1
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Nicastro G, Abis G, Klein P, Esteban-Serna S, Gallagher C, Chaves-Arquero B, Cai Y, Figueiredo AM, Martin SR, Patani R, Taylor IA, Ramos A. Direct m6A recognition by IMP1 underlays an alternative model of target selection for non-canonical methyl-readers. Nucleic Acids Res 2023; 51:8774-8786. [PMID: 37377445 PMCID: PMC10484666 DOI: 10.1093/nar/gkad534] [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: 02/24/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
m6A methylation provides an essential layer of regulation in organismal development, and is aberrant in a range of cancers and neuro-pathologies. The information encoded by m6A methylation is integrated into existing RNA regulatory networks by RNA binding proteins that recognise methylated sites, the m6A readers. m6A readers include a well-characterised class of dedicated proteins, the YTH proteins, as well as a broader group of multi-functional regulators where recognition of m6A is only partially understood. Molecular insight in this recognition is essential to build a mechanistic understanding of global m6A regulation. In this study, we show that the reader IMP1 recognises the m6A using a dedicated hydrophobic platform that assembles on the methyl moiety, creating a stable high-affinity interaction. This recognition is conserved across evolution and independent from the underlying sequence context but is layered upon the strong sequence specificity of IMP1 for GGAC RNA. This leads us to propose a concept for m6A regulation where methylation plays a context-dependent role in the recognition of selected IMP1 targets that is dependent on the cellular concentration of available IMP1, differing from that observed for the YTH proteins.
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Affiliation(s)
- Giuseppe Nicastro
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Giancarlo Abis
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Pierre Klein
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Sofia Esteban-Serna
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Christopher Gallagher
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Belen Chaves-Arquero
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Yuyang Cai
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Angelo Miguel Figueiredo
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Stephen R Martin
- Structural Biology Technology Platform, The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Rickie Patani
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andres Ramos
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
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2
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Doyon TJ, Buller AR. Site-Selective Deuteration of Amino Acids through Dual-Protein Catalysis. J Am Chem Soc 2022; 144:7327-7336. [PMID: 35416652 PMCID: PMC10634506 DOI: 10.1021/jacs.2c00608] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Deuterated amino acids have been recognized for their utility in drug development, for facilitating nuclear magnetic resonance (NMR) analysis, and as probes for enzyme mechanism. Small molecule-based methods for the site-selective synthesis of deuterated amino acids typically involve de novo synthesis of the compound from deuterated precursors. In comparison, enzymatic methods for introducing deuterium offer improved efficiency, operating directly on free amino acids to achieve hydrogen-deuterium (H/D) exchange. However, site selectivity remains a significant challenge for enzyme-mediated deuteration, limiting access to desirable deuteration motifs. Here, we use enzyme-catalyzed deuteration, combined with steady-state kinetic analysis and ultraviolet (UV)-vis spectroscopy to probe the mechanism of a two-protein system responsible for the biosynthesis of l-allo-Ile. We show that an aminotransferase (DsaD) can pair with a small partner protein (DsaE) to catalyze Cα and Cβ H/D exchange of amino acids, while reactions without DsaE lead exclusively to Cα-deuteration. With conditions for improved catalysis, we evaluate the substrate scope for Cα/Cβ-deuteration and demonstrate the utility of this system for preparative-scale, selective labeling of amino acids.
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Affiliation(s)
- Tyler J Doyon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Andrew R Buller
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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3
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Kuenze G, Bonneau R, Leman JK, Meiler J. Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints. Structure 2019; 27:1721-1734.e5. [PMID: 31522945 DOI: 10.1016/j.str.2019.08.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/05/2019] [Accepted: 08/23/2019] [Indexed: 12/17/2022]
Abstract
Computational methods to predict protein structure from nuclear magnetic resonance (NMR) restraints that only require assignment of backbone signals, hold great potential to study larger proteins. Ideally, computational methods designed to work with sparse data need to add atomic detail that is missing in the experimental restraints. We introduce a comprehensive framework into the Rosetta suite that uses NMR restraints derived from paramagnetic labeling. Specifically, RosettaNMR incorporates pseudocontact shifts, residual dipolar couplings, and paramagnetic relaxation enhancements. It continues to use backbone chemical shifts and nuclear Overhauser effect distance restraints. We assess RosettaNMR for protein structure prediction by folding 28 monomeric proteins and 8 homo-oligomeric proteins. Furthermore, the general applicability of RosettaNMR is demonstrated on two protein-protein and three protein-ligand docking examples. Paramagnetic restraints generated more accurate models for 85% of the benchmark proteins and, when combined with chemical shifts, sampled high-accuracy models (≤2Å) in 50% of the cases.
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Affiliation(s)
- Georg Kuenze
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA.
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA; Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Department of Computer Science, New York University, New York, NY 10012, USA
| | - Julia Koehler Leman
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA; Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA.
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA.
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4
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Sheveleva NN, Markelov DA, Vovk MA, Tarasenko II, Mikhailova ME, Ilyash MY, Neelov IM, Lahderanta E. Stable Deuterium Labeling of Histidine-Rich Lysine-Based Dendrimers. Molecules 2019; 24:E2481. [PMID: 31284551 PMCID: PMC6651089 DOI: 10.3390/molecules24132481] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 01/02/2023] Open
Abstract
Peptide dendrimers, due to their biocompatibility and low toxicity, are highly promising candidates as nanocarriers for drugs and genes. The development of this kind of delivery system requires reliable monitoring of their metabolic and biological pathways. In this respect, hydrogen isotope labeling has tremendous importance, being a safe tool for detection of the labeled nanocarriers. In this work, we have synthesized new histidine-rich lysine-based dendrimers (Lys-2His dendrimer) with two linear histidine (His) residues in every inner segment. The presence of His residues has enabled us to perform controlled deuteration of Lys-2His dendrimers. The high deuteration degree (around 70%) does not practically change after redissolving the samples in H2O and heating them at 40 °C, which indicates the isotopic label stability.
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Affiliation(s)
- Nadezhda N Sheveleva
- Saint Petersburg State University, 7/9 Universitetskaya nab, 199034 Saint Petersburg, Russia
| | - Denis A Markelov
- Saint Petersburg State University, 7/9 Universitetskaya nab, 199034 Saint Petersburg, Russia.
| | - Mikhail A Vovk
- Saint Petersburg State University, 7/9 Universitetskaya nab, 199034 Saint Petersburg, Russia
| | - Irina I Tarasenko
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect 31, V.O., 199004 Saint Petersburg, Russia
| | - Mariya E Mikhailova
- Saint Petersburg State University, 7/9 Universitetskaya nab, 199034 Saint Petersburg, Russia
| | - Maxim Yu Ilyash
- Saint Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO University), Kronverkskiy pr. 49, 197101 Saint Petersburg, Russia
| | - Igor M Neelov
- Saint Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO University), Kronverkskiy pr. 49, 197101 Saint Petersburg, Russia
| | - Erkki Lahderanta
- Department of Physics, LUT University, Box 20, 53851 Lappeenranta, Finland
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5
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Movellan KT, Najbauer EE, Pratihar S, Salvi M, Giller K, Becker S, Andreas LB. Alpha protons as NMR probes in deuterated proteins. JOURNAL OF BIOMOLECULAR NMR 2019; 73:81-91. [PMID: 30762170 PMCID: PMC6441447 DOI: 10.1007/s10858-019-00230-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 01/28/2019] [Indexed: 05/08/2023]
Abstract
We describe a new labeling method that allows for full protonation at the backbone Hα position, maintaining protein side chains with a high level of deuteration. We refer to the method as alpha proton exchange by transamination (α-PET) since it relies on transaminase activity demonstrated here using Escherichia coli expression. We show that α-PET labeling is particularly useful in improving structural characterization of solid proteins by introduction of an additional proton reporter, while eliminating many strong dipolar couplings. The approach benefits from the high sensitivity associated with 1.3 mm samples, more abundant information including Hα resonances, and the narrow proton linewidths encountered for highly deuterated proteins. The labeling strategy solves amide proton exchange problems commonly encountered for membrane proteins when using perdeuteration and backexchange protocols, allowing access to alpha and all amide protons including those in exchange-protected regions. The incorporation of Hα protons provides new insights, as the close Hα-Hα and Hα-HN contacts present in β-sheets become accessible, improving the chance to determine the protein structure as compared with HN-HN contacts alone. Protonation of the Hα position higher than 90% is achieved for Ile, Leu, Phe, Tyr, Met, Val, Ala, Gln, Asn, Thr, Ser, Glu, Asp even though LAAO is only active at this degree for Ile, Leu, Phe, Tyr, Trp, Met. Additionally, the glycine methylene carbon is labeled preferentially with a single deuteron, allowing stereospecific assignment of glycine alpha protons. In solution, we show that the high deuteration level dramatically reduces R2 relaxation rates, which is beneficial for the study of large proteins and protein dynamics. We demonstrate the method using two model systems, as well as a 32 kDa membrane protein, hVDAC1, showing the applicability of the method to study membrane proteins.
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Affiliation(s)
- Kumar Tekwani Movellan
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Eszter E Najbauer
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Supriya Pratihar
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Michele Salvi
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Karin Giller
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Stefan Becker
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Loren B Andreas
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany.
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6
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Schörghuber J, Geist L, Platzer G, Konrat R, Lichtenecker RJ. Highly Selective Stable Isotope Labeling of Histidine Residues by Using a Novel Precursor in E. coli-Based Overexpression Systems. Chembiochem 2017; 18:1487-1491. [PMID: 28489326 DOI: 10.1002/cbic.201700192] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Indexed: 12/14/2022]
Abstract
The importance of NMR spectroscopy in unraveling the structural and dynamic properties of proteins is ever-expanding owing to progress in experimental techniques, hardware development, and novel labeling approaches. Multiple sophisticated methods of aliphatic residue labeling can be found in the literature, whereas the selective incorporation of NMR active isotopes into other amino acids still holds the potential for improvement. In order to close this methodological gap, we present a novel metabolic precursor for cell-based protein overexpression to assemble 13 C/2 H isotope patterns in the peptide backbone, as well as in side chain positions of a mechanistically distinguished histidine residue.
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Affiliation(s)
- Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, Währingerstrasse 38, 1090, Vienna, Austria
| | - Leonhard Geist
- Christian Doppler Laboratory for High-Content Structural Biology, and Biotechnology/Department of Structural and Computational Biology, University of Vienna, 1090, Vienna, Austria
| | - Gerald Platzer
- Christian Doppler Laboratory for High-Content Structural Biology, and Biotechnology/Department of Structural and Computational Biology, University of Vienna, 1090, Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology, and Biotechnology/Department of Structural and Computational Biology, University of Vienna, 1090, Vienna, Austria
| | - Roman J Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Währingerstrasse 38, 1090, Vienna, Austria
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7
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Hein C, Löhr F, Schwarz D, Dötsch V. Acceleration of protein backbone NMR assignment by combinatorial labeling: Application to a small molecule binding study. Biopolymers 2017; 107. [PMID: 28035667 DOI: 10.1002/bip.23013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 12/21/2022]
Abstract
Selective labeling with stable isotopes has long been recognized as a valuable tool in protein NMR to alleviate signal overlap and sensitivity limitations. In this study, combinatorial 15 N-, 13 Cα -, and 13 C'-selective labeling has been used during the backbone assignment of human cyclophilin D to explore binding of an inhibitor molecule. Using a cell-free expression system, a scheme that involves 15 N, 1-13 C, 2-13 C, fully 15 N/13 C, and unlabeled amino acids was optimized to gain a maximum of assignment information from three samples. This scheme was combined with time-shared triple-resonance NMR experiments, which allows a fast and efficient backbone assignment by giving the unambiguous assignment of unique amino acid pairs in the protein, the identity of ambiguous pairs and information about all 19 non-proline amino acid types. It is therefore well suited for binding studies where de novo assignments of amide 1 H and 15 N resonances need to be obtained, even in cases where sensitivity is the limiting factor.
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Affiliation(s)
- Christopher Hein
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, 60438, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, 60438, Germany
| | - Daniel Schwarz
- Merck KGaA, Discovery Pharmacology, Global Research and Development, Darmstadt, 64293, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, 60438, Germany
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8
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Augustyniak R, Stanek J, Colaux H, Bodenhausen G, Koźmiński W, Herrmann T, Ferrage F. Nuclear overhauser spectroscopy of chiral CHD methylene groups. JOURNAL OF BIOMOLECULAR NMR 2016; 64:27-37. [PMID: 26614488 DOI: 10.1007/s10858-015-0002-0] [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: 06/23/2015] [Accepted: 11/12/2015] [Indexed: 06/05/2023]
Abstract
Nuclear magnetic resonance spectroscopy (NMR) can provide a great deal of information about structure and dynamics of biomolecules. The quality of an NMR structure strongly depends on the number of experimental observables and on their accurate conversion into geometric restraints. When distance restraints are derived from nuclear Overhauser effect spectroscopy (NOESY), stereo-specific assignments of prochiral atoms can contribute significantly to the accuracy of NMR structures of proteins and nucleic acids. Here we introduce a series of NOESY-based pulse sequences that can assist in the assignment of chiral CHD methylene protons in random fractionally deuterated proteins. Partial deuteration suppresses spin-diffusion between the two protons of CH2 groups that normally impedes the distinction of cross-relaxation networks for these two protons in NOESY spectra. Three and four-dimensional spectra allow one to distinguish cross-relaxation pathways involving either of the two methylene protons so that one can obtain stereospecific assignments. In addition, the analysis provides a large number of stereospecific distance restraints. Non-uniform sampling was used to ensure optimal signal resolution in 4D spectra and reduce ambiguities of the assignments. Automatic assignment procedures were modified for efficient and accurate stereospecific assignments during automated structure calculations based on 3D spectra. The protocol was applied to calcium-loaded calbindin D9k. A large number of stereospecific assignments lead to a significant improvement of the accuracy of the structure.
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Affiliation(s)
- Rafal Augustyniak
- Département de chimie, Ecole Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 6, 4 Place Jussieu, 75005, Paris, France
- UMR 7203 LBM, CNRS, 75005, Paris, France
| | - Jan Stanek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Henri Colaux
- Département de chimie, Ecole Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 6, 4 Place Jussieu, 75005, Paris, France
- UMR 7203 LBM, CNRS, 75005, Paris, France
| | - Geoffrey Bodenhausen
- Département de chimie, Ecole Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 6, 4 Place Jussieu, 75005, Paris, France
- UMR 7203 LBM, CNRS, 75005, Paris, France
- Ecole Polytechnique Fédérale de Lausanne, Institut des Sciences et Ingénierie Chimiques, BCH, 1015, Lausanne, Switzerland
| | - Wiktor Koźmiński
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Torsten Herrmann
- Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, Université de Lyon/UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Fabien Ferrage
- Département de chimie, Ecole Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005, Paris, France.
- Sorbonne Universités, UPMC Université Paris 6, 4 Place Jussieu, 75005, Paris, France.
- UMR 7203 LBM, CNRS, 75005, Paris, France.
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9
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Milbradt AG, Arthanari H, Takeuchi K, Boeszoermenyi A, Hagn F, Wagner G. Increased resolution of aromatic cross peaks using alternate 13C labeling and TROSY. JOURNAL OF BIOMOLECULAR NMR 2015; 62:291-301. [PMID: 25957757 PMCID: PMC4782774 DOI: 10.1007/s10858-015-9944-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 05/02/2015] [Indexed: 05/21/2023]
Abstract
For typical globular proteins, contacts involving aromatic side chains would constitute the largest number of distance constraints that could be used to define the structure of proteins and protein complexes based on NOE contacts. However, the (1)H NMR signals of aromatic side chains are often heavily overlapped, which hampers extensive use of aromatic NOE cross peaks. Some of this overlap can be overcome by recording (13)C-dispersed NOESY spectra. However, the resolution in the carbon dimension is rather low due to the narrow dispersion of the carbon signals, large one-bond carbon-carbon (C-C) couplings, and line broadening due to chemical shift anisotropy (CSA). Although it has been noted that the CSA of aromatic carbons could be used in TROSY experiments for enhancing resolution, this has not been used much in practice because of complications arising from large aromatic one-bond C-C couplings, and 3D or 4D carbon dispersed NOESY are typically recorded at low resolution hampering straightforward peak assignments. Here we show that the aromatic TROSY effect can optimally be used when employing alternate (13)C labeling using 2-(13)C glycerol, 2-(13)C pyruvate, or 3-(13)C pyruvate as the carbon source. With the elimination of the strong one-bond C-C coupling, the TROSY effect can easily be exploited. We show that (1)H-(13)C TROSY spectra of alternately (13)C labeled samples can be recorded at high resolution, and we employ 3D NOESY aromatic-TROSY spectra to obtain valuable intramolecular and intermolecular cross peaks on a protein complex.
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Affiliation(s)
- Alexander G. Milbradt
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Koh Takeuchi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Andras Boeszoermenyi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Franz Hagn
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dept. of Chemistry and Institute for Advanced Study, Technische Universität München, 85748 Garching, Germany
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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10
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Tugarinov V. Indirect use of deuterium in solution NMR studies of protein structure and hydrogen bonding. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 77:49-68. [PMID: 24411830 DOI: 10.1016/j.pnmrs.2013.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 08/15/2013] [Indexed: 06/03/2023]
Abstract
A description of the utility of deuteration in protein NMR is provided with an emphasis on quantitative evaluation of the effects of deuteration on a number of NMR parameters of proteins: (1) chemical shifts, (2) scalar coupling constants, (3) relaxation properties (R1 and R2 rates) of nuclei directly attached to one or more deuterons as well as protons of methyl groups in a highly deuterated environment, (4) scalar relaxation of 15N and 13C nuclei in 15N-D and 13C-D spin systems as a measure of hydrogen bonding strength, and (5) NOE-based applications of deuteration in NMR studies of protein structure. The discussion is restricted to the 'indirect' use of deuterium in the sense that the description of NMR parameters and properties of the nuclei affected by nearby deuterons (15N, 13C, 1H) is provided rather than those of deuterium itself.
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Affiliation(s)
- Vitali Tugarinov
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States.
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11
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Lundström P, Ahlner A, Blissing AT. Isotope labeling methods for relaxation measurements. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 992:63-82. [PMID: 23076579 DOI: 10.1007/978-94-007-4954-2_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Nuclear magnetic spin relaxation has emerged as a powerful technique for probing molecular dynamics. Not only is it possible to use it for determination of time constant(s) for molecular reorientation but it can also be used to characterize internal motions on time scales from picoseconds to seconds. Traditionally, uniformly (15)N labeled samples have been used for these experiments but it is clear that this limits the applications. For instance, sensitivity for large systems is dramatically increased if dynamics is probed at methyl groups and structural characterization of low-populated states requires measurements on (13)Cα, (13)Cβ or (13)CO or (1)Hα. Unfortunately, homonuclear scalar couplings may lead to artifacts in the latter types of experiments and selective isotopic labeling schemes that only label the desired position are necessary. Both selective and uniform labeling schemes for measurements of relaxation rates for a large number of positions in proteins are discussed in this chapter.
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Affiliation(s)
- Patrik Lundström
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.
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12
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Sastry M, Bewley CA, Kwong PD. Mammalian expression of isotopically labeled proteins for NMR spectroscopy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 992:197-211. [PMID: 23076586 DOI: 10.1007/978-94-007-4954-2_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
NMR spectroscopic characterization of biologically interesting proteins generally requires the incorporation of (15)N/(13)C and/or (2)H stable isotopes. While prokaryotic incorporation systems are regularly used, mammalian ones are not: of the nearly 9,000 NMR macromolecular structures currently deposited in the Protein Data Bank, only a handful (<0.5%) were solved with proteins expressed in mammalian systems. This low number of structures is largely a reflection of the difficulty in producing uniformly labeled, mammalian-expressed proteins. This is unfortunate, as many interesting proteins require mammalian cofactors, chaperons, or post-translational modifications such as N-linked glycosylation, and mammalian cells have the necessary machinery to produce them correctly. Here we describe recent advances in mammalian expression, including an efficient adenoviral vector-based system, for the production of isotopically enriched proteins. This system allows for the expression of mammalian proteins and their complexes, including proteins that require post-translational modifications. We describe how this system can produce isotopically labeled (15)N and (13)C post-translationally modified proteins, such as the outer domain of HIV-1 gp120, which has 15 sites of N-linked glycosylation. Selective amino-acid labeling is also described. These developments should reduce barriers to the determination of NMR structures with isotopically labeled proteins from mammalian expression systems.
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Affiliation(s)
- Mallika Sastry
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-3027, USA.
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13
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Su XC, Loh CT, Qi R, Otting G. Suppression of isotope scrambling in cell-free protein synthesis by broadband inhibition of PLP enymes for selective 15N-labelling and production of perdeuterated proteins in H2O. JOURNAL OF BIOMOLECULAR NMR 2011; 50:35-42. [PMID: 21318579 DOI: 10.1007/s10858-011-9477-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 01/26/2011] [Indexed: 05/30/2023]
Abstract
Selectively isotope labelled protein samples can be prepared in vivo or in vitro from selectively labelled amino acids but, in many cases, metabolic conversions between different amino acids result in isotope scrambling. The best results are obtained by cell-free protein synthesis, where metabolic enzymes are generally less active, but isotope scrambling can never be suppressed completely. We show that reduction of E. coli S30 extracts with NaBH(4) presents a simple and inexpensive way to achieve cleaner selective isotope labelling in cell-free protein synthesis reactions. The purpose of the NaBH(4) is to inactivate all pyridoxal-phosphate (PLP) dependent enzymes by irreversible reduction of the Schiff bases formed between PLP and lysine side chains of the enzymes or amino groups of free amino acids. The reduced S30 extracts retain their activity of protein synthesis, can be stored as well as conventional S30 extracts and effectively suppress conversions between different amino acids. In addition, inactivation of PLP-dependent enzymes greatly stabilizes hydrogens bound to α-carbons against exchange with water, minimizing the loss of α-deuterons during cell-free production of proteins from perdeuterated amino acids in H(2)O solution. This allows the production of highly perdeuterated proteins that contain protons at all exchangeable positions, without having to back-exchange labile deuterons for protons as required for proteins that have been synthesized in D(2)O.
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Affiliation(s)
- Xun-Cheng Su
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
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14
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Enhanced, simplified expression of perdeuterated hemoglobin for NMR structure and dynamics. Protein Expr Purif 2010; 72:8-18. [DOI: 10.1016/j.pep.2010.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 02/19/2010] [Accepted: 03/05/2010] [Indexed: 02/02/2023]
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15
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Vögeli B, Friedmann M, Leitz D, Sobol A, Riek R. Quantitative determination of NOE rates in perdeuterated and protonated proteins: practical and theoretical aspects. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 204:290-302. [PMID: 20381391 DOI: 10.1016/j.jmr.2010.03.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 03/10/2010] [Accepted: 03/10/2010] [Indexed: 05/27/2023]
Abstract
Precision and accuracy are the limiting factors in extracting structural and dynamic information from experimental NOEs. In this study, error sources at all stages of such an analysis are identified and errors are estimated. The data set of H(N)-H(N) cross-relaxation rates obtained from triple-labeled ubiquitin presented in [B. Vögeli, T.F. Segawa, D. Leitz, A. Sobol, A. Choutko, D. Trzesniak, W. van Gunsteren, R. Riek, J. Am. Chem. Soc. 131 (47) (2009) 17215-17225] is extended to rates obtained from a double-labeled sample. Analog data sets are presented for GB3. It is shown that quantitative NOE rates can be determined with high accuracy from both triple-labeled as well as double-labeled samples. The quality of experimental cross-relaxation rates obtained from 3D HXQC-NOESY and NOESY-HXQC experiments is discussed. It is shown that NOESY-HXQC experiments provide rates of the same quality as HXQC-NOESY if both diagonal and cross peaks for a spin pair can be resolved. Expressions for cross-relaxation rates for anisotropically tumbling molecules exhibiting fast and slow motion are derived. The impact of anisotropy on the prediction of cross-relaxation rates and on the conversion of experimental rates into effective distances is discussed. For molecules with anisotropy D(II)/D( perpendicular) up to five the distance error is smaller than 2%. Finally, "averaged order parameters" are calculated for specific secondary-structural elements showing similar trends for ubiquitin and GB3.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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16
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Abstract
BACKGROUND: Drug discovery is a complex and unpredictable endeavor with a high failure rate. Current trends in the pharmaceutical industry have exasperated these challenges and are contributing to the dramatic decline in productivity observed over the last decade. The industrialization of science by forcing the drug discovery process to adhere to assembly-line protocols is imposing unnecessary restrictions, such as short project time-lines. Recent advances in nuclear magnetic resonance are responding to these self-imposed limitations and are providing opportunities to increase the success rate of drug discovery. OBJECTIVE/METHOD: A review of recent advancements in NMR technology that have the potential of significantly impacting and benefiting the drug discovery process will be presented. These include fast NMR data collection protocols and high-throughput protein structure determination, rapid protein-ligand co-structure determination, lead discovery using fragment-based NMR affinity screens, NMR metabolomics to monitor in vivo efficacy and toxicity for lead compounds, and the identification of new therapeutic targets through the functional annotation of proteins by FAST-NMR. CONCLUSION: NMR is a critical component of the drug discovery process, where the versatility of the technique enables it to continually expand and evolve its role. NMR is expected to maintain this growth over the next decade with advancements in automation, speed of structure calculation, in-cell imaging techniques, and the expansion of NMR amenable targets.
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Affiliation(s)
- Robert Powers
- Department of Chemistry, University of Nebraska Lincoln, Lincoln, NE 68588
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17
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Lundström P, Lin H, Kay LE. Measuring 13Cbeta chemical shifts of invisible excited states in proteins by relaxation dispersion NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2009; 44:139-155. [PMID: 19448976 DOI: 10.1007/s10858-009-9321-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 04/20/2009] [Indexed: 05/26/2023]
Abstract
A labeling scheme is introduced that facilitates the measurement of accurate (13)C(beta) chemical shifts of invisible, excited states of proteins by relaxation dispersion NMR spectroscopy. The approach makes use of protein over-expression in a strain of E. coli in which the TCA cycle enzyme succinate dehydrogenase is knocked out, leading to the production of samples with high levels of (13)C enrichment (30-40%) at C(beta) side-chain carbon positions for 15 of the amino acids with little (13)C label at positions one bond removed (approximately 5%). A pair of samples are produced using [1-(13)C]-glucose/NaH(12)CO(3) or [2-(13)C]-glucose as carbon sources with isolated and enriched (>30%) (13)C(beta) positions for 11 and 4 residues, respectively. The efficacy of the labeling procedure is established by NMR spectroscopy. The utility of such samples for measurement of (13)C(beta) chemical shifts of invisible, excited states in exchange with visible, ground conformations is confirmed by relaxation dispersion studies of a protein-ligand binding exchange reaction in which the extracted chemical shift differences from dispersion profiles compare favorably with those obtained directly from measurements on ligand free and fully bound protein samples.
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Affiliation(s)
- Patrik Lundström
- Molecular Biotechnology/IFM, Linköping University, 581 83, Linköping, Sweden
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18
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Abstract
Information on local dynamics of antibodies is important to evaluate stability, to rationally design variants, and to clarify conformational disorders at the epitope binding sites. Such information may also be useful for improved understanding of antigen recognition. NMR can be used for characterization of local protein dynamics at the atomic level through relaxation measurements. Due to the complexity of the NMR spectra, an extensive use of this method is limited to small protein molecules, for example, antibody domains and some scFv. Here, we describe a protocol that was used to study the dynamics of an antibody domain in solution using NMR. We describe protein preparation for NMR studies, NMR sample optimization, signal assignments, and dynamics experiments.
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Affiliation(s)
- Bang K Vu
- NCI-Frederick, National Institutes of Health, Frederick, MD, USA
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19
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Key labeling technologies to tackle sizeable problems in RNA structural biology. Int J Mol Sci 2008; 9:1214-1240. [PMID: 19325801 PMCID: PMC2635727 DOI: 10.3390/ijms9071214] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Revised: 06/06/2008] [Accepted: 07/14/2008] [Indexed: 01/09/2023] Open
Abstract
The ability to adopt complex three-dimensional (3D) structures that can rapidly interconvert between multiple functional states (folding and dynamics) is vital for the proper functioning of RNAs. Consequently, RNA structure and dynamics necessarily determine their biological function. In the post-genomic era, it is clear that RNAs comprise a larger proportion (>50%) of the transcribed genome compared to proteins (< or =2%). Yet the determination of the 3D structures of RNAs lags considerably behind those of proteins and to date there are even fewer investigations of dynamics in RNAs compared to proteins. Site specific incorporation of various structural and dynamic probes into nucleic acids would likely transform RNA structural biology. Therefore, various methods for introducing probes for structural, functional, and biotechnological applications are critically assessed here. These probes include stable isotopes such as (2)H, (13)C, (15)N, and (19)F. Incorporation of these probes using improved RNA ligation strategies promises to change the landscape of structural biology of supramacromolecules probed by biophysical tools such as nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography and Raman spectroscopy. Finally, some of the structural and dynamic problems that can be addressed using these technological advances are outlined.
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20
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Wang Y, Filippov I, Richter C, Luo R, Kriwacki RW. Solution NMR studies of an intrinsically unstructured protein within a dilute, 75 kDa eukaryotic protein assembly; probing the practical limits for efficiently assigning polypeptide backbone resonances. Chembiochem 2006; 6:2242-6. [PMID: 16270364 DOI: 10.1002/cbic.200500260] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This paper describes an efficient NMR strategy for assigning the backbone resonances of an intrinsically unstructured protein (IUP), p21-KID, bound to its biological target, Cdk2/cyclin A. In order to overcome the challenges associated with the high molecular weight (75 kDa) and low solubility of the ternary complex (0.2 mM), we used perdeuteration, TROSY, and high-sensitivity cryogenic NMR probes at high magnetic-field strengths (i.e. 16.4, 18.8 and 21.1 Tesla). p21-KID was also prepared by using specific amino acid isotope labels. Most importantly, we studied binary, subcomplexes that allowed resonance assignments to be made in stages. We show that subdomains of p21-KID folded within binary complexes into the same conformations as observed in the ternary, Cdk2/cyclin A complex. This is a general feature of IUPs, which often adopt highly extended conformations when bound to other proteins. This strategy is suitable for studies of IUPs within considerably larger biomolecular assemblies as long as the IUP can be uniformly and selectively isotope labeled.
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Affiliation(s)
- Yuefeng Wang
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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21
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Paliy O, Gunasekera TS. Growth of E. coli BL21 in minimal media with different gluconeogenic carbon sources and salt contents. Appl Microbiol Biotechnol 2006; 73:1169-72. [PMID: 16944129 DOI: 10.1007/s00253-006-0554-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Revised: 06/20/2006] [Accepted: 06/21/2006] [Indexed: 11/26/2022]
Abstract
Escherichia coli strain BL21 is commonly used as a host strain for protein expression and purification. For structural analysis, proteins are frequently isotopically labeled with deuterium (2H), 13C, or 15N by growing E. coli cultures in a medium containing the appropriate isotope. When large quantities of fully deuterated proteins are required, E. coli is often grown in minimal media with deuterated succinate or acetate as the carbon source because these are less expensive. Despite the widespread use of BL21, we found no data on the effect of different minimal media and carbon sources on BL21 growth. In this study, we assessed the growth behavior of E. coli BL21 in minimal media with different gluconeogenic carbon sources. Though BL21 grew reasonably well on glycerol and pyruvate, it had a prolonged lag-phase on succinate (20 h), acetate (10 h), and fumarate (20 h), attributed to the physiological adaptation of E. coli cells. Wild-type strain NCM3722 (K12) grew well on all the substrates. We also examined the growth of E. coli BL21 in minimal media that differed in their salt composition but not in their source of carbon. The commonly used M9 medium did not support the optimum growth of E. coli BL21 in minimal medium. The addition of ferrous sulphate to M9 medium (otherwise lacking it) increased the growth rate of E. coli cultures and significantly increased their cell density in the stationary phase.
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Affiliation(s)
- Oleg Paliy
- Department of Biochemistry and Molecular Biology, Wright State University, 256 BioSciences, 3640 Col. Glenn Hwy, Dayton, OH 45435, USA.
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22
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Haon S, Augé S, Tropis M, Milon A, Lindley ND. Low cost production of perdeuterated biomass using methylotrophic yeasts. J Labelled Comp Radiopharm 2006. [DOI: 10.1002/jlcr.2580331108] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Pierce A, deWaal E, Van Remmen H, VanRemmen H, Richardson A, Chaudhuri A. A Novel Approach for Screening the Proteome for Changes in Protein Conformation. Biochemistry 2006; 45:3077-85. [PMID: 16503663 DOI: 10.1021/bi052031i] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Changes in surface hydrophobicity are generally considered as a sensitive indicator for monitoring the structural alterations of proteins that are often associated with changes in function. Currently, no technique has been developed to screen a complex mixture of proteins for changes in the conformation of specific proteins. In this study, we adapted a UV photolabeling approach, using an apolar fluorescent probe, 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (BisANS), to monitor changes in surface hydrophobic domains in either purified rhodanese or skeletal muscle cytosolic proteins by urea-induced unfolding or in response to in vitro metal-catalyzed oxidation. Using two-dimensional polyacrylamide gel electrophoresis (2D PAGE), we identified two specific proteins in skeletal muscle cytosol that exhibited a marked loss of incorporation of BisANS after exposure to in vitro oxidative stress: creatine kinase (CK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). We found that the activities of both enzymes were also reduced significantly in response to oxidative stress. We then determined if this method could detect changes in surface hydrophobicity in specific proteins arising from oxidative stress generated in vivo by muscle denervation. A loss in surface hydrophobic domains in CK and GAPDH was again observed as measured by the BisANS photoincorporation approach. In addition, the CK and GAPDH activity in denervated muscle was markedly reduced. These data demonstrate for the first time that this assay can screen a complex mixture of proteins for alterations in surface hydrophobic domains of individual proteins.
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Affiliation(s)
- Anson Pierce
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
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24
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Tugarinov V, Kay LE. Methyl groups as probes of structure and dynamics in NMR studies of high-molecular-weight proteins. Chembiochem 2006; 6:1567-77. [PMID: 16075427 DOI: 10.1002/cbic.200500110] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Vitali Tugarinov
- Department of Medical Genetics and Microbiology, University of Toronto, Medical Sciences Building, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
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25
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Bromek K, Lee D, Hauhart R, Krych-Goldberg M, Atkinson JP, Barlow PN, Pervushin K. Polychromatic Selective Population Inversion for TROSY Experiments with Large Proteins. J Am Chem Soc 2004; 127:405-11. [PMID: 15631491 DOI: 10.1021/ja0462326] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper presents polychromatic selective polarization inversion (PC-SPI) as an alternative to the polarization transfer methods recently developed for the application of NMR to large biological molecules. Theoretical and numerical considerations indicate that PC-SPI has the potential for more efficient polarization transfer under conditions of rapid transverse relaxation compared to J coupling- and cross-correlated relaxation-based transfers. The main advantage offered by the method presented here is the maintenance of near-optimal trajectories of inversion of the individual components of the spin magnetization while using broadband optimized pulses. A 2D experiment was implemented combining PC-SPI with TROSY-based chemical shift correlation. The experiment was applied to detect (15)N-(1)H chemical shift correlation spectra of a 200 kDa complex consisting of an 80% (2)H- and uniformly (15)N,(13)C-labeled 22 kDa portion of complement receptor type 1 and unlabeled C3b of complement (180 kDa).
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Affiliation(s)
- Krystyna Bromek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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26
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Zheng Y, Giovannelli JL, Ho NT, Ho C, Yang D. Side-chain assignments of methyl-containing residues in a uniformly 13C-labeled hemoglobin in the carbonmonoxy form. JOURNAL OF BIOMOLECULAR NMR 2004; 30:423-429. [PMID: 15630562 DOI: 10.1007/s10858-004-4345-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2004] [Accepted: 09/28/2004] [Indexed: 05/24/2023]
Abstract
Sequence-specific assignment of the methyl groups in large proteins can be obtained from an MQ-(H)CC(m)H(m)-TOCSY experiment on uniformly (13)C-labeled proteins without deuteration (Yang et al., 2004). Here the procedure is further demonstrated on a uniformly (13)C-labeled alpha-chain or beta-chain of human normal adult hemoglobin (65 kDa) in the carbonmonoxy form. In addition, a strategy is presented for assigning protons of methyl-containing residues of uniformly (13)C-labeled large proteins, on the basis of prior methyl assignments based on MQ-(H)CCH-TOCSY and H(C)C(m)H(m)-TOCSY experiments. Assignment of about 80% of the side-chain resonances of methyl-containing residues of carbonmonoxyhemoglobin has been obtained.
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Affiliation(s)
- Yu Zheng
- Department of Biological Sciences, The National University of Singapore, 14 Science Drive 4, Singapore, 117543
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27
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Abstract
Recent developments in NMR spectroscopy, which include new experiments that increase the lifetimes of NMR signals or that precisely define the orientation of internuclear bond vectors with respect to a common molecular frame, have significantly increased the size of proteins for which quantitative structural and dynamic information can be obtained. These experiments have, in turn, benefited from new labeling strategies that continue to drive the field. The utility of the new methodology is illustrated by considering applications to malate synthase G, a 723 residue enzyme, which is the largest single polypeptide chain for which chemical shift assignments have been obtained to date. New experiments developed specifically to address the complexity and low sensitivity of spectra recorded on this protein are presented. A discussion of the chemical information that is readily available from studies of systems in the 100 kDa mol wt range is included. Prospects for membrane protein structure determination are discussed briefly in the context of an application to an Escherichia coli enzyme, PagP, localized to the outer membrane of gram-negative bacteria.
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Affiliation(s)
- Vitali Tugarinov
- Department of Medical Genetics, University of Toronto, Ontario, Canada M5S 1A8.
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28
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Hajduk PJ, Mack JC, Olejniczak ET, Park C, Dandliker PJ, Beutel BA. SOS-NMR: a saturation transfer NMR-based method for determining the structures of protein-ligand complexes. J Am Chem Soc 2004; 126:2390-8. [PMID: 14982445 DOI: 10.1021/ja039480v] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An NMR-based alternative to traditional X-ray crystallography and NMR methods for structure-based drug design is described that enables the structure determination of ligands complexed to virtually any biomolecular target regardless of size, composition, or oligomeric state. The method utilizes saturation transfer difference (STD) NMR spectroscopy performed on a ligand complexed to a series of target samples that have been deuterated everywhere except for specific amino acid types. In this way, the amino acid composition of the ligand-binding site can be defined, and, given the three-dimensional structure of the protein target, the three-dimensional structure of the protein-ligand complex can be determined. Unlike earlier NMR methods for solving the structures of protein-ligand complexes, no protein resonance assignments are necessary. Thus, the approach has broad potential applications--especially in cases where X-ray crystallography and traditional NMR methods have failed to produce structural data. The method is called SOS-NMR for structural information using Overhauser effects and selective labeling and is validated on two protein-ligand complexes: FKBP complexed to 2-(3'-pyridyl)-benzimidazole and MurA complexed to uridine diphosphate N-acetylglucosamine.
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Affiliation(s)
- Philip J Hajduk
- Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, Illinois 60064, USA.
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29
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Vögeli B, Kovacs H, Pervushin K. Measurements of side-chain 13C-13C residual dipolar couplings in uniformly deuterated proteins. J Am Chem Soc 2004; 126:2414-20. [PMID: 14982448 DOI: 10.1021/ja0381813] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
13C-only spectroscopy was used to measure multiple residual (13)C-(13)C dipolar couplings (RDCs) in uniformly deuterated and (13)C-labeled proteins. We demonstrate that (13)C-start and (13)C-observe spectra can be routinely used to measure an extensive set of the side-chain residual (13)C-(13)C dipolar couplings upon partial alignment of human ubiquitin in the presence of bacteriophages Pf1. We establish that, among different broadband polarization transfer schemes, the FLOPSY family can be used to exchange magnetization between a J coupled network of spins while largely decoupling dipolar interactions between these spins. An excellent correlation between measured RDCs and the 3D structure of the protein was observed, indicating a potential use of the (13)C-(13)C RDCs in the structure determination of perdeuterated proteins.
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Affiliation(s)
- Beat Vögeli
- Laboratorium für Physikalische Chemie, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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30
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Paliy O, Bloor D, Brockwell D, Gilbert P, Barber J. Improved methods of cultivation and production of deuteriated proteins from E. coli strains grown on fully deuteriated minimal medium. J Appl Microbiol 2003; 94:580-6. [PMID: 12631193 DOI: 10.1046/j.1365-2672.2003.01866.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS The aim was to develop reliable and economical protocols for the production of fully deuteriated biomolecules by bacteria. This required the preparation of deuterium-tolerant bacterial strains and an understanding of the physiological mechanisms of acquisition of deuterium tolerance. METHODS AND RESULTS We report here improved methods for the cultivation of Escherichia coli on fully deuteriated minimal medium. A multi-stage adaptation protocol was developed; this included repeated plating and selection of colonies and resulted in highly deuterium-tolerant cell cultures. Three E. coli strains, JM109, MRE600 and MRE600Rif, were adapted to growth on deuteriated succinate medium. This is the first report of JM109 being adapted to deuteriated minimal media. The adapted strains showed good, consistent growth rates and were capable of being transformed with plasmids. Expression of heterologous proteins in these strains was reliable and yields were consistently high (100-200 mg l-1). We also show that all E. coli cells are inherently capable of growth on deuteriated media. CONCLUSIONS We have developed a new adaptation protocol that resulted in three highly deuterium-tolerant E. coli strains. Deuterium-adapted cultures produced good yields of a deuteriated recombinant protein. We suggest that E. coli cells are inherently capable of growth on deuteriated media, but that non-specific mutations enhance deuterium tolerance. Thus plating and selection of colonies leads to highly deuterium-tolerant strains. SIGNIFICANCE AND IMPACT OF STUDY An understanding of the mechanism of adaptation of E. coli to growth on deuteriated media allows strategies for the development of disabled deuterium-tolerant strains suitable for high-level production of deuteriated recombinant proteins and other biomolecules. This is of particular importance for nuclear magnetic resonance and neutron scattering studies of biomolecules.
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Affiliation(s)
- O Paliy
- School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
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31
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Lippens G, Bodart PR, Taulelle F, Amoureux JP. Restricted linear least square treatment processing of heteronuclear spectra of biomolecules using the ANAFOR strategy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2003; 161:174-182. [PMID: 12713967 DOI: 10.1016/s1090-7807(03)00005-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We explore the use of a processing procedure based on restricted least square minimization as a tool for reducing the time versus resolution dilemma often encountered for biomolecular multidimensional spectra. Using a 2D spectrum as a reference, we obtain the necessary input of frequency components and linewidths. Combined even with a limited time evolution in the indirect dimension, the amplitudes of the correlation peaks in all planes of the 3D spectra can be extracted, and can be used to reconstruct the interferograms in the third dimension. Parameters such as number of lines, threshold choice, resolution, lineshape, number of experimental data points and finally signal to noise ratio of the spectrum are examined starting from a triple-resonance HNCA spectrum of ubiquitin.
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Affiliation(s)
- Guy Lippens
- Université de Lille2, CNRS-UMR 8525, Institut Pasteur de Lille, 1 rue du Professeur Calmette BP447, 59021, Lille Cedex, France.
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32
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Stereoselective route to 15N-labeled-β-deuterated amino acids: synthesis of (2S,3R)-[3-2H,15N]-phenylalanine. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0957-4166(02)00487-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Shekhtman A, Ghose R, Goger M, Cowburn D. NMR structure determination and investigation using a reduced proton (REDPRO) labeling strategy for proteins. FEBS Lett 2002; 524:177-82. [PMID: 12135763 DOI: 10.1016/s0014-5793(02)03051-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present here a stable isotope labeling technique for proteins, which seeks the appropriate compromise between the advantages of (a) random isotope labeling, with its large number of protons available for structure determination, and (b) selective labeling to generate isolated proton spins decreasing spectral complexity and improving relaxation properties of NMR experiments. The described reduced proton (REDPRO) procedure results in side-chain specific protonation of overexpressed proteins, which is highly selective. The REDPRO labeling scheme provides a sufficient number of NOE constraints for structure calculation. Dramatically improved relaxation properties of the heteronuclear magnetization transfer coupled with TROSY advantages make the proposed labeling scheme an attractive approach for study of high molecular weight protein targets, their ligand sites, and interdomain interactions.
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35
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Lee AL, Flynn PF, Wand AJ. Comparison of 2H and 13C NMR Relaxation Techniques for the Study of Protein Methyl Group Dynamics in Solution. J Am Chem Soc 1999. [DOI: 10.1021/ja983758f] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew L. Lee
- Contribution from the The Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059
| | - Peter F. Flynn
- Contribution from the The Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059
| | - A. Joshua Wand
- Contribution from the The Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059
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36
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McCallum SA, Hitchens TK, Rule GS. Unambiguous correlations of backbone amide and aliphatic gamma resonances in deuterated proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1998; 134:350-354. [PMID: 9761709 DOI: 10.1006/jmre.1998.1525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Two 3D NMR pulse sequences that correlate aliphatic gamma carbon resonance frequencies to amide proton and nitrogen chemical shifts in perdeuterated proteins are presented. The HN(COCACB)CG provides only interresidue connectivities (NH(i) and Cgamma(i-1)) while the HN(CACB)CG detects both the inter- and intraresidue (NH(i) and Cgamma(i) or Cgamma(i-1)) correlations. These two experiments are useful for sequential assignments and the identification of residue type from the Cgamma shifts. Spectra acquired on a perdeuterated 53-kDa protein illustrate the sensitivity and utility of these experiments.
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Affiliation(s)
- S A McCallum
- Department of Biochemistry, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
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37
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McKay RT, Pearlstone JR, Corson DC, Gagné SM, Smillie LB, Sykes BD. Structure and interaction site of the regulatory domain of troponin-C when complexed with the 96-148 region of troponin-I. Biochemistry 1998; 37:12419-30. [PMID: 9730814 DOI: 10.1021/bi9809019] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The structure of the regulatory domain of chicken skeletal troponin-C (residues 1-90) when complexed with the major inhibitory region (residues 96-148) of chicken skeletal troponin-I was determined using multinuclear, multidimensional NMR spectroscopy. This complex represents the first interaction formed between the regulatory domain of troponin-C and troponin-I after calcium binding in the regulation of muscle contraction. The stoichiometry of the complex was determined to be 1:1, with a dissociation constant in the 1-40 microM range. The structure of troponin-C in the complex was calculated from 1039 NMR distance and 111 dihedral angle restraints. When compared to the structure of this domain in the calcium saturated "open" form but in the absence of troponin-I, the bound structure appears to be slightly more "closed". The troponin-I peptide-binding site was found to be in the hydrophobic pocket of calcium saturated troponin-C, using edited/filtered NMR experiments and chemical shift mapping of changes induced in the regulatory domain upon peptide binding. The troponin-I peptide (residues 96-148) was found to bind to the regulatory domain of troponin-C very similarly, but not identically, to a shorter troponin-I peptide (region 115-131) thought to represent the major interaction site of troponin-I for this domain of troponin-C.
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Affiliation(s)
- R T McKay
- MRC Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Canada
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38
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Briercheck DM, Rule GS. Effect of deuteration on the accuracy of HN-HN distance constraints. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1998; 134:52-56. [PMID: 9740730 DOI: 10.1006/jmre.1998.1511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The effect of deuteration on the measurement of HN-HN distances in moderately sized (15 kDa) proteins is discussed. Data are presented for a 15 kDa protein which is 95% deuterated on the Halpha position, and partially (70%) deuterated at other aliphatic sites. Deuteration of the protein increases the signal intensity of HN-HN cross peaks in NOESY spectra such that dipolar couplings between protons 4-5 A apart are readily detected. Experimental data and computer simulations show that either perdeuteration or partial deuteration of the protein increases the accuracy of amide-amide distance constraints. Thus, partial deuteration can be used to obtain more accurate long-range distance constraints for structure determination by NMR.
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Affiliation(s)
- D M Briercheck
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania, USA
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39
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Gardner KH, Kay LE. The use of 2H, 13C, 15N multidimensional NMR to study the structure and dynamics of proteins. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 1998; 27:357-406. [PMID: 9646872 DOI: 10.1146/annurev.biophys.27.1.357] [Citation(s) in RCA: 510] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the past thirty years, deuterium labeling has been used to improve the resolution and sensitivity of protein NMR spectra used in a wide variety of applications. Most recently, the combination of triple resonance experiments and 2H, 13C, 15N labeled samples has been critical to the solution structure determination of several proteins with molecular weights on the order of 30 kDa. Here we review the developments in isotopic labeling strategies, NMR pulse sequences, and structure-determination protocols that have facilitated this advance and hold promise for future NMR-based structural studies of even larger systems. As well, we detail recent progress in the use of solution 2H NMR methods to probe the dynamics of protein sidechains.
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Affiliation(s)
- K H Gardner
- Protein Engineering Network Centres of Excellence, University of Toronto, Ontario, Canada.
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40
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Tolbert TJ, Williamson JR. Preparation of Specifically Deuterated and 13C-Labeled RNA for NMR Studies Using Enzymatic Synthesis. J Am Chem Soc 1997. [DOI: 10.1021/ja9725054] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas J. Tolbert
- Contribution from the Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - James R. Williamson
- Contribution from the Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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41
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Evans PD, Jaseja M, Jeeves M, Hyde EI. NMR studies of the Escherichia coli Trp repressor.trpRs operator complex. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 242:567-75. [PMID: 9022683 DOI: 10.1111/j.1432-1033.1996.0567r.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
To understand the specificity of the Escherichia coli Trp repressor for its operators, we have begun to study complexes of the protein with alternative DNA sequences, using 1H-NMR spectroscopy. We report here the 1H-NMR chemical shifts of a 20-bp oligodeoxynucleotide containing the sequence of a symmetrised form of the trpR operator in the presence and absence of the holorepressor. Deuterated protein was used to assign the spectrum of the oligodeoxynucleotide in a 37-kDa complex with the Trp holorepressor. Many of the resonances of the DNA shift on binding to the protein, which suggests changes in conformation throughout the sequence. The largest changes in shifts for the aromatic protons in the major groove are for A15 and G16, which are thought to hydrogen bond to the protein, possibly via water molecules. We have also examined the effect of DNA binding on the corepressor, tryptophan, in this complex. The indole proton resonance of the tryptophan undergoes a downfield shift of 1.2 ppm upon binding of DNA. This large shift is consistent with hydrogen bonding of the tryptophan to the phosphate backbone of the trpR operator DNA, as in the crystal structure of the holoprotein with the trp operator.
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Affiliation(s)
- P D Evans
- School of Biochemistry, University of Birmingham, Edgbaston, UK
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42
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Tropis M, Bardou F, Bersch B, Daffé M, Milon A. Composition and phase behaviour of polar lipids isolated from Spirulina maxima cells grown in a perdeuterated medium. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1284:196-202. [PMID: 8914584 DOI: 10.1016/s0005-2736(96)00129-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The lipid composition of Spirulina maxima cells grown in a perdeuterated medium was determined by using nuclear magnetic resonance spectroscopy, fast atom-bombardment-mass spectrometry, gas chromatography-mass spectrometry as well as conventional chemical methods. The extent of deuteration was determined by mass spectrometry and was superior to 97.5%. The major lipids identified in the strain were: non-polar lipids (9%), monogalactosyldiacylglycerol (5%), digalactosyldiacylglycerol (22%), phosphatidylglycerol (31%), sulfoquinovosyldiacylglycerol (32%), phosphatidylinositol (traces). The major fatty acids were 16:0 (80%) and 18:1 (15%). These results demonstrate that the adaptation of the cells to D2O did not imply a profound modification of the lipid composition. The perdeuterated polar lipid mixture dispersed into an excess of water organises spontaneously in a lamellar phase as seen by 31P and deuterium solid state NMR and can therefore be used to prepare perdeuterated model membranes with a well defined composition. Liposomes made using these lipids have a gel to liquid-crystalline phase transition in the range 15-27 degrees C and are in a fluid L alpha phase above this temperature.
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Affiliation(s)
- M Tropis
- Laboratoire de Pharmacologie et de Toxicologie Fondamentales du CNRS, Université Paul Sabatier, Toulouse, France
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43
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Smith BO, Ito Y, Raine A, Teichmann S, Ben-Tovim L, Nietlispach D, Broadhurst RW, Terada T, Kelly M, Oschkinat H, Shibata T, Yokoyama S, Laue ED. An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types. JOURNAL OF BIOMOLECULAR NMR 1996; 8:360-368. [PMID: 20686886 DOI: 10.1007/bf00410335] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/1996] [Accepted: 10/02/1996] [Indexed: 05/29/2023]
Abstract
A combination of calculation and experiment is used to demonstrate that the global fold of larger proteins can be rapidly determined using limited NMR data. The approach involves a combination of heteronuclear triple resonance NMR experiments with protonation of selected residue types in an otherwise completely deuterated protein. This method of labelling produces proteins with alpha-specific deuteration in the protonated residues, and the results suggest that this will improve the sensitivity of experiments involving correlation of side-chain ((1)H and (13)C) and backbone ((1)H and (15)N) amide resonances. It will allow the rapid assignment of backbone resonances with high sensitivity and the determination of a reasonable structural model of a protein based on limited NOE restraints, an application that is of increasing importance as data from the large number of genome sequencing projects accumulates. The method that we propose should also be of utility in extending the use of NMR spectroscopy to determine the structures of larger proteins.
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Affiliation(s)
- B O Smith
- Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QW, Cambridge, UK
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44
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Deuteration of amino acids in basic deuterium oxide solution at supercritical temperatures. J Supercrit Fluids 1996. [DOI: 10.1016/s0896-8446(96)90006-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Ramesh V, Syed SE, Frederick RO, Sutcliffe MJ, Barnes M, Roberts GC. NMR studies of the mode of binding of corepressors and inducers to Escherichia coli trp repressor. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 235:804-13. [PMID: 8654432 DOI: 10.1111/j.1432-1033.1996.00804.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The binding of the corepressors tryptophan and 5-methyltryptophan and of the inducers 3-indolepropionate, 3-indoleacrylate and 5-methylindole to the Escherichia coli trp repressor have been studied by 1H-NMR spectroscopy. Identification of the resonances of the protons of bound ligands and their NOEs to protons of the protein (measured as transferred NOE) was greatly facilitated by the use of samples of the protein in which the hydrogens of all residues except alanine, isoleucine and threonine was replaced by deuterium. Chemical-shift changes of protein-backbone resonances and side-chain-amide resonances on ligand binding were measured with generally or selectively 15N-labelled protein. The patterns of changes in the chemical shifts of protein resonances and, particularly, ligand resonances distinguish the corepressors from the inducers, indicating, in agreement with earlier work, that corepressors and inducers bind to the protein in different ways. The NOEs observed for the bond ligands have been used to determine the position of the ligands in the crystallographically determined binding site, by means of a simulated-annealing molecular-dynamics protocol. The structures obtained show that the orientation in the binding site of the indole rings of tryptophan and 5-methyltryptophan and of 3-indolepropionate and 3-indoleacrylate differ by approximately 180 degrees in solution (in agreement with the crystallographic data for complexes of the trp repressor with tryptophan or with 3-indolepropionate). The value and limitations of calculating ligand positions based on transferred NOE are discussed.
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Affiliation(s)
- V Ramesh
- Department of Biochemistry and Biological NMR Centre, University of Leicester, UK
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46
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Nietlispach D, Clowes RT, Broadhurst RW, Ito Y, Keeler J, Kelly M, Ashurst J, Oschkinat H, Domaille PJ, Laue ED. An Approach to the Structure Determination of Larger Proteins Using Triple Resonance NMR Experiments in Conjunction with Random Fractional Deuteration. J Am Chem Soc 1996. [DOI: 10.1021/ja952207b] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Daniel Nietlispach
- Contribution from the Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K., the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, and the Du Pont Merck Pharmaceutical Company, Box 80328, Wilmington, Delaware 19880-0328
| | - Robin T. Clowes
- Contribution from the Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K., the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, and the Du Pont Merck Pharmaceutical Company, Box 80328, Wilmington, Delaware 19880-0328
| | - R. William Broadhurst
- Contribution from the Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K., the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, and the Du Pont Merck Pharmaceutical Company, Box 80328, Wilmington, Delaware 19880-0328
| | - Yutaka Ito
- Contribution from the Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K., the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, and the Du Pont Merck Pharmaceutical Company, Box 80328, Wilmington, Delaware 19880-0328
| | - James Keeler
- Contribution from the Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K., the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, and the Du Pont Merck Pharmaceutical Company, Box 80328, Wilmington, Delaware 19880-0328
| | - Mark Kelly
- Contribution from the Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K., the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, and the Du Pont Merck Pharmaceutical Company, Box 80328, Wilmington, Delaware 19880-0328
| | - Jennifer Ashurst
- Contribution from the Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K., the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, and the Du Pont Merck Pharmaceutical Company, Box 80328, Wilmington, Delaware 19880-0328
| | - Hartmut Oschkinat
- Contribution from the Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K., the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, and the Du Pont Merck Pharmaceutical Company, Box 80328, Wilmington, Delaware 19880-0328
| | - Peter J. Domaille
- Contribution from the Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K., the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, and the Du Pont Merck Pharmaceutical Company, Box 80328, Wilmington, Delaware 19880-0328
| | - Ernest D. Laue
- Contribution from the Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K., the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, and the Du Pont Merck Pharmaceutical Company, Box 80328, Wilmington, Delaware 19880-0328
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47
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Farmer BT, Venters RA. Assignment of aliphatic side-chain 1HN/15N resonances in perdeuterated proteins. JOURNAL OF BIOMOLECULAR NMR 1996; 7:59-71. [PMID: 8720832 DOI: 10.1007/bf00190457] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The perdeuteration of aliphatic sites in large proteins has been shown to greatly facilitate the process of sequential backbone and side-chain 13C assignments and has also been utilized in obtaining long-range NOE distance restraints for structure calculations. To obtain the maximum information from a 4D 15N/15N-separated NOESY, as many main-chain and side-chain 1HN/15N resonances as possible must be assigned. Traditionally, only backbone amide 1HN/15N resonances are assigned by correlation experiments, whereas slowly exchanging side-chain amide, amino, and guanidino protons are assigned by NOEs to side-chain aliphatic protons. In a perdeuterated protein, however, there is a minimal number of such protons. We have therefore developed several gradient-enhanced and sensitivity-enhanced pulse sequences, containing water-flipback pulses, to provide through-bond correlations of the aliphatic side-chain 1HN/15N resonances to side-chain 13C resonances with high sensitivity: NH2-filtered 2D 1H-15N HSQC(H2N-HSQC), 3D H2N(CO)C gamma/beta and 3D H2N(COC gamma/beta)C beta/alpha for glutamine and asparagine side-chain amide groups; 2D refocused H(N epsilon/zeta)C delta/epsilon and H(N epsilon/zeta C delta/epsilon)C gamma/delta for arginine side-chain amino groups and non-refocused versions for lysine side-chain amino groups; and 2D refocused H(N epsilon)C zeta and nonrefocused H(N epsilon, eta)C zeta for arginine side-chain guanidino groups. These pulse sequences have been applied to perdeuterated 13C-/15N-labeled human carbonic anhydrase II (2H-HCA II). Because more than 95% of all side-chain 13C resonances in 2H-HCA II have already been assigned with the C(CC)(CO)NH experiment, the assignment of the side-chain 1HN/15N resonances has been straightforward using the pulse sequences mentioned above. The importance of assigning these side-chain HN protons has been demonstrated by recent studies in which the calculation of protein global folds was simulated using only 1HN-1HN NOE restraints. In these studies, the inclusion of NOE restraints to side-chain HN protons significantly improved the quality of the global fold that could be determined for a perdeuterated protein [R.A. Venters et al. (1995) J. Am. Chem. Soc., 117, 9592-9593].
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Affiliation(s)
- B T Farmer
- Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543-4000, USA
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48
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Hsu VL, Jia X, Kearns DR. Multidimensional NMR spectroscopy of DNA-binding proteins: structure and function of a transcription factor. Toxicol Lett 1995; 82-83:577-89. [PMID: 8597113 DOI: 10.1016/0378-4274(95)03585-0] [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] [Indexed: 01/31/2023]
Abstract
The solution structure of a type II DNA-binding protein (DBPII), transcription factor 1 (TF1), has been determined using NMR spectroscopy. A multidimensional, heteronuclear strategy was employed to overcome assignment ambiguities due to resonance overlap and broadened crosspeaks. This approach involved the use of selectively deuteriated, 13C- and 15N-labeled samples and 'isotopic heterodimers' to distinguish between intra- and intermonomeric NOEs. A comparison with the crystal structure and NMR analysis of the E. coli HU protein suggests that other homologous proteins in this family will possess similar tertiary structures. This NMR strategy is applicable to the study of other proteins and their biomolecular complexes.
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Affiliation(s)
- V L Hsu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331-7305, USA
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49
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Dyson HJ. Nuclear magnetic resonance of thioredoxin and glutaredoxin. Methods Enzymol 1995; 252:293-306. [PMID: 7476364 DOI: 10.1016/0076-6879(95)52032-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- H J Dyson
- Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA
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50
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Perlman ME, Davis DG, Koszalka GW, Tuttle JV, London RE. Studies of inhibitor binding to Escherichia coli purine nucleoside phosphorylase using the transferred nuclear Overhauser effect and rotating-frame nuclear Overhauser enhancement. Biochemistry 1994; 33:7547-59. [PMID: 8011620 DOI: 10.1021/bi00190a007] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
NMR studies of the adenosine analog tubercidin have been carried out in the presence of Escherichia coli purine nucleoside phosphorylase (PNP) in order to characterize the conformation of the enzyme-complexed nucleoside. Although analysis of transferred NOE data at various enzyme/inhibitor ratios indicated a predominantly syn nucleoside conformation in the enzyme-complexed state, the results, particularly the 8(1') and 8(3') NOE interactions, were not quantitatively consistent with any single bound conformation. Dissociation rate constants for the tubercidin-PNP complex were determined based on analysis of chemical shift and line width data as a function of enzyme/inhibitor ratio, Carr-Purcell-Meiboom-Gill measurements of the transverse relaxation rate as a function of pulse rate, and T1 rho experiments as a function of the spin-lock field strength. Dissociation rate constants of 2100 s-1 at 20 degrees C and 1400 s-1 at 10 degrees C were determined using the latter two methods. These rates are sufficiently high to justify the validity of the transferred NOE method for an enzyme as large as PNP. The possible significance of spin diffusion was investigated by the use of the deuterated analog [2'-2H]tubercidin, for which many of the intraligand spin diffusion pathways are eliminated, and by performing a series of transferred ROE experiments. A comparison of data obtained using transferred NOE and ROE measurements provides a basis for separating direct and indirect relaxation pathways. Both approaches indicated that the relatively significant 8(3') NOE interaction was not dominated by spin diffusion. Furthermore, analysis of chemical shift and transverse relaxation data for the tubercidin H-2 resonance gave inconsistent results for the chemical shift of the bound species and was inconsistent with the assumption of a single, bound conformation. These results were interpreted in terms of a 2:1 ratio of a syn, 3'-exo:anti, 3'-endo geometry for bound tubercidin. Ligand competition experiments using 9-deazainosine show that all of the tubercidin TRNOE effects are reversed by addition of the second nucleoside, suggesting that the TRNOE data for tubercidin arise due to interactions at the active sites of PNP rather than as a consequence of nonspecific binding to the enzyme.
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Affiliation(s)
- M E Perlman
- Laboratory of Molecular Biophysics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
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