1
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Dudas EF, Tully MD, Foldes T, Kelly G, Tartaglia GG, Pastore A. The structural properties of full-length annexin A11. Front Mol Biosci 2024; 11:1347741. [PMID: 38516187 PMCID: PMC10955470 DOI: 10.3389/fmolb.2024.1347741] [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: 12/01/2023] [Accepted: 01/17/2024] [Indexed: 03/23/2024] Open
Abstract
Annexin A11 (ANXA11) is a calcium-dependent phospholipid-binding protein belonging to the annexin protein family and implicated in the neurodegenerative amyotrophic lateral sclerosis. Structurally, ANXA11 contains a conserved calcium-binding C-terminal domain common to all annexins and a putative intrinsically unfolded N-terminus specific for ANXA11. Little is known about the structure and functions of this region of the protein. By analogy with annexin A1, it was suggested that residues 38 to 59 within the ANXA11 N-terminus could form a helical region that would be involved in interactions. Interestingly, this region contains residues that, when mutated, may lead to clinical manifestations. In the present study, we have studied the structural features of the full-length protein with special attention to the N-terminal region using a combination of biophysical techniques which include nuclear magnetic resonance and small angle X-ray scattering. We show that the N-terminus is intrinsically disordered and that the overall features of the protein are not markedly affected by the presence of calcium. We also analyzed the 38-59 helix hypothesis using synthetic peptides spanning both the wild-type sequence and clinically relevant mutations. We show that the peptides have a remarkable character typical of a native helix and that mutations do not alter the behaviour suggesting that they are required for interactions rather than being structurally important. Our work paves the way to a more thorough understanding of the ANXA11 functions.
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Affiliation(s)
- Erika F. Dudas
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- European Synchrotron Radiation Facility, Grenoble, France
| | - Mark D. Tully
- European Synchrotron Radiation Facility, Grenoble, France
| | - Tamas Foldes
- University College London, Department of Physics and Astronomy, University College London, London, United Kingdom
- Institut de Biologie Structurale (IBS), Institut Laue-Langevin, University Grenoble Alpes, Grenoble, France
| | - Geoff Kelly
- MRC Biomedical NMR Centre, The Francis Crick Institute, London, United Kingdom
| | | | - Annalisa Pastore
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- European Synchrotron Radiation Facility, Grenoble, France
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2
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Felli IC, Bermel W, Pierattelli R. Exclusively heteronuclear NMR experiments for the investigation of intrinsically disordered proteins: focusing on proline residues. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:511-522. [PMID: 37904768 PMCID: PMC10539766 DOI: 10.5194/mr-2-511-2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/02/2021] [Indexed: 11/01/2023]
Abstract
NMR represents a key spectroscopic technique that contributes to the emerging field of highly flexible, intrinsically disordered proteins (IDPs) or protein regions (IDRs) that lack a stable three-dimensional structure. A set of exclusively heteronuclear NMR experiments tailored for proline residues, highly abundant in IDPs/IDRs, are presented here. They provide a valuable complement to the widely used approach based on amide proton detection, filling the gap introduced by the lack of amide protons in proline residues within polypeptide chains. The novel experiments have very interesting properties for the investigations of IDPs/IDRs of increasing complexity.
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Affiliation(s)
- Isabella C. Felli
- CERM and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Roberta Pierattelli
- CERM and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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3
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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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4
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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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5
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Wong LE, Maier J, Wienands J, Becker S, Griesinger C. Sensitivity-Enhanced Four-Dimensional Amide–Amide Correlation NMR Experiments for Sequential Assignment of Proline-Rich Disordered Proteins. J Am Chem Soc 2018; 140:3518-3522. [DOI: 10.1021/jacs.8b00215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Leo E. Wong
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Joachim Maier
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Jürgen Wienands
- Institute of Cellular and Molecular Immunology, Georg August University of Göttingen, Humboldtallee 34, 37073 Göttingen, Germany
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Christian Griesinger
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
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6
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Wiedemann C, Bellstedt P, Häfner S, Herbst C, Bordusa F, Görlach M, Ohlenschläger O, Ramachandran R. A Set of Efficient nD NMR Protocols for Resonance Assignments of Intrinsically Disordered Proteins. Chemphyschem 2016; 17:1961-8. [PMID: 27061973 DOI: 10.1002/cphc.201600155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 11/07/2022]
Abstract
The RF pulse scheme RN[N-CA HEHAHA]NH, which provides a convenient approach to the acquisition of different multidimensional chemical shift correlation NMR spectra leading to backbone resonance assignments, including those of the proline residues of intrinsically disordered proteins (IDPs), is experimentally demonstrated. Depending on the type of correlation data required, the method involves the generation of in-phase ((15) N)(x) magnetisation via different magnetisation transfer pathways such as H→N→CO→N, HA→CA→CO→N, H→N→CA→N and H→CA→N, the subsequent application of (15) N-(13) C(α) heteronuclear Hartmann-Hahn mixing over a period of ≈100 ms, chemical-shift labelling of relevant nuclei before and after the heteronuclear mixing step and amide proton detection in the acquisition dimension. It makes use of the favourable relaxation properties of IDPs and the presence of (1) JCαN and (2) JCαN couplings to achieve efficient correlation of the backbone resonances of each amino acid residue "i" with the backbone amide resonances of residues "i-1" and "i+1". It can be implemented in a straightforward way through simple modifications of the RF pulse schemes commonly employed in protein NMR studies. The efficacy of the approach is demonstrated using a uniformly ((15) N,(13) C) labelled sample of α-synuclein. The different possibilities for obtaining the amino-acid-type information, simultaneously with the connectivity data between the backbone resonances of sequentially neighbouring residues, have also been outlined.
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Affiliation(s)
- Christoph Wiedemann
- Institute of Biochemistry/Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Peter Bellstedt
- Faculty of Chemistry and Earth Sciences, Friedrich Schiller University Jena, Humboldstr. 10, 07743, Jena, Germany
| | - Sabine Häfner
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Christian Herbst
- Department of Physics, Faculty of Science, Ubon Ratchathani University, 34190, Ubon Ratchathani, Thailand
| | - Frank Bordusa
- Institute of Biochemistry/Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Matthias Görlach
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Oliver Ohlenschläger
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Ramadurai Ramachandran
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
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7
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DeForte S, Reddy KD, Uversky VN. Quarterly intrinsic disorder digest (January-February-March, 2014). INTRINSICALLY DISORDERED PROTEINS 2016; 4:e1153395. [PMID: 28232896 DOI: 10.1080/21690707.2016.1153395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This is the 5th issue of the Digested Disorder series that represents a reader's digest of the scientific literature on intrinsically disordered proteins. We continue to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the first quarter of 2014; i.e., during the period of January, February, and March of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida , Tampa, FL, USA
| | - Krishna D Reddy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida , Tampa, FL, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Biology Department, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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8
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Human adenosine A2A receptor binds calmodulin with high affinity in a calcium-dependent manner. Biophys J 2015; 108:903-917. [PMID: 25692595 DOI: 10.1016/j.bpj.2014.12.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 12/02/2014] [Accepted: 12/16/2014] [Indexed: 12/22/2022] Open
Abstract
Understanding how ligands bind to G-protein-coupled receptors and how binding changes receptor structure to affect signaling is critical for developing a complete picture of the signal transduction process. The adenosine A2A receptor (A2AR) is a particularly interesting example, as it has an exceptionally long intracellular carboxyl terminus, which is predicted to be mainly disordered. Experimental data on the structure of the A2AR C-terminus is lacking, because published structures of A2AR do not include the C-terminus. Calmodulin has been reported to bind to the A2AR C-terminus, with a possible binding site on helix 8, next to the membrane. The biological meaning of the interaction as well as its calcium dependence, thermodynamic parameters, and organization of the proteins in the complex are unclear. Here, we characterized the structure of the A2AR C-terminus and the A2AR C-terminus-calmodulin complex using different biophysical methods, including native gel and analytical gel filtration, isothermal titration calorimetry, NMR spectroscopy, and small-angle X-ray scattering. We found that the C-terminus is disordered and flexible, and it binds with high affinity (Kd = 98 nM) to calmodulin without major conformational changes in the domain. Calmodulin binds to helix 8 of the A2AR in a calcium-dependent manner that can displace binding of A2AR to lipid vesicles. We also predicted and classified putative calmodulin-binding sites in a larger group of G-protein-coupled receptors.
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9
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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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10
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Tossavainen H, Hellman M, Piirainen H, Jaakola VP, Permi P. H(N), N, C(α), C(β) and C' assignments of the intrinsically disordered C-terminus of human adenosine A2A receptor. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:403-406. [PMID: 25952762 DOI: 10.1007/s12104-015-9618-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/03/2015] [Indexed: 06/04/2023]
Abstract
The C-terminus of the human adenosine A2A receptor differs from the other human adenosine receptors by its exceptional length and lack of a canonical cysteine residue. We have previously structurally characterized this C-terminal domain and its interaction with calmodulin. It was shown to be structurally disordered and flexible, and to bind calmodulin with high affinity in a calcium-dependent manner. Interaction with calmodulin takes place at the N-terminal end of the A2A C-terminal domain without major conformational changes in the latter. NMR was one of the biophysical methods used in the study. Here we present the H(N), N, C(α), C(β) and C' chemical shift assignments of the free form of the C-terminus residues 293-412, used in the NMR spectroscopic characterization of the domain.
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Affiliation(s)
- Helena Tossavainen
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, 00014, Helsinki, Finland
| | - Maarit Hellman
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, 00014, Helsinki, Finland
| | - Henni Piirainen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Veli-Pekka Jaakola
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Perttu Permi
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, 00014, Helsinki, Finland.
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11
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Wiedemann C, Goradia N, Häfner S, Herbst C, Görlach M, Ohlenschläger O, Ramachandran R. HN-NCA heteronuclear TOCSY-NH experiment for (1)H(N) and (15)N sequential correlations in ((13)C, (15)N) labelled intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2015; 63:201-212. [PMID: 26282620 DOI: 10.1007/s10858-015-9976-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/08/2015] [Indexed: 06/04/2023]
Abstract
A simple triple resonance NMR experiment that leads to the correlation of the backbone amide resonances of each amino acid residue 'i' with that of residues 'i-1' and 'i+1' in ((13)C, (15)N) labelled intrinsically disordered proteins (IDPs) is presented. The experimental scheme, {HN-NCA heteronuclear TOCSY-NH}, exploits the favourable relaxation properties of IDPs and the presence of (1) J CαN and (2) J CαN couplings to transfer the (15)N x magnetisation from amino acid residue 'i' to adjacent residues via the application of a band-selective (15)N-(13)C(α) heteronuclear cross-polarisation sequence of ~100 ms duration. Employing non-uniform sampling in the indirect dimensions, the efficacy of the approach has been demonstrated by the acquisition of 3D HNN chemical shift correlation spectra of α-synuclein. The experimental performance of the RF pulse sequence has been compared with that of the conventional INEPT-based HN(CA)NH pulse scheme. As the availability of data from both the HCCNH and HNN experiments will make it possible to use the information extracted from one experiment to simplify the analysis of the data of the other and lead to a robust approach for unambiguous backbone and side-chain resonance assignments, a time-saving strategy for the simultaneous collection of HCCNH and HNN data is also described.
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Affiliation(s)
- Christoph Wiedemann
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
- Institute of Biochemistry/Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle/Salle, Germany
| | - Nishit Goradia
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Sabine Häfner
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Christian Herbst
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
- Department of Physics, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Matthias Görlach
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Oliver Ohlenschläger
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Ramadurai Ramachandran
- Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
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12
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Dziekański P, Grudziąż K, Jarvoll P, Koźmiński W, Zawadzka-Kazimierczuk A. (13)C-detected NMR experiments for automatic resonance assignment of IDPs and multiple-fixing SMFT processing. JOURNAL OF BIOMOLECULAR NMR 2015; 62:179-90. [PMID: 25902761 PMCID: PMC4451475 DOI: 10.1007/s10858-015-9932-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/15/2015] [Indexed: 05/13/2023]
Abstract
Intrinsically disordered proteins (IDPs) have recently attracted much interest, due to their role in many biological processes, including signaling and regulation mechanisms. High-dimensional (13)C direct-detected NMR experiments have proven exceptionally useful in case of IDPs, providing spectra with superior peak dispersion. Here, two such novel experiments recorded with non-uniform sampling are introduced, these are 5D HabCabCO(CA)NCO and 5D HNCO(CA)NCO. Together with the 4D (HACA)CON(CA)NCO, an extension of the previously published 3D experiments (Pantoja-Uceda and Santoro in J Biomol NMR 59:43-50, 2014. doi: 10.1007/s10858-014-9827-1), they form a set allowing for complete and reliable resonance assignment of difficult IDPs. The processing is performed with sparse multidimensional Fourier transform based on the concept of restricting (fixing) some of spectral dimensions to a priori known resonance frequencies. In our study, a multiple-fixing method was developed, that allows easy access to spectral data. The experiments were tested on a resolution-demanding alpha-synuclein sample. Due to superior peak dispersion in high-dimensional spectrum and availability of the sequential connectivities between four consecutive residues, the overwhelming majority of resonances could be assigned automatically using the TSAR program.
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Affiliation(s)
- Paweł Dziekański
- />Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
- />Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Katarzyna Grudziąż
- />Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Patrik Jarvoll
- />Agilent Technologies, 10 Mead Road, Yarnton, OX5 1QU UK
| | - 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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13
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Goradia N, Wiedemann C, Herbst C, Görlach M, Heinemann SH, Ohlenschläger O, Ramachandran R. An Approach to NMR Assignment of Intrinsically Disordered Proteins. Chemphyschem 2015; 16:739-46. [DOI: 10.1002/cphc.201402872] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Indexed: 01/06/2023]
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14
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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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