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Schiavina M, Bracaglia L, Rodella MA, Kümmerle R, Konrat R, Felli IC, Pierattelli R. Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz. Nat Protoc 2024; 19:406-440. [PMID: 38087081 DOI: 10.1038/s41596-023-00921-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/20/2023] [Indexed: 02/12/2024]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for characterizing biomolecules such as proteins and nucleic acids at atomic resolution. Increased magnetic field strengths drive progress in biomolecular NMR applications, leading to improved performance, e.g., higher resolution. A new class of NMR spectrometers with a 28.2 T magnetic field (1.2 GHz 1H frequency) has been commercially available since the end of 2019. The availability of ultra-high-field NMR instrumentation makes it possible to investigate more complex systems using NMR. This is especially true for highly flexible intrinsically disordered proteins (IDPs) and highly flexible regions (IDRs) of complex multidomain proteins. Indeed, the investigation of these proteins is frequently hampered by the crowding of NMR spectra. The advantages, however, are accompanied by challenges that the user must overcome when conducting experiments at such a high field (e.g., large spectral widths, radio frequency bandwidth, performance of decoupling schemes). This protocol presents strategies and tricks for optimising high-field NMR experiments for IDPs/IDRs based on the analysis of the relaxation properties of the investigated protein. The protocol, tested on three IDPs of different molecular weight and structural complexity, focuses on 13C-detected NMR at 1.2 GHz. A set of experiments, including some multiple receiver experiments, and tips to implement versions tailored for IDPs/IDRs are described. However, the general approach and most considerations can also be applied to experiments that acquire 1H or 15N nuclei and to experiments performed at lower field strengths.
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Affiliation(s)
- Marco Schiavina
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy.
| | - Lorenzo Bracaglia
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy
| | - Maria Anna Rodella
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy
| | | | - Robert Konrat
- Department of Computational and Structural Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Isabella C Felli
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy.
| | - Roberta Pierattelli
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy.
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Kupče Ē, Mote KR, Webb A, Madhu PK, Claridge TDW. Multiplexing experiments in NMR and multi-nuclear MRI. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 124-125:1-56. [PMID: 34479710 DOI: 10.1016/j.pnmrs.2021.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 05/22/2023]
Abstract
Multiplexing NMR experiments by direct detection of multiple free induction decays (FIDs) in a single experiment offers a dramatic increase in the spectral information content and often yields significant improvement in sensitivity per unit time. Experiments with multi-FID detection have been designed with both homonuclear and multinuclear acquisition, and the advent of multiple receivers on commercial spectrometers opens up new possibilities for recording spectra from different nuclear species in parallel. Here we provide an extensive overview of such techniques, designed for applications in liquid- and solid-state NMR as well as in hyperpolarized samples. A brief overview of multinuclear MRI is also provided, to stimulate cross fertilization of ideas between the two areas of research (NMR and MRI). It is shown how such techniques enable the design of experiments that allow structure elucidation of small molecules from a single measurement. Likewise, in biomolecular NMR experiments multi-FID detection allows complete resonance assignment in proteins. Probes with multiple RF microcoils routed to multiple NMR receivers provide an alternative way of increasing the throughput of modern NMR systems, effectively reducing the cost of NMR analysis and increasing the information content at the same time. Solid-state NMR experiments have also benefited immensely from both parallel and sequential multi-FID detection in a variety of multi-dimensional pulse schemes. We are confident that multi-FID detection will become an essential component of future NMR methodologies, effectively increasing the sensitivity and information content of NMR measurements.
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Affiliation(s)
- Ēriks Kupče
- Bruker UK Ltd., Banner Lane, Coventry CV4 9GH, United Kingdom.
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research-Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Andrew Webb
- Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Perunthiruthy K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research-Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
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3
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Joseph D, Sukumaran S, Chandra K, Pudakalakatti SM, Dubey A, Singh A, Atreya HS. Rapid nuclear magnetic resonance data acquisition with improved resolution and sensitivity for high-throughput metabolomic analysis. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:300-314. [PMID: 33030750 DOI: 10.1002/mrc.5106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/18/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
Nuclear magnetic resonance (NMR)-based metabolomics has witnessed rapid advancements in recent years with the continuous development of new methods to enhance the sensitivity, resolution, and speed of data acquisition. Some of the approaches were earlier used for peptide and protein resonance assignments and have now been adapted to metabolomics. At the same time, new NMR methods involving novel data acquisition techniques, suited particularly for high-throughput analysis in metabolomics, have been developed. In this review, we focus on the different sampling strategies or data acquisition methods that have been developed in our laboratory and other groups to acquire NMR spectra rapidly with high sensitivity and resolution for metabolomics. In particular, we focus on the use of multiple receivers, phase modulation NMR spectroscopy, and fast-pulsing methods for identification and assignments of metabolites.
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Affiliation(s)
- David Joseph
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India
| | - Sujeesh Sukumaran
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India
| | - Kousik Chandra
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India
| | | | - Abhinav Dubey
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India
| | - Amrinder Singh
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India
| | - Hanudatta S Atreya
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India
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4
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Di Pietro ME, Castiglione F, Mele A. Polar/apolar domains' dynamics in alkylimidazolium ionic liquids unveiled by the dual receiver NMR 1H and 19F relaxation experiment. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114567] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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5
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Kupče Ē, Mote KR, Madhu PK. Experiments with direct detection of multiple FIDs. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 304:16-34. [PMID: 31077929 DOI: 10.1016/j.jmr.2019.04.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/26/2019] [Accepted: 04/29/2019] [Indexed: 05/04/2023]
Abstract
Pulse schemes with direct observation of multiple free induction decays (FIDs) offer a dramatic increase in the spectral information content of NMR experiments and often yield substantial improvement in measurement sensitivity per unit time. Availability of multiple receivers on the state-of-the-art commercial spectrometers allows spectra from different nuclear species to be recorded in parallel routinely. Experiments with multi-FID detection have been designed with both, homonuclear and multinuclear acquisition. We provide a brief overview of such techniques designed for applications in liquid- and solid- state NMR as well as in hyperpolarized samples. Here we show how these techniques have led to design of experiments that allow structure elucidation of small molecules and resonance assignment in proteins from a single measurement. Probes with multiple RF micro-coils routed to multiple NMR receivers provide an alternative way of increasing the throughput of modern NMR systems. Solid-state NMR experiments have also benefited immensely from both parallel and simultaneous FID acquisition in a variety of multi-dimensional pulse schemes. We believe that multi-FID detection will become an essential component of the future NMR methodologies effectively increasing the information content of NMR experiments and reducing the cost of NMR analysis.
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Affiliation(s)
- Ēriks Kupče
- Bruker UK Ltd., Banner Lane, Coventry CV4 9GH, United Kingdom.
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad 500107, India
| | - Perunthiruthy K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad 500107, India
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6
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Edison AS, Le Guennec A, Delaglio F, Kupče Ē. Practical Guidelines for 13C-Based NMR Metabolomics. Methods Mol Biol 2019; 2037:69-95. [PMID: 31463840 DOI: 10.1007/978-1-4939-9690-2_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
We present an overview of 13C-based NMR metabolomics. At first glance, the low sensitivity of 13C relative to 1H NMR might seem like too great an obstacle to use this approach. However, there are several advantages to 13C NMR, whether samples can be isotopically enriched or not. At natural abundance, peaks are sharp and largely resolved, and peak frequencies are more stable to pH and other sample conditions. Statistical approaches can be used to obtain C-C and C-H correlation maps, which greatly aid in compound identification. With 13C isotopic enrichment, other experiments are possible, including both 13C-J-RES and INADEQUATE, which can be used for de novo identification of metabolites not in databases.NMR instrumentation and software has significantly improved, and probes are now commercially available that can record useful natural abundance 1D 13C spectra from real metabolomics samples in 2 h or less. Probe technology continues to improve, and the next generation should be even better. Combined with new methods of simultaneous data acquisition, which allows for two or more 1D or 2D NMR experiments to be collected using multiple receivers, very rich datasets can be collected in a reasonable amount of time that should improve metabolomics data analysis and compound identification.
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Affiliation(s)
- Arthur S Edison
- Department of Biochemistry, University of Georgia, Athens, GA, USA. .,Department of Genetics, University of Georgia, Athens, GA, USA. .,Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
| | - Adrien Le Guennec
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.,NMR Facility, Guy's Campus, King's College London, London, UK
| | - Frank Delaglio
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, University of Maryland, Rockville, MD, USA
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Singh A, Dubey A, Adiga SK, Atreya HS. Phase modulated 2D HSQC-TOCSY for unambiguous assignment of overlapping spin systems. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 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] [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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8
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Sharma K, Madhu PK, Mote KR. A suite of pulse sequences based on multiple sequential acquisitions at one and two radiofrequency channels for solid-state magic-angle spinning NMR studies of proteins. JOURNAL OF BIOMOLECULAR NMR 2016; 65:127-141. [PMID: 27364976 DOI: 10.1007/s10858-016-0043-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/14/2016] [Indexed: 05/04/2023]
Abstract
One of the fundamental challenges in the application of solid-state NMR is its limited sensitivity, yet a majority of experiments do not make efficient use of the limited polarization available. The loss in polarization in a single acquisition experiment is mandated by the need to select out a single coherence pathway. In contrast, sequential acquisition strategies can encode more than one pathway in the same experiment or recover unused polarization to supplement a standard experiment. In this article, we present pulse sequences that implement sequential acquisition strategies on one and two radiofrequency channels with a combination of proton and carbon detection to record multiple experiments under magic-angle spinning. We show that complementary 2D experiments such as [Formula: see text] and [Formula: see text] or DARR and [Formula: see text], and 3D experiments such as [Formula: see text] and [Formula: see text], or [Formula: see text] and [Formula: see text] can be combined in a single experiment to ensure time savings of at least 40 %. These experiments can be done under fast or slow-moderate magic-angle spinning frequencies aided by windowed [Formula: see text] acquisition and homonulcear decoupling. The pulse sequence suite is further expanded by including pathways that allow the recovery of residual polarization, the so-called 'afterglow' pathways, to encode a number of pulse sequences to aid in assignments and chemical-shift mapping.
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Affiliation(s)
- Kshama Sharma
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, 21, Brundavan Colony, Narsingi, Hyderabad, 500 075, India
| | - Perunthiruthy K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, 21, Brundavan Colony, Narsingi, Hyderabad, 500 075, India.
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, 400 005, India.
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, 21, Brundavan Colony, Narsingi, Hyderabad, 500 075, India.
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Kovacs H, Kupče Ē. Parallel NMR spectroscopy with simultaneous detection of (1) H and (19) F nuclei. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:544-60. [PMID: 27021630 DOI: 10.1002/mrc.4428] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 02/10/2016] [Accepted: 02/17/2016] [Indexed: 05/22/2023]
Abstract
Recording NMR signals of several nuclear species simultaneously by using parallel receivers provides more information from a single measurement and at the same time increases the measurement sensitivity per unit time. Here we present a comprehensive series of the most frequently used NMR experiments modified for simultaneous direct detection of two of the most sensitive NMR nuclei - (1) H and (19) F. We hope that the presented material will stimulate interest in and further development of this technique.
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Affiliation(s)
- Helena Kovacs
- Bruker BioSpin AG, Industriestrasse 26, CH-8117, Fällanden, Switzerland
| | - Ēriks Kupče
- Bruker UK Limited, Banner Lane, Coventry, CV4 9GH, UK
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10
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Wiedemann C, Bellstedt P, Häfner S, Herbst C, Bordusa F, Görlach M, Ohlenschläger O, Ramachandran R. A Set of Efficient nD NMR Protocols for Resonance Assignments of Intrinsically Disordered Proteins. Chemphyschem 2016; 17:1961-8. [PMID: 27061973 DOI: 10.1002/cphc.201600155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 11/07/2022]
Abstract
The RF pulse scheme RN[N-CA HEHAHA]NH, which provides a convenient approach to the acquisition of different multidimensional chemical shift correlation NMR spectra leading to backbone resonance assignments, including those of the proline residues of intrinsically disordered proteins (IDPs), is experimentally demonstrated. Depending on the type of correlation data required, the method involves the generation of in-phase ((15) N)(x) magnetisation via different magnetisation transfer pathways such as H→N→CO→N, HA→CA→CO→N, H→N→CA→N and H→CA→N, the subsequent application of (15) N-(13) C(α) heteronuclear Hartmann-Hahn mixing over a period of ≈100 ms, chemical-shift labelling of relevant nuclei before and after the heteronuclear mixing step and amide proton detection in the acquisition dimension. It makes use of the favourable relaxation properties of IDPs and the presence of (1) JCαN and (2) JCαN couplings to achieve efficient correlation of the backbone resonances of each amino acid residue "i" with the backbone amide resonances of residues "i-1" and "i+1". It can be implemented in a straightforward way through simple modifications of the RF pulse schemes commonly employed in protein NMR studies. The efficacy of the approach is demonstrated using a uniformly ((15) N,(13) C) labelled sample of α-synuclein. The different possibilities for obtaining the amino-acid-type information, simultaneously with the connectivity data between the backbone resonances of sequentially neighbouring residues, have also been outlined.
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Affiliation(s)
- Christoph Wiedemann
- Institute of Biochemistry/Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Peter Bellstedt
- Faculty of Chemistry and Earth Sciences, Friedrich Schiller University Jena, Humboldstr. 10, 07743, Jena, Germany
| | - Sabine Häfner
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Christian Herbst
- Department of Physics, Faculty of Science, Ubon Ratchathani University, 34190, Ubon Ratchathani, Thailand
| | - Frank Bordusa
- Institute of Biochemistry/Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Matthias Görlach
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Oliver Ohlenschläger
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Ramadurai Ramachandran
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
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11
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Gierth P, Codina A, Schumann F, Kovacs H, Kupče Ē. Fast experiments for structure elucidation of small molecules: Hadamard NMR with multiple receivers. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:940-944. [PMID: 26302997 DOI: 10.1002/mrc.4292] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/07/2015] [Accepted: 06/15/2015] [Indexed: 06/04/2023]
Abstract
We propose several significant improvements to the PANSY (Parallel NMR SpectroscopY) experiments-PANSY COSY and PANSY-TOCSY. The improved versions of these experiments provide sufficient spectral information for structure elucidation of small organic molecules from just two 2D experiments. The PANSY-TOCSY-Q experiment has been modified to allow for simultaneous acquisition of three different types of NMR spectra-1D C-13 of non-protonated carbon sites, 2D TOCSY and multiplicity edited 2D HETCOR. In addition the J-filtered 2D PANSY-gCOSY experiment records a 2D HH gCOSY spectrum in parallel with a (1) J-filtered HC long-range HETCOR spectrum as well as offers a simplified data processing. In addition to parallel acquisition, further time savings are feasible because of significantly smaller F1 spectral windows as compared to the indirect detection experiments. Use of cryoprobes and multiple receivers can significantly alleviate the sensitivity issues that are usually associated with the so called direct detection experiments. In cases where experiments are sampling limited rather than sensitivity limited further reduction of experiment time is achieved by using Hadamard encoding. In favorable cases the total recording time for the two PANSY experiments can be reduced to just 40 s. The proposed PANSY experiments provide sufficient information to allow the CMCse software package (Bruker) to solve structures of small organic molecules.
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Affiliation(s)
- Peter Gierth
- Bruker UK Limited, Banner Lane, Coventry, CV4 9GH, UK
| | - Anna Codina
- Bruker UK Limited, Banner Lane, Coventry, CV4 9GH, UK
| | - Frank Schumann
- Bruker BioSpin AG, Industriestrasse 26, Fällanden, 8117, Switzerland
| | - Helena Kovacs
- Bruker BioSpin AG, Industriestrasse 26, Fällanden, 8117, Switzerland
| | - Ēriks Kupče
- Bruker UK Limited, Banner Lane, Coventry, CV4 9GH, UK
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Chen Y, Zhang Z, Lin Y, Cai C, Cai S, Chen Z. Localised two-dimensional correlated spectroscopy based on Hadamard encoding technique. Mol Phys 2014. [DOI: 10.1080/00268976.2014.897397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Yushan Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surface, Xiamen University, Xiamen, China
| | - Zhiyong Zhang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surface, Xiamen University, Xiamen, China
| | - Yanqin Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surface, Xiamen University, Xiamen, China
| | - Congbo Cai
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surface, Xiamen University, Xiamen, China
| | - Shuhui Cai
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surface, Xiamen University, Xiamen, China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surface, Xiamen University, Xiamen, China
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Pudakalakatti SM, Dubey A, Jaipuria G, Shubhashree U, Adiga SK, Moskau D, Atreya HS. A fast NMR method for resonance assignments: application to metabolomics. JOURNAL OF BIOMOLECULAR NMR 2014; 58:165-173. [PMID: 24488481 DOI: 10.1007/s10858-014-9814-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/22/2014] [Indexed: 06/03/2023]
Abstract
We present a new method for rapid NMR data acquisition and assignments applicable to unlabeled ((12)C) or (13)C-labeled biomolecules/organic molecules in general and metabolomics in particular. The method involves the acquisition of three two dimensional (2D) NMR spectra simultaneously using a dual receiver system. The three spectra, namely: (1) G-matrix Fourier transform (GFT) (3,2)D [(13)C, (1)H] HSQC-TOCSY, (2) 2D (1)H-(1)H TOCSY and (3) 2D (13)C-(1)H HETCOR are acquired in a single experiment and provide mutually complementary information to completely assign individual metabolites in a mixture. The GFT (3,2)D [(13)C, (1)H] HSQC-TOCSY provides 3D correlations in a reduced dimensionality manner facilitating high resolution and unambiguous assignments. The experiments were applied for complete (1)H and (13)C assignments of a mixture of 21 unlabeled metabolites corresponding to a medium used in assisted reproductive technology. Taken together, the experiments provide time gain of order of magnitudes compared to the conventional data acquisition methods and can be combined with other fast NMR techniques such as non-uniform sampling and covariance spectroscopy. This provides new avenues for using multiple receivers and projection NMR techniques for high-throughput approaches in metabolomics.
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Martineau C, Decker F, Engelke F, Taulelle F. Parallelizing acquisitions of solid-state NMR spectra with multi-channel probe and multi-receivers: applications to nanoporous solids. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2013; 55-56:48-53. [PMID: 24011557 DOI: 10.1016/j.ssnmr.2013.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/03/2013] [Accepted: 08/13/2013] [Indexed: 05/04/2023]
Abstract
A five-channel ((1)H, (19)F, (31)P, (27)Al, (13)C) 2.5 mm magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) probe is used in combination with three separate receivers for the parallel acquisitions of one (1D) and two-dimensional (2D) NMR spectra in model fluorinated aluminophosphate and porous Al-based metal-organic framework (MOF). Possible combinations to record simultaneously spectra using this set-up are presented, including (i) parallel acquisitions of quantitative 1D NMR spectra of solids containing nuclei with contrasted T1 relaxation rates and (ii) parallel acquisitions of 2D heteronuclear NMR spectra. In solids containing numerous different NMR-accessible nuclei, the number of NMR experiments that have to be acquired to get accurate structural information is high. The strategy we present here, i.e. the multiplication of both the number of irradiation channels in the probe and the number of parallel receivers, offers one possibility to optimize this measurement time.
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Affiliation(s)
- Charlotte Martineau
- Tectospin, Institut Lavoisier de Versailles (ILV), UMR CNRS 8180, Université de Versailles Saint-Quentin-en-Yvelines, 45 Avenue des États-Unis, 78035 Versailles cedex, France.
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Giraud N, Pitoux D, Ouvrard JM, Merlet D. CombiningJ-Edited and Correlation Spectroscopies Within a Multi-dimensional Spatial Frequency Encoding: Toward Fully Resolved1H NMR Spectra. Chemistry 2013; 19:12221-4. [DOI: 10.1002/chem.201302005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Reddy JG, Hosur RV. Parallel acquisition of 3D-HA(CA)NH and 3D-HACACO spectra. JOURNAL OF BIOMOLECULAR NMR 2013; 56:77-84. [PMID: 23645113 DOI: 10.1007/s10858-013-9735-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Accepted: 04/25/2013] [Indexed: 06/02/2023]
Abstract
We present here an NMR pulse sequence with 5 independent incrementable time delays within the frame of a 3-dimensional experiment, by incorporating polarization sharing and dual receiver concepts. This has been applied to directly record 3D-HA(CA)NH and 3D-HACACO spectra of proteins simultaneously using parallel detection of (1)H and (13)C nuclei. While both the experiments display intra-residue backbone correlations, the 3D-HA(CA)NH provides also sequential 'i - 1 → i' correlation along the (1)Hα dimension. Both the spectra contain special peak patterns at glycine locations which serve as check points during the sequential assignment process. The 3D-HACACO spectrum contains, in addition, information on prolines and side chains of residues having H-C-CO network (i.e., (1)Hβ, (13)Cβ and (13)COγ of Asp and Asn, and (1)Hγ, (13)Cγ and (13)COδ of Glu and Gln), which are generally absent in most conventional proton detected experiments.
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Affiliation(s)
- Jithender G Reddy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
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Donovan KJ, Kupče E, Frydman L. Multiple Parallel 2D NMR Acquisitions in a Single Scan. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201210070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Donovan KJ, Kupče E, Frydman L. Multiple parallel 2D NMR acquisitions in a single scan. Angew Chem Int Ed Engl 2013; 52:4152-5. [PMID: 23460245 DOI: 10.1002/anie.201210070] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Kevin J Donovan
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
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Structure elucidation of indole–indoline type alkaloids: A retrospective account from the point of view of current NMR and MS technology. J Pharm Biomed Anal 2012; 69:106-24. [DOI: 10.1016/j.jpba.2012.02.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Revised: 02/14/2012] [Accepted: 02/15/2012] [Indexed: 11/23/2022]
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Kupče E, Kay LE. Parallel acquisition of multi-dimensional spectra in protein NMR. JOURNAL OF BIOMOLECULAR NMR 2012; 54:1-7. [PMID: 22802131 DOI: 10.1007/s10858-012-9646-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 06/15/2012] [Indexed: 06/01/2023]
Abstract
We introduce the use of multiple receivers applied in parallel for simultaneously recording multi-dimensional data sets of proteins in a single experiment. The utility of the approach is established through the introduction of the 2D (15)N,(1)H(N)||(13)CO HSQC experiment in which a pair of two-dimensional (15)N,(1)H(N) and (15)N,(13)CO spectra are recorded. The methodology is further extended to higher dimensionality via the 3D (1)H(N)||(13)CO HNCA in which a pair of data sets recording (13)C(α),(15)N,(1)H(N) and (13)C(α),(15)N,(13)CO chemical shifts are acquired. With the anticipated increases in probe sensitivity it is expected that multiple receiver experiments will become an important approach for efficient recording of NMR data.
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Affiliation(s)
- Eriks Kupče
- Agilent Technologies, 6 Mead Road, Yarnton, Oxford, OX5 1QU, UK
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