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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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Querci L, Grifagni D, Trindade IB, Silva JM, Louro RO, Cantini F, Piccioli M. Paramagnetic NMR to study iron sulfur proteins: 13C detected experiments illuminate the vicinity of the metal center. JOURNAL OF BIOMOLECULAR NMR 2023; 77:247-259. [PMID: 37853207 PMCID: PMC10687126 DOI: 10.1007/s10858-023-00425-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023]
Abstract
The robustness of NMR coherence transfer in proximity of a paramagnetic center depends on the relaxation properties of the nuclei involved. In the case of Iron-Sulfur Proteins, different pulse schemes or different parameter sets often provide complementary results. Tailored versions of HCACO and CACO experiments significantly increase the number of observed Cα/C' connectivities in highly paramagnetic systems, by recovering many resonances that were lost due to paramagnetic relaxation. Optimized 13C direct detected experiments can significantly extend the available assignments, improving the overall knowledge of these systems. The different relaxation properties of Cα and C' nuclei are exploited in CACO vs COCA experiments and the complementarity of the two experiments is used to obtain structural information. The two [Fe2S2]+ clusters containing NEET protein CISD3 and the one [Fe4S4]2+ cluster containing HiPIP protein PioC have been taken as model systems. We show that tailored experiments contribute to decrease the blind sphere around the cluster, to extend resonance assignment of cluster bound cysteine residues and to retrieve details on the topology of the iron-bound ligand residues.
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Affiliation(s)
- Leonardo Querci
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Deborah Grifagni
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Inês B Trindade
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Av. da República (EAN), 2780-157, Oeiras, Portugal
- Division of Biology and Biological Engineering, California Institute of Technology, CA 91125, Pasadena, USA
| | - José Malanho Silva
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Av. da República (EAN), 2780-157, Oeiras, Portugal
| | - Francesca Cantini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Mario Piccioli
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
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3
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Fraser OA, Dewing SM, Usher ET, George C, Showalter SA. A direct nuclear magnetic resonance method to investigate lysine acetylation of intrinsically disordered proteins. Front Mol Biosci 2023; 9:1074743. [PMID: 36685286 PMCID: PMC9853081 DOI: 10.3389/fmolb.2022.1074743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
Intrinsically disordered proteins are frequent targets for functional regulation through post-translational modification due to their high accessibility to modifying enzymes and the strong influence of changes in primary structure on their chemical properties. While lysine Nε-acetylation was first observed as a common modification of histone tails, proteomic data suggest that lysine acetylation is ubiquitous among both nuclear and cytosolic proteins. However, compared with our biophysical understanding of the other common post-translational modifications, mechanistic studies to document how lysine Nε-acetyl marks are placed, utilized to transduce signals, and eliminated when signals need to be turned off, have not kept pace with proteomic discoveries. Herein we report a nuclear magnetic resonance method to monitor Nε-lysine acetylation through enzymatic installation of a13C-acetyl probe on a protein substrate, followed by detection through 13C direct-detect spectroscopy. We demonstrate the ease and utility of this method using histone H3 tail acetylation as a model. The clearest advantage to this method is that it requires no exogenous tags that would otherwise add steric bulk, change the chemical properties of the modified lysine, or generally interfere with downstream biochemical processes. The non-perturbing nature of this tagging method is beneficial for application in any system where changes to local structure and chemical properties beyond those imparted by lysine modification are unacceptable, including intrinsically disordered proteins, bromodomain containing protein complexes, and lysine deacetylase enzyme assays.
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Affiliation(s)
- Olivia A. Fraser
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Sophia M. Dewing
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Emery T. Usher
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Christy George
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Scott A. Showalter
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
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4
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Dal Colle MCS, Fittolani G, Delbianco M. Synthetic Approaches to Break the Chemical Shift Degeneracy of Glycans. Chembiochem 2022; 23:e202200416. [PMID: 36005282 PMCID: PMC10087674 DOI: 10.1002/cbic.202200416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/24/2022] [Indexed: 01/25/2023]
Abstract
NMR spectroscopy is the leading technique for determining glycans' three-dimensional structure and dynamic in solution as well as a fundamental tool to study protein-glycan interactions. To overcome the severe chemical shift degeneracy of these compounds, synthetic probes carrying NMR-active nuclei (e. g., 13 C or 19 F) or lanthanide tags have been proposed. These elegant strategies permitted to simplify the complex NMR analysis of unlabeled analogues, shining light on glycans' conformational aspects and interaction with proteins. Here, we highlight some key achievements in the synthesis of specifically labeled glycan probes and their contribution towards the fundamental understanding of glycans.
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Affiliation(s)
- Marlene C S Dal Colle
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Giulio Fittolani
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
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5
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Haller JD, Bodor A, Luy B. Pure shift amide detection in conventional and TROSY-type experiments of 13C, 15N-labeled proteins. JOURNAL OF BIOMOLECULAR NMR 2022; 76:213-221. [PMID: 36399207 PMCID: PMC9712348 DOI: 10.1007/s10858-022-00406-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Large coupling networks in uniformly 13C,15N-labeled biomolecules induce broad multiplets that even in flexible proteins are frequently not recognized as such. The reason is that given multiplets typically consist of a large number of individual resonances that result in a single broad line, in which individual components are no longer resolved. We here introduce a real-time pure shift acquisition scheme for the detection of amide protons which is based on 13C-BIRDr,X. As a result the full homo- and heteronuclear coupling network can be suppressed at low power leading to real singlets at substantially improved resolution and uncompromised sensitivity. The method is tested on a small globular and an intrinsically disordered protein (IDP) where the average spectral resolution is increased by a factor of ~ 2 and higher. Equally important, the approach works without saturation of water magnetization for solvent suppression and exchanging amide protons are not affected by saturation transfer.
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Affiliation(s)
- Jens D. Haller
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Hermann-Von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Andrea Bodor
- Institute of Chemistry, Analytical and BioNMR Laboratory, ELTE –Eötvös Loránd University, Pázmány Péter Sétány 1/A, 1117 Budapest, Hungary
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Hermann-Von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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6
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Lenard AJ, Mulder FAA, Madl T. Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:113-139. [PMID: 36496256 DOI: 10.1016/j.pnmrs.2022.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on solvent accessibility of NMR-active nuclei. Addition of soluble paramagnetic probes to the solution of a biomolecule leads to paramagnetic relaxation enhancement in a concentration-dependent manner. Here we review recent progress in the sPRE-based characterization of structural and dynamic properties of biomolecules and their complexes, and aim to deliver a comprehensive illustration of a growing number of applications of the method to various biological systems. We discuss the physical principles of sPRE measurements and provide an overview of available co-solute paramagnetic probes. We then explore how sPRE, in combination with complementary biophysical techniques, can further advance biomolecular structure determination, identification of interaction surfaces within protein complexes, and probing of conformational changes and low-population transient states, as well as deliver insights into weak, nonspecific, and transient interactions between proteins and co-solutes. In addition, we present examples of how the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and discuss the prospects of applying sPRE to NMR metabolomics, drug discovery, and the study of intrinsically disordered proteins.
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Affiliation(s)
- Aneta J Lenard
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria.
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center and Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark; Institute of Biochemistry, Johannes Kepler Universität Linz, 4040 Linz, Austria.
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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7
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Beniamino Y, Cenni V, Piccioli M, Ciurli S, Zambelli B. The Ni(II)-Binding Activity of the Intrinsically Disordered Region of Human NDRG1, a Protein Involved in Cancer Development. Biomolecules 2022; 12:biom12091272. [PMID: 36139110 PMCID: PMC9496542 DOI: 10.3390/biom12091272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Nickel exposure is associated with tumors of the respiratory tract such as lung and nasal cancers, acting through still-uncharacterized mechanisms. Understanding the molecular basis of nickel-induced carcinogenesis requires unraveling the mode and the effects of Ni(II) binding to its intracellular targets. A possible Ni(II)-binding protein and a potential focus for cancer treatment is hNDRG1, a protein induced by Ni(II) through the hypoxia response pathway, whose expression correlates with higher cancer aggressiveness and resistance to chemotherapy in lung tissue. The protein sequence contains a unique C-terminal sequence of 83 residues (hNDRG1*C), featuring a three-times-repeated decapeptide, involved in metal binding, lipid interaction and post-translational phosphorylation. In the present work, the biochemical and biophysical characterization of unmodified hNDRG1*C was performed. Bioinformatic analysis assigned it to the family of the intrinsically disordered regions and the absence of secondary and tertiary structure was experimentally proven by circular dichroism and NMR. Isothermal titration calorimetry revealed the occurrence of a Ni(II)-binding event with micromolar affinity. Detailed information on the Ni(II)-binding site and on the residues involved was obtained in an extensive NMR study, revealing an octahedral paramagnetic metal coordination that does not cause any major change of the protein backbone, which is coherent with CD analysis. hNDRG1*C was found in a monomeric form by light-scattering experiments, while the full-length hNDRG1 monomer was found in equilibrium between the dimer and tetramer, both in solution and in human cell lines. The results are the first essential step for understanding the cellular function of hNDRG1*C at the molecular level, with potential future applications to clarify its role and the role of Ni(II) in cancer development.
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Affiliation(s)
- Ylenia Beniamino
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, 40127 Bologna, Italy
| | - Vittoria Cenni
- CNR Institute of Molecular Genetics “Luigi-Luca Cavalli-Sforza” Unit of Bologna, Via di Barbiano 1/10, 40136 Bologna, Italy
| | - Mario Piccioli
- Department of Chemistry, Center for Magnetic Resonance, University of Florence, 50121 Florence, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, 40127 Bologna, Italy
- Correspondence: (S.C.); (B.Z.); Tel.: +38-051-2096204 (S.C.); +38-051-2096233 (B.Z.)
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, 40127 Bologna, Italy
- Correspondence: (S.C.); (B.Z.); Tel.: +38-051-2096204 (S.C.); +38-051-2096233 (B.Z.)
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8
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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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9
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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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10
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Kurzawa-Akanbi M, Tammireddy S, Fabrik I, Gliaudelytė L, Doherty MK, Heap R, Matečko-Burmann I, Burmann BM, Trost M, Lucocq JM, Gherman AV, Fairfoul G, Singh P, Burté F, Green A, McKeith IG, Härtlova A, Whitfield PD, Morris CM. Altered ceramide metabolism is a feature in the extracellular vesicle-mediated spread of alpha-synuclein in Lewy body disorders. Acta Neuropathol 2021; 142:961-984. [PMID: 34514546 PMCID: PMC8568874 DOI: 10.1007/s00401-021-02367-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023]
Abstract
Mutations in glucocerebrosidase (GBA) are the most prevalent genetic risk factor for Lewy body disorders (LBD)-collectively Parkinson's disease, Parkinson's disease dementia and dementia with Lewy bodies. Despite this genetic association, it remains unclear how GBA mutations increase susceptibility to develop LBD. We investigated relationships between LBD-specific glucocerebrosidase deficits, GBA-related pathways, and α-synuclein levels in brain tissue from LBD and controls, with and without GBA mutations. We show that LBD is characterised by altered sphingolipid metabolism with prominent elevation of ceramide species, regardless of GBA mutations. Since extracellular vesicles (EV) could be involved in LBD pathogenesis by spreading disease-linked lipids and proteins, we investigated EV derived from post-mortem cerebrospinal fluid (CSF) and brain tissue from GBA mutation carriers and non-carriers. EV purified from LBD CSF and frontal cortex were heavily loaded with ceramides and neurodegeneration-linked proteins including alpha-synuclein and tau. Our in vitro studies demonstrate that LBD EV constitute a "pathological package" capable of inducing aggregation of wild-type alpha-synuclein, mediated through a combination of alpha-synuclein-ceramide interaction and the presence of pathological forms of alpha-synuclein. Together, our findings indicate that abnormalities in ceramide metabolism are a feature of LBD, constituting a promising source of biomarkers, and that GBA mutations likely accelerate the pathological process occurring in sporadic LBD through endolysosomal deficiency.
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11
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Karunanithy G, Mackenzie HW, Hansen DF. Virtual Homonuclear Decoupling in Direct Detection Nuclear Magnetic Resonance Experiments Using Deep Neural Networks. J Am Chem Soc 2021; 143:16935-16942. [PMID: 34633815 DOI: 10.1021/jacs.1c04010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nuclear magnetic resonance (NMR) experiments are frequently complicated by the presence of homonuclear scalar couplings. For the growing body of biomolecular 13C-detected NMR methods, one-bond 13C-13C couplings significantly reduce sensitivity and resolution. The solution to this problem has typically been to perform virtual decoupling by recording multiple spectra and taking linear combinations. Here, we propose an alternative method of virtual decoupling using deep neural networks, which only requires a single spectrum and gives a significant boost in resolution while reducing the minimum effective phase cycles of the experiments by at least a factor of 2. We successfully apply this methodology to virtually decouple in-phase CON (13CO-15N) protein NMR spectra, 13C-13C correlation spectra of protein side chains, and 13Cα-detected protein 13Cα-13CO spectra where two large homonuclear couplings are present. The deep neural network approach effectively decouples spectra with a high degree of flexibility, including in cases where existing methods fail, and facilitates the use of simpler pulse sequences.
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Affiliation(s)
- Gogulan Karunanithy
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom WC1E 6BT
| | - Harold W Mackenzie
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom WC1E 6BT
| | - D Flemming Hansen
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom WC1E 6BT
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12
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Grasso EM, Majumdar A, Wrabl JO, Frueh DP, Hilser VJ. Conserved allosteric ensembles in disordered proteins using TROSY/anti-TROSY R 2-filtered spectroscopy. Biophys J 2021; 120:2498-2510. [PMID: 33901472 PMCID: PMC8390865 DOI: 10.1016/j.bpj.2021.04.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/11/2021] [Accepted: 04/16/2021] [Indexed: 11/22/2022] Open
Abstract
Defining the role of intrinsic disorder in proteins in the myriad of biological processes with which it is involved represents a significant goal in modern biophysics. Toward this end, NMR is uniquely suited for molecular studies of dynamic and disordered regions, but studying these regions in concert with their more structured domains and binding partners presents spectroscopic challenges. Here, we investigate the interactions between the structured and disordered regions of the human glucocorticoid receptor (GR). To do this, we developed an NMR strategy that relies on a novel relaxation filter for the simultaneous study of structured and unstructured regions. Using this approach, we conducted a comparative analysis of three translational isoforms of GR containing a folded DNA-binding domain (DBD) and two disordered regions that flank the DBD, one of which varies in size in the different isoforms. Notably, we were able to assign resonances that had previously been inaccessible because of the spectral complexity of the translational isoforms, which in turn allowed us to 1) identify a region of the structured DBD that undergoes significant changes in the local chemical environment in the presence of the disordered region and 2) determine differences in the conformational ensembles of the disordered regions of the translational isoforms. Furthermore, an ensemble-based thermodynamic analysis of the isoforms reveals conserved patterns of stability within the N-terminal domain of GR that persist despite low sequence conservation. These studies provide an avenue for further investigations of the mechanistic underpinnings of the functional relevance of the translational isoforms of GR while also providing a general NMR strategy for studying systems containing both structured and disordered regions.
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Affiliation(s)
- Emily M Grasso
- Department of Biology, Johns Hopkins University, Baltimore, Maryland; T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Ananya Majumdar
- The Biomolecular NMR Center, Johns Hopkins University, Baltimore, Maryland
| | - James O Wrabl
- Department of Biology, Johns Hopkins University, Baltimore, Maryland
| | - Dominique P Frueh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, Baltimore, Maryland; T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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13
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Furuita K, Sugiki T, Takamuku M, Hattori Y, So M, Kawata Y, Ikegami T, Fujiwara T, Kojima C. Sensitivity enhancement by sequential data acquisition for 13C-direct detection NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 322:106878. [PMID: 33285399 DOI: 10.1016/j.jmr.2020.106878] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
13C-direct detection NMR has several advantages compared to proton detection, including a tendency to relax slower and wider chemical shift range. However, the sensitivity of 13C-direct detection is much lower than that of proton detection because of its lower gyromagnetic ratio. In addition, a virtual decoupling procedure is often performed to remove peak splitting in the 13C-direct detection axis, which further reduces the sensitivity to 1/√2. In this study, to enhance the sensitivity of 13C-direct detection experiments, we developed a HCACO-type new pulse sequence in which anti-phase (AP) and in-phase (IP) signals are acquired sequentially in a single scan. The developed experiment was tested on an amino acid (valine) and two proteins (streptococcal protein G B1 domain (GB1) and α-synuclein). The AP and IP spectra were successfully obtained in all cases. Using these spectra, IPAP virtual decoupling was performed, and peak splitting was successfully removed. The sensitivity of the experiment was increased by 1.43, 1.26 and 1.26 times for valine, GB1 and α-synuclein, respectively, compared to the conventional HCACO experiment. In addition, we developed another HCACO-type pulse sequence, where AP and IP signals are simultaneously acquired in a single FID. The sensitivity of the experiment was increased by 1.40 and 1.35 times for valine and GB1, respectively. These methods are potentially applicable to other 13C-direct detection experiments that measure one-bond correlations and will further extend the utility of the 13C-direct detection method, especially for structural analyses of intrinsically disordered proteins.
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Affiliation(s)
- Kyoko Furuita
- Institute for Protein Research, Osaka University, Japan.
| | | | - Mika Takamuku
- Institute for Protein Research, Osaka University, Japan
| | - Yoshikazu Hattori
- Institute for Protein Research, Osaka University, Japan; Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Japan
| | - Masatomo So
- Institute for Protein Research, Osaka University, Japan
| | - Yasushi Kawata
- Graduate School of Engineering, Tottori University, Japan
| | - Takahisa Ikegami
- Institute for Protein Research, Osaka University, Japan; Graduate School of Medical Life Science, Yokohama City University, Japan
| | | | - Chojiro Kojima
- Institute for Protein Research, Osaka University, Japan; Graduate School of Engineering Science, Yokohama National University, Japan.
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14
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Karjalainen M, Tossavainen H, Hellman M, Permi P. HACANCOi: a new H α-detected experiment for backbone resonance assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2020; 74:741-752. [PMID: 33118136 PMCID: PMC7701164 DOI: 10.1007/s10858-020-00347-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Unidirectional coherence transfer is highly efficient in intrinsically disordered proteins (IDPs). Their elevated ps-ns timescale dynamics ensures long transverse (T2) relaxation times allowing sophisticated coherence transfer pathway selection in comparison to folded proteins. 1Hα-detection ensures non-susceptibility to chemical exchange with the solvent and enables chemical shift assignment of consecutive proline residues, typically abundant in IDPs. However, many IDPs undergo a disorder-to-order transition upon interaction with their target protein, which leads to the loss of the favorable relaxation properties. Long coherence transfer routes now result in prohibitively large decrease in sensitivity. We introduce a novel 4D 1Hα-detected experiment HACANCOi, together with its 3D implementation, which warrant high sensitivity for the assignment of proline-rich regions in IDPs in complex with a globular protein. The experiment correlates 1Hαi, 13Cαi, 15Ni and [Formula: see text] spins by transferring the magnetization concomitantly from 13Cαi to 15Ni and [Formula: see text]. The B1 domain of protein G (GB1), and the enteropathogenic E. coli EspF in complex with human SNX9 SH3, serve as model systems to demonstrate the attainable sensitivity and successful sequential assignment.
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Affiliation(s)
- Mikael Karjalainen
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Helena Tossavainen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Maarit Hellman
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Perttu Permi
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.
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15
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Alik A, Bouguechtouli C, Julien M, Bermel W, Ghouil R, Zinn‐Justin S, Theillet F. Sensitivity‐Enhanced
13
C‐NMR Spectroscopy for Monitoring Multisite Phosphorylation at Physiological Temperature and pH. Angew Chem Int Ed Engl 2020; 59:10411-10415. [DOI: 10.1002/anie.202002288] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/12/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Ania Alik
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Chafiaa Bouguechtouli
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Manon Julien
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Wolfgang Bermel
- Bruker BioSpin GmbH Silberstreifen 76287 Rheinstetten Germany
| | - Rania Ghouil
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Sophie Zinn‐Justin
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Francois‐Xavier Theillet
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
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16
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Alik A, Bouguechtouli C, Julien M, Bermel W, Ghouil R, Zinn‐Justin S, Theillet F. Sensitivity‐Enhanced
13
C‐NMR Spectroscopy for Monitoring Multisite Phosphorylation at Physiological Temperature and pH. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002288] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ania Alik
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Chafiaa Bouguechtouli
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Manon Julien
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Wolfgang Bermel
- Bruker BioSpin GmbH Silberstreifen 76287 Rheinstetten Germany
| | - Rania Ghouil
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Sophie Zinn‐Justin
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Francois‐Xavier Theillet
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
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17
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Tossavainen H, Salovaara S, Hellman M, Ihalin R, Permi P. Dispersion from C α or N H: 4D experiments for backbone resonance assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2020; 74:147-159. [PMID: 31932991 PMCID: PMC7080685 DOI: 10.1007/s10858-020-00299-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/02/2020] [Indexed: 05/07/2023]
Abstract
Resonance assignment of intrinsically disordered proteins is remarkably challenging due to scant chemical shift dispersion arising from conformational heterogeneity. The challenge is even greater if repeating segments are present in the amino acid sequence. To forward unambiguous resonance assignment of intrinsically disordered proteins, we present iHACANCO, HACACON and (HACA)CONCAHA, three Hα-detected 4D experiments with Cα as an additional dimension. In addition, we present (HACA)CON(CA)NH and (HACA)N(CA)CONH, new 4D Hα-start, HN-detect experiments which have two NH dimensions to enhance peak dispersion in a sequential walk through C', NH and HN, and provide more accurate NH/HN chemical shifts than those that can be obtained from a crowded 1H, 15N-HSQC spectrum. Application of these 4D experiments is demonstrated using BilRI (165 aa), an outer-membrane intrinsically disordered protein from the opportunistic oral pathogen Aggregatibacter actinomycetemcomitans. BilRI amino acid sequence encompasses three very similar repeats with a 13-residue identical stretch in two of them.
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Affiliation(s)
- Helena Tossavainen
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Santeri Salovaara
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Maarit Hellman
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Riikka Ihalin
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Perttu Permi
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.
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18
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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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19
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Sciolino N, Burz DS, Shekhtman A. In-Cell NMR Spectroscopy of Intrinsically Disordered Proteins. Proteomics 2019; 19:e1800055. [PMID: 30489014 DOI: 10.1002/pmic.201800055] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/29/2018] [Indexed: 01/14/2023]
Abstract
This review summarizes the results of in-cell Nuclear Magnetic Resonance, NMR, spectroscopic investigations of the eukaryotic and prokaryotic intrinsically disordered proteins, IDPs: α-synuclein, prokaryotic ubiquitin-like protein, Pup, tubulin-related neuronal protein, Tau, phenylalanyl-glycyl-repeat-rich nucleoporins, FG Nups, and the negative regulator of flagellin synthesis, FlgM. The results show that the cellular behavior of IDPs may differ significantly from that observed in the test tube.
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Affiliation(s)
- Nicholas Sciolino
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
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20
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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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21
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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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22
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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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23
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Jansen S, Melková K, Trošanová Z, Hanáková K, Zachrdla M, Nováček J, Župa E, Zdráhal Z, Hritz J, Žídek L. Quantitative mapping of microtubule-associated protein 2c (MAP2c) phosphorylation and regulatory protein 14-3-3ζ-binding sites reveals key differences between MAP2c and its homolog Tau. J Biol Chem 2017; 292:6715-6727. [PMID: 28258221 DOI: 10.1074/jbc.m116.771097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/01/2017] [Indexed: 11/06/2022] Open
Abstract
Microtubule-associated protein 2c (MAP2c) is involved in neuronal development and is less characterized than its homolog Tau, which has various roles in neurodegeneration. Using NMR methods providing single-residue resolution and quantitative comparison, we investigated molecular interactions important for the regulatory roles of MAP2c in microtubule dynamics. We found that MAP2c and Tau significantly differ in the position and kinetics of sites that are phosphorylated by cAMP-dependent protein kinase (PKA), even in highly homologous regions. We determined the binding sites of unphosphorylated and phosphorylated MAP2c responsible for interactions with the regulatory protein 14-3-3ζ. Differences in phosphorylation and in charge distribution between MAP2c and Tau suggested that both MAP2c and Tau respond to the same signal (phosphorylation by PKA) but have different downstream effects, indicating a signaling branch point for controlling microtubule stability. Although the interactions of phosphorylated Tau with 14-3-3ζ are supposed to be a major factor in microtubule destabilization, the binding of 14-3-3ζ to MAP2c enhanced by PKA-mediated phosphorylation is likely to influence microtubule-MAP2c binding much less, in agreement with the results of our tubulin co-sedimentation measurements. The specific location of the major MAP2c phosphorylation site in a region homologous to the muscarinic receptor-binding site of Tau suggests that MAP2c also may regulate processes other than microtubule dynamics.
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Affiliation(s)
- Séverine Jansen
- From the National Centre for Biomolecular Research, Faculty of Science, and.,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Kateřina Melková
- From the National Centre for Biomolecular Research, Faculty of Science, and.,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Zuzana Trošanová
- From the National Centre for Biomolecular Research, Faculty of Science, and.,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Kateřina Hanáková
- the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Milan Zachrdla
- From the National Centre for Biomolecular Research, Faculty of Science, and.,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jiří Nováček
- the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Erik Župa
- From the National Centre for Biomolecular Research, Faculty of Science, and.,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Zbyněk Zdráhal
- the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jozef Hritz
- From the National Centre for Biomolecular Research, Faculty of Science, and .,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Lukáš Žídek
- From the National Centre for Biomolecular Research, Faculty of Science, and .,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
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24
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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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25
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Żerko S, Byrski P, Włodarczyk-Pruszyński P, Górka M, Ledolter K, Masliah E, Konrat R, Koźmiński W. Five and four dimensional experiments for robust backbone resonance assignment of large intrinsically disordered proteins: application to Tau3x protein. JOURNAL OF BIOMOLECULAR NMR 2016; 65:193-203. [PMID: 27430223 PMCID: PMC4983291 DOI: 10.1007/s10858-016-0048-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/09/2016] [Indexed: 05/04/2023]
Abstract
New experiments dedicated for large IDPs backbone resonance assignment are presented. The most distinctive feature of all described techniques is the employment of MOCCA-XY16 mixing sequences to obtain effective magnetization transfers between carbonyl carbon backbone nuclei. The proposed 4 and 5 dimensional experiments provide a high dispersion of obtained signals making them suitable for use in the case of large IDPs (application to 354 a. a. residues of Tau protein 3x isoform is presented) as well as provide both forward and backward connectivities. What is more, connecting short chains interrupted with proline residues is also possible. All the experiments employ non-uniform sampling.
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Affiliation(s)
- Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093, Warsaw, Poland
| | - Piotr Byrski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093, Warsaw, Poland
| | | | - Michał Górka
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093, Warsaw, Poland
- Section of Biophysics, Faculty of Physics, University of Warsaw, 02093, Warsaw, Poland
| | - Karin Ledolter
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Eliezer Masliah
- Departments of Neuroscience and Pathology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Robert Konrat
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093, Warsaw, Poland.
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Kakita VMR, Hosur RV. Non-Uniform-Sampling Ultrahigh Resolution TOCSY NMR: Analysis of Complex Mixtures at Microgram Levels. Chemphyschem 2016; 17:2304-8. [DOI: 10.1002/cphc.201600255] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Veera M. R. Kakita
- UM-DAE Centre for Excellence in Basic Sciences; Mumbai University Campus, Kalina, Santa Cruz Mumbai 400 098 India
| | - Ramakrishna V. Hosur
- UM-DAE Centre for Excellence in Basic Sciences; Mumbai University Campus, Kalina, Santa Cruz Mumbai 400 098 India
- Department of Chemical Sciences; Tata Institute of Fundamental Research (TIFR); 1-Homi Bhabha Road, Colaba Mumbai 400 005 India
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27
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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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28
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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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29
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Piai A, Gonnelli L, Felli IC, Pierattelli R, Kazimierczuk K, Grudziąż K, Koźmiński W, Zawadzka-Kazimierczuk A. Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2016; 64:239-53. [PMID: 26891900 PMCID: PMC4824835 DOI: 10.1007/s10858-016-0024-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/11/2016] [Indexed: 05/07/2023]
Abstract
Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical shifts dispersion and generally low resolution. For these systems, sequence specific assignment is highly time-consuming, so the prospect of using automatic strategies for their assignment is very attractive. In this article we present a new version of the automatic assignment program TSAR dedicated to intrinsically disordered proteins. In particular, we demonstrate how the automatic procedure can be improved by incorporating methods for amino acid recognition and information on chemical shifts in selected amino acids. The approach was tested in silico on 16 disordered proteins and experimentally on α-synuclein, with remarkably good results.
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Affiliation(s)
- Alessandro Piai
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | - Leonardo Gonnelli
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | - Isabella C Felli
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | - Roberta Pierattelli
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | | | - Katarzyna Grudziąż
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Anna Zawadzka-Kazimierczuk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.
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30
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Zhang Z, Smith PES, Frydman L. Reducing acquisition times in multidimensional NMR with a time-optimized Fourier encoding algorithm. J Chem Phys 2015; 141:194201. [PMID: 25416883 DOI: 10.1063/1.4901561] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Speeding up the acquisition of multidimensional nuclear magnetic resonance (NMR) spectra is an important topic in contemporary NMR, with central roles in high-throughput investigations and analyses of marginally stable samples. A variety of fast NMR techniques have been developed, including methods based on non-uniform sampling and Hadamard encoding, that overcome the long sampling times inherent to schemes based on fast-Fourier-transform (FFT) methods. Here, we explore the potential of an alternative fast acquisition method that leverages a priori knowledge, to tailor polychromatic pulses and customized time delays for an efficient Fourier encoding of the indirect domain of an NMR experiment. By porting the encoding of the indirect-domain to the excitation process, this strategy avoids potential artifacts associated with non-uniform sampling schemes and uses a minimum number of scans equal to the number of resonances present in the indirect dimension. An added convenience is afforded by the fact that a usual 2D FFT can be used to process the generated data. Acquisitions of 2D heteronuclear correlation NMR spectra on quinine and on the anti-inflammatory drug isobutyl propionic phenolic acid illustrate the new method's performance. This method can be readily automated to deal with complex samples such as those occurring in metabolomics, in in-cell as well as in in vivo NMR applications, where speed and temporal stability are often primary concerns.
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Affiliation(s)
- Zhiyong Zhang
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Pieter E S Smith
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lucio Frydman
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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31
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Żerko S, Koźmiński W. Six- and seven-dimensional experiments by combination of sparse random sampling and projection spectroscopy dedicated for backbone resonance assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2015; 63:283-90. [PMID: 26403428 PMCID: PMC4642589 DOI: 10.1007/s10858-015-9987-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/16/2015] [Indexed: 05/04/2023]
Abstract
Two novel six- and seven-dimensional NMR experiments are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in four indirectly detected dimensions and synchronous sampling in the additional dimensions using projection spectroscopy principle. The resulted data sets could be processed as five-dimensional data using existing software. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel experiments were successfully tested using 1 mM sample of α-synuclein on 600 and 800 MHz NMR spectrometers equipped with standard room temperature probes. The experiments allowed backbone assignment from a 1-day acquisition.
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Affiliation(s)
- Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02089, Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02089, Warsaw, Poland.
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32
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Miotto MC, Valiente-Gabioud AA, Rossetti G, Zweckstetter M, Carloni P, Selenko P, Griesinger C, Binolfi A, Fernández CO. Copper Binding to the N-Terminally Acetylated, Naturally Occurring Form of Alpha-Synuclein Induces Local Helical Folding. J Am Chem Soc 2015; 137:6444-7. [DOI: 10.1021/jacs.5b01911] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Giulia Rossetti
- Computational
Biophysics, German Research School for Simulation Sciences and Computational
Biomedicine, Institute for Advanced Simulations IAS-5, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Markus Zweckstetter
- Department
of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen, 37077 Göttingen, Germany
- Center for
the Molecular Physiology of the Brain, University Medical Center, 37077 Göttingen, Germany
| | - Paolo Carloni
- Computational
Biophysics, German Research School for Simulation Sciences and Computational
Biomedicine, Institute for Advanced Simulations IAS-5, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Philipp Selenko
- Department
of NMR-assisted Structural Biology, In-cell NMR, Leibniz Institute of Molecular Pharmacology, Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Christian Griesinger
- Department
of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Andres Binolfi
- Department
of NMR-assisted Structural Biology, In-cell NMR, Leibniz Institute of Molecular Pharmacology, Robert-Roessle-Strasse 10, 13125 Berlin, Germany
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33
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Hošek T, Gil-Caballero S, Pierattelli R, Brutscher B, Felli IC. Longitudinal relaxation properties of (1)H(N) and (1)H(α) determined by direct-detected (13)C NMR experiments to study intrinsically disordered proteins (IDPs). JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 254:19-26. [PMID: 25771525 DOI: 10.1016/j.jmr.2015.01.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 06/04/2023]
Abstract
Intrinsically disordered proteins (IDPs) are functional proteins containing large fragments characterized by high local mobility. Bioinformatic studies have suggested that a significant fraction (more than 30%) of eukaryotic proteins has disordered regions of more than 50 amino acids in length. Hence, NMR methods for the characterization of local compactness and solvent accessibility in such highly disordered proteins are of high importance. Among the available approaches, the HET-SOFAST/BEST experiments (Schanda et al., 2006, Rennella et al., 2014) provide semi-quantitative information by monitoring longitudinal (1)H relaxation of amide protons under different initial conditions. However, when approaching physiological sample conditions, the potential of these amide (1)H detected experiments is reduced due to rapid amide proton solvent exchange. (13)C direct detection methods therefore provide a valuable alternative thanks to a higher chemical shift dispersion and their intrinsic insensitivity toward solvent exchange. Here we present two sets of (13)C-detected experiments, which indirectly measure (1)H(N) and (1)H(α) inversion recovery profiles. The experiments consist of an initial spin inversion-recovery block optimized for selective manipulation of different types of proton spins followed by a CON read-out scheme. The proposed experiments were tested on human α-synuclein and ubiquitin, two representative examples of unfolded and folded proteins.
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Affiliation(s)
- Tomáš Hošek
- 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
| | - 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, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
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34
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Solution NMR Structure Determination of Polytopic α-Helical Membrane Proteins: A Guide to Spin Label Paramagnetic Relaxation Enhancement Restraints. Methods Enzymol 2015; 557:329-48. [PMID: 25950972 DOI: 10.1016/bs.mie.2014.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Solution nuclear magnetic resonance structures of polytopic α-helical membrane proteins require additional restraints beyond the traditional Nuclear Overhauser Effect (NOE) restraints. Several methods have been developed and this review focuses on paramagnetic relaxation enhancement (PRE). Important aspects of spin labeling, PRE measurements, structure calculations, and structural quality are discussed.
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35
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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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36
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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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37
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Hsu STD. NMR assignments of PI3-SH3 domain aided by protonless NMR spectroscopy. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:291-295. [PMID: 23832674 DOI: 10.1007/s12104-013-9503-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 06/29/2013] [Indexed: 06/02/2023]
Abstract
We report here the near complete assignments of native bovine PI3-SH3 domain, which has been a model system for protein folding, misfolding and amyloid fibril formation. The use of (13)C-detected protonless NMR spectroscopy is instrumental in assigning the spin system of the proline residue at the C-terminus in addition to the missing resonances in proton-based NMR spectra due to rapid solvent exchange. It also helps assign the resonances of all three proline amine nitrogen nuclei, which are underrepresented in the database. Comparison of the backbone (13)C resonances of PI3-SH3 in its native and amyloid fibril states shows that the aggregation of PI3-SH3 is accompanied by major conformational rearrangements.
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Affiliation(s)
- Shang-Te Danny Hsu
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK,
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38
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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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39
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Alvarado LJ, LeBlanc RM, Longhini AP, Keane SC, Jain N, Yildiz ZF, Tolbert BS, D'Souza VM, Summers MF, Kreutz C, Dayie TK. Regio-selective chemical-enzymatic synthesis of pyrimidine nucleotides facilitates RNA structure and dynamics studies. Chembiochem 2014; 15:1573-7. [PMID: 24954297 DOI: 10.1002/cbic.201402130] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Indexed: 12/16/2022]
Abstract
Isotope labeling has revolutionized NMR studies of small nucleic acids, but to extend this technology to larger RNAs, site-specific labeling tools to expedite NMR structural and dynamics studies are required. Using enzymes from the pentose phosphate pathway, we coupled chemically synthesized uracil nucleobase with specifically (13) C-labeled ribose to synthesize both UTP and CTP in nearly quantitative yields. This chemoenzymatic method affords a cost-effective preparation of labels that are unattainable by current methods. The methodology generates versatile (13) C and (15) N labeling patterns which, when employed with relaxation-optimized NMR spectroscopy, effectively mitigate problems of rapid relaxation that result in low resolution and sensitivity. The methodology is demonstrated with RNAs of various sizes, complexity, and function: the exon splicing silencer 3 (27 nt), iron responsive element (29 nt), Pro-tRNA (76 nt), and HIV-1 core encapsidation signal (155 nt).
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Affiliation(s)
- Luigi J Alvarado
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, 1115 Biomolecular Sciences Building, College Park, MD 20782 (USA)
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40
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Fontana C, Kovacs H, Widmalm G. NMR structure analysis of uniformly 13C-labeled carbohydrates. JOURNAL OF BIOMOLECULAR NMR 2014; 59:95-110. [PMID: 24771296 DOI: 10.1007/s10858-014-9830-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 04/16/2014] [Indexed: 05/26/2023]
Abstract
In this study, a set of nuclear magnetic resonance experiments, some of them commonly used in the study of (13)C-labeled proteins and/or nucleic acids, is applied for the structure determination of uniformly (13)C-enriched carbohydrates. Two model substances were employed: one compound of low molecular weight [(UL-(13)C)-sucrose, 342 Da] and one compound of medium molecular weight ((13)C-enriched O-antigenic polysaccharide isolated from Escherichia coli O142, ~10 kDa). The first step in this approach involves the assignment of the carbon resonances in each monosaccharide spin system using the anomeric carbon signal as the starting point. The (13)C resonances are traced using (13)C-(13)C correlations from homonuclear experiments, such as (H)CC-CT-COSY, (H)CC-NOESY, CC-CT-TOCSY and/or virtually decoupled (H)CC-TOCSY. Based on the assignment of the (13)C resonances, the (1)H chemical shifts are derived in a straightforward manner using one-bond (1)H-(13)C correlations from heteronuclear experiments (HC-CT-HSQC). In order to avoid the (1) J CC splitting of the (13)C resonances and to improve the resolution, either constant-time (CT) in the indirect dimension or virtual decoupling in the direct dimension were used. The monosaccharide sequence and linkage positions in oligosaccharides were determined using either (13)C or (1)H detected experiments, namely CC-CT-COSY, band-selective (H)CC-TOCSY, HC-CT-HSQC-NOESY or long-range HC-CT-HSQC. However, due to the short T2 relaxation time associated with larger polysaccharides, the sequential information in the O-antigen polysaccharide from E. coli O142 could only be elucidated using the (1)H-detected experiments. Exchanging protons of hydroxyl groups and N-acetyl amides in the (13)C-enriched polysaccharide were assigned by using HC-H2BC spectra. The assignment of the N-acetyl groups with (15)N at natural abundance was completed by using HN-SOFAST-HMQC, HNCA, HNCO and (13)C-detected (H)CACO spectra.
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Affiliation(s)
- Carolina Fontana
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 106 91, Stockholm, Sweden
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41
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Pantoja-Uceda D, Santoro J. New 13C-detected experiments for the assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2014; 59:43-50. [PMID: 24699834 DOI: 10.1007/s10858-014-9827-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 03/27/2014] [Indexed: 05/21/2023]
Abstract
NMR assignment of intrinsically disordered proteins (IDPs) by conventional HN-detected methods is hampered by the small dispersion of the amide protons chemical shifts and exchange broadening of amide proton signals. Therefore several alternative assignment strategies have been proposed in the last years. Attempting to seize that dispersion of (13)C' and (15)N chemical shifts holds even in IDPs, we recently proposed two (13)C-detected experiments to directly correlate the chemical shifts of two consecutive (13)C'-(15)N groups in proteins, i.e. without mediation of other nuclei. Main drawback of these experiments is the interruption of the connection at prolines. Here we present new (13)C-detected experiments to correlate consecutive (13)C'-(15)N groups in IDPs, hacacoNcaNCO and hacaCOncaNCO, that overcome this limitation. Moreover, the experiments provide recognition of glycine residues, thereby facilitating the assignment process.
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Affiliation(s)
- David Pantoja-Uceda
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006, Madrid, Spain
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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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Sahu D, Bastidas M, Showalter SA. Generating NMR chemical shift assignments of intrinsically disordered proteins using carbon-detected NMR methods. Anal Biochem 2013; 449:17-25. [PMID: 24333248 DOI: 10.1016/j.ab.2013.12.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 11/26/2013] [Accepted: 12/02/2013] [Indexed: 10/25/2022]
Abstract
There is an extraordinary need to describe the structures of intrinsically disordered proteins (IDPs) due to their role in various biological processes involved in signaling and transcription. However, general study of IDPs by NMR spectroscopy is limited by the poor (1)H amide chemical shift dispersion typically observed in their spectra. Recently, (13)C direct-detected NMR spectroscopy has been recognized as enabling broad structural study of IDPs. Most notably, multidimensional experiments based on the (15)N,(13)C CON spectrum make complete chemical shift assignment feasible. Here we document a collection of NMR-based tools that efficiently lead to chemical shift assignment of IDPs, motivated by a case study of the C-terminal disordered region from the human pancreatic transcription factor Pdx1. Our strategy builds on the combination of two three-dimensional (3D) experiments, (HN-flip)N(CA)CON and 3D (HN-flip)N(CA)NCO, that enable daisy chain connections to be built along the IDP backbone, facilitated by acquisition of amino acid-specific (15)N,(13)C CON-detected experiments. Assignments are completed through carbon-detected, total correlation spectroscopy (TOCSY)-based side chain chemical shift measurement. Conducting our study required producing valuable modifications to many previously published pulse sequences, motivating us to announce the creation of a database of our pulse programs, which we make freely available through our website.
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Affiliation(s)
- Debashish Sahu
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Monique Bastidas
- 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.
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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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45
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Pérez-Trujillo M, Monteagudo E, Parella T. 13C NMR Spectroscopy for the Differentiation of Enantiomers Using Chiral Solvating Agents. Anal Chem 2013; 85:10887-94. [DOI: 10.1021/ac402580j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Míriam Pérez-Trujillo
- Servei
de Ressonància Magnètica Nuclear, Facultat de Ciències
i Biociències, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain
- Departament
de Química, Facultat de Ciències i Biociències, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain
| | - Eva Monteagudo
- Servei
de Ressonància Magnètica Nuclear, Facultat de Ciències
i Biociències, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain
| | - Teodor Parella
- Servei
de Ressonància Magnètica Nuclear, Facultat de Ciències
i Biociències, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain
- Departament
de Química, Facultat de Ciències i Biociències, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain
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Gil S, Hošek T, Solyom Z, Kümmerle R, Brutscher B, Pierattelli R, Felli IC. NMR Spectroscopic Studies of Intrinsically Disordered Proteins at Near-Physiological Conditions. Angew Chem Int Ed Engl 2013; 52:11808-12. [DOI: 10.1002/anie.201304272] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/30/2013] [Indexed: 11/11/2022]
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Gil S, Hošek T, Solyom Z, Kümmerle R, Brutscher B, Pierattelli R, Felli IC. NMR Spectroscopic Studies of Intrinsically Disordered Proteins at Near-Physiological Conditions. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304272] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Pantoja-Uceda D, Santoro J. Direct correlation of consecutive C'-N groups in proteins: a method for the assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 57:57-63. [PMID: 23929272 DOI: 10.1007/s10858-013-9765-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/24/2013] [Indexed: 05/21/2023]
Abstract
Two novel 3D (13)C-detected experiments, hNcocaNCO and hnCOcaNCO, are proposed to facilitate the resonance assignment of intrinsically disordered proteins. The experiments correlate the (15)N and (13)C' chemical shifts of two consecutive amide moieties without involving other nuclei, thus taking advantage of the good dispersion shown by the (15)N-(13)C' correlations, even for proteins that lack a well defined tertiary structure. The new pulse sequences were successfully tested using Nupr1, an intrinsically disordered protein of 93 residues.
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Affiliation(s)
- David Pantoja-Uceda
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006, Madrid, Spain
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Nováček J, Janda L, Dopitová R, Žídek L, Sklenář V. Efficient protocol for backbone and side-chain assignments of large, intrinsically disordered proteins: transient secondary structure analysis of 49.2 kDa microtubule associated protein 2c. JOURNAL OF BIOMOLECULAR NMR 2013; 56:291-301. [PMID: 23877929 DOI: 10.1007/s10858-013-9761-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 07/07/2013] [Indexed: 05/21/2023]
Abstract
Microtubule-associated proteins (MAPs) are abundantly present in axons and dendrites, and have been shown to play crucial role during the neuronal morphogenesis. The period of main dendritic outgrowth and synaptogenesis coincides with high expression levels of one of MAPs, the MAP2c, in rats. The MAP2c is a 49.2 kDa intrinsically disordered protein. To achieve an atomic resolution characterization of such a large protein, we have developed a protocol based on the acquisition of two five-dimensional (13)C-directly detected NMR experiments. Our previously published 5D CACONCACO experiment (Nováček et al. in J Biomol NMR 50(1):1-11, 2011) provides the sequential assignment of the backbone resonances, which is not interrupted by the presence of the proline residues in the amino acid sequence. A novel 5D HC(CC-TOCSY)CACON experiment facilitates the assignment of the aliphatic side chain resonances. To streamline the data analysis, we have developed a semi-automated procedure for signal assignments. The obtained data provides the first atomic resolution insight into the conformational state of MAP2c and constitutes a model for further functional studies of MAPs.
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Affiliation(s)
- Jiří Nováček
- Faculty of Science, NCBR, and CEITEC, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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Popovic M, Zlatev V, Hodnik V, Anderluh G, Felli IC, Pongor S, Pintar A. Flexibility of the PDZ-binding motif in the micelle-bound form of Jagged-1 cytoplasmic tail. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1818:1706-16. [PMID: 22465068 DOI: 10.1016/j.bbamem.2012.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 01/07/2023]
Abstract
Human Jagged-1, one of the ligands of Notch receptors, is a transmembrane protein composed of a large extracellular region and a 125-residue cytoplasmic tail which bears a C-terminal PDZ recognition motif. To investigate the interaction between Jagged-1 cytoplasmic tail and the inner leaflet of the plasma membrane we determined, by solution NMR, the secondary structure and dynamics of the recombinant protein corresponding to the intracellular region of Jagged-1, J1_tmic, bound to negatively charged lysophospholipid micelles. NMR showed that the PDZ binding motif is preceded by four alpha-helical segments and that, despite the extensive interaction between J1_tmic and the micelle, the PDZ binding motif remains highly flexible. Binding of J1_tmic to negatively charged, but not to zwitterionic vesicles, was confirmed by surface plasmon resonance. To study the PDZ binding region in more detail, we prepared a peptide corresponding to the last 24 residues of Jagged-1, J1C24, and different phosphorylated variants of it. J1C24 displays a marked helical propensity and undergoes a coil-helix transition in the presence of negatively charged, but not zwitterionic, lysophospholipid micelles. Phosphorylation at different positions drastically decreases the helical propensity of the peptides and abolishes the coil-helix transition triggered by lysophospholipid micelles. We propose that phosphorylation of residues upstream of the PDZ binding motif may shift the equilibrium from an ordered, membrane-bound, interfacial form of Jagged-1 C-terminal region to a more disordered form with an increased accessibility of the PDZ recognition motif, thus playing an indirect role in the interaction between Jagged-1 and the PDZ-containing target protein.
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Affiliation(s)
- Matija Popovic
- International Centre for Genetic Engineering and Biotechnology, AREA Science Park Padriciano 99, 1-34149 Trieste, Italy
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