1
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Vedel IM, Prestel A, Zhang Z, Skawinska NT, Stark H, Harris P, Kragelund BB, Peters GHJ. Structural characterization of human tryptophan hydroxylase 2 reveals that L-Phe is superior to L-Trp as the regulatory domain ligand. Structure 2023:S0969-2126(23)00127-2. [PMID: 37119821 DOI: 10.1016/j.str.2023.04.004] [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: 12/17/2022] [Revised: 03/03/2023] [Accepted: 04/04/2023] [Indexed: 05/01/2023]
Abstract
Tryptophan hydroxylase 2 (TPH2) catalyzes the rate-limiting step in serotonin biosynthesis in the brain. Consequently, regulation of TPH2 is relevant for serotonin-related diseases, yet the regulatory mechanism of TPH2 is poorly understood and structural and dynamical insights are missing. We use NMR spectroscopy to determine the structure of a 47 N-terminally truncated variant of the regulatory domain (RD) dimer of human TPH2 in complex with L-Phe, and show that L-Phe is the superior RD ligand compared with the natural substrate, L-Trp. Using cryo-EM, we obtain a low-resolution structure of a similarly truncated variant of the complete tetrameric enzyme with dimerized RDs. The cryo-EM two-dimensional (2D) class averages additionally indicate that the RDs are dynamic in the tetramer and likely exist in a monomer-dimer equilibrium. Our results provide structural information on the RD as an isolated domain and in the TPH2 tetramer, which will facilitate future elucidation of TPH2's regulatory mechanism.
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Affiliation(s)
- Ida M Vedel
- Department of Chemistry, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Andreas Prestel
- Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark
| | - Zhenwei Zhang
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Natalia T Skawinska
- Department of Chemistry, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Pernille Harris
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Birthe B Kragelund
- Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark.
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
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2
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Yoshimura Y, Mulder FAA. Sensitive and simplified: a combinatorial acquisition of five distinct 2D constant-time 13C- 1H NMR protein correlation spectra. JOURNAL OF BIOMOLECULAR NMR 2020; 74:695-706. [PMID: 32804297 DOI: 10.1007/s10858-020-00341-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
A procedure is presented for the substantial simplification of 2D constant-time 13C-1H heteronuclear single-quantum correlation (HSQC) spectra of 13C-enriched proteins. In this approach, a single pulse sequence simultaneously records eight sub-spectra wherein the phases of the NMR signals depend on spin topology. Signals from different chemical groups are then stratified into different sub-spectra through linear combination based on Hadamard encoding of 13CHn multiplicity (n = 1, 2, and 3) and the chemical nature of neighboring 13C nuclei (aliphatic, carbonyl/carboxyl, aromatic). This results in five sets of 2D NMR spectra containing mutually exclusive signals from: (i) 13Cβ-1Hβ correlations of asparagine and aspartic acid, 13Cγ-1Hγ correlations of glutamine and glutamic acid, and 13Cα-1Hα correlations of glycine, (ii) 13Cα-1Hα correlations of all residues but glycine, and (iii) 13Cβ-1Hβ correlations of phenylalanine, tyrosine, histidine, and tryptophan, and the remaining (iv) aliphatic 13CH2 and (v) aliphatic 13CH/13CH3 resonances. As HSQC is a common element of many NMR experiments, the spectral simplification proposed in this article can be straightforwardly implemented in experiments for resonance assignment and structure determination and should be of widespread utility.
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Affiliation(s)
- Yuichi Yoshimura
- Lifematics West-Japan Branch, Hirano-machi 4-6-16, Chuo-ku, Osaka, 541-0046, Japan
- Institute for Protein Research, Osaka University, Yamada-oka 3-2, Suita, Osaka, 565-0871, Japan
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Frans A A Mulder
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark.
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3
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Behera SP, Dubey A, Chen WN, De Paula VS, Zhang M, Sgourakis NG, Bermel W, Wagner G, Coote PW, Arthanari H. Nearest-neighbor NMR spectroscopy: categorizing spectral peaks by their adjacent nuclei. Nat Commun 2020; 11:5547. [PMID: 33144564 PMCID: PMC7642304 DOI: 10.1038/s41467-020-19325-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/01/2020] [Indexed: 01/12/2023] Open
Abstract
Methyl-NMR enables atomic-resolution studies of structure and dynamics of large proteins in solution. However, resonance assignment remains challenging. The problem is to combine existing structural informational with sparse distance restraints and search for the most compatible assignment among the permutations. Prior classification of peaks as either from isoleucine, leucine, or valine reduces the search space by many orders of magnitude. However, this is hindered by overlapped leucine and valine frequencies. In contrast, the nearest-neighbor nuclei, coupled to the methyl carbons, resonate in distinct frequency bands. Here, we develop a framework to imprint additional information about passively coupled resonances onto the observed peaks. This depends on simultaneously orchestrating closely spaced bands of resonances along different magnetization trajectories, using principles from control theory. For methyl-NMR, the method is implemented as a modification to the standard fingerprint spectrum (the 2D-HMQC). The amino acid type is immediately apparent in the fingerprint spectrum. There is no additional relaxation loss or an increase in experimental time. The method is validated on biologically relevant proteins. The idea of generating new spectral information using passive, adjacent resonances is applicable to other contexts in NMR spectroscopy.
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Affiliation(s)
- Soumya P Behera
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Abhinav Dubey
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Wan-Na Chen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Viviane S De Paula
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Meng Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Nikolaos G Sgourakis
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Wolfgang Bermel
- Magnetic Resonance Spectroscopy NMR Application, Bruker BioSpin GmbH, 76287, Rheinstetten, Germany
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Paul W Coote
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
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4
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Christou NE, Ayala I, Giandoreggio-Barranco K, Byrdin M, Adam V, Bourgeois D, Brutscher B. NMR Reveals Light-Induced Changes in the Dynamics of a Photoswitchable Fluorescent Protein. Biophys J 2019; 117:2087-2100. [PMID: 31733726 DOI: 10.1016/j.bpj.2019.10.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/20/2019] [Accepted: 10/25/2019] [Indexed: 12/22/2022] Open
Abstract
The availability of fluorescent proteins with distinct phototransformation properties is crucial for a wide range of applications in advanced fluorescence microscopy and biotechnology. To rationally design new variants optimized for specific applications, a detailed understanding of the mechanistic features underlying phototransformation is essential. At present, little is known about the conformational dynamics of fluorescent proteins at physiological temperature and how these dynamics contribute to the observed phototransformation properties. Here, we apply high-resolution NMR spectroscopy in solution combined with in situ sample illumination at different wavelengths to investigate the conformational dynamics of rsFolder, a GFP-derived protein that can be reversibly switched between a green fluorescent state and a nonfluorescent state. Our results add a dynamic view to the static structures obtained by x-ray crystallography. Including a custom-tailored NMR toolbox in fluorescent protein research provides new opportunities for investigating the effect of mutations or changes in the environmental conditions on the conformational dynamics of phototransformable fluorescent proteins and their correlation with the observed photochemical and photophysical properties.
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Affiliation(s)
- Nina-Eleni Christou
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Isabel Ayala
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | - Martin Byrdin
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Virgile Adam
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Bernhard Brutscher
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
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5
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Favier A, Brutscher B. NMRlib: user-friendly pulse sequence tools for Bruker NMR spectrometers. JOURNAL OF BIOMOLECULAR NMR 2019; 73:199-211. [PMID: 31076970 DOI: 10.1007/s10858-019-00249-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
We present NMRlib, a suite of jython-based tools designed for Bruker spectrometers (TopSpin versions 3.2-4.0) that allow easy setup, management, and exchange of NMR experiments. A NMR experiment can be set up and executed in a few clicks by navigating through the NMRlib GUI tree structure, without any further parameter adjustment. NMRlib is magnetic-field independent, and thus particularly helpful for laboratories operating multiple NMR spectrometers. NMRlib is easily personalized by adding, deleting, or reorganizing experiments. Additional tools are provided for data processing, visualization, and analysis. In particular, NMRlib contains all the polarization-enhanced fast-pulsing NMR experiments (SOFAST, BEST, HADAMAC,…) developed in our laboratory over the last decade. We also discuss some specific features that have been implemented to make these experiments most efficient and user friendly.
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Affiliation(s)
- Adrien Favier
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France.
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6
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Jean NL, Bougault CM, Egan AJF, Vollmer W, Simorre JP. Solution NMR assignment of LpoB, an outer-membrane anchored Penicillin-Binding Protein activator from Escherichia coli. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:123-127. [PMID: 24691651 PMCID: PMC4351441 DOI: 10.1007/s12104-014-9557-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/25/2014] [Indexed: 06/03/2023]
Abstract
Bacteria surround their cytoplasmic membrane with the essential heteropolymer peptidoglycan (PG), which is made of glycan chains cross-linked by short peptides, to maintain osmotic stability and cell shape. PG is assembled from lipid II precursor by glycosyltransferase and transpeptidase reactions catalyzed by PG synthases, which are anchored to the cytoplasmic membrane and are controlled from inside the cell by cytoskeletal elements. Recently, two lipoproteins, LpoA and LpoB, were shown to be required in Escherichia coli for activating the main peptidoglycan synthases, Penicillin-Binding Proteins 1A and 1B, from the outer membrane. Here we present the backbone and side-chain assignment of the (1)H, (13)C and (15)N resonances of LpoB from E. coli. We also provide evidence for a two-domain organization of LpoB and a largely disordered, 64 amino acid-long N-terminal domain.
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Affiliation(s)
- Nicolas L. Jean
- />Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes, EPN Campus, 6 rue Jules Horowitz, 38027 Grenoble, France
- />CNRS, IBS, 38027 Grenoble, France
- />CEA, DSV, IBS, 38027 Grenoble, France
| | - Catherine M. Bougault
- />Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes, EPN Campus, 6 rue Jules Horowitz, 38027 Grenoble, France
- />CNRS, IBS, 38027 Grenoble, France
- />CEA, DSV, IBS, 38027 Grenoble, France
| | - Alexander J. F. Egan
- />Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX UK
| | - Waldemar Vollmer
- />Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX UK
| | - Jean-Pierre Simorre
- />Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes, EPN Campus, 6 rue Jules Horowitz, 38027 Grenoble, France
- />CNRS, IBS, 38027 Grenoble, France
- />CEA, DSV, IBS, 38027 Grenoble, France
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7
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Bersch B, Bougault C, Roux L, Favier A, Vernet T, Durmort C. New insights into histidine triad proteins: solution structure of a Streptococcus pneumoniae PhtD domain and zinc transfer to AdcAII. PLoS One 2013; 8:e81168. [PMID: 24312273 PMCID: PMC3842936 DOI: 10.1371/journal.pone.0081168] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/09/2013] [Indexed: 12/18/2022] Open
Abstract
Zinc (Zn2+) homeostasis is critical for pathogen host colonization and invasion. Polyhistidine triad (Pht) proteins, located at the surface of various streptococci, have been proposed to be involved in Zn2+ homeostasis. The phtD gene, coding for a Zn2+-binding protein, is organized in an operon with adcAII coding for the extracellular part of a Zn2+ transporter. In the present work, we investigate the relationship between PhtD and AdcAII using biochemical and structural biology approaches. Immuno-precipitation experiments on purified membranes of Streptococcus pneumoniae (S. pneumoniae) demonstrate that native PhtD and AdcAII interact in vivo confirming our previous in vitro observations. NMR was used to demonstrate Zn2+ transfer from the Zn2+-bound form of a 137 amino acid N-terminal domain of PhtD (t-PhtD) to AdcAII. The high resolution NMR structure of t-PhtD shows that Zn2+ is bound in a tetrahedral site by histidines 83, 86, and 88 as well as by glutamate 63. Comparison of the NMR parameters measured for apo- and Zn2+-t-PhtD shows that the loss of Zn2+ leads to a diminished helical propensity at the C-terminus and increases the local dynamics and overall molecular volume. Structural comparison with the crystal structure of a 55-long fragment of PhtA suggests that Pht proteins are built from short repetitive units formed by three β-strands containing the conserved HxxHxH motif. Taken together, these results support a role for S. pneumoniae PhtD as a Zn2+ scavenger for later release to the surface transporter AdcAII, leading to Zn2+ uptake.
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Affiliation(s)
- Beate Bersch
- Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France ; Institut de Biologie Structurale, Direction des Sciences du Vivant, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France ; Institut de Biologie Structurale, Centre National de la Recherche Scientifique, Grenoble, France
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8
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Lichtenecker RJ, Coudevylle N, Konrat R, Schmid W. Selective isotope labelling of leucine residues by using α-ketoacid precursor compounds. Chembiochem 2013; 14:818-21. [PMID: 23564734 DOI: 10.1002/cbic.201200737] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Indexed: 01/26/2023]
Abstract
You can have one without the other: A new metabolic precursor compound can selectively introduce (13)C and (2)H patterns at leucine residues in proteins in cell-based expression systems without interfering with valine metabolism. The protocol provides selectively labelled macromolecules well suited for probing structure and dynamics in high-molecular-weight proteins by NMR spectroscopy.
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Affiliation(s)
- Roman J Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Währingerstrasse 38, 1090 Vienna, Austria.
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9
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Lecoq L, Bougault C, Kern T, Hugonnet JE, Veckerlé C, Pessey O, Arthur M, Simorre JP. Backbone and side-chain 1H, 15N and 13C assignment of apo- and imipenem-acylated L,D-transpeptidase from Bacillus subtilis. BIOMOLECULAR NMR ASSIGNMENTS 2012; 6:205-208. [PMID: 22278298 DOI: 10.1007/s12104-012-9358-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 01/17/2012] [Indexed: 05/31/2023]
Abstract
The D,D-transpeptidase activity of Penicillin Binding Proteins (PBPs) is essential to maintain cell wall integrity. PBPs catalyze the final step of the peptidoglycan synthesis by forming 4 → 3 cross-links between two peptide stems. Recently, a novel β-lactam resistance mechanism involving L,D-transpeptidases has been identified in Enterococcus faecium and Mycobacterium tuberculosis. In this resistance pathway, the classical 4 → 3 cross-links are replaced by 3 → 3 cross-links, whose formation are catalyzed by the L,D-transpeptidases. To date, only one class of the entire β-lactam family, the carbapenems, is able to inhibit the L,D-transpeptidase activity. Nevertheless, the specificity of this inactivation is still not understood. Hence, the study of this new transpeptidase family is of considerable interest in order to understand the mechanism of the L,D-transpeptidases inhibition by carbapenems. In this context, we present herein the backbone and side-chain (1)H, (15)N and (13)C NMR assignment of the L,D-transpeptidase from Bacillus subtilis (Ldt(Bs)) in the apo and in the acylated form with a carbapenem, the imipenem.
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Affiliation(s)
- L Lecoq
- CEA, Institut de Biologie Structurale Jean-Pierre Ebel, 41, rue Jules Horowitz, 38027 Grenoble, France
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10
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Lecoq L, Bougault C, Hugonnet JE, Veckerlé C, Pessey O, Arthur M, Simorre JP. Dynamics induced by β-lactam antibiotics in the active site of Bacillus subtilis L,D-transpeptidase. Structure 2012; 20:850-61. [PMID: 22579252 DOI: 10.1016/j.str.2012.03.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 02/29/2012] [Accepted: 03/05/2012] [Indexed: 11/18/2022]
Abstract
β-lactams inhibit peptidoglycan polymerization by acting as suicide substrates of essential d,d-transpeptidases. Bypass of these enzymes by unrelated l,d-transpeptidases results in β-lactam resistance, although carbapenems remain unexpectedly active. To gain insight into carbapenem specificity of l,d-transpeptidases (Ldts), we solved the nuclear magnetic resonance (NMR) structures of apo and imipenem-acylated Bacillus subtilis Ldt and show that the cysteine nucleophile is present as a neutral imidazole-sulfhydryl pair in the substrate-free enzyme. NMR relaxation dispersion does not reveal any preexisting conformational exchange in the apoenzyme, and change in flexibility is not observed upon noncovalent binding of β-lactams (K(D) > 37.5 mM). In contrast, covalent modification of active cysteine by both carbapenems and 2-nitro-5-thiobenzoate induces backbone flexibility that does not result from disruption of the imidazole-sulfhydryl proton interaction or steric hindrance. The chemical step of the reaction determines enzyme specificity since no differences in drug affinity were observed.
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Affiliation(s)
- Lauriane Lecoq
- CEA, DSV, Institut de Biologie Structurale (IBS), Grenoble F-38027, France
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11
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Hu W, Namanja AT, Wong S, Chen Y. Selective editing of Val and Leu methyl groups in high molecular weight protein NMR. JOURNAL OF BIOMOLECULAR NMR 2012; 53:113-24. [PMID: 22532128 PMCID: PMC3764919 DOI: 10.1007/s10858-012-9629-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Accepted: 04/10/2012] [Indexed: 05/21/2023]
Abstract
The development of methyl-TROSY approaches and specific (13)C-(1)H labeling of Ile, Leu and Val methyl groups in highly deuterated proteins has made it possible to study high molecular weight proteins, either alone or in complexes, using solution nuclear magnetic resonance (NMR) spectroscopy. Here we present 2-dimensional (2D) and 3-dimensional (3D) NMR experiments designed to achieve complete separation of the methyl resonances of Val and Leu, labeled using the same precursor, α-ketoisovalerate or acetolactate. The 2D experiment can further select the methyl resonances of Val or Leu based on the C(α) or C(β) chemical shift values of Val or Leu, respectively. In the 3D spectrum, the methyl cross peaks of Val and Leu residues have opposite signs; thus, not only can the residue types be easily distinguished, but the methyl pairs from the same residue can also be identified. The feasibility of this approach, implemented in both 2D and 3D experiments, has been demonstrated on an 82 kDa protein, malate synthase G. The methods developed in this study will reduce resonance overlaps and also facilitate structure-guided resonance assignments.
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12
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Sarret G, Favier A, Covès J, Hazemann JL, Mergeay M, Bersch B. CopK from Cupriavidus metallidurans CH34 binds Cu(I) in a tetrathioether site: characterization by X-ray absorption and NMR spectroscopy. J Am Chem Soc 2010; 132:3770-7. [PMID: 20192263 DOI: 10.1021/ja9083896] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cupriavidus metallidurans CH34 is a bacterium that is resistant to high metal concentrations in the environment. Increased copper resistance is associated with the cop cluster on the large plasmid pMOL30 that is composed of at least 21 genes. The copK gene encodes a 74 residue periplasmic protein whose expression is strongly upregulated in the presence of copper. CopK was previously shown to cooperatively bind Cu(I) and Cu(II) in distinct, specific sites. The solution structure of Cu(I)-CopK and the characterization of the Cu(I) site by X-ray absorption spectroscopy and NMR are reported here. EXAFS spectra are in agreement with a tetrathioether Cu(I) site, providing so far unique spectral information on a 4S-coordinated Cu(I) in a protein. The methionine residues forming the Cu(I) site, M28, M38, M44, and M54, are identified by NMR. We propose the chemical shift of the methionine C(epsilon) as a new and sensitive probe for the detection of Cu(I) bound to thioether groups. The solution structure of Cu(I)-CopK demonstrates that Cu(I) binding induces a complete structural modification with the disruption of the second beta-sheet and a rotation of the C-terminal part of nearly 180 degrees around a hinge formed by asparagine 57. This conformational change is directly related to the loss of the dimer interface and most probably to the formation of the Cu(II) site involving histidine 70. The solution structure of Cu(I)-CopK therefore provides the molecular basis for the understanding of the Cu(I)/Cu(II) binding cooperativity.
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Affiliation(s)
- Géraldine Sarret
- Environmental Geochemistry Group, LGIT, UMR 5559, Université Joseph Fourier and CNRS, BP 53, 38041 Grenoble, France
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13
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Felli IC, Brutscher B. Recent Advances in Solution NMR: Fast Methods and Heteronuclear Direct Detection. Chemphyschem 2009; 10:1356-68. [DOI: 10.1002/cphc.200900133] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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14
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Sibille N, Hanoulle X, Bonachera F, Verdegem D, Landrieu I, Wieruszeski JM, Lippens G. Selective backbone labelling of ILV methyl labelled proteins. JOURNAL OF BIOMOLECULAR NMR 2009; 43:219-227. [PMID: 19288066 DOI: 10.1007/s10858-009-9307-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 02/10/2009] [Accepted: 02/13/2009] [Indexed: 05/27/2023]
Abstract
Adding the 13C labelled 2-keto-isovalerate and 2-oxobutanoate precursors to a minimal medium composed of 12C labelled glucose instead of the commonly used (2D, 13C) glucose leads not only to the 13C labelling of (I, L, V) methyls but also to the selective 13C labelling of the backbone C(alpha) and CO carbons of the Ile and Val residues. As a result, the backbone (1H, 15N) correlations of the Ile and Val residues and their next neighbours in the (i + 1) position can be selectively identified in HN(CA) and HN(CO) planes. The availability of a selective HSQC spectrum corresponding to the sole amide resonances of the Ile and Val residues allows connecting them to their corresponding methyls by the intra-residue NOE effect, and should therefore be applicable to larger systems.
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Affiliation(s)
- Nathalie Sibille
- CNRS UMR 8576-Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille 1, 59655, Villeneuve d'Ascq Cedex, France
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15
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Mueller L. Alternate HMQC experiments for recording HN and HC-correlation spectra in proteins at high throughput. JOURNAL OF BIOMOLECULAR NMR 2008; 42:129-137. [PMID: 18820839 DOI: 10.1007/s10858-008-9270-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Accepted: 08/13/2008] [Indexed: 05/26/2023]
Abstract
Alternate implementations of the SOFAST-HMQC experiment are described. In these alternate SOFAST-HMQC experiments (ALSOFAST-HMQC) excitation of the magnetization of interest is achieved by non-selective rf pulses while preserving the equilibrium polarization of passive spins. This alternate excitation scheme also allows the incorporation of a novel sensitivity enhancement protocol which has been most recently developed by Brutscher and coworkers and which permits simultaneous detection of both the x- and y-components of the indirectly detected t(1)-interferograms without the need to introduce additional rf pulses and delays. We show that the ALSOFAST HC-HMQC experiment, which implements an alternate means of frequency selection, enables the detection of methyl resonances with large secondary proton chemical shifts. This is achieved by selecting coherences of interest via a frequency selective carbon inversion pulse. Detailed comparisons between SOFAST- and the presented ALSOFAST-HMQC experiment reveals a considerable degree of mutual complementarity.
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Affiliation(s)
- Luciano Mueller
- Bristol-Myers Squibb, Route 206 and Province Line Road, Princeton, NJ 08543-4000, USA.
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16
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Ribeiro EA, Favier A, Gerard FCA, Leyrat C, Brutscher B, Blondel D, Ruigrok RWH, Blackledge M, Jamin M. Solution structure of the C-terminal nucleoprotein-RNA binding domain of the vesicular stomatitis virus phosphoprotein. J Mol Biol 2008; 382:525-38. [PMID: 18657547 DOI: 10.1016/j.jmb.2008.07.028] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Accepted: 07/07/2008] [Indexed: 10/21/2022]
Abstract
Beyond common features in their genome organization and replication mechanisms, the evolutionary relationships among viruses of the Rhabdoviridae family are difficult to decipher because of the great variability in the amino acid sequence of their proteins. The phosphoprotein (P) of vesicular stomatitis virus (VSV) is an essential component of the RNA transcription and replication machinery; in particular, it contains binding sites for the RNA-dependent RNA polymerase and for the nucleoprotein. Here, we devised a new method for defining boundaries of structured domains from multiple disorder prediction algorithms, and we identified an autonomous folding C-terminal domain in VSV P (P(CTD)). We show that, like the C-terminal domain of rabies virus (RV) P, VSV P(CTD) binds to the viral nucleocapsid (nucleoprotein-RNA complex). We solved the three-dimensional structure of VSV P(CTD) by NMR spectroscopy and found that the topology of its polypeptide chain resembles that of RV P(CTD). The common part of both proteins could be superimposed with a backbone RMSD from mean atomic coordinates of 2.6 A. VSV P(CTD) has a shorter N-terminal helix (alpha(1)) than RV P(CTD); it lacks two alpha-helices (helices alpha(3) and alpha(6) of RV P), and the loop between strands beta(1) and beta(2) is longer than that in RV. Dynamical properties measured by NMR relaxation revealed the presence of fast motions (below the nanosecond timescale) in loop regions (amino acids 209-214) and slower conformational exchange in the N- and C-terminal helices. Characterization of a longer construct indicated that P(CTD) is preceded by a flexible linker. The results presented here support a modular organization of VSV P, with independent folded domains separated by flexible linkers, which is conserved among different genera of Rhabdoviridae and is similar to that proposed for the P proteins of the Paramyxoviridae.
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Affiliation(s)
- Euripedes A Ribeiro
- UJF-EMBL-CNRS-UMR 5233-Unit of Virus Host Cell Interactions, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
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17
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Bersch B, Favier A, Schanda P, van Aelst S, Vallaeys T, Covès J, Mergeay M, Wattiez R. Molecular Structure and Metal-binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus metallidurans CH34 During Copper Challenge. J Mol Biol 2008; 380:386-403. [DOI: 10.1016/j.jmb.2008.05.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Revised: 05/06/2008] [Accepted: 05/08/2008] [Indexed: 11/16/2022]
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18
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Lescop E, Rasia R, Brutscher B. Hadamard amino-acid-type edited NMR experiment for fast protein resonance assignment. J Am Chem Soc 2008; 130:5014-5. [PMID: 18345629 DOI: 10.1021/ja800914h] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An original Hadamard-encoding scheme allows discrimination among seven amino acid types in a single two-dimensional NMR experiment. Combined with hyperdimensional NMR techniques, this presents a promising new method for fast, automated backbone resonance assignment of proteins in only a few hours time.
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Affiliation(s)
- Ewen Lescop
- IBS, Institut de Biologie Structurale Jean-Pierre Ebel, 41 rue Jules Horowitz, F-38027 Grenoble, France
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19
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Traaseth NJ, Verardi R, Veglia G. Asymmetric methyl group labeling as a probe of membrane protein homo-oligomers by NMR spectroscopy. J Am Chem Soc 2008; 130:2400-1. [PMID: 18247624 DOI: 10.1021/ja711499r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nathaniel J Traaseth
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
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20
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Burnley BT, Kalverda AP, Paisey SJ, Berry A, Homans SW. Hadamard NMR spectroscopy for relaxation measurements of large (>35 kDa) proteins. JOURNAL OF BIOMOLECULAR NMR 2007; 39:239-45. [PMID: 17882509 DOI: 10.1007/s10858-007-9192-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 08/31/2007] [Indexed: 05/17/2023]
Abstract
Here we present a suite of pulse sequences for the measurement of (15)N T(1), T(1rho) and NOE data that combine traditional TROSY-based pulse sequences with band-selective Hadamard frequency encoding. The additive nature of the Hadamard matrix produces much reduced resonance overlap without the need for an increase in the dimensionality of the experiment or a significant decrease in the signal to noise ratio. We validate the accuracy of these sequences in application to ubiquitin and demonstrate their utility for relaxation measurements in Escherichia coli Class II fructose 1,6-bisphosphate aldolase (FBP-aldolase), a 358 residue 78 kDa dimeric enzyme.
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Affiliation(s)
- B Tom Burnley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
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21
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Feliz M, García J, Aragón E, Pons M. Fast 2D NMR ligand screening using Hadamard spectroscopy. J Am Chem Soc 2007; 128:7146-7. [PMID: 16734452 DOI: 10.1021/ja0608949] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fast 2D NMR-based screening can be achieved using Hadamard encoded spectroscopy to focus on the signals of interest (e.g., enzyme active or ligand recognition sites). By recording a set of Hadamard spectra (a "Hadamard constellation") with relative offsets comparable to the excitation bandwidth, quantitative ligand-induced shifts can be obtained from peak intensities.
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Affiliation(s)
- Miguel Feliz
- Laboratory of Biomolecular NMR, Institute of Research in Biomedicine, Science Research Park, Josep Samitier 1-5, 08028 Barcelona, Spain
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22
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Boudet J, Chouquet A, Chahboune A, Giustini C, Joris B, Simorre JP, Bougault C. 1H, 13C and 15N resonance assignments of YajG, an Escherichia coli protein of unknown structure and function. BIOMOLECULAR NMR ASSIGNMENTS 2007; 1:89-91. [PMID: 19636835 DOI: 10.1007/s12104-007-9025-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Accepted: 06/09/2007] [Indexed: 05/26/2023]
Abstract
The ampG gene codes for a permease required to uptake anhydro-muropeptides into bacterial cytoplasm. Located upstream in the same operon, is another 579-base-pair-long open reading frame encoding a putative lipoprotein YajG, whose nearly complete 1H,13C,15N assignments are reported here.
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Affiliation(s)
- Julien Boudet
- Laboratoire de Résonance Magnétique Nucléaire, CEA, CNRS, Université Joseph Fourier, Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, 38027 Grenoble, France
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23
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Manon F, Favier A, Núñez G, Simorre JP, Cusack S. Solution structure of NOD1 CARD and mutational analysis of its interaction with the CARD of downstream kinase RICK. J Mol Biol 2006; 365:160-74. [PMID: 17054981 DOI: 10.1016/j.jmb.2006.09.067] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2006] [Revised: 09/18/2006] [Accepted: 09/25/2006] [Indexed: 01/01/2023]
Abstract
NOD1 is a cytosolic signalling host pattern-recognition receptor composed of a caspase-activating and recruitment domain (CARD), a nucleotide-binding and oligomerization domain (NOD) and leucine-rich repeats. It plays a crucial role in innate immunity by activating the NF-kappaB pathway via its downstream effector the kinase RICK (RIP2) following the recognition of a specific bacterial ligand. RICK is recruited by NOD1 through interaction of their respective CARDs. Here we present the high resolution NMR structure of the NOD1 CARD. It is generally similar to other CARDs of known structure, consisting of six tightly packed helices, although the length and orientation of the last helix is unusual. Mutations in both the NOD1 and RICK CARD domains were assayed by immuno-precipitation of cell lysates and in vivo NF-kappaB activation in order to define residues important for CARD-CARD interaction and downstream signalling. The results show that the interaction is critically dependent on three acidic residues on NOD1 CARD and three basic residues on RICK CARD and thus is likely to have a strong electrostatic component, similar to other characterised CARD-CARD interactions.
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Affiliation(s)
- Florence Manon
- Grenoble Outstation, European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9, France
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24
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Marion D. Processing of ND NMR spectra sampled in polar coordinates: a simple Fourier transform instead of a reconstruction. JOURNAL OF BIOMOLECULAR NMR 2006; 36:45-54. [PMID: 16964531 DOI: 10.1007/s10858-006-9066-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Revised: 05/30/2006] [Accepted: 07/11/2006] [Indexed: 05/11/2023]
Abstract
In order to reduce the acquisition time of multidimensional NMR spectra of biological macromolecules, projected spectra (or in other words, spectra sampled in polar coordinates) can be used. Their standard processing involves a regular FFT of the projections followed by a reconstruction, i.e. a non-linear process. In this communication, we show that a 2D discrete Fourier transform can be implemented in polar coordinates to obtain directly a frequency domain spectrum. Aliasing due to local violations of the Nyquist sampling theorem gives rise to base line ridges but the peak line-shapes are not distorted as in most reconstruction methods. The sampling scheme is not linear and the data points in the time domain should thus be weighted accordingly in the polar FT; however, artifacts can be reduced by additional data weighting of the undersampled regions. This processing does not require any parameter tuning and is straightforward to use. The algorithm written for polar sampling can be adapted to any sampling scheme and will permit to investigate better compromises in terms of experimental time and lack of artifacts.
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Affiliation(s)
- Dominique Marion
- Institut de Biologie Structurale Jean-Pierre Ebel, CNRS-CEA-UJF, 41, Rue Jules Horowitz, 38027, Grenoble Cedex 1, France.
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25
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Schanda P, Kupce E, Brutscher B. SOFAST-HMQC experiments for recording two-dimensional heteronuclear correlation spectra of proteins within a few seconds. JOURNAL OF BIOMOLECULAR NMR 2005; 33:199-211. [PMID: 16341750 DOI: 10.1007/s10858-005-4425-x] [Citation(s) in RCA: 500] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Accepted: 10/13/2005] [Indexed: 05/05/2023]
Abstract
Fast multidimensional NMR with a time resolution of a few seconds provides a new tool for high throughput screening and site-resolved real-time studies of kinetic molecular processes by NMR. Recently we have demonstrated the feasibility to record protein 1H-15N correlation spectra in a few seconds of acquisition time using a new SOFAST-HMQC experiment (Schanda and Brutscher (2005) J. Am. Chem. Soc. 127, 8014). Here, we investigate in detail the performance of SOFAST-HMQC to record 1H-15N and 1H-13C correlation spectra of proteins of different size and at different magnetic field strengths. Compared to standard 1H-15N correlation experiments SOFAST-HMQC provides a significant gain in sensitivity, especially for fast repetition rates. Guidelines are provided on how to set up SOFAST-HMQC experiments for a given protein sample. In addition, an alternative pulse scheme, IPAP-SOFAST-HMQC is presented that allows application on NMR spectrometers equipped with cryogenic probes, and fast measurement of one-bond 1H-13C and 1H-15N scalar and residual dipolar coupling constants.
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Affiliation(s)
- Paul Schanda
- Institut de Biologie Structurale-Jean-Pierre Ebel, UMR5075 CNRS-CEA-UJF, 41, rue Jules Horowitz, 38027, Grenoble Cedex, France
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26
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Van Melckebeke H, Pardi A, Boisbouvier J, Simorre JP, Brutscher B. Resolution-enhanced base-type-edited HCN experiment for RNA. JOURNAL OF BIOMOLECULAR NMR 2005; 32:263-71. [PMID: 16211480 DOI: 10.1007/s10858-005-8872-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2005] [Accepted: 06/07/2005] [Indexed: 05/04/2023]
Abstract
New base-type-edited transverse-relaxation optimized CT-HCN(C) experiments are presented that yield intra-base and sugar-to-base correlations for 13C-15N labeled RNA. High spectral resolution in the 13C and 15N dimensions is achieved by constant time (CT) frequency editing. A spectral editing filter applied during the CT 15N labeling period separates the correlation peaks arising from G/U and A/C nucleotide bases. This provides the increased spectral resolution required to unambiguously connect the 1H and 13C resonances in sugar and base moieties of RNA nucleotides. In addition, the experiment allows base type identification for each residue, and therefore presents an attractive spectroscopic alternative to nucleotide-specific isotope labeling. Application to a 33-nucleotide RNA aptamer demonstrates the performance of the new pulse scheme.
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Affiliation(s)
- Hélène Van Melckebeke
- Laboratoire de RMN, Institut de Biologie Structurale--Jean-Pierre Ebel, UMR, 5075 CNRS-CEA-UJF, 41, rue Jules Horowitz, 38027, Cedex, Grenoble, France
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27
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Steinbeck CA, Chmelka BF. Rapid 1H{13C}-Resolved Diffusion and Spin-Relaxation Measurements by NMR Spectroscopy. J Am Chem Soc 2005; 127:11624-35. [PMID: 16104738 DOI: 10.1021/ja0439064] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hadamard-encoded heteronuclear-resolved NMR diffusion and relaxation measurements allow overlapping signal decays to be resolved with substantially shorter measuring times than are generally associated with 2D heteronuclear cross-correlation experiments. Overall measuring time requirements can be reduced by approximately an order of magnitude, compared to typical 2D heteronuclear single-quantum correlation-resolved diffusion or relaxation measurements. Specifically, in cases where chemical shift correlation information provides enhanced spectral resolution, the use of Hadamard encoding can be used to overcome uniqueness challenges that are associated with the analysis of concurrent dynamic processes and the extraction of time constants from overlapping exponential signal decays. This leads to substantially improved resolution of similar time constants than can be achieved solely through the use of post-acquisition processing techniques. In the ideal case of complete spectral separation of the signal decays, the usual constraint that time constants must be sufficiently different to resolve by exponential analysis can be circumvented entirely. Hadamard-based pulse sequences have been used to determine 1H[13C]-resolved diffusion coefficients and spin-relaxation time constants for the chemically similar components of an aqueous solution of ethanol, glycerol, and poly(ethylene glycol), and a dye-containing block-copolymer solution, which exhibit significant spectral overlap in their 1H NMR spectra.
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Affiliation(s)
- Christian A Steinbeck
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
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28
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Van Melckebeke H, Simorre JP, Brutscher B. Suppression of artifacts induced by homonuclear decoupling in amino-acid-type edited methyl 1H-13C correlation experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 170:199-205. [PMID: 15388081 DOI: 10.1016/j.jmr.2004.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2004] [Revised: 06/24/2004] [Indexed: 05/24/2023]
Abstract
A detailed theoretical and experimental analysis of the artifacts induced by homonuclear band-selective decoupling during CT frequency labeling is presented. The effects are discussed in the context of an amino-acid-type editing filter implemented in (1)H-(13)C CT-HSQC experiments of methyl groups in proteins. It is shown that both Bloch-Siegert shifts and modulation sidebands are efficiently suppressed by using additional off-resonance decoupling as proposed by Zhang and Gorenstein [J. Magn. Reson. 132 (1998) 81], and appropriate adjustment of a set of pulse sequence parameters. The theoretical predictions are confirmed by experiments performed on (13)C-labeled protein samples, yielding artifact-free amino-acid-type edited methyl spectra.
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Affiliation(s)
- Hélène Van Melckebeke
- Institut de Biologie Structurale, Jean-Pierre Ebel C.N.R.S.-C.E.A.-UJF 41, rue Jules Horowitz, 38027 Grenoble Cedex, France
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