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Abstract
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Thanks to recent
improvements in NMR spectrometer hardware and
pulse sequence design, modern 13C NMR has become a useful
tool for biomolecular applications. The complete assignment of a protein
can be accomplished by using 13C detected multinuclear
experiments and it can provide unique information relevant for the
study of a variety of different biomolecules including paramagnetic
proteins and intrinsically disordered proteins. A wide range of NMR
observables can be measured, concurring to the structural and dynamic
characterization of a protein in isolation, as part of a larger complex,
or even inside a living cell. We present the different properties
of 13C with respect to 1H, which provide the
rationale for the experiments developed and their application, the
technical aspects that need to be faced, and the many experimental
variants designed to address different cases. Application areas where
these experiments successfully complement proton NMR are also described.
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Affiliation(s)
- Isabella C Felli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
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2
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Arthanari H, Takeuchi K, Dubey A, Wagner G. Emerging solution NMR methods to illuminate the structural and dynamic properties of proteins. Curr Opin Struct Biol 2019; 58:294-304. [PMID: 31327528 PMCID: PMC6778509 DOI: 10.1016/j.sbi.2019.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 06/03/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022]
Abstract
The first recognition of protein breathing was more than 50 years ago. Today, we are able to detect the multitude of interaction modes, structural polymorphisms, and binding-induced changes in protein structure that direct function. Solution-state NMR spectroscopy has proved to be a powerful technique, not only to obtain high-resolution structures of proteins, but also to provide unique insights into the functional dynamics of proteins. Here, we summarize recent technical landmarks in solution NMR that have enabled characterization of key biological macromolecular systems. These methods have been fundamental to atomic resolution structure determination and quantitative analysis of dynamics over a wide range of time scales by NMR. The ability of NMR to detect lowly populated protein conformations and transiently formed complexes plays a critical role in its ability to elucidate functionally important structural features of proteins and their dynamics.
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Affiliation(s)
- Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States.
| | - Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 135-0064 Tokyo, Japan.
| | - Abhinav Dubey
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States.
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3
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Takeuchi K, Baskaran K, Arthanari H. Structure determination using solution NMR: Is it worth the effort? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:195-201. [PMID: 31345771 DOI: 10.1016/j.jmr.2019.07.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
It has been almost 40 years since solution NMR joined X-ray crystallography as a technique for determining high-resolution structures of proteins. Since then NMR derived structure has contributed in fundamental ways to our understanding of the function of biomolecules. With the already existing mature field of X-ray crystallography and the emergence of cryo-EM as techniques to tackle high-resolution structures of large protein complexes, the role of NMR in structure determination has been questioned. However, NMR has the unique ability to recapitulate the dynamic motion of proteins in their structures, while size limitations of the biomolecular systems that can be routinely studied still present challenges. The field has continually developed methodology and instrumentation since its introduction, pushing its frontiers and redefining its limits. Here we present a brief overview of NMR-based structure determination over the past 40 years. We outline the current state of the field and look ahead to the challenges that still need to be addressed to realize the future potential of NMR as a structural technique.
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Affiliation(s)
- Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery (Molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Kumaran Baskaran
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr, Madison, WI 53706, United States
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, United States.
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Hawk LML, Gee CT, Urick AK, Hu H, Pomerantz WCK. Paramagnetic relaxation enhancement for protein-observed 19F NMR as an enabling approach for efficient fragment screening. RSC Adv 2016; 6:95715-95721. [PMID: 28496971 PMCID: PMC5421645 DOI: 10.1039/c6ra21226c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Protein-observed 19F (PrOF) NMR is an emerging tool for ligand discovery. To optimize the efficiency of PrOF NMR experiments, paramagnetic relaxation enhancement through the addition of chelated Ni(II) was used to shorten longitudinal relaxation time without causing significant line broadening. Thus enhancing relaxation time leads to shorter experiments without perturbing the binding of low- or high-affinity ligands. This method allows for time-efficient screening of potential ligands for a wide variety of proteins in the growing field of fragment-based ligand discovery.
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Affiliation(s)
- Laura M L Hawk
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
| | - Clifford T Gee
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
| | - Andrew K Urick
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, United States
| | - Haitao Hu
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
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5
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Takeuchi K, Arthanari H, Imai M, Wagner G, Shimada I. Nitrogen-detected TROSY yields comparable sensitivity to proton-detected TROSY for non-deuterated, large proteins under physiological salt conditions. JOURNAL OF BIOMOLECULAR NMR 2016; 64:143-51. [PMID: 26800993 PMCID: PMC4871712 DOI: 10.1007/s10858-016-0015-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/16/2016] [Indexed: 05/12/2023]
Abstract
Direct detection of the TROSY component of proton-attached (15)N nuclei ((15)N-detected TROSY) yields high quality spectra with high field magnets, by taking advantage of the slow (15)N transverse relaxation. The slow transverse relaxation and narrow line width of the (15)N-detected TROSY resonances are expected to compensate for the inherently low (15)N sensitivity. However, the sensitivity of (15)N-detected TROSY in a previous report was one-order of magnitude lower than in the conventional (1)H-detected version. This could be due to the fact that the previous experiments were performed at low salt (0-50 mM), which is advantageous for (1)H-detected experiments. Here, we show that the sensitivity gap between (15)N and (1)H becomes marginal for a non-deuterated, large protein (τ c = 35 ns) at a physiological salt concentration (200 mM). This effect is due to the high salt tolerance of the (15)N-detected TROSY. Together with the previously reported benefits of the (15)N-detected TROSY, our results provide further support for the significance of this experiment for structural studies of macromolecules when using high field magnets near and above 1 GHz.
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Affiliation(s)
- Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute for Advanced Industrial Science and Technology, Tokyo, 135-0063, Japan
- PRESTO, JST, Tokyo, 135-0063, Japan
| | - Haribabu Arthanari
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Misaki Imai
- Research and Development Department, Japan Biological Informatics Consortium, Tokyo, 135-0063, Japan
| | - Gerhard Wagner
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
| | - Ichio Shimada
- Molecular Profiling Research Center for Drug Discovery, National Institute for Advanced Industrial Science and Technology, Tokyo, 135-0063, Japan.
- Graduate Schools of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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Takeuchi K, Arthanari H, Shimada I, Wagner G. Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR. JOURNAL OF BIOMOLECULAR NMR 2015; 63:323-331. [PMID: 26497830 PMCID: PMC4749451 DOI: 10.1007/s10858-015-9991-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 10/01/2015] [Indexed: 05/18/2023]
Abstract
Detection of (15)N in multidimensional NMR experiments of proteins has sparsely been utilized because of the low gyromagnetic ratio (γ) of nitrogen and the presumed low sensitivity of such experiments. Here we show that selecting the TROSY components of proton-attached (15)N nuclei (TROSY (15)NH) yields high quality spectra in high field magnets (>600 MHz) by taking advantage of the slow (15)N transverse relaxation and compensating for the inherently low (15)N sensitivity. The (15)N TROSY transverse relaxation rates increase modestly with molecular weight but the TROSY gain in peak heights depends strongly on the magnetic field strength. Theoretical simulations predict that the narrowest line width for the TROSY (15)NH component can be obtained at 900 MHz, but sensitivity reaches its maximum around 1.2 GHz. Based on these considerations, a (15)N-detected 2D (1)H-(15)N TROSY-HSQC ((15)N-detected TROSY-HSQC) experiment was developed and high-quality 2D spectra were recorded at 800 MHz in 2 h for 1 mM maltose-binding protein at 278 K (τc ~ 40 ns). Unlike for (1)H detected TROSY, deuteration is not mandatory to benefit (15)N detected TROSY due to reduced dipolar broadening, which facilitates studies of proteins that cannot be deuterated, especially in cases where production requires eukaryotic expression systems. The option of recording (15)N TROSY of proteins expressed in H2O media also alleviates the problem of incomplete amide proton back exchange, which often hampers the detection of amide groups in the core of large molecular weight proteins that are expressed in D2O culture media and cannot be refolded for amide back exchange. These results illustrate the potential of (15)NH-detected TROSY experiments as a means to exploit the high resolution offered by high field magnets near and above 1 GHz.
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Affiliation(s)
- Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute for Advanced Industrial Science and Technology, Tokyo, 135-0063, Japan
- PRESTO, JST, Tokyo, 135-0063, Japan
| | - Haribabu Arthanari
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Ichio Shimada
- Molecular Profiling Research Center for Drug Discovery, National Institute for Advanced Industrial Science and Technology, Tokyo, 135-0063, Japan.
- Graduate Schools of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Gerhard Wagner
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
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Felli IC, Pierattelli R. Spin-state-selective methods in solution- and solid-state biomolecular 13C NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 84-85:1-13. [PMID: 25669738 DOI: 10.1016/j.pnmrs.2014.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 10/26/2014] [Indexed: 06/04/2023]
Abstract
Spin-state-selective methods to achieve homonuclear decoupling in the direct acquisition dimension of (13)C detected NMR experiments have been one of the key contributors to converting (13)C detected NMR experiments into really useful tools for studying biomolecules. We discuss here in detail the various methods that have been proposed, summarize the large array of new experiments that have been developed and present applications to different kinds of proteins in different aggregation states.
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Affiliation(s)
- Isabella C Felli
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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8
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Yao X, Becker S, Zweckstetter M. A six-dimensional alpha proton detection-based APSY experiment for backbone assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2014; 60:231-40. [PMID: 25367087 DOI: 10.1007/s10858-014-9872-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 10/30/2014] [Indexed: 05/21/2023]
Abstract
Sequence specific resonance assignment is the prerequisite for the NMR-based analysis of the conformational ensembles and their underlying dynamics of intrinsically disordered proteins. However, rapid solvent exchange in intrinsically disordered proteins often complicates assignment strategies based on HN-detection. Here we present a six-dimensional alpha proton detection-based automated projection spectroscopy (APSY) experiment for backbone assignment of intrinsically disordered proteins. The 6D HCACONCAH APSY correlates the six different chemical shifts, H(α)(i - 1), C(α)(i - 1), C'(i - 1), N(i), Cα(i) and Hα(i). Application to two intrinsically disordered proteins, 140-residue α-synuclein and a 352-residue isoform of Tau, demonstrates that the chemical shift information provided by the 6D HCACONCAH APSY allows efficient backbone resonance assignment of intrinsically disordered proteins.
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Affiliation(s)
- Xuejun Yao
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
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9
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Göbl C, Madl T, Simon B, Sattler M. NMR approaches for structural analysis of multidomain proteins and complexes in solution. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 80:26-63. [PMID: 24924266 DOI: 10.1016/j.pnmrs.2014.05.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/14/2014] [Indexed: 05/22/2023]
Abstract
NMR spectroscopy is a key method for studying the structure and dynamics of (large) multidomain proteins and complexes in solution. It plays a unique role in integrated structural biology approaches as especially information about conformational dynamics can be readily obtained at residue resolution. Here, we review NMR techniques for such studies focusing on state-of-the-art tools and practical aspects. An efficient approach for determining the quaternary structure of multidomain complexes starts from the structures of individual domains or subunits. The arrangement of the domains/subunits within the complex is then defined based on NMR measurements that provide information about the domain interfaces combined with (long-range) distance and orientational restraints. Aspects discussed include sample preparation, specific isotope labeling and spin labeling; determination of binding interfaces and domain/subunit arrangements from chemical shift perturbations (CSP), nuclear Overhauser effects (NOEs), isotope editing/filtering, cross-saturation, and differential line broadening; and based on paramagnetic relaxation enhancements (PRE) using covalent and soluble spin labels. Finally, the utility of complementary methods such as small-angle X-ray or neutron scattering (SAXS, SANS), electron paramagnetic resonance (EPR) or fluorescence spectroscopy techniques is discussed. The applications of NMR techniques are illustrated with studies of challenging (high molecular weight) protein complexes.
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Affiliation(s)
- Christoph Göbl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Tobias Madl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Molecular Biology, University of Graz, Graz, Austria.
| | - Bernd Simon
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.
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10
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Mayzel M, Rosenlöw J, Isaksson L, Orekhov VY. Time-resolved multidimensional NMR with non-uniform sampling. JOURNAL OF BIOMOLECULAR NMR 2014; 58:129-39. [PMID: 24435565 PMCID: PMC3929766 DOI: 10.1007/s10858-013-9811-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 12/30/2013] [Indexed: 05/11/2023]
Abstract
Time-resolved experiments demand high resolution both in spectral dimensions and in time of the studied kinetic process. The latter requirement traditionally prohibits applications of the multidimensional experiments, which, although capable of providing invaluable information about structure and dynamics and almost unlimited spectral resolution, require too lengthy data collection. Our work shows that the problem has a solution in using modern methods of NMR data collection and signal processing. A continuous fast pulsing three-dimensional experiment is acquired using non-uniform sampling during full time of the studied reaction. High sensitivity and time-resolution of a few minutes is achieved by simultaneous processing of the full data set with the multi-dimensional decomposition. The method is verified and illustrated in realistic simulations and by measuring deuterium exchange rates of amide protons in ubiquitin. We applied the method for characterizing kinetics of in vitro phosphorylation of two tyrosine residues in an intrinsically disordered cytosolic domain of the B cell receptor protein CD79b. Signals of many residues including tyrosines in both phosphorylated and unmodified forms of CD79b are found in a heavily crowded region of 2D ¹H-¹⁵N correlation spectrum and the significantly enhanced spectral resolution provided by the 3D time-resolved approach was essential for the quantitative site-specific analysis.
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Affiliation(s)
- Maxim Mayzel
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
| | - Joakim Rosenlöw
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
| | - Linnéa Isaksson
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
| | - Vladislav Y. Orekhov
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
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Bermel W, Bruix M, Felli IC, Kumar M V V, Pierattelli R, Serrano S. Improving the chemical shift dispersion of multidimensional NMR spectra of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 55:231-237. [PMID: 23314728 DOI: 10.1007/s10858-013-9704-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 01/02/2013] [Indexed: 06/01/2023]
Abstract
Intrinsically disordered proteins (IDPs) have recently attracted the attention of the scientific community challenging the well accepted structure-function paradigm. In the characterization of the dynamic features of proteins nuclear magnetic resonance spectroscopy (NMR) is a strategic tool of investigation. However the peculiar properties of IDPs, with the lack of a unique 3D structure and their high flexibility, have a strong impact on NMR observables (low chemical shift dispersion, efficient solvent exchange broadening) and thus on the quality of NMR spectra. Key aspects to be considered in the design of new NMR experiments optimized for the study of IDPs are discussed. A new experiment, based on direct detection of (13)C(α), is proposed.
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Sibille N, Bellot G, Wang J, Déméné H. Low concentration of a Gd-chelate increases the signal-to-noise ratio in fast pulsing BEST experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 224:32-37. [PMID: 23010449 DOI: 10.1016/j.jmr.2012.07.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 07/17/2012] [Accepted: 07/31/2012] [Indexed: 06/01/2023]
Abstract
Despite numerous developments in the past few years that aim to increase the sensitivity of NMR multidimensional experiments, NMR spectroscopy still suffers from intrinsic low sensitivity. In this report, we show that the combination of two developments in the field, the Band-selective Excitation Short-Transient (BEST) experiment [Schanda et al., J. Am. Chem. Soc., 128 (2006) 9042] and the addition of the nonionic paramagnetic gadolinium chelate gadodiamide into NMR samples, enhances the signal-to-noise ratio. This effect is shown here for four different proteins, three globular and one unfolded, of molecular weights ranging from 6.5 kDa to 40 kDa, using 2D BEST HSQC and 3D BEST triple resonance sequences. Moreover, we show that the increase in signal-to-noise ratio provided by the gadodiamide is higher for peak resonances with lower than average intensity in BEST experiments. It is interesting to note that these residues are on average the weakest ones in those experiments. In this case, the gadodiamide-mediated increase can reach a value of 60% for low and 30% for high molecular weight proteins respectively. An investigation into the origin of this "paramagnetic gain" in BEST experiments is presented.
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Affiliation(s)
- Nathalie Sibille
- CNRS UMR 5048, Centre de Biochimie Structurale, Montpellier, France
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13
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Chakraborty S, Susmitha AL, Hosur RV. Selective lighting up of segments around Gly, Ala and Ser/Thr in proteins. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50:587-91. [PMID: 22806716 DOI: 10.1002/mrc.3843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 06/12/2012] [Accepted: 06/14/2012] [Indexed: 05/23/2023]
Abstract
Direct detection of (13) C nucleus can be used as a valuable alternative where (1) H detection poses a challenge due to relaxation effects, chemical exchange and poor chemical shift dispersion. In this context, we have designed a suite of 2D (13) C(α) -detected hNCA experiments that provide sequential correlations of (13) C(α) with (15) N on one hand and efficient spectroscopic labeling of certain groups of residues, namely, Gly, Ala, Ser and Thr, on the other. These residues act as checkpoints in the sequential walk, which in turn offer new possibilities of backbone assignment of small proteins from a set of 2D experiments, thereby providing great economy in terms of spectrometer time. The direct identification of peptide segments around Gly, Ala, Ser and Thr residues along a protein chain will be highly valuable for deriving important information on sites of ligand binding, phosphorylation, inhibitor/substrate binding, understanding protein folding pathways, comprehending local conformational dynamics etc. without having to obtain complete sequence-specific assignments, which can be time consuming and at times formidable, especially in large proteins. We have illustratively demonstrated the multifaceted applications of these variants of 2D experiments on ubiquitin and M-crystallin. We foresee that these 2D hNCA experiments will provide economic and efficient strategies for studying the structure and function of proteins.
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Affiliation(s)
- Swagata Chakraborty
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
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14
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Theillet FX, Binolfi A, Liokatis S, Verzini S, Selenko P. Paramagnetic relaxation enhancement to improve sensitivity of fast NMR methods: application to intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2011; 51:487-495. [PMID: 22008951 DOI: 10.1007/s10858-011-9577-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 09/28/2011] [Indexed: 05/31/2023]
Abstract
We report enhanced sensitivity NMR measurements of intrinsically disordered proteins in the presence of paramagnetic relaxation enhancement (PRE) agents such as Ni(2+)-chelated DO2A. In proton-detected (1)H-(15)N SOFAST-HMQC and carbon-detected (H-flip)(13)CO-(15)N experiments, faster longitudinal relaxation enables the usage of even shorter interscan delays. This results in higher NMR signal intensities per units of experimental time, without adverse line broadening effects. At 40 mmol·L(-1) of the PRE agent, we obtain a 1.7- to 1.9-fold larger signal to noise (S/N) for the respective 2D NMR experiments. High solvent accessibility of intrinsically disordered protein (IDP) residues renders this class of proteins particularly amenable to the outlined approach.
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Affiliation(s)
- François-Xavier Theillet
- Department of NMR-assisted Structural Biology, In-cell NMR Group, Leibniz Institute of Molecular Pharmacology (FMP), Berlin, Germany
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15
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Barb AW, Freedberg DI, Battistel MD, Prestegard JH. NMR detection and characterization of sialylated glycoproteins and cell surface polysaccharides. JOURNAL OF BIOMOLECULAR NMR 2011; 51:163-71. [PMID: 21947924 PMCID: PMC3199143 DOI: 10.1007/s10858-011-9550-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 06/25/2011] [Indexed: 05/03/2023]
Abstract
Few solution NMR pulse sequences exist that are explicitly designed to characterize carbohydrates (glycans). This is despite the essential role carbohydrate motifs play in cell-cell communication, microbial pathogenesis, autoimmune disease progression and cancer metastasis, and despite that fact that glycans, often shed to extra-cellular fluids, can be diagnostic of disease. Here we present a suite of two dimensional coherence experiments to measure three different correlations (H3-C2, H3-C1, and C1-C2) on sialic acids, a group of nine-carbon carbohydrates found on eukaryotic cell surfaces that often play a key role in disease processes. The chemical shifts of the H3, C2, and C1 nuclei of sialic acids are sensitive to carbohydrate linkage, linkage conformation, and ionization state of the C1 carboxylate. The experiments reported include rigorous filter elements to enable detection and characterization of isotopically labeled sialic acids with high sensitivity in living cells and crude isolates with minimal interference from unwanted signals arising from the ~1% (13)C-natural abundance of cellular metabolites. Application is illustrated with detection of sialic acids on living cells, in unpurified mixtures, and at the terminus of the N-glycan on the 55 kDa immunoglobulin G Fc.
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Affiliation(s)
- Adam W. Barb
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602
| | - Darón I. Freedberg
- Laboratory of Bacterial Polysaccharides, Building 29, Room 115 Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, HFM-419, Rockville, MD 20852
| | - Marcos D. Battistel
- Laboratory of Bacterial Polysaccharides, Building 29, Room 115 Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, HFM-419, Rockville, MD 20852
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Wang X, Tash B, Flanagan JM, Tian F. RDC derived protein backbone resonance assignment using fragment assembly. JOURNAL OF BIOMOLECULAR NMR 2011; 49:85-98. [PMID: 21191805 PMCID: PMC6936109 DOI: 10.1007/s10858-010-9467-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 12/15/2010] [Indexed: 05/23/2023]
Abstract
Experimental residual dipolar couplings (RDCs) in combination with structural models have the potential for accelerating the protein backbone resonance assignment process because RDCs can be measured accurately and interpreted quantitatively. However, this application has been limited due to the need for very high-resolution structural templates. Here, we introduce a new approach to resonance assignment based on optimal agreement between the experimental and calculated RDCs from a structural template that contains all assignable residues. To overcome the inherent computational complexity of such a global search, we have adopted an efficient two-stage search algorithm and included connectivity data from conventional assignment experiments. In the first stage, a list of strings of resonances (CA-links) is generated via exhaustive searches for short segments of sequentially connected residues in a protein (local templates), and then ranked by the agreement of the experimental (13)C(α) chemical shifts and (15)N-(1)H RDCs to the predicted values for each local template. In the second stage, the top CA-links for different local templates in stage I are combinatorially connected to produce CA-links for all assignable residues. The resulting CA-links are ranked for resonance assignment according to their measured RDCs and predicted values from a tertiary structure. Since the final RDC ranking of CA-links includes all assignable residues and the assignment is derived from a "global minimum", our approach is far less reliant on the quality of experimental data and structural templates. The present approach is validated with the assignments of several proteins, including a 42 kDa maltose binding protein (MBP) using RDCs and structural templates of varying quality. Since backbone resonance assignment is an essential first step for most of biomolecular NMR applications and is often a bottleneck for large systems, we expect that this new approach will improve the efficiency of the assignment process for small and medium size proteins and will extend the size limits assignable by current methods for proteins with structural models.
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Affiliation(s)
- Xingsheng Wang
- Department of Biochemistry and Molecular Biology, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
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17
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Thakur CS, Sama JN, Jackson ME, Chen B, Dayie TK. Selective 13C labeling of nucleotides for large RNA NMR spectroscopy using an E. coli strain disabled in the TCA cycle. JOURNAL OF BIOMOLECULAR NMR 2010; 48:179-92. [PMID: 21057854 PMCID: PMC2988204 DOI: 10.1007/s10858-010-9454-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 07/28/2010] [Indexed: 05/05/2023]
Abstract
Escherichia coli (E. coli) is an ideal organism to tailor-make labeled nucleotides for biophysical studies of RNA. Recently, we showed that adding labeled formate enhanced the isotopic enrichment at protonated carbon sites in nucleotides. In this paper, we show that growth of a mutant E. coli strain DL323 (lacking succinate and malate dehydrogenases) on (13)C-2-glycerol and (13)C-1,3-glycerol enables selective labeling at many useful sites for RNA NMR spectroscopy. For DL323 E. coli grown in (13)C-2-glycerol without labeled formate, all the ribose carbon atoms are labeled except the C3' and C5' carbon positions. Consequently the C1', C2' and C4' positions remain singlet. In addition, only the pyrimidine base C6 atoms are substantially labeled to ~96% whereas the C2 and C8 atoms of purine are labeled to ~5%. Supplementing the growth media with (13)C-formate increases the labeling at C8 to ~88%, but not C2. Not unexpectedly, addition of exogenous formate is unnecessary for attaining the high enrichment levels of ~88% for the C2 and C8 purine positions in a (13)C-1,3-glycerol based growth. Furthermore, the ribose ring is labeled in all but the C4' carbon position, such that the C2' and C3' positions suffer from multiplet splitting but the C5' position remains singlet and the C1' position shows a small amount of residual C1'-C2' coupling. As expected, all the protonated base atoms, except C6, are labeled to ~90%. In addition, labeling with (13)C-1,3-glycerol affords an isolated methylene ribose with high enrichment at the C5' position (~90%) that makes it particularly attractive for NMR applications involving CH(2)-TROSY modules without the need for decoupling the C4' carbon. To simulate the tumbling of large RNA molecules, perdeuterated glycerol was added to a mixture of the four nucleotides, and the methylene TROSY experiment recorded at various temperatures. Even under conditions of slow tumbling, all the expected carbon correlations were observed, which indicates this approach of using nucleotides obtained from DL323 E. coli will be applicable to high molecular weight RNA systems.
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Affiliation(s)
- Chandar S. Thakur
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure & Organization, University of Maryland, 1115 Biomolecular Sciences Bldg (#296), College Park, MD 20742-3360 USA
| | - Jacob N. Sama
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure & Organization, University of Maryland, 1115 Biomolecular Sciences Bldg (#296), College Park, MD 20742-3360 USA
| | - Melantha E. Jackson
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure & Organization, University of Maryland, 1115 Biomolecular Sciences Bldg (#296), College Park, MD 20742-3360 USA
| | - Bin Chen
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure & Organization, University of Maryland, 1115 Biomolecular Sciences Bldg (#296), College Park, MD 20742-3360 USA
| | - T. Kwaku Dayie
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure & Organization, University of Maryland, 1115 Biomolecular Sciences Bldg (#296), College Park, MD 20742-3360 USA
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18
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Takeuchi K, Heffron G, Sun ZYJ, Frueh DP, Wagner G. Nitrogen-detected CAN and CON experiments as alternative experiments for main chain NMR resonance assignments. JOURNAL OF BIOMOLECULAR NMR 2010; 47:271-82. [PMID: 20556482 PMCID: PMC2946331 DOI: 10.1007/s10858-010-9430-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 06/01/2010] [Indexed: 05/12/2023]
Abstract
Heteronuclear direct-detection experiments, which utilize the slower relaxation properties of low gamma nuclei, such as (13)C have recently been proposed for sequence-specific assignment and structural analyses of large, unstructured, and/or paramagnetic proteins. Here we present two novel (15)N direct-detection experiments. The CAN experiment sequentially connects amide (15)N resonances using (13)C(alpha) chemical shift matching, and the CON experiment connects the preceding (13)C' nuclei. When starting from the same carbon polarization, the intensities of nitrogen signals detected in the CAN or CON experiments would be expected four times lower than those of carbon resonances observed in the corresponding (13)C-detecting experiment, NCA-DIPAP or NCO-IPAP (Bermel et al. 2006b; Takeuchi et al. 2008). However, the disadvantage due to the lower gamma is counteracted by the slower (15)N transverse relaxation during detection, the possibility for more efficient decoupling in both dimensions, and relaxation optimized properties of the pulse sequences. As a result, the median S/N in the (15)N observe CAN experiment is 16% higher than in the (13)C observe NCA-DIPAP experiment. In addition, significantly higher sensitivity was observed for those residues that are hard to detect in the NCA-DIPAP experiment, such as Gly, Ser and residues with high-field C(alpha) resonances. Both CAN and CON experiments are able to detect Pro resonances that would not be observed in conventional proton-detected experiments. In addition, those experiments are free from problems of incomplete deuterium-to-proton back exchange in amide positions of perdeuterated proteins expressed in D(2)O. Thus, these features and the superior resolution of (15)N-detected experiments provide an attractive alternative for main chain assignments. The experiments are demonstrated with the small model protein GB1 at conditions simulating a 150 kDa protein, and the 52 kDa glutathione S-transferase dimer, GST.
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Affiliation(s)
- Koh Takeuchi
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Gregory Heffron
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Zhen-Yu J. Sun
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Dominique P. Frueh
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gerhard Wagner
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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Takeuchi K, Frueh DP, Sun ZYJ, Hiller S, Wagner G. CACA-TOCSY with alternate 13C-12C labeling: a 13Calpha direct detection experiment for mainchain resonance assignment, dihedral angle information, and amino acid type identification. JOURNAL OF BIOMOLECULAR NMR 2010; 47:55-63. [PMID: 20383561 PMCID: PMC2868269 DOI: 10.1007/s10858-010-9410-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 03/19/2010] [Indexed: 05/29/2023]
Abstract
We present a (13)C direct detection CACA-TOCSY experiment for samples with alternate (13)C-(12)C labeling. It provides inter-residue correlations between (13)C(alpha) resonances of residue i and adjacent C(alpha)s at positions i - 1 and i + 1. Furthermore, longer mixing times yield correlations to C(alpha) nuclei separated by more than one residue. The experiment also provides C(alpha)-to-sidechain correlations, some amino acid type identifications and estimates for psi dihedral angles. The power of the experiment derives from the alternate (13)C-(12)C labeling with [1,3-(13)C] glycerol or [2-(13)C] glycerol, which allows utilizing the small scalar (3)J(CC) couplings that are masked by strong (1)J(CC) couplings in uniformly (13)C labeled samples.
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