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Bence Farkas L, Timári I, Kövér KE, Sørensen OW. Four-in-one: HSQC, HSQC-TOCSY (or H2BC), TOCSY, and enhanced HMBC spectra integrated into a single NO Relaxation Delay (NORD) NMR experiment. J Magn Reson 2022; 343:107297. [PMID: 36174396 DOI: 10.1016/j.jmr.2022.107297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
The NMR pulse sequence design strategy of NORD (NO Relaxation Delay) is extended to design of two new three-module experiments, NORD {HMBC}-{HSQC-TOCSY}-{TOCSY} and NORD {HMBC}-{2BOB}-{TOCSY}, each delivering four spectra - HMBC, HSQC, TOCSY, and either HSQC-TOCSY or H2BC. Compared to individual recording of these spectra particularly the sensitivity of the least sensitive module, HMBC, is enhanced by designing the homonuclear TOCSY module to allow buildup of magnetization pertinent to HMBC during its execution. Effectively, the sensitivity of the heteronuclear modules is boosted at the expense of the inherently much higher TOCSY sensitivity, thus resulting in a significant saving in spectrometer time.
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Affiliation(s)
- László Bence Farkas
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - István Timári
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Katalin E Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Hungary.
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Yong JRJ, Hansen AL, Kupče Ē, Claridge TDW. Increasing sensitivity and versatility in NMR supersequences with new HSQC-based modules. J Magn Reson 2021; 329:107027. [PMID: 34246882 DOI: 10.1016/j.jmr.2021.107027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 05/22/2023]
Abstract
The sensitivity-enhanced HSQC, as well as HSQC-TOCSY, experiments have been modified for incorporation into NOAH (NMR by Ordered Acquisition using 1H detection) supersequences, adding diversity for 13C and 15N modules. Importantly, these heteronuclear modules have been specifically tailored to preserve the magnetisation required for subsequent acquisition of other heteronuclear or homonuclear modules in a supersequence. In addition, we present protocols for optimally combining HSQC and HSQC-TOCSY elements within the same supersequences, yielding high-quality 2D spectra suitable for structure characterisation but with greatly reduced experiment durations. We further demonstrate that these time savings can translate to increased detection sensitivity per unit time.
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Affiliation(s)
- Jonathan R J Yong
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH 43210, USA
| | - Ēriks Kupče
- Bruker UK Ltd., Banner Lane, Coventry CV4 9GH, UK
| | - Tim D W Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK.
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Hargett AA, Marcella AM, Yu H, Li C, Orwenyo J, Battistel MD, Wang LX, Freedberg DI. Glycosylation States on Intact Proteins Determined by NMR Spectroscopy. Molecules 2021; 26:molecules26144308. [PMID: 34299586 PMCID: PMC8303171 DOI: 10.3390/molecules26144308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/23/2022] Open
Abstract
Protein glycosylation is important in many organisms for proper protein folding, signaling, cell adhesion, protein-protein interactions, and immune responses. Thus, effectively determining the extent of glycosylation in glycoprotein therapeutics is crucial. Up to now, characterizing protein glycosylation has been carried out mostly by liquid chromatography mass spectrometry (LC-MS), which requires careful sample processing, e.g., glycan removal or protein digestion and glycopeptide enrichment. Herein, we introduce an NMR-based method to better characterize intact glycoproteins in natural abundance. This non-destructive method relies on exploiting differences in nuclear relaxation to suppress the NMR signals of the protein while maintaining glycan signals. Using RNase B Man5 and RNase B Man9, we establish reference spectra that can be used to determine the different glycoforms present in heterogeneously glycosylated commercial RNase B.
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Affiliation(s)
- Audra A. Hargett
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Aaron M. Marcella
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Huifeng Yu
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (C.L.); (J.O.); (L.-X.W.)
| | - Jared Orwenyo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (C.L.); (J.O.); (L.-X.W.)
| | - Marcos D. Battistel
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (C.L.); (J.O.); (L.-X.W.)
| | - Darón I. Freedberg
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
- Correspondence:
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Becker J, Koos MRM, Schulze-Sünninghausen D, Luy B. ASAP- HSQC-TOCSY for fast spin system identification and extraction of long-range couplings. J Magn Reson 2019; 300:76-83. [PMID: 30711785 DOI: 10.1016/j.jmr.2018.12.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 06/09/2023]
Abstract
Based on Ernst-angle-type excitation and Acceleration by Sharing Adjacent Polarization (ASAP), a fast HSQC-TOCSY experiment is introduced. In the approach, the DIPSI-2 isotropic mixing period of the ASAP-HSQC is simply shifted, which provides a TOCSY period without additional application of rf-energy. The ASAP-HSQC-TOCSY allows the acquisition of a conventional 2D in about 30 s. Alternatively, it allows the acquisition of highly carbon-resolved spectra (several Hz digital resolution) on the order of minutes. An ASAP-HSQC-TOCSY-IPAP variant, finally, allows the sign-sensitive extraction of heteronuclear long-range coupling constants from a pair of highly resolved spectra in less than an hour. Pulse sequences, several example spectra, and a discussion of results are given.
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Affiliation(s)
- Johanna Becker
- Institut für Organische Chemie and Institut für Biologische Grenzflächen, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Martin R M Koos
- Institut für Organische Chemie and Institut für Biologische Grenzflächen, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - David Schulze-Sünninghausen
- Institut für Organische Chemie and Institut für Biologische Grenzflächen, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Burkhard Luy
- Institut für Organische Chemie and Institut für Biologische Grenzflächen, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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Brodaczewska N, Košťálová Z, Uhrín D. (3, 2)D 1H, 13C BIRD r,X- HSQC-TOCSY for NMR structure elucidation of mixtures: application to complex carbohydrates. J Biomol NMR 2018; 70:115-122. [PMID: 29327222 DOI: 10.1007/s10858-018-0163-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/04/2018] [Indexed: 06/07/2023]
Abstract
Overlap of NMR signals is the major cause of difficulties associated with NMR structure elucidation of molecules contained in complex mixtures. A 2D homonuclear correlation spectroscopy in particular suffers from low dispersion of 1H chemical shifts; larger dispersion of 13C chemical shifts is often used to reduce this overlap, while still providing the proton-proton correlation information e.g. in the form of a 2D 1H, 13C HSQC-TOCSY experiment. For this methodology to work, 13C chemical shift must be resolved. In case of 13C chemical shifts overlap, 1H chemical shifts can be used to achieve the desired resolution. The proposed (3, 2)D 1H, 13C BIRDr,X-HSQC-TOCSY experiment achieves this while preserving singlet character of cross peaks in the F1 dimension. The required high-resolution in the 13C dimension is thus retained, while the cross peak overlap occurring in a regular HSQC-TOCSY experiment is eliminated. The method is illustrated on the analysis of a complex carbohydrate mixture obtained by depolymerisation of a fucosylated chondroitin sulfate isolated from the body wall of the sea cucumber Holothuria forskali.
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Affiliation(s)
- Natalia Brodaczewska
- EastChem School of Chemistry, University of Edinburgh Joseph Black Building, David Brewster Rd, Edinburgh, EH9 3FJ, UK
| | - Zuzana Košťálová
- EastChem School of Chemistry, University of Edinburgh Joseph Black Building, David Brewster Rd, Edinburgh, EH9 3FJ, UK
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Dušan Uhrín
- EastChem School of Chemistry, University of Edinburgh Joseph Black Building, David Brewster Rd, Edinburgh, EH9 3FJ, UK.
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Singh A, Dubey A, Adiga SK, Atreya HS. Phase modulated 2D HSQC-TOCSY for unambiguous assignment of overlapping spin systems. J Magn Reson 2018; 286:10-16. [PMID: 29169027 DOI: 10.1016/j.jmr.2017.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/12/2017] [Accepted: 11/13/2017] [Indexed: 06/07/2023]
Abstract
We present a new method that allows one to unambiguously resolve overlapping spin systems often encountered in biomolecular systems such as peptides and proteins or in samples containing a mixture of different molecules such as in metabolomics. We address this problem using the recently proposed phase modulation approach. By evolving the 1H chemical shifts in a conventional two dimensional (2D) HSQC-TOCSY experiment for a fixed delay period, the phase/intensity of set of cross peaks belonging to one spin system are modulated differentially relative to those of its overlapping counterpart, resulting in their discrimination and recognition. The method thus accelerates the process of identification and resonance assignment of individual compounds in complex mixtures. This approach facilitated the assignment of molecules in the embryo culture medium used in human assisted reproductive technology.
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Affiliation(s)
- Amrinder Singh
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India
| | - Abhinav Dubey
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India
| | - Satish K Adiga
- Department of Clinical Embryology, Kasturba Medical College, Manipal University, Manipal 576104, India
| | - Hanudatta S Atreya
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India.
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Saurí J, Marcó N, Williamson RT, Martin GE, Parella T. Extending long-range heteronuclear NMR connectivities by HSQMBC-COSY and HSQMBC-TOCSY experiments. J Magn Reson 2015; 258:25-32. [PMID: 26160012 DOI: 10.1016/j.jmr.2015.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 06/04/2023]
Abstract
The detection of long-range heteronuclear correlations presenting J(CH) coupling values smaller than 1-2Hz is a challenge in the structural analysis of small molecules and natural products. HSQMBC-COSY and HSQMBC-TOCSY pulse schemes are evaluated as complementary NMR methods to standard HMBC/HSQMBC experiments. Incorporation of an additional J(HH) transfer step in the basic HSQMBC pulse scheme can favor the sensitive observation of traditionally missing or very weak correlations and, in addition, facilitates the detection of a significant number of still longer-range connectivities to both protonated and non-protonated carbons under optimum sensitivity conditions. A comparative (1)H-(13)C study is performed using strychnine as a model compound and several examples are also provided including (1)H-(15)N applications.
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Affiliation(s)
- Josep Saurí
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain; NMR Structure Elucidation, Process and Analytical Chemistry, Merck & Co. Inc., 126 E. Lincoln Avenue, Rahway, NJ 07065, USA
| | - Núria Marcó
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - R Thomas Williamson
- NMR Structure Elucidation, Process and Analytical Chemistry, Merck & Co. Inc., 126 E. Lincoln Avenue, Rahway, NJ 07065, USA
| | - Gary E Martin
- NMR Structure Elucidation, Process and Analytical Chemistry, Merck & Co. Inc., 126 E. Lincoln Avenue, Rahway, NJ 07065, USA
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain.
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Rath P, Saurel O, Tropis M, Daffé M, Demange P, Milon A. NMR localization of the O-mycoloylation on PorH, a channel forming peptide from Corynebacterium glutamicum. FEBS Lett 2013; 587:3687-91. [PMID: 24100136 DOI: 10.1016/j.febslet.2013.09.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/04/2013] [Accepted: 09/25/2013] [Indexed: 11/28/2022]
Abstract
PorH and PorA are two small peptides that, in complex, form a voltage-dependent ion channel in the outer membrane of Corynebacterium glutamicum. Specific post-translational modifications on PorA and PorH are required for the formation of a functional ion channel. The assignment of PorH proton NMR chemical shifts in DMSO, allowed identifying unambiguously the exact position of the PorH O-mycoloylation on Ser 56 side chain. This was further confirmed by site directed mutagenesis and mass spectrometry. Together with the previously published localization of PorA mycoloylation, this provides the complete primary structure characterization of this outer membrane porin.
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Affiliation(s)
- Parthasarathi Rath
- Institute of Pharmacology and Structural Biology, Université de Toulouse, UPS, 205 route de Narbonne, 31077 Toulouse, France; IPBS, UMR 5089, CNRS, 205 route de Narbonne, BP 64182, 31077 Toulouse, France
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Parella T, Espinosa JF. Long-range proton-carbon coupling constants: NMR methods and applications. Prog Nucl Magn Reson Spectrosc 2013; 73:17-55. [PMID: 23962883 DOI: 10.1016/j.pnmrs.2013.07.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/03/2013] [Accepted: 07/03/2013] [Indexed: 06/02/2023]
Abstract
A general review of novel NMR methods to measure heteronuclear long-range proton-carbon coupling constants ((n)JCH; n>1) in small molecules is made. NMR experiments are classified in terms of NMR pulse scheme and cross-peak nature. A discussion about simplicity, general applicability and accuracy for each particular NMR experiment is presented and exemplified. Important aspects such as the sign determination and measurement of very small coupling values involving protonated and non-protonated carbons as well as the complementarity between different experiments are also discussed. Finally, a compilation of applications in structural and conformational analysis of different types of molecules since 2000 is surveyed.
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Affiliation(s)
- Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
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