1
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Waudby C, Christodoulou J. Analysis of conformational exchange processes using methyl-TROSY-based Hahn echo measurements of quadruple-quantum relaxation. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:777-793. [PMID: 37905227 PMCID: PMC10583286 DOI: 10.5194/mr-2-777-2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/14/2021] [Indexed: 11/02/2023]
Abstract
Transverse nuclear spin relaxation is a sensitive probe of chemical exchange on timescales on the order of microseconds to milliseconds. Here we present an experiment for the simultaneous measurement of the relaxation rates of two quadruple-quantum transitions in 13 CH3 -labelled methyl groups. These coherences are protected against relaxation by intra-methyl dipolar interactions and so have unexpectedly long lifetimes within perdeuterated biomacromolecules. However, these coherences also have an order of magnitude higher sensitivity to chemical exchange broadening than lower order coherences and therefore provide ideal probes of dynamic processes. We show that analysis of the static magnetic field dependence of zero-, double- and quadruple-quantum Hahn echo relaxation rates provides a robust indication of chemical exchange and can determine the signed relative magnitudes of proton and carbon chemical shift differences between ground and excited states. We also demonstrate that this analysis can be combined with established Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion measurements, providing improved precision in parameter estimates, particularly in the determination of 1 H chemical shift differences.
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Affiliation(s)
- Christopher A. Waudby
- Institute of Structural and Molecular Biology, University College
London, London, WC1E 6BT, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College
London, London, WC1E 6BT, UK
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
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2
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Liu B, Rangadurai A, Shi H, Al-Hashimi H. Rapid assessment of Watson-Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE imino 1H CEST. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:715-731. [PMID: 37905209 PMCID: PMC10539785 DOI: 10.5194/mr-2-715-2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/05/2021] [Indexed: 11/01/2023]
Abstract
In duplex DNA, Watson-Crick A-T and G-C base pairs (bp's) exist in dynamic equilibrium with an alternative Hoogsteen conformation, which is low in abundance and short-lived. Measuring how the Hoogsteen dynamics varies across different DNA sequences, structural contexts and physiological conditions is key for identifying potential Hoogsteen hot spots and for understanding the potential roles of Hoogsteen base pairs in DNA recognition and repair. However, such studies are hampered by the need to prepare 13 C or 15 N isotopically enriched DNA samples for NMR relaxation dispersion (RD) experiments. Here, using SELective Optimized Proton Experiments (SELOPE) 1 H CEST experiments employing high-power radiofrequency fields (B 1 > 250 Hz) targeting imino protons, we demonstrate accurate and robust characterization of Watson-Crick to Hoogsteen exchange, without the need for isotopic enrichment of the DNA. For 13 residues in three DNA duplexes under different temperature and pH conditions, the exchange parameters deduced from high-power imino 1 H CEST were in very good agreement with counterparts measured using off-resonance 13 C / 15 N spin relaxation in the rotating frame (R 1 ρ ). It is shown that 1 H-1 H NOE effects which typically introduce artifacts in 1 H-based measurements of chemical exchange can be effectively suppressed by selective excitation, provided that the relaxation delay is short (≤ 100 ms). The 1 H CEST experiment can be performed with ∼ 10× higher throughput and ∼ 100× lower cost relative to 13 C / 15 N R 1 ρ and enabled Hoogsteen chemical exchange measurements undetectable by R 1 ρ . The results reveal an increased propensity to form Hoogsteen bp's near terminal ends and a diminished propensity within A-tract motifs. The 1 H CEST experiment provides a basis for rapidly screening Hoogsteen breathing in duplex DNA, enabling identification of unusual motifs for more in-depth characterization.
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Affiliation(s)
- Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
- Department of Chemistry, Duke University, Durham, NC, USA
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3
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Overbeck JH, Kremer W, Sprangers R. A suite of 19F based relaxation dispersion experiments to assess biomolecular motions. JOURNAL OF BIOMOLECULAR NMR 2020; 74:753-766. [PMID: 32997265 PMCID: PMC7701166 DOI: 10.1007/s10858-020-00348-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/18/2020] [Indexed: 05/08/2023]
Abstract
Proteins and nucleic acids are highly dynamic bio-molecules that can populate a variety of conformational states. NMR relaxation dispersion (RD) methods are uniquely suited to quantify the associated kinetic and thermodynamic parameters. Here, we present a consistent suite of 19F-based CPMG, on-resonance R1ρ and off-resonance R1ρ RD experiments. We validate these experiments by studying the unfolding transition of a 7.5 kDa cold shock protein. Furthermore we show that the 19F RD experiments are applicable to very large molecular machines by quantifying dynamics in the 360 kDa half-proteasome. Our approach significantly extends the timescale of chemical exchange that can be studied with 19F RD, adds robustness to the extraction of exchange parameters and can determine the absolute chemical shifts of excited states. Importantly, due to the simplicity of 19F NMR spectra, it is possible to record complete datasets within hours on samples that are of very low costs. This makes the presented experiments ideally suited to complement static structural information from cryo-EM and X-ray crystallography with insights into functionally relevant motions.
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Affiliation(s)
- Jan H Overbeck
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany
| | - Werner Kremer
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany
| | - Remco Sprangers
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany.
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4
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Köhler C, Carlström G, Gunnarsson A, Weininger U, Tångefjord S, Ullah V, Lepistö M, Karlsson U, Papavoine T, Edman K, Akke M. Dynamic allosteric communication pathway directing differential activation of the glucocorticoid receptor. SCIENCE ADVANCES 2020; 6:eabb5277. [PMID: 32832645 PMCID: PMC7439413 DOI: 10.1126/sciadv.abb5277] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 06/05/2020] [Indexed: 05/07/2023]
Abstract
Allosteric communication within proteins is a hallmark of biochemical signaling, but the dynamic transmission pathways remain poorly characterized. We combined NMR spectroscopy and surface plasmon resonance to reveal these pathways and quantify their energetics in the glucocorticoid receptor, a transcriptional regulator controlling development, metabolism, and immune response. Our results delineate a dynamic communication network of residues linking the ligand-binding pocket to the activation function-2 interface, where helix 12, a switch for transcriptional activation, exhibits ligand- and coregulator-dependent dynamics coupled to graded activation. The allosteric free energy responds to variations in ligand structure: subtle changes gradually tune allostery while preserving the transmission pathway, whereas substitution of the entire pharmacophore leads to divergent allosteric control by apparently rewiring the communication network. Our results provide key insights that should aid in the design of mechanistically differentiated ligands.
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Affiliation(s)
- C. Köhler
- Respiratory, Inflammation and Autoimmunity, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - G. Carlström
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - A. Gunnarsson
- Discovery Sciences, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - U. Weininger
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P. O. Box 124, 221 00 Lund, Sweden
| | - S. Tångefjord
- Respiratory, Inflammation and Autoimmunity, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
- Discovery Sciences, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - V. Ullah
- Respiratory, Inflammation and Autoimmunity, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - M. Lepistö
- Respiratory, Inflammation and Autoimmunity, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - U. Karlsson
- Discovery Sciences, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - T. Papavoine
- Respiratory, Inflammation and Autoimmunity, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - K. Edman
- Discovery Sciences, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - M. Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P. O. Box 124, 221 00 Lund, Sweden
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5
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Pritišanac I, Alderson TR, Güntert P. Automated assignment of methyl NMR spectra from large proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 118-119:54-73. [PMID: 32883449 DOI: 10.1016/j.pnmrs.2020.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 05/05/2023]
Abstract
As structural biology trends towards larger and more complex biomolecular targets, a detailed understanding of their interactions and underlying structures and dynamics is required. The development of methyl-TROSY has enabled NMR spectroscopy to provide atomic-resolution insight into the mechanisms of large molecular assemblies in solution. However, the applicability of methyl-TROSY has been hindered by the laborious and time-consuming resonance assignment process, typically performed with domain fragmentation, site-directed mutagenesis, and analysis of NOE data in the context of a crystal structure. In response, several structure-based automatic methyl assignment strategies have been developed over the past decade. Here, we present a comprehensive analysis of all available methods and compare their input data requirements, algorithmic strategies, and reported performance. In general, the methods fall into two categories: those that primarily rely on inter-methyl NOEs, and those that utilize methyl PRE- and PCS-based restraints. We discuss their advantages and limitations, and highlight the potential benefits from standardizing and combining different methods.
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Affiliation(s)
- Iva Pritišanac
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - T Reid Alderson
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Güntert
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany; Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland; Department of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan.
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6
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Liu Y, Wang Z, Li X, Kang F, Ma X, Yang W, Ma W, Wang J. A Uniquely Modified DKL-based Peptide Probe for Positron Emission Tomography Imaging. Curr Pharm Des 2020; 25:96-103. [PMID: 30931855 DOI: 10.2174/1381612825666190329151326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 03/20/2019] [Indexed: 11/22/2022]
Abstract
Peptides containing the asparagine-glycine-arginine (NGR) motif can target the tumor neovascular biomarker CD13/aminopeptidase N receptor. D-K6L9 is a tumor-selective anti-cancer peptide. To improve the capacity of NGR peptides to target tumors, we joined the NGR and D-K6L9 peptides to form NKL. Next, we linked 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) to NKL and labeled it with gallium 68 (68Ga, t1/2 = 67.7 min) to form 68Ga-DOTA-NKL. This novel probe was characterized in vitro. 68Ga-DOTA-NKL was stable in phosphate buffered saline at room temperature and in human serum at 37°C. We determined that the uptake rate of 68Ga-DOTA-NKL in CD13 receptor-positive 22Rv1 tumor cells was 3.15% ± 0.04 after 2 h, and tested 68Ga-DOTA-NKL using positron emission tomography (PET)/computed tomography imaging in vivo. MicroPET imaging results revealed that 22Rv1 tumor uptake of 68Ga-DOTA-NKL was 8.69 ± 0.20, 6.61 ± 0.22, 3.85 ± 0.06, and 1.41 ± 0.23 percentage injected dose per gram of tissue (%ID/g) at 0.5, 1, 2, and 3 h postinjection (pi), respectively. The tumor-to-background contrast in the subcutaneous human prostate cancer 22Rv1 mouse model was 9.97 ± 1.90. The 68Ga-DOTA-NKL probe has combined tumor-targeting and tumor-selective properties, and may be used to diagnose CD13-positive tumors.
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Affiliation(s)
- Yi Liu
- Department of Nuclear Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Zhengjie Wang
- Department of Nuclear Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Xiang Li
- Department of Nuclear Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Fei Kang
- Department of Nuclear Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Xiaowei Ma
- Department of Nuclear Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Weidong Yang
- Department of Nuclear Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Wenhui Ma
- Department of Nuclear Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Jing Wang
- Department of Nuclear Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
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7
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Schütz S, Sprangers R. Methyl TROSY spectroscopy: A versatile NMR approach to study challenging biological systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:56-84. [PMID: 32130959 DOI: 10.1016/j.pnmrs.2019.09.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/09/2019] [Accepted: 09/25/2019] [Indexed: 05/21/2023]
Abstract
A major goal in structural biology is to unravel how molecular machines function in detail. To that end, solution-state NMR spectroscopy is ideally suited as it is able to study biological assemblies in a near natural environment. Based on methyl TROSY methods, it is now possible to record high-quality data on complexes that are far over 100 kDa in molecular weight. In this review, we discuss the theoretical background of methyl TROSY spectroscopy, the information that can be extracted from methyl TROSY spectra and approaches that can be used to assign methyl resonances in large complexes. In addition, we touch upon insights that have been obtained for a number of challenging biological systems, including the 20S proteasome, the RNA exosome, molecular chaperones and G-protein-coupled receptors. We anticipate that methyl TROSY methods will be increasingly important in modern structural biology approaches, where information regarding static structures is complemented with insights into conformational changes and dynamic intermolecular interactions.
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Affiliation(s)
- Stefan Schütz
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
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8
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Weininger U, Modig K, Ishida H, Vogel HJ, Akke M. Rotamer Jumps, Proton Exchange, and Amine Inversion Dynamics of Dimethylated Lysine Residues in Proteins Resolved by pH-Dependent 1H and 13C NMR Relaxation Dispersion. J Phys Chem B 2019; 123:9742-9750. [PMID: 31580078 DOI: 10.1021/acs.jpcb.9b06408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Post-translational methylation of lysine side chains is of great importance for protein regulation, including epigenetic control. Here, we present specific 13CHD2 labeling of dimethylated lysines as a sensitive probe of the structure, interactions, and dynamics of these groups, and outline a theoretical and experimental framework for analyzing their conformational dynamics using 1H and 13C CPMG relaxation dispersion experiments. Dimethylated lysine side chains in calcium-loaded calmodulin show a marked pH dependence of their Carr-Purcell-Meiboom-Gill (CPMG) dispersion profiles, indicating complex exchange behavior. Combined analysis of 1H and 13C CPMG relaxation dispersions requires consideration of 12-state correlated exchange of the two methyl groups due to circular three-state rotamer jumps around the Cε-Nζ axis combined with proton exchange and amine inversion. Taking into account a number of fundamental constraints, the exchange model can be reduced to include only three fitted parameters, namely, the geometric average of the rotamer-jump rate constants, the rate constant of deprotonation of Nζ, and the chemical shift difference between the trans and gauge positions of the 13C or 1H nuclei. The pH dependence indicates that protonation of the end group dramatically slows down rotamer exchange for some lysine residues, whereas deprotonation leads to rapid amine inversion coupled with rotamer scrambling. The observed variation among residues in their exchange behavior appears to depend on the structural environment of the side chain. Understanding this type of exchange process is critical to correctly interpreting NMR spectra of methylated lysine side chains. The exchange model presented here forms the basis for studying the structure and dynamics of epigenetically modified lysine side chains and perturbations caused by changes in pH or interactions with target proteins.
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Affiliation(s)
- Ulrich Weininger
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry , Lund University , P.O. Box 124, SE-221 00 Lund , Sweden
| | - Kristofer Modig
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry , Lund University , P.O. Box 124, SE-221 00 Lund , Sweden
| | - Hiroaki Ishida
- Department of Biological Sciences, Biochemistry Research Group , University of Calgary , 2500 University Drive NW , Calgary , Alberta , T2N 1N4 Canada
| | - Hans J Vogel
- Department of Biological Sciences, Biochemistry Research Group , University of Calgary , 2500 University Drive NW , Calgary , Alberta , T2N 1N4 Canada
| | - Mikael Akke
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry , Lund University , P.O. Box 124, SE-221 00 Lund , Sweden
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9
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Raum HN, Dreydoppel M, Weininger U. Conformational exchange of aromatic side chains by 1H CPMG relaxation dispersion. JOURNAL OF BIOMOLECULAR NMR 2018; 72:105-114. [PMID: 30229369 PMCID: PMC6209042 DOI: 10.1007/s10858-018-0210-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
Aromatic side chains are attractive probes of protein dynamics on the millisecond time scale, because they are often key residues in enzyme active sites and protein binding sites. Further they allow to study specific processes, like histidine tautomerization and ring flips. Till now such processes have been studied by aromatic 13C CPMG relaxation dispersion experiments. Here we investigate the possibility of aromatic 1H CPMG relaxation dispersion experiments as a complementary method. Artifact-free dispersions are possible on uniformly 1H and 13C labeled samples for histidine δ2 and ε1, as well as for tryptophan δ1. The method has been validated by measuring fast folding-unfolding kinetics of the small protein CspB under native conditions. The determined rate constants and populations agree well with previous results from 13C CPMG relaxation dispersion experiments. The CPMG-derived chemical shift differences between the folded and unfolded states are in good agreement with those obtained directly from the spectra. In contrast, the 1H relaxation dispersion profiles in phenylalanine, tyrosine and the six-ring moiety of tryptophan, display anomalous behavior caused by 3J 1H-1H couplings and, if present, strong 13C-13C couplings. Therefore they require site-selective 1H/2H and, in case of strong couplings, 13C/12C labeling. In summary, aromatic 1H CPMG relaxation dispersion experiments work on certain positions (His δ2, His ε1 and Trp δ1) in uniformly labeled samples, while other positions require site-selective isotope labeling.
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Affiliation(s)
- Heiner N Raum
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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10
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Schörghuber J, Geist L, Platzer G, Feichtinger M, Bisaccia M, Scheibelberger L, Weber F, Konrat R, Lichtenecker RJ. Late metabolic precursors for selective aromatic residue labeling. JOURNAL OF BIOMOLECULAR NMR 2018; 71:129-140. [PMID: 29808436 PMCID: PMC6096522 DOI: 10.1007/s10858-018-0188-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/19/2018] [Indexed: 06/08/2023]
Abstract
In recent years, we developed a toolbox of heavy isotope containing compounds, which serve as metabolic amino acid precursors in the E. coli-based overexpression of aromatic residue labeled proteins. Our labeling techniques show excellent results both in terms of selectivity and isotope incorporation levels. They are additionally distinguished by low sample production costs and meet the economic demands to further implement protein NMR spectroscopy as a routinely used method in drug development processes. Different isotopologues allow for the assembly of optimized protein samples, which fulfill the requirements of various NMR experiments to elucidate protein structures, analyze conformational dynamics, or probe interaction surfaces. In the present article, we want to summarize the precursors we developed so far and give examples of their special value in the probing of protein-ligand interaction.
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Affiliation(s)
- Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Leonhard Geist
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Gerald Platzer
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Michael Feichtinger
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Marilena Bisaccia
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Lukas Scheibelberger
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Frederik Weber
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Roman J Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria.
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11
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Ye L, Van Eps N, Li X, Ernst OP, Prosser RS. Utilizing tagged paramagnetic shift reagents to monitor protein dynamics by NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1555-1563. [PMID: 28951313 DOI: 10.1016/j.bbapap.2017.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/11/2017] [Accepted: 09/18/2017] [Indexed: 10/18/2022]
Abstract
Calmodulin is a ubiquitous calcium sensor protein, known to serve as a critical interaction hub with a wide range of signaling partners. While the holo form of calmodulin (CaM-4Ca2+) has a well-defined ground state structure, it has been shown to undergo exchange, on a millisecond timescale, to a conformation resembling that of the peptide bound state. Tagged paramagnetic relaxation agents have been previously used to identify long-range dipolar interactions through relaxation effects on nuclear spins of interest. In the case of calmodulin, this lead to the determination of the relative orientation of the N- and C-terminal domains and the presence of a weakly populated peptide bound like state. Here, we make use of pseudocontact shifts from a tagged paramagnetic shift reagent which allows us to define minor states both in 13C and 15N NMR spectra and through 13C- and 15N-edited 1H-CPMG relaxation dispersion measurements. This is validated by pulsed EPR (DEER) spectroscopy which reveals an ensemble consisting of a compact peptide-bound like conformer, an intermediate peptide-bound like conformer, and a (dumbbell-like) extended ground state conformer of CaM-4Ca2+, where addition of the MLCK peptide increases the population of the peptide-bound conformers. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Libin Ye
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Xiang Li
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - R Scott Prosser
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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12
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Weininger U. Site-selective 13C labeling of histidine and tryptophan using ribose. JOURNAL OF BIOMOLECULAR NMR 2017; 69:23-30. [PMID: 28856561 PMCID: PMC5626788 DOI: 10.1007/s10858-017-0130-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
Experimental studies on protein dynamics at atomic resolution by NMR-spectroscopy in solution require isolated 1H-X spin pairs. This is the default scenario in standard 1H-15N backbone experiments. Side chain dynamic experiments, which allow to study specific local processes like proton-transfer, or tautomerization, require isolated 1H-13C sites which must be produced by site-selective 13C labeling. In the most general way this is achieved by using site-selectively 13C-enriched glucose as the carbon source in bacterial expression systems. Here we systematically investigate the use of site-selectively 13C-enriched ribose as a suitable precursor for 13C labeled histidines and tryptophans. The 13C incorporation in nearly all sites of all 20 amino acids was quantified and compared to glucose based labeling. In general the ribose approach results in more selective labeling. 1-13C ribose exclusively labels His δ2 and Trp δ1 in aromatic side chains and helps to resolve possible overlap problems. The incorporation yield is however only 37% in total and 72% compared to yields of 2-13C glucose. A combined approach of 1-13C ribose and 2-13C glucose maximizes 13C incorporation to 75% in total and 150% compared to 2-13C glucose only. Further histidine positions β, α and CO become significantly labeled at around 50% in total by 3-, 4- or 5-13C ribose. Interestingly backbone CO of Gly, Ala, Cys, Ser, Val, Phe and Tyr are labeled at 40-50% in total with 3-13C ribose, compared to 5% and below for 1-13C and 2-13C glucose. Using ribose instead of glucose as a source for site-selective 13C labeling enables a very selective labeling of certain positions and thereby expanding the toolbox for customized isotope labeling of amino-acids.
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Affiliation(s)
- Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P. O. Box 124, 22100, Lund, Sweden.
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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13
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Juen MA, Wunderlich CH, Nußbaumer F, Tollinger M, Kontaxis G, Konrat R, Hansen DF, Kreutz C. Excited States of Nucleic Acids Probed by Proton Relaxation Dispersion NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:12008-12. [PMID: 27533469 PMCID: PMC5082494 DOI: 10.1002/anie.201605870] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Indexed: 11/16/2022]
Abstract
In this work an improved stable isotope labeling protocol for nucleic acids is introduced. The novel building blocks eliminate/minimize homonuclear (13) C and (1) H scalar couplings thus allowing proton relaxation dispersion (RD) experiments to report accurately on the chemical exchange of nucleic acids. Using site-specific (2) H and (13) C labeling, spin topologies are introduced into DNA and RNA that make (1) H relaxation dispersion experiments applicable in a straightforward manner. The novel RNA/DNA building blocks were successfully incorporated into two nucleic acids. The A-site RNA was previously shown to undergo a two site exchange process in the micro- to millisecond time regime. Using proton relaxation dispersion experiments the exchange parameters determined earlier could be recapitulated, thus validating the proposed approach. We further investigated the dynamics of the cTAR DNA, a DNA transcript that is involved in the viral replication cycle of HIV-1. Again, an exchange process could be characterized and quantified. This shows the general applicablility of the novel labeling scheme for (1) H RD experiments of nucleic acids.
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Affiliation(s)
- Michael Andreas Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | | | - Felix Nußbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Martin Tollinger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Georg Kontaxis
- Computational Biology and Biomolecular NMR, Max F. Perutz Laboratories (MFPL), University of Vienna, Dr. Bohr Gasse 9 (VBC 5), 1030, Vienna, Austria
| | - Robert Konrat
- Computational Biology and Biomolecular NMR, Max F. Perutz Laboratories (MFPL), University of Vienna, Dr. Bohr Gasse 9 (VBC 5), 1030, Vienna, Austria
| | - D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Room 612, Gower Street, London, WC1E 6BT, UK.
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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14
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Takeda M, Miyanoiri Y, Terauchi T, Kainosho M. (13)C-NMR studies on disulfide bond isomerization in bovine pancreatic trypsin inhibitor (BPTI). JOURNAL OF BIOMOLECULAR NMR 2016; 66:37-53. [PMID: 27566173 DOI: 10.1007/s10858-016-0055-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
Conformational isomerization of disulfide bonds is associated with the dynamics and thus the functional aspects of proteins. However, our understanding of the isomerization is limited by experimental difficulties in probing it. We explored the disulfide conformational isomerization of the Cys14-Cys38 disulfide bond in bovine pancreatic trypsin inhibitor (BPTI), by performing an NMR line-shape analysis of its Cys carbon peaks. In this approach, 1D (13)C spectra were recorded at small temperature intervals for BPTI samples selectively labeled with site-specifically (13)C-enriched Cys, and the recorded peaks were displayed in the order of the temperature after the spectral scales were normalized to a carbon peak. Over the profile of the line-shape, exchange broadening that altered with temperature was manifested for the carbon peaks of Cys14 and Cys38. The Cys14-Cys38 disulfide bond reportedly exists in equilibrium between a high-populated (M) and two low-populated states (m c14 and m c38). Consistent with the three-site exchange model, biphasic exchange broadening arising from the two processes was observed for the peak of the Cys14 α-carbon. As the exchange broadening is maximized when the exchange rate equals the chemical shift difference in Hz between equilibrating sites, semi-quantitative information that was useful for establishing conditions for (13)C relaxation dispersion experiments was obtained through the carbon line-shape profile. With respect to the m c38 isomerization, the (1)H-(13)C signals at the β-position of the minor state were resolved from the major peaks and detected by exchange experiments at a low temperature.
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Affiliation(s)
- Mitsuhiro Takeda
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
- Department of Structural BioImaging, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Yohei Miyanoiri
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Tsutomu Terauchi
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo, 192-0397, Japan
- SAIL Technologies Inc., 2008-2 Wada, Tama, Tokyo, 206-0001, Japan
| | - Masatsune Kainosho
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo, 192-0397, Japan.
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15
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Juen MA, Wunderlich CH, Nußbaumer F, Tollinger M, Kontaxis G, Konrat R, Hansen DF, Kreutz C. Excited States of Nucleic Acids Probed by Proton Relaxation Dispersion NMR Spectroscopy. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605870] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michael Andreas Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI); University of Innsbruck; Innrain 80/82 6020 Innsbruck Austria
| | | | - Felix Nußbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI); University of Innsbruck; Innrain 80/82 6020 Innsbruck Austria
| | - Martin Tollinger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI); University of Innsbruck; Innrain 80/82 6020 Innsbruck Austria
| | - Georg Kontaxis
- Computational Biology and Biomolecular NMR; Max F. Perutz Laboratories (MFPL); University of Vienna; Dr. Bohr Gasse 9 (VBC 5) 1030 Vienna Austria
| | - Robert Konrat
- Computational Biology and Biomolecular NMR; Max F. Perutz Laboratories (MFPL); University of Vienna; Dr. Bohr Gasse 9 (VBC 5) 1030 Vienna Austria
| | - D. Flemming Hansen
- Institute of Structural and Molecular Biology; Division of Biosciences; University College London; Darwin Building, Room 612, Gower Street London WC1E 6BT UK
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI); University of Innsbruck; Innrain 80/82 6020 Innsbruck Austria
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16
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Gu Y, Li DW, Brüschweiler R. Decoding the Mobility and Time Scales of Protein Loops. J Chem Theory Comput 2016; 11:1308-14. [PMID: 26579776 DOI: 10.1021/ct501085y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The flexible nature of protein loops and the time scales of their dynamics are critical for many biologically important events at the molecular level, such as protein interaction and recognition processes. In order to obtain a predictive understanding of the dynamic properties of loops, 500 ns molecular dynamics (MD) computer simulations of 38 different proteins were performed and validated using NMR chemical shifts. A total of 169 loops were analyzed and classified into three types, namely fast loops with correlation times <10 ns, slow loops with correlation times between 10 and 500 ns, and loops that are static over the course of the whole trajectory. Chemical and biophysical loop descriptors, such as amino-acid sequence, average 3D structure, charge distribution, hydrophobicity, and local contacts were used to develop and parametrize the ToeLoop algorithm for the prediction of the flexibility and motional time scale of every protein loop, which is also implemented as a public Web server (http://spin.ccic.ohio-state.edu/index.php/loop). The results demonstrate that loop dynamics with their time scales can be predicted rapidly with reasonable accuracy, which will allow the screening of average protein structures to help better understand the various roles loops can play in the context of protein-protein interactions and binding.
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Affiliation(s)
- Yina Gu
- Department of Chemistry and Biochemistry and ‡Campus Chemical Instrument Center, The Ohio State University , Columbus, Ohio 43210, United States
| | - Da-Wei Li
- Department of Chemistry and Biochemistry and ‡Campus Chemical Instrument Center, The Ohio State University , Columbus, Ohio 43210, United States
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry and ‡Campus Chemical Instrument Center, The Ohio State University , Columbus, Ohio 43210, United States
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17
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Toyama Y, Osawa M, Yokogawa M, Shimada I. NMR Method for Characterizing Microsecond-to-Millisecond Chemical Exchanges Utilizing Differential Multiple-Quantum Relaxation in High Molecular Weight Proteins. J Am Chem Soc 2016; 138:2302-11. [PMID: 26855064 DOI: 10.1021/jacs.5b12954] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical exchange processes of proteins on the order of microseconds (μs) to milliseconds (ms) play critical roles in biological functions. Developments in methyl-transverse relaxation optimized spectroscopy (methyl-TROSY), which observes the slowly relaxing multiple quantum (MQ) coherences, have enabled the studies of biologically important large proteins. However, the analyses of μs to ms chemical exchange processes based on the methyl-TROSY principle are still challenging, because the interpretation of the chemical exchange contributions to the MQ relaxation profiles is complicated, as significant chemical shift differences occur in both (1)H and (13)C nuclei. Here, we report a new methyl-based NMR method for characterizing chemical exchanges, utilizing differential MQ relaxation rates and a heteronuclear double resonance pulse technique. The method enables quantitative evaluations of the chemical exchange processes, in which significant chemical shift differences exist in both the (1)H and (13)C nuclei. The versatility of the method is demonstrated with the application to KirBac1.1, with an apparent molecular mass of 200 kDa.
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Affiliation(s)
- Yuki Toyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Japan Biological Informatics Consortium (JBIC) , Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mariko Yokogawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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18
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Hoang J, Prosser RS. Conformational Selection and Functional Dynamics of Calmodulin: A 19F Nuclear Magnetic Resonance Study. Biochemistry 2014; 53:5727-36. [DOI: 10.1021/bi500679c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joshua Hoang
- Department
of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
| | - R. Scott Prosser
- Department
of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
- Department
of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, ON M5S
1A8, Canada
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19
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Weininger U, Brath U, Modig K, Teilum K, Akke M. Off-resonance rotating-frame relaxation dispersion experiment for 13C in aromatic side chains using L-optimized TROSY-selection. JOURNAL OF BIOMOLECULAR NMR 2014; 59:23-9. [PMID: 24706175 PMCID: PMC4003406 DOI: 10.1007/s10858-014-9826-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/25/2014] [Indexed: 05/04/2023]
Abstract
Protein dynamics on the microsecond-millisecond time scales often play a critical role in biological function. NMR relaxation dispersion experiments are powerful approaches for investigating biologically relevant dynamics with site-specific resolution, as shown by a growing number of publications on enzyme catalysis, protein folding, ligand binding, and allostery. To date, the majority of studies has probed the backbone amides or side-chain methyl groups, while experiments targeting other sites have been used more sparingly. Aromatic side chains are useful probes of protein dynamics, because they are over-represented in protein binding interfaces, have important catalytic roles in enzymes, and form a sizable part of the protein interior. Here we present an off-resonance R 1ρ experiment for measuring microsecond to millisecond conformational exchange of aromatic side chains in selectively (13)C labeled proteins by means of longitudinal- and transverse-relaxation optimization. Using selective excitation and inversion of the narrow component of the (13)C doublet, the experiment achieves significant sensitivity enhancement in terms of both signal intensity and the fractional contribution from exchange to transverse relaxation; additional signal enhancement is achieved by optimizing the longitudinal relaxation recovery of the covalently attached (1)H spins. We validated the L-TROSY-selected R 1ρ experiment by measuring exchange parameters for Y23 in bovine pancreatic trypsin inhibitor at a temperature of 328 K, where the ring flip is in the fast exchange regime with a mean waiting time between flips of 320 μs. The determined chemical shift difference matches perfectly with that measured from the NMR spectrum at lower temperatures, where separate peaks are observed for the two sites. We further show that potentially complicating effects of strong scalar coupling between protons (Weininger et al. in J Phys Chem B 117: 9241-9247, 2013b) can be accounted for using a simple expression, and provide recommendations for data acquisition when the studied system exhibits this behavior. The present method extends the repertoire of relaxation methods tailored for aromatic side chains by enabling studies of faster processes and improved control over artifacts due to strong coupling.
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Affiliation(s)
- Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Ulrika Brath
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
- Present Address: Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Göteborg, Sweden
| | - Kristofer Modig
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Kaare Teilum
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Mikael Akke
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
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20
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Frueh DP. Practical aspects of NMR signal assignment in larger and challenging proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 78:47-75. [PMID: 24534088 PMCID: PMC3951217 DOI: 10.1016/j.pnmrs.2013.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 12/05/2013] [Accepted: 12/06/2013] [Indexed: 05/03/2023]
Abstract
NMR has matured into a technique routinely employed for studying proteins in near physiological conditions. However, applications to larger proteins are impeded by the complexity of the various correlation maps necessary to assign NMR signals. This article reviews the data analysis techniques traditionally employed for resonance assignment and describes alternative protocols necessary for overcoming challenges in large protein spectra. In particular, simultaneous analysis of multiple spectra may help overcome ambiguities or may reveal correlations in an indirect manner. Similarly, visualization of orthogonal planes in a multidimensional spectrum can provide alternative assignment procedures. We describe examples of such strategies for assignment of backbone, methyl, and nOe resonances. We describe experimental aspects of data acquisition for the related experiments and provide guidelines for preliminary studies. Focus is placed on large folded monomeric proteins and examples are provided for 37, 48, 53, and 81 kDa proteins.
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Affiliation(s)
- Dominique P Frueh
- Johns Hopkins University School of Medicine, Biophysics and Biophysical Chemistry, 725 N. Wolfe Street, 701 Hunterian, Baltimore, MD 21205-2105, United States.
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21
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Palmer AG. Chemical exchange in biomacromolecules: past, present, and future. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:3-17. [PMID: 24656076 PMCID: PMC4049312 DOI: 10.1016/j.jmr.2014.01.008] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/09/2014] [Accepted: 01/10/2014] [Indexed: 05/08/2023]
Abstract
The perspective reviews quantitative investigations of chemical exchange phenomena in proteins and other biological macromolecules using NMR spectroscopy, particularly relaxation dispersion methods. The emphasis is on techniques and applications that quantify the populations, interconversion kinetics, and structural features of sparsely populated conformational states in equilibrium with a highly populated ground state. Applications to folding, molecular recognition, catalysis, and allostery by proteins and nucleic acids are highlighted.
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Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, United States.
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22
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Frueh DP, Goodrich AC, Mishra SH, Nichols SR. NMR methods for structural studies of large monomeric and multimeric proteins. Curr Opin Struct Biol 2013; 23:734-9. [PMID: 23850141 PMCID: PMC3805735 DOI: 10.1016/j.sbi.2013.06.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 06/13/2013] [Accepted: 06/21/2013] [Indexed: 12/16/2022]
Abstract
NMR structural studies of large monomeric and multimeric proteins face distinct challenges. In large monomeric proteins, the common occurrence of frequency degeneracies between residues impedes unambiguous assignment of NMR signals. To overcome this barrier, nonuniform sampling (NUS) is used to measure spectra with optimal resolution within reasonable time, new correlation maps resolve previous impasses in assignment strategies, and novel selective methyl labeling schemes provide additional structural probes without cluttering NMR spectra. These advances push the limits of NMR studies of large monomeric proteins. Large multimeric and multidomain proteins are studied by NMR when individual components can also be studied by NMR and have known structures. The structural properties of large assemblies are obtained by identifying binding surfaces, by orienting domains, and employing limited distance constraints. Segmental labeling and the combination of NMR with other methods have helped popularize NMR studies of such systems.
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Affiliation(s)
- Dominique P Frueh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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23
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Weininger U, Blissing AT, Hennig J, Ahlner A, Liu Z, Vogel HJ, Akke M, Lundström P. Protein conformational exchange measured by 1H R1ρ relaxation dispersion of methyl groups. JOURNAL OF BIOMOLECULAR NMR 2013; 57:47-55. [PMID: 23904100 DOI: 10.1007/s10858-013-9764-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 07/17/2013] [Indexed: 06/02/2023]
Abstract
Activated dynamics plays a central role in protein function, where transitions between distinct conformations often underlie the switching between active and inactive states. The characteristic time scales of these transitions typically fall in the microsecond to millisecond range, which is amenable to investigations by NMR relaxation dispersion experiments. Processes at the faster end of this range are more challenging to study, because higher RF field strengths are required to achieve refocusing of the exchanging magnetization. Here we describe a rotating-frame relaxation dispersion experiment for (1)H spins in methyl (13)CHD2 groups, which improves the characterization of fast exchange processes. The influence of (1)H-(1)H rotating-frame nuclear Overhauser effects (ROE) is shown to be negligible, based on a comparison of R 1ρ relaxation data acquired with tilt angles of 90° and 35°, in which the ROE is maximal and minimal, respectively, and on samples containing different (1)H densities surrounding the monitored methyl groups. The method was applied to ubiquitin and the apo form of calmodulin. We find that ubiquitin does not exhibit any (1)H relaxation dispersion of its methyl groups at 10 or 25 °C. By contrast, calmodulin shows significant conformational exchange of the methionine methyl groups in its C-terminal domain, as previously demonstrated by (1)H and (13)C CPMG experiments. The present R 1ρ experiment extends the relaxation dispersion profile towards higher refocusing frequencies, which improves the definition of the exchange correlation time, compared to previous results.
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Affiliation(s)
- Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100, Lund, Sweden
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