1
|
Yong JRJ, Kupče Ē, Claridge TDW. The NOAH HSQC-COSY module revisited: A theoretical and practical comparison of pulse sequences. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 367:107759. [PMID: 39216461 DOI: 10.1016/j.jmr.2024.107759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/19/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
NMR supersequences, as exemplified by the NOAH (NMR by Ordered Acquisition using 1H detection) technique, are a powerful way of acquiring multiple 2D data sets in much shorter durations. This is accomplished through targeted excitation and detection of the magnetisation belonging to specific isotopologues ('magnetisation pools'). Separately, the HSQC-COSY experiment has recently seen an increase in popularity due to the high signal dispersion in the indirect dimension and the removal of ambiguity traditionally associated with HSQC-TOCSY experiments. Here, we describe how the HSQC-COSY experiment can be integrated as a 'module' within NOAH supersequences. The benefits and drawbacks of several different pulse sequence implementations are discussed, with a particular focus on how sensitivities of other modules in the same supersequence are affected.
Collapse
Affiliation(s)
- Jonathan R J Yong
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; The Alan Turing Institute, The British Library, 96 Euston Road, London NW1 2DB, United Kingdom(1)
| | - Ēriks Kupče
- Bruker UK Ltd, R&D, Coventry CV4 9GH, United Kingdom; Latvian Academy of Sciences, Akadēmijas Laukums 1, Riga LV-1050, Latvia(1)
| | - Tim D W Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, United Kingdom(1).
| |
Collapse
|
2
|
Nedvedova S, Guillière F, Miele AE, Cantrelle FX, Dvorak J, Walker O, Hologne M. Divide, conquer and reconstruct: How to solve the 3D structure of recalcitrant Micro-Exon Gene (MEG) protein from Schistosoma mansoni. PLoS One 2023; 18:e0289444. [PMID: 37535563 PMCID: PMC10399815 DOI: 10.1371/journal.pone.0289444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023] Open
Abstract
Micro-Exon Genes are a widespread class of genes known for their high variability, widespread in the genome of parasitic trematodes such as Schistosoma mansoni. In this study, we present a strategy that allowed us to solve the structures of three alternatively spliced isoforms from the Schistoma mansoni MEG 2.1 family for the first time. All isoforms are hydrophobic, intrinsically disordered, and recalcitrant to be expressed in high yield in heterologous hosts. We resorted to the chemical synthesis of shorter pieces, before reconstructing the entire sequence. Here, we show that isoform 1 partially folds in a-helix in the presence of trifluoroethanol while isoform 2 features two rigid elbows, that maintain the peptide as disordered, preventing any structuring. Finally, isoform 3 is dominated by the signal peptide, which folds into a-helix. We demonstrated that combining biophysical techniques, like circular dichroism and nuclear magnetic resonance at natural abundance, with in silico molecular dynamics simulation for isoform 1 only, was the key to solve the structure of MEG 2.1. Our results provide a crucial piece to the puzzle of this elusive and highly variable class of proteins.
Collapse
Affiliation(s)
- Stepanka Nedvedova
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne, France
- Department of Chemistry, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
- Department of Zoology and Fisheries, Center of Infectious Animal Diseases, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Florence Guillière
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne, France
| | - Adriana Erica Miele
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne, France
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - François-Xavier Cantrelle
- Université de Lille, CNRS, UMR8576 -UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Jan Dvorak
- Department of Zoology and Fisheries, Center of Infectious Animal Diseases, Czech University of Life Sciences Prague, Prague, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
- Faculty of Environmental Sciences, Center of Infectious Animal Diseases, Czech University of Life Sciences in Prague, Prague, Czech Republic
| | - Olivier Walker
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne, France
| | - Maggy Hologne
- Université de Lyon, CNRS, UCB Lyon1, Institut des Sciences Analytiques, UMR5280, 5 rue de la Doua, Villeurbanne, France
| |
Collapse
|
3
|
Abstract
Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.
Collapse
Affiliation(s)
- Carolina Fontana
- Departamento
de Química del Litoral, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| |
Collapse
|
4
|
Yong JRJ, Hansen AL, Kupče Ē, Claridge TDW. Increasing sensitivity and versatility in NMR supersequences with new HSQC-based modules. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 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] [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.
Collapse
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.
| |
Collapse
|
5
|
Hansen AL, Kupče E, Li DW, Bruschweiler-Li L, Wang C, Brüschweiler R. 2D NMR-Based Metabolomics with HSQC/TOCSY NOAH Supersequences. Anal Chem 2021; 93:6112-6119. [DOI: 10.1021/acs.analchem.0c05205] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alexandar L. Hansen
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - E̅riks Kupče
- Bruker UK Ltd., Banner Lane, Coventry, CV4 9GH, U.K
| | - Da-Wei Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Cheng Wang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Rafael Brüschweiler
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| |
Collapse
|