced in the 1H- than in the 15N-dimension. Further, we could experimentally validate the difference in relaxation behavior of imino groups in AU and GC base pairs. Additionally, we showed that 15N-detected experiments theoretically should benefit from sensitivity and resolution advantages at higher static fields but that the latter is obscured by exchange dynamics within the RNAs.
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Affiliation(s)
- Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Sven Warhaut
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Sara Keyhani
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt, Germany
| | - Heiko Keller
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt, Germany
| | - Lars T Kuhn
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287, Rheinstetten, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
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20
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Gibbs EB, Cook EC, Showalter SA. Application of NMR to studies of intrinsically disordered proteins. Arch Biochem Biophys 2017; 628:57-70. [PMID: 28502465 DOI: 10.1016/j.abb.2017.05.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 12/20/2022]
Abstract
The prevalence of intrinsically disordered protein regions, particularly in eukaryotic proteins, and their clear functional advantages for signaling and gene regulation have created an imperative for high-resolution structural and mechanistic studies. NMR spectroscopy has played a central role in enhancing not only our understanding of the intrinsically disordered native state, but also how that state contributes to biological function. While pathological functions associated with protein aggregation are well established, it has recently become clear that disordered regions also mediate functionally advantageous assembly into high-order structures that promote the formation of membrane-less sub-cellular compartments and even hydrogels. Across the range of functional assembly states accessed by disordered regions, post-translational modifications and regulatory macromolecular interactions, which can also be investigated by NMR spectroscopy, feature prominently. Here we will explore the many ways in which NMR has advanced our understanding of the physical-chemical phase space occupied by disordered protein regions and provide prospectus for the future role of NMR in this emerging and exciting field.
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Affiliation(s)
- Eric B Gibbs
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Erik C Cook
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Scott A Showalter
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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21
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Takeuchi K, Arthanari H, Wagner G. Perspective: revisiting the field dependence of TROSY sensitivity. JOURNAL OF BIOMOLECULAR NMR 2016; 66:221-225. [PMID: 27866370 PMCID: PMC5218892 DOI: 10.1007/s10858-016-0075-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/01/2016] [Indexed: 05/03/2023]
Abstract
The discovery of the TROSY effect (Pervushin et al. in Proc Natl Acad Sci USA 94:12366-12371, 1997) for reducing transverse relaxation and line sharpening through selecting pathways in which dipole-dipole and CSA Hamiltonians partially cancel each other had a tremendous impact on solution NMR studies of macromolecules. Together with the methyl TROSY (Tugarinov and Kay in J Biomol NMR 28:165-172, 2004) it enabled structural and functional studies of significantly larger systems. The optimal field strengths for TROSY have been estimated to be on spectrometers operating around 900 MHz (21.14 T) for the 1HN TROSY (Pervushin et al. in Proc Natl Acad Sci USA 94:12366-12371, 1997) while the aromatic 13C (13Caro) TROSY is posited to be optimal at around 600 MHz (14.09 T) (Pervushin et al. in J Am Chem Soc 120:6394-6400, 1998b; Pervushin in Q Rev Biophys 33:161-197, 2000). The initial rational was based on the consideration of where the quadratic B0 field dependences of the TROSY relaxation rates reach a minimum. For sensitivity consideration, however, it is interesting to estimate which field strengths yield the tallest peaks. Recent studies of 15N-detected TROSYs suggested that maximal peak heights are expected at 1.15 GHz (27.01 T) although the slowest relaxation rates or longest transverse relaxation times T2 are indeed expected around 900 MHz (21.14 T) (Takeuchi in J Biomol NMR 63:323-331, 2015; Takeuchi et al. in J Biomol NMR 64:143-151, 2016). This was based on the fact that the heights of Lorentzian lines are proportional to B o3/2 * T2 (Bo). Thus, multiplying the parabolic T2(Bo) dependence with the increasing function of B o3/2 shifts the maxima of peak-height field dependence from the T2 maximum at 900 MHz to higher fields. Moreover, besides shifting the peak height maximum for 15N TROSY, this analysis yields estimates for optimal peak heights for 1HN detected TROSY to 1.5 GHz, and to 900 MHz for 13C-detected 13CaroTROSY as is detailed below. To our knowledge, this aspect of field dependence of TROSY sensitivity has not been in the attention of the NMR community but may affect perspectives of NMR at ultra-high fields.
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Affiliation(s)
- Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, 135-0064, Japan
- PRESTO, Japan Science and Technology Agency, Tokyo, 135-0064, Japan
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
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Takeuchi K, Arthanari H, Imai M, Wagner G, Shimada I. Nitrogen-detected TROSY yields comparable sensitivity to proton-detected TROSY for non-deuterated, large proteins under physiological salt conditions. JOURNAL OF BIOMOLECULAR NMR 2016; 64:143-51. [PMID: 26800993 PMCID: PMC4871712 DOI: 10.1007/s10858-016-0015-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/16/2016] [Indexed: 05/12/2023]
Abstract
Direct detection of the TROSY component of proton-attached (15)N nuclei ((15)N-detected TROSY) yields high quality spectra with high field magnets, by taking advantage of the slow (15)N transverse relaxation. The slow transverse relaxation and narrow line width of the (15)N-detected TROSY resonances are expected to compensate for the inherently low (15)N sensitivity. However, the sensitivity of (15)N-detected TROSY in a previous report was one-order of magnitude lower than in the conventional (1)H-detected version. This could be due to the fact that the previous experiments were performed at low salt (0-50 mM), which is advantageous for (1)H-detected experiments. Here, we show that the sensitivity gap between (15)N and (1)H becomes marginal for a non-deuterated, large protein (τ c = 35 ns) at a physiological salt concentration (200 mM). This effect is due to the high salt tolerance of the (15)N-detected TROSY. Together with the previously reported benefits of the (15)N-detected TROSY, our results provide further support for the significance of this experiment for structural studies of macromolecules when using high field magnets near and above 1 GHz.
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Affiliation(s)
- Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute for Advanced Industrial Science and Technology, Tokyo, 135-0063, Japan
- PRESTO, JST, Tokyo, 135-0063, Japan
| | - Haribabu Arthanari
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Misaki Imai
- Research and Development Department, Japan Biological Informatics Consortium, Tokyo, 135-0063, Japan
| | - Gerhard Wagner
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
| | - Ichio Shimada
- Molecular Profiling Research Center for Drug Discovery, National Institute for Advanced Industrial Science and Technology, Tokyo, 135-0063, Japan.
- Graduate Schools of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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Takeuchi K, Arthanari H, Shimada I, Wagner G. Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR. JOURNAL OF BIOMOLECULAR NMR 2015; 63:323-331. [PMID: 26497830 PMCID: PMC4749451 DOI: 10.1007/s10858-015-9991-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 10/01/2015] [Indexed: 05/18/2023]
Abstract
Detection of (15)N in multidimensional NMR experiments of proteins has sparsely been utilized because of the low gyromagnetic ratio (γ) of nitrogen and the presumed low sensitivity of such experiments. Here we show that selecting the TROSY components of proton-attached (15)N nuclei (TROSY (15)NH) yields high quality spectra in high field magnets (>600 MHz) by taking advantage of the slow (15)N transverse relaxation and compensating for the inherently low (15)N sensitivity. The (15)N TROSY transverse relaxation rates increase modestly with molecular weight but the TROSY gain in peak heights depends strongly on the magnetic field strength. Theoretical simulations predict that the narrowest line width for the TROSY (15)NH component can be obtained at 900 MHz, but sensitivity reaches its maximum around 1.2 GHz. Based on these considerations, a (15)N-detected 2D (1)H-(15)N TROSY-HSQC ((15)N-detected TROSY-HSQC) experiment was developed and high-quality 2D spectra were recorded at 800 MHz in 2 h for 1 mM maltose-binding protein at 278 K (τc ~ 40 ns). Unlike for (1)H detected TROSY, deuteration is not mandatory to benefit (15)N detected TROSY due to reduced dipolar broadening, which facilitates studies of proteins that cannot be deuterated, especially in cases where production requires eukaryotic expression systems. The option of recording (15)N TROSY of proteins expressed in H2O media also alleviates the problem of incomplete amide proton back exchange, which often hampers the detection of amide groups in the core of large molecular weight proteins that are expressed in D2O culture media and cannot be refolded for amide back exchange. These results illustrate the potential of (15)NH-detected TROSY experiments as a means to exploit the high resolution offered by high field magnets near and above 1 GHz.
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Affiliation(s)
- Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute for Advanced Industrial Science and Technology, Tokyo, 135-0063, Japan
- PRESTO, JST, Tokyo, 135-0063, Japan
| | - Haribabu Arthanari
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Ichio Shimada
- Molecular Profiling Research Center for Drug Discovery, National Institute for Advanced Industrial Science and Technology, Tokyo, 135-0063, Japan.
- Graduate Schools of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Gerhard Wagner
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
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Oktaviani NA, Risør MW, Lee YH, Megens RP, de Jong DH, Otten R, Scheek RM, Enghild JJ, Nielsen NC, Ikegami T, Mulder FAA. Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide. JOURNAL OF BIOMOLECULAR NMR 2015; 62:129-42. [PMID: 25820763 DOI: 10.1007/s10858-015-9925-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 03/20/2015] [Indexed: 05/21/2023]
Abstract
Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T 1 relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form Fe(DO3A) as a suitable PRE agent. Fe(DO3A) effectively reduces the T 1 values across the entire sequence of the intrinsically disordered protein α-synuclein with negligible impact on line width. The agent is better suited than currently used alternatives, shows no specific interaction with the polypeptide chain and, due to its high relaxivity, is effective at low concentrations and in 'proton-less' NMR experiments. By using Fe(DO3A) we were able to complete the backbone resonance assignment of a highly fibrillogenic peptide from α1-antitrypsin by acquiring the necessary suite of multidimensional NMR datasets in 3 h.
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Affiliation(s)
- Nur Alia Oktaviani
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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25
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Brutscher B, Felli IC, Gil-Caballero S, Hošek T, Kümmerle R, Piai A, Pierattelli R, Sólyom Z. NMR Methods for the Study of Instrinsically Disordered Proteins Structure, Dynamics, and Interactions: General Overview and Practical Guidelines. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:49-122. [PMID: 26387100 DOI: 10.1007/978-3-319-20164-1_3] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Thanks to recent improvements in NMR instrumentation, pulse sequence design, and sample preparation, a panoply of new NMR tools has become available for atomic resolution characterization of intrinsically disordered proteins (IDPs) that are optimized for the particular chemical and spectroscopic properties of these molecules. A wide range of NMR observables can now be measured on increasingly complex IDPs that report on their structural and dynamic properties in isolation, as part of a larger complex, or even inside an entire living cell. Herein we present basic NMR concepts, as well as optimised tools available for the study of IDPs in solution. In particular, the following sections are discussed hereafter: a short introduction to NMR spectroscopy and instrumentation (Sect. 3.1), the effect of order and disorder on NMR observables (Sect. 3.2), particular challenges and bottlenecks for NMR studies of IDPs (Sect. 3.3), 2D HN and CON NMR experiments: the fingerprint of an IDP (Sect. 3.4), tools for overcoming major bottlenecks of IDP NMR studies (Sect. 3.5), 13C detected experiments (Sect. 3.6), from 2D to 3D: from simple snapshots to site-resolved characterization of IDPs (Sect. 3.7), sequential NMR assignment: 3D experiments (Sect. 3.8), high-dimensional NMR experiments (nD, with n>3) (Sect. 3.9) and conclusions and perspectives (Sect. 3.10).
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Affiliation(s)
- Bernhard Brutscher
- Institut de Biologie Structurale, Université Grenoble 1, CNRS, CEA, 71 avenue des Martyrs, 38044, Grenoble Cedex 9, France.
| | - Isabella C Felli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy.
| | | | - Tomáš Hošek
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy
| | - Rainer Kümmerle
- Bruker BioSpin AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Alessandro Piai
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy
| | - Roberta Pierattelli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy.
| | - Zsófia Sólyom
- Institut de Biologie Structurale, Université Grenoble 1, CNRS, CEA, 71 avenue des Martyrs, 38044, Grenoble Cedex 9, France
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26
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Theillet FX, Binolfi A, Liokatis S, Verzini S, Selenko P. Paramagnetic relaxation enhancement to improve sensitivity of fast NMR methods: application to intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2011; 51:487-495. [PMID: 22008951 DOI: 10.1007/s10858-011-9577-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 09/28/2011] [Indexed: 05/31/2023]
Abstract
We report enhanced sensitivity NMR measurements of intrinsically disordered proteins in the presence of paramagnetic relaxation enhancement (PRE) agents such as Ni(2+)-chelated DO2A. In proton-detected (1)H-(15)N SOFAST-HMQC and carbon-detected (H-flip)(13)CO-(15)N experiments, faster longitudinal relaxation enables the usage of even shorter interscan delays. This results in higher NMR signal intensities per units of experimental time, without adverse line broadening effects. At 40 mmol·L(-1) of the PRE agent, we obtain a 1.7- to 1.9-fold larger signal to noise (S/N) for the respective 2D NMR experiments. High solvent accessibility of intrinsically disordered protein (IDP) residues renders this class of proteins particularly amenable to the outlined approach.
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Affiliation(s)
- François-Xavier Theillet
- Department of NMR-assisted Structural Biology, In-cell NMR Group, Leibniz Institute of Molecular Pharmacology (FMP), Berlin, Germany
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Gal M, Edmonds KA, Milbradt AG, Takeuchi K, Wagner G. Speeding up direct (15)N detection: hCaN 2D NMR experiment. JOURNAL OF BIOMOLECULAR NMR 2011; 51:497-504. [PMID: 22038648 PMCID: PMC3338130 DOI: 10.1007/s10858-011-9580-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 10/11/2011] [Indexed: 05/05/2023]
Abstract
Experiments detecting low gyromagnetic nuclei have recently been proposed to utilize the relatively slow relaxation properties of these nuclei in comparison to (1)H. Here we present a new type of (15)N direct-detection experiment. Like the previously proposed CaN experiment (Takeuchi et al. in J Biomol NMR 47:271-282, 2010), the hCaN experiment described here sequentially connects amide (15)N resonances, but utilizes the initial high polarization and the faster recovery of the (1)H nucleus to shorten the recycling delay. This allows recording 2D (15)N-detected NMR experiments on proteins within a few hours, while still obtaining superior resolution for (13)C and (15)N, establishing sequential assignments through prolines, and at conditions where amide protons exchange rapidly. The experiments are demonstrated on various biomolecules, including the small globular protein GB1, the 22 kDa HEAT2 domain of eIF4G, and an unstructured polypeptide fragment of NFAT1, which contains many SerPro sequence repeats.
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Affiliation(s)
- Maayan Gal
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Katherine A. Edmonds
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Alexander G. Milbradt
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Koh Takeuchi
- Biomedicinal Information Research Center, National institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Gerhard Wagner
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
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Barb AW, Freedberg DI, Battistel MD, Prestegard JH. NMR detection and characterization of sialylated glycoproteins and cell surface polysaccharides. JOURNAL OF BIOMOLECULAR NMR 2011; 51:163-71. [PMID: 21947924 PMCID: PMC3199143 DOI: 10.1007/s10858-011-9550-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 06/25/2011] [Indexed: 05/03/2023]
Abstract
Few solution NMR pulse sequences exist that are explicitly designed to characterize carbohydrates (glycans). This is despite the essential role carbohydrate motifs play in cell-cell communication, microbial pathogenesis, autoimmune disease progression and cancer metastasis, and despite that fact that glycans, often shed to extra-cellular fluids, can be diagnostic of disease. Here we present a suite of two dimensional coherence experiments to measure three different correlations (H3-C2, H3-C1, and C1-C2) on sialic acids, a group of nine-carbon carbohydrates found on eukaryotic cell surfaces that often play a key role in disease processes. The chemical shifts of the H3, C2, and C1 nuclei of sialic acids are sensitive to carbohydrate linkage, linkage conformation, and ionization state of the C1 carboxylate. The experiments reported include rigorous filter elements to enable detection and characterization of isotopically labeled sialic acids with high sensitivity in living cells and crude isolates with minimal interference from unwanted signals arising from the ~1% (13)C-natural abundance of cellular metabolites. Application is illustrated with detection of sialic acids on living cells, in unpurified mixtures, and at the terminus of the N-glycan on the 55 kDa immunoglobulin G Fc.
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Affiliation(s)
- Adam W. Barb
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602
| | - Darón I. Freedberg
- Laboratory of Bacterial Polysaccharides, Building 29, Room 115 Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, HFM-419, Rockville, MD 20852
| | - Marcos D. Battistel
- Laboratory of Bacterial Polysaccharides, Building 29, Room 115 Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, HFM-419, Rockville, MD 20852
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