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Kampmeyer C, Larsen-Ledet S, Wagnkilde MR, Michelsen M, Iversen HKM, Nielsen SV, Lindemose S, Caregnato A, Ravid T, Stein A, Teilum K, Lindorff-Larsen K, Hartmann-Petersen R. Disease-linked mutations cause exposure of a protein quality control degron. Structure 2022; 30:1245-1253.e5. [PMID: 35700725 DOI: 10.1016/j.str.2022.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/08/2022] [Accepted: 05/18/2022] [Indexed: 10/18/2022]
Abstract
More than half of disease-causing missense variants are thought to lead to protein degradation, but the molecular mechanism of how these variants are recognized by the cell remains enigmatic. Degrons are stretches of amino acids that help mediate recognition by E3 ligases and thus confer protein degradation via the ubiquitin-proteasome system. While degrons that mediate controlled degradation of, for example, signaling components and cell-cycle regulators are well described, so-called protein-quality-control degrons that mediate the degradation of destabilized proteins are poorly understood. Here, we show that disease-linked dihydrofolate reductase (DHFR) missense variants are structurally destabilized and chaperone-dependent proteasome targets. We find two regions in DHFR that act as degrons, and the proteasomal turnover of one of these was dependent on the molecular chaperone Hsp70. Structural analyses by nuclear magnetic resonance (NMR) and hydrogen/deuterium exchange revealed that this degron is buried in wild-type DHFR but becomes transiently exposed in the disease-linked missense variants.
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Affiliation(s)
- Caroline Kampmeyer
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Sven Larsen-Ledet
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Morten Rose Wagnkilde
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Mathias Michelsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Henriette K M Iversen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Sofie V Nielsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Søren Lindemose
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Alberto Caregnato
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Tommer Ravid
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, 91904 Jerusalem, Israel
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Kaare Teilum
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
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2
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Lin E, Bai Z, Yuan Y, Chen Z, Yang Y, Huang Y, Chen Z. A General Reconstruction Method for Multidimensional Sparse Sampling Nuclear Magnetic Resonance Spectroscopy. J Phys Chem Lett 2021; 12:10622-10630. [PMID: 34699231 DOI: 10.1021/acs.jpclett.1c03063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Multidimensional NMR spectroscopy provides a powerful tool for structure elucidation and dynamic analysis of complex samples, particularly for biological macromolecules. Multidimensional sparse sampling effectively accelerates NMR experiments while an efficient reconstruction method is generally required for unraveling spectra. Various reconstruction methods were proposed for pure Fourier NMR (only involving chemical shifts and J couplings detection). However, reconstruction concerned with Laplace-related NMR (i.e., involving relaxation or diffusion detection) is more challenging due to its ill-posed property. The existing Laplace-related NMR sparse sampling reconstruction methods suffer from poor resolution and possible artifacts in the resulting spectra owing to the pitfalls of the optimization algorithms. Herein, we propose a general approach for fast high-resolution reconstruction of multidimensional sparse sampling NMR, including pure Fourier, mixed Fourier-Laplace, and pure Laplace NMR, benefiting from the comprehensive sparse constraint and effective optimization algorithm and thus showing the promising prospects of multidimensional NMR.
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Affiliation(s)
- Enping Lin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Electronic Science, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhemin Bai
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Electronic Science, Xiamen University, Xiamen, Fujian 361005, China
| | - Yifei Yuan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Electronic Science, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhiwei Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Electronic Science, Xiamen University, Xiamen, Fujian 361005, China
| | - Yu Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Electronic Science, Xiamen University, Xiamen, Fujian 361005, China
| | - Yuqing Huang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Electronic Science, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhong Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Electronic Science, Xiamen University, Xiamen, Fujian 361005, China
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3
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Definition of the immune evasion-replication interface of rabies virus P protein. PLoS Pathog 2021; 17:e1009729. [PMID: 34237115 PMCID: PMC8291714 DOI: 10.1371/journal.ppat.1009729] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/20/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022] Open
Abstract
Rabies virus phosphoprotein (P protein) is a multifunctional protein that plays key roles in replication as the polymerase cofactor that binds to the complex of viral genomic RNA and the nucleoprotein (N protein), and in evading the innate immune response by binding to STAT transcription factors. These interactions are mediated by the C-terminal domain of P (PCTD). The colocation of these binding sites in the small globular PCTD raises the question of how these interactions underlying replication and immune evasion, central to viral infection, are coordinated and, potentially, coregulated. While direct data on the binding interface of the PCTD for STAT1 is available, the lack of direct structural data on the sites that bind N protein limits our understanding of this interaction hub. The PCTD was proposed to bind via two sites to a flexible loop of N protein (Npep) that is not visible in crystal structures, but no direct analysis of this interaction has been reported. Here we use Nuclear Magnetic Resonance, and molecular modelling to show N protein residues, Leu381, Asp383, Asp384 and phosphor-Ser389, are likely to bind to a ‘positive patch’ of the PCTD formed by Lys211, Lys214 and Arg260. Furthermore, in contrast to previous predictions we identify a single site of interaction on the PCTD by this Npep. Intriguingly, this site is proximal to the defined STAT1 binding site that includes Ile201 to Phe209. However, cell-based assays indicate that STAT1 and N protein do not compete for P protein. Thus, it appears that interactions critical to replication and immune evasion can occur simultaneously with the same molecules of P protein so that the binding of P protein to activated STAT1 can potentially occur without interrupting interactions involved in replication. These data suggest that replication complexes might be directly involved in STAT1 antagonism. For viruses to infect cells and generate progeny, they must be able to mediate replication, while simultaneously evading the innate immune system. Viruses with small genomes often achieve this through multifunctional proteins that have roles in both replication and immune evasion, such as the phosphoprotein (P protein) of rabies virus. P protein is an essential cofactor in genome replication and transcription, dependent on the well-folded C-terminal domain (PCTD), which binds to the nucleoprotein (N protein) when complexed with RNA. The PCTD can also bind and antagonize signal transducers and activators of transcription (STAT) proteins, that are essential for activating antiviral mechanisms. Here we show using Nuclear Magnetic Resonance spectroscopy and cell-based assays, that the STAT1-binding and N-binding interfaces are proximal but, nevertheless, it appears that the same molecule of PCTD can simultaneously bind STAT1 and N protein. These data suggest that P-protein-STAT1 interaction, critical to immune evasion, can occur without interrupting interactions underlying replication, and so replication complexes might be directly involved in STAT1 antagonism.
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4
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Shchukina A, Małecki P, Mateos B, Nowakowski M, Urbańczyk M, Kontaxis G, Kasprzak P, Conrad-Billroth C, Konrat R, Kazimierczuk K. Temperature as an Extra Dimension in Multidimensional Protein NMR Spectroscopy. Chemistry 2021; 27:1753-1767. [PMID: 32985764 DOI: 10.1002/chem.202003678] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Indexed: 11/07/2022]
Abstract
NMR spectroscopy is a particularly informative method for studying protein structures and dynamics in solution; however, it is also one of the most time-consuming. Modern approaches to biomolecular NMR spectroscopy are based on lengthy multidimensional experiments, the duration of which grows exponentially with the number of dimensions. The experimental time may even be several days in the case of 3D and 4D spectra. Moreover, the experiment often has to be repeated under several different conditions, for example, to measure the temperature-dependent effects in a spectrum (temperature coefficients (TCs)). Herein, a new approach that involves joint sampling of indirect evolution times and temperature is proposed. This allows TCs to be measured through 3D spectra in even less time than that needed to acquire a single spectrum by using the conventional approach. Two signal processing methods that are complementary, in terms of sensitivity and resolution, 1) dividing data into overlapping subsets followed by compressed sensing reconstruction, and 2) treating the complete data set with a variant of the Radon transform, are proposed. The temperature-swept 3D HNCO spectra of two intrinsically disordered proteins, osteopontin and CD44 cytoplasmic tail, show that this new approach makes it possible to determine TCs and their non-linearities effectively. Non-linearities, which indicate the presence of a compact state, are particularly interesting. The complete package of data acquisition and processing software for this new approach are provided.
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Affiliation(s)
- Alexandra Shchukina
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Paweł Małecki
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Borja Mateos
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Michał Nowakowski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Mateusz Urbańczyk
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Georg Kontaxis
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Paweł Kasprzak
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland.,Department of Mathematical Methods in Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Clara Conrad-Billroth
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
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5
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Romero JA, Nawrocka EK, Shchukina A, Blanco FJ, Diercks T, Kazimierczuk K. Non‐Stationary Complementary Non‐Uniform Sampling (NOSCO NUS) for Fast Acquisition of Serial 2D NMR Titration Data. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Javier A. Romero
- Centre of New Technologies University of Warsaw Banacha 2C 02-097 Warsaw Poland
| | - Ewa K. Nawrocka
- Centre of New Technologies University of Warsaw Banacha 2C 02-097 Warsaw Poland
- Faculty of Chemistry University of Warsaw Pasteura 1 02-093 Warsaw Poland
| | - Alexandra Shchukina
- Faculty of Chemistry Biological and Chemical Research Centre University of Warsaw Zwirki i Wigury 101 02-089 Warsaw Poland
| | - Francisco J. Blanco
- Structural and Chemical Biology Department Centro de Investigaciones Biológicas CIB-CSIC 28040 Madrid Spain
| | - Tammo Diercks
- CIC bioGUNE Parque Tecnológico de Bizkaia, Ed. 800 48160- Derio Spain
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6
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Romero JA, Nawrocka EK, Shchukina A, Blanco FJ, Diercks T, Kazimierczuk K. Non-Stationary Complementary Non-Uniform Sampling (NOSCO NUS) for Fast Acquisition of Serial 2D NMR Titration Data. Angew Chem Int Ed Engl 2020; 59:23496-23499. [PMID: 32852098 PMCID: PMC7756666 DOI: 10.1002/anie.202009479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Indexed: 11/13/2022]
Abstract
NMR spectroscopy offers unique benefits for ligand binding studies on isotopically labelled target proteins. These benefits include atomic resolution, direct distinction of binding sites and modes, a lowest detectable affinity limit, and function independent setup. Yet, retracing protein signal assignments from apo to holo states to derive exact dissociation constants and chemical shift perturbation amplitudes (for ligand docking and structure‐based optimization) requires lengthy titration series of 2D heteronuclear correlation spectra at variable ligand concentration that may exceed the protein's lifetime and available spectrometer time. We present a novel method to overcome this critical limitation, based on non‐stationary complementary non‐uniform sampling (NOSCO NUS) combined with a robust particle swarm optimization algorithm. We illustrate its potential in two challenging studies with very distinct protein sizes and binding affinities, showing that NOSCO NUS can reduce measurement times by an order of magnitude to make such highly informative NMR titration studies more broadly feasible.
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Affiliation(s)
- Javier A Romero
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Ewa K Nawrocka
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland.,Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Alexandra Shchukina
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Francisco J Blanco
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas, CIB-CSIC, 28040, Madrid, Spain
| | - Tammo Diercks
- CIC bioGUNE, Parque Tecnológico de Bizkaia, Ed. 800, 48160-, Derio, Spain
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7
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Chen D, Wang Z, Guo D, Orekhov V, Qu X. Review and Prospect: Deep Learning in Nuclear Magnetic Resonance Spectroscopy. Chemistry 2020; 26:10391-10401. [PMID: 32251549 DOI: 10.1002/chem.202000246] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/03/2020] [Indexed: 01/08/2023]
Abstract
Since the concept of deep learning (DL) was formally proposed in 2006, it has had a major impact on academic research and industry. Nowadays, DL provides an unprecedented way to analyze and process data with demonstrated great results in computer vision, medical imaging, natural language processing, and so forth. Herein, applications of DL in NMR spectroscopy are summarized, and a perspective for DL as an entirely new approach that is likely to transform NMR spectroscopy into a much more efficient and powerful technique in chemistry and life sciences is outlined.
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Affiliation(s)
- Dicheng Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, P.O. Box 979, Xiamen, 361005, P.R. China
| | - Zi Wang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, P.O. Box 979, Xiamen, 361005, P.R. China
| | - Di Guo
- School of Computer and Information Engineering, Xiamen University of Technology, Xiamen, 361024, P.R. China
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, Gothenburg, 40530, Sweden
| | - Xiaobo Qu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, P.O. Box 979, Xiamen, 361005, P.R. China
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8
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Alik A, Bouguechtouli C, Julien M, Bermel W, Ghouil R, Zinn‐Justin S, Theillet F. Sensitivity‐Enhanced
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C‐NMR Spectroscopy for Monitoring Multisite Phosphorylation at Physiological Temperature and pH. Angew Chem Int Ed Engl 2020; 59:10411-10415. [DOI: 10.1002/anie.202002288] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/12/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Ania Alik
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Chafiaa Bouguechtouli
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Manon Julien
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Wolfgang Bermel
- Bruker BioSpin GmbH Silberstreifen 76287 Rheinstetten Germany
| | - Rania Ghouil
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Sophie Zinn‐Justin
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Francois‐Xavier Theillet
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
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9
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Alik A, Bouguechtouli C, Julien M, Bermel W, Ghouil R, Zinn‐Justin S, Theillet F. Sensitivity‐Enhanced
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C‐NMR Spectroscopy for Monitoring Multisite Phosphorylation at Physiological Temperature and pH. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002288] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ania Alik
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Chafiaa Bouguechtouli
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Manon Julien
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Wolfgang Bermel
- Bruker BioSpin GmbH Silberstreifen 76287 Rheinstetten Germany
| | - Rania Ghouil
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Sophie Zinn‐Justin
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Francois‐Xavier Theillet
- Université Paris-Saclay CEA CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
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10
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Qu X, Huang Y, Lu H, Qiu T, Guo D, Agback T, Orekhov V, Chen Z. Accelerated Nuclear Magnetic Resonance Spectroscopy with Deep Learning. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201908162] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xiaobo Qu
- Department of Electronic Science Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance State Key Laboratory of Physical Chemistry of Solid Surfaces Xiamen University P.O.Box 979 Xiamen 361005 China
| | - Yihui Huang
- Department of Electronic Science Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance State Key Laboratory of Physical Chemistry of Solid Surfaces Xiamen University P.O.Box 979 Xiamen 361005 China
| | - Hengfa Lu
- Department of Electronic Science Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance State Key Laboratory of Physical Chemistry of Solid Surfaces Xiamen University P.O.Box 979 Xiamen 361005 China
| | - Tianyu Qiu
- Department of Electronic Science Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance State Key Laboratory of Physical Chemistry of Solid Surfaces Xiamen University P.O.Box 979 Xiamen 361005 China
| | - Di Guo
- School of Computer and Information Engineering Xiamen University of Technology China
| | - Tatiana Agback
- Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology University of Gothenburg Box 465 Gothenburg 40530 Sweden
| | - Zhong Chen
- Department of Electronic Science Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance State Key Laboratory of Physical Chemistry of Solid Surfaces Xiamen University P.O.Box 979 Xiamen 361005 China
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11
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Qu X, Huang Y, Lu H, Qiu T, Guo D, Agback T, Orekhov V, Chen Z. Accelerated Nuclear Magnetic Resonance Spectroscopy with Deep Learning. Angew Chem Int Ed Engl 2020; 59:10297-10300. [PMID: 31490596 DOI: 10.1002/anie.201908162] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Indexed: 11/11/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy serves as an indispensable tool in chemistry and biology but often suffers from long experimental times. We present a proof-of-concept of the application of deep learning and neural networks for high-quality, reliable, and very fast NMR spectra reconstruction from limited experimental data. We show that the neural network training can be achieved using solely synthetic NMR signals, which lifts the prohibiting demand for a large volume of realistic training data usually required for a deep learning approach.
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Affiliation(s)
- Xiaobo Qu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, P.O.Box 979, Xiamen, 361005, China
| | - Yihui Huang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, P.O.Box 979, Xiamen, 361005, China
| | - Hengfa Lu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, P.O.Box 979, Xiamen, 361005, China
| | - Tianyu Qiu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, P.O.Box 979, Xiamen, 361005, China
| | - Di Guo
- School of Computer and Information Engineering, Xiamen University of Technology, China
| | - Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, Gothenburg, 40530, Sweden
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, P.O.Box 979, Xiamen, 361005, China
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12
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Féraud B, Martineau E, Leenders J, Govaerts B, de Tullio P, Giraudeau P. Combining rapid 2D NMR experiments with novel pre-processing workflows and MIC quality measures for metabolomics. Metabolomics 2020; 16:42. [PMID: 32189152 DOI: 10.1007/s11306-020-01662-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/10/2020] [Indexed: 11/28/2022]
Abstract
INTRODUCTION The use of 2D NMR data sources (COSY in this paper) allows to reach general metabolomics results which are at least as good as the results obtained with 1D NMR data, and this with a less advanced and less complex level of pre-processing. But a major issue still exists and can largely slow down a generalized use of 2D data sources in metabolomics: the experiment duration. OBJECTIVE The goal of this paper is to overcome the experiment duration issue in our recently published MIC strategy by considering faster 2D COSY acquisition techniques: a conventional COSY with a reduced number of transients and the use of the Non-Uniform Sampling (NUS) method. These faster alternatives are all submitted to novel 2D pre-processing workflows and to Metabolomic Informative Content analyses. Eventually, results are compared to those obtained with conventional COSY spectra. METHODS To pre-process the 2D data sources, the Global Peak List (GPL) workflow and the Vectorization workflow are used. To compare this data sources and to detect the more informative one(s), MIC (Metabolomic Informative Content) indexes are used, based on clustering and inertia measures of quality. RESULTS Results are discussed according to a multi-factor experimental design (which is unsupervised and based on human urine samples). Descriptive PCA results and MIC indexes are shown, leading to the direct and objective comparison of the different data sets. CONCLUSION In conclusion, it is demonstrated that conventional COSY spectra recorded with only one transient per increment and COSY spectra recorded with 50% of non-uniform sampling provide very similar MIC results as the initial COSY recorded with four transients, but in a much shorter time. Consequently, using techniques like the reduction of the number of transients or NUS can really open the door to a potential high-throughput use of 2D COSY spectra in metabolomics.
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Affiliation(s)
- Baptiste Féraud
- Institute of Statistics, Biostatistics and Actuarial Sciences (ISBA), Université Catholique de Louvain (UCL), Voie du Roman Pays 20, bte L1.04.01, 1348, Louvain-la-Neuve, Belgium.
- Machine Learning Group, Université Catholique de Louvain (UCL), 1348, Louvain-la-Neuve, Belgium.
| | - Estelle Martineau
- Université de Nantes, CNRS, CEISAM UMR 6230, 44000, Nantes, France
- Spectromaîtrise, CAPACITES SAS, 26 Bd Vincent Gâche, 44200, Nantes, France
| | - Justine Leenders
- Metabolomics Group, Center for Interdisciplinary Research on Medicines (CIRM), Université de Liège (ULG), Liège, Belgium
| | - Bernadette Govaerts
- Institute of Statistics, Biostatistics and Actuarial Sciences (ISBA), Université Catholique de Louvain (UCL), Voie du Roman Pays 20, bte L1.04.01, 1348, Louvain-la-Neuve, Belgium
| | - Pascal de Tullio
- Metabolomics Group, Center for Interdisciplinary Research on Medicines (CIRM), Université de Liège (ULG), Liège, Belgium
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Rovny J, Blum RL, Loria JP, Barrett SE. Accelerating 2D NMR relaxation dispersion experiments using iterated maps. JOURNAL OF BIOMOLECULAR NMR 2019; 73:561-576. [PMID: 31280454 PMCID: PMC7370911 DOI: 10.1007/s10858-019-00263-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/19/2019] [Indexed: 05/08/2023]
Abstract
NMR relaxation dispersion experiments play a central role in exploring molecular motion over an important range of timescales, and are an example of a broader class of multidimensional NMR experiments that probe important biomolecules. However, resolving the spectral features of these experiments using the Fourier transform requires sampling the full Nyquist grid of data, making these experiments very costly in time. Practitioners often reduce the experiment time by omitting 1D experiments in the indirectly observed dimensions, and reconstructing the spectra using one of a variety of post-processing algorithms. In prior work, we described a fast, Fourier-based reconstruction method using iterated maps according to the Difference Map algorithm of Veit Elser (DiffMap). Here we describe coDiffMap, a new reconstruction method that is based on DiffMap, but which exploits the strong correlations between 2D data slices in a pseudo-3D experiment. We apply coDiffMap to reconstruct dispersion curves from an [Formula: see text] relaxation dispersion experiment, and demonstrate that the method provides fast reconstructions and accurate relaxation curves down to very low numbers of sparsely-sampled data points.
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Affiliation(s)
- Jared Rovny
- Department of Physics, Yale University, 217 Prospect St., New Haven, CT, 06511, USA
| | - Robert L Blum
- Department of Physics, Yale University, 217 Prospect St., New Haven, CT, 06511, USA
| | - J Patrick Loria
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, CT, 06511, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 225 Prospect St., New Haven, CT, 06511, USA
| | - Sean E Barrett
- Department of Physics, Yale University, 217 Prospect St., New Haven, CT, 06511, USA.
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14
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Blum RL, Rovny J, Loria JP, Barrett SE. Reaching the sparse-sampling limit for reconstructing a single peak in a 2D NMR spectrum using iterated maps. JOURNAL OF BIOMOLECULAR NMR 2019; 73:545-560. [PMID: 31292847 PMCID: PMC7384587 DOI: 10.1007/s10858-019-00262-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/19/2019] [Indexed: 05/08/2023]
Abstract
Many of the ubiquitous experiments of biomolecular NMR, including [Formula: see text], [Formula: see text], and CEST, involve acquiring repeated 2D spectra under slightly different conditions. Such experiments are amenable to acceleration using non-uniform sampling spectral reconstruction methods that take advantage of prior information. We previously developed one such technique, an iterated maps method (DiffMap) that we successfully applied to 2D NMR spectra, including [Formula: see text] relaxation dispersion data. In that prior work, we took a top-down approach to reconstructing the 2D spectrum with a minimal number of sparse samples, reaching an undersampling fraction that appeared to leave some room for improvement. In this study, we develop an in-depth understanding of the action of the DiffMap algorithm, identifying the factors that cause reconstruction errors for different undersampling fractions. This improved understanding allows us to formulate a bottom-up approach to finding the lowest number of sparse samples required to accurately reconstruct individual spectral features with DiffMap. We also discuss the difficulty of extending this method to reconstructing many peaks at once, and suggest a way forward.
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Affiliation(s)
- Robert L Blum
- Department of Physics, Yale University, 217 Prospect St., New Haven, CT, 06511, USA
| | - Jared Rovny
- Department of Physics, Yale University, 217 Prospect St., New Haven, CT, 06511, USA
| | - J Patrick Loria
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, CT, 06511, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 225 Prospect St., New Haven, CT, 06511, USA
| | - Sean E Barrett
- Department of Physics, Yale University, 217 Prospect St., New Haven, CT, 06511, USA.
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15
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Pustovalova Y, Mayzel M, Orekhov VY. XLSY: Extra-Large NMR Spectroscopy. Angew Chem Int Ed Engl 2018; 57:14043-14045. [PMID: 30175546 PMCID: PMC6585689 DOI: 10.1002/anie.201806144] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/24/2018] [Indexed: 11/23/2022]
Abstract
NMR studies of intrinsically disordered proteins and other complex biomolecular systems require spectra with the highest resolution and dimensionality. An efficient approach, extra‐large NMR spectroscopy, is presented for experimental data collection, reconstruction, and handling of very large NMR spectra by a combination of the radial and non‐uniform sampling, a new processing algorithm, and rigorous statistical validation. We demonstrate the first high‐quality reconstruction of a full seven‐dimensional HNCOCACONH and two five‐dimensional HACACONH and HN(CA)CONH experiments for a representative intrinsically disordered protein α‐synuclein. XLSY will significantly enhance the NMR toolbox in challenging biomolecular studies.
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Affiliation(s)
- Yulia Pustovalova
- Department of Chemistry and Molecular Biology, University of Gothenburg, P.O. Box 465, Gothenburg, 405 30, Sweden
| | - Maxim Mayzel
- Swedish NMR Centre, University of Gothenburg, P.O. Box 465, Gothenburg, 405 30, Sweden
| | - Vladislav Yu Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, P.O. Box 465, Gothenburg, 405 30, Sweden.,Swedish NMR Centre, University of Gothenburg, P.O. Box 465, Gothenburg, 405 30, Sweden
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16
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Affiliation(s)
- Yulia Pustovalova
- Department of Chemistry and Molecular Biology; University of Gothenburg; P.O. Box 465 Gothenburg 405 30 Sweden
| | - Maxim Mayzel
- Swedish NMR Centre; University of Gothenburg; P.O. Box 465 Gothenburg 405 30 Sweden
| | - Vladislav Yu. Orekhov
- Department of Chemistry and Molecular Biology; University of Gothenburg; P.O. Box 465 Gothenburg 405 30 Sweden
- Swedish NMR Centre; University of Gothenburg; P.O. Box 465 Gothenburg 405 30 Sweden
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17
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Li D, Hansen AL, Bruschweiler-Li L, Brüschweiler R. Non-Uniform and Absolute Minimal Sampling for High-Throughput Multidimensional NMR Applications. Chemistry 2018; 24:11535-11544. [PMID: 29566285 PMCID: PMC6488043 DOI: 10.1002/chem.201800954] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Indexed: 11/10/2022]
Abstract
Many biomolecular NMR applications can benefit from the faster acquisition of multidimensional NMR data with high resolution and their automated analysis and interpretation. In recent years, a number of non-uniform sampling (NUS) approaches have been introduced for the reconstruction of multidimensional NMR spectra, such as compressed sensing, thereby bypassing traditional Fourier-transform processing. Such approaches are applicable to both biomacromolecules and small molecules and their complex mixtures and can be combined with homonuclear decoupling (pure shift) and covariance processing. For homonuclear 2D TOCSY experiments, absolute minimal sampling (AMS) permits the drastic shortening of measurement times necessary for high-throughput applications for identification and quantification of components in complex biological mixtures in the field of metabolomics. Such TOCSY spectra can be comprehensively represented by graphic theoretical maximal cliques for the identification of entire spin systems and their subsequent query against NMR databases. Integration of these methods in webservers permits the rapid and reliable identification of mixture components. Recent progress is reviewed in this Minireview.
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Affiliation(s)
- Dawei Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, U.S.A
| | - Alexandar L. Hansen
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, U.S.A
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, U.S.A
| | - Rafael Brüschweiler
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, U.S.A
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, U.S.A
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
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18
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Zinke M, Fricke P, Samson C, Hwang S, Wall JS, Lange S, Zinn‐Justin S, Lange A. Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR. Angew Chem Int Ed Engl 2017; 56:9497-9501. [PMID: 28644511 PMCID: PMC5582604 DOI: 10.1002/anie.201706060] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Indexed: 01/03/2023]
Abstract
Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH, (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.
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Affiliation(s)
- Maximilian Zinke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Pascal Fricke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Camille Samson
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRSUniversité Paris-Sud, Université Paris-SaclayGif-sur-Yvette CedexFrance
| | - Songhwan Hwang
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | | | - Sascha Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Sophie Zinn‐Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRSUniversité Paris-Sud, Université Paris-SaclayGif-sur-Yvette CedexFrance
| | - Adam Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
- Institut für BiologieHumboldt-Universität zu BerlinBerlinGermany
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19
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Zinke M, Fricke P, Samson C, Hwang S, Wall JS, Lange S, Zinn-Justin S, Lange A. Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Maximilian Zinke
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Pascal Fricke
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Camille Samson
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris-Sud, Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Songhwan Hwang
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | | | - Sascha Lange
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Sophie Zinn-Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris-Sud, Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Adam Lange
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
- Institut für Biologie; Humboldt-Universität zu Berlin; Berlin Germany
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20
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Hansen AL, Li D, Wang C, Brüschweiler R. Absolute Minimal Sampling of Homonuclear 2D NMR TOCSY Spectra for High-Throughput Applications of Complex Mixtures. Angew Chem Int Ed Engl 2017; 56:8149-8152. [PMID: 28543988 PMCID: PMC5663451 DOI: 10.1002/anie.201703587] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Indexed: 11/08/2022]
Abstract
Modern applications of 2D NMR spectroscopy to diagnostic screening, metabolomics, quality control, and other high-throughput applications are often limited by the time-consuming sampling requirements along the indirect time domain t1 . 2D total correlation spectroscopy (TOCSY) provides unique spin connectivity information for the analysis of a large number of compounds in complex mixtures, but standard methods typically require >100 t1 increments for an accurate spectral reconstruction, rendering these experiments ineffective for high-throughput applications. For a complex metabolite mixture it is demonstrated that absolute minimal sampling (AMS), based on direct fitting of resonance frequencies and amplitudes in the time domain, yields an accurate spectral reconstruction of TOCSY spectra using as few as 16 t1 points. This permits the rapid collection of homonuclear 2D NMR experiments at high resolution with measurement times that previously were only the realm of 1D experiments.
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Affiliation(s)
- Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Dawei Li
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Cheng Wang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Rafael Brüschweiler
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, 1645 Neil Avenue, Columbus, OH, 43210, USA
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21
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Hansen AL, Li D, Wang C, Brüschweiler R. Absolute Minimal Sampling of Homonuclear 2D NMR TOCSY Spectra for High-Throughput Applications of Complex Mixtures. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703587] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alexandar L. Hansen
- Campus Chemical Instrument Center; The Ohio State University; 460 W. 12th Avenue Columbus OH 43210 USA
| | - Dawei Li
- Campus Chemical Instrument Center; The Ohio State University; 460 W. 12th Avenue Columbus OH 43210 USA
| | - Cheng Wang
- Department of Chemistry and Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
| | - Rafael Brüschweiler
- Campus Chemical Instrument Center; The Ohio State University; 460 W. 12th Avenue Columbus OH 43210 USA
- Department of Chemistry and Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
- Department of Biological Chemistry and Pharmacology; The Ohio State University; 1645 Neil Avenue Columbus OH 43210 USA
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22
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Ndukwe IE, Shchukina A, Zorin V, Cobas C, Kazimierczuk K, Butts CP. Enabling Fast Pseudo-2D NMR Spectral Acquisition for Broadband Homonuclear Decoupling: The EXACT NMR Approach. Chemphyschem 2017; 18:2081-2087. [DOI: 10.1002/cphc.201700474] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Ikenna E. Ndukwe
- Department of Chemistry; University of Bristol; Cantocks Close Bristol. BS8 1TS UK
- Department of Pure and Industrial Chemistry; Abia State University; Uturu PMB 2000. Abia State Nigeria
| | - Alexandra Shchukina
- Centre of New Technologies; University of Warsaw; Banacha 2C 02089 Warszawa Poland
- Institute for Spectroscopy; Russian Academy of Sciences; Fizicheskaya 5 142190, Moscow Troitsk Russia
| | - Vadim Zorin
- Mestrelab Research S.L.; Feliciano Barrera 9B-Bajo 15706 Santiago de Compostela Spain
| | - Carlos Cobas
- Mestrelab Research S.L.; Feliciano Barrera 9B-Bajo 15706 Santiago de Compostela Spain
| | | | - Craig P. Butts
- Department of Chemistry; University of Bristol; Cantocks Close Bristol. BS8 1TS UK
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23
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Shchukina A, Kasprzak P, Dass R, Nowakowski M, Kazimierczuk K. Pitfalls in compressed sensing reconstruction and how to avoid them. JOURNAL OF BIOMOLECULAR NMR 2017; 68:79-98. [PMID: 27837295 PMCID: PMC5504175 DOI: 10.1007/s10858-016-0068-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 10/01/2016] [Indexed: 05/04/2023]
Abstract
Multidimensional NMR can provide unmatched spectral resolution, which is crucial when dealing with samples of biological macromolecules. The resolution, however, comes at the high price of long experimental time. Non-uniform sampling (NUS) of the evolution time domain allows to suppress this limitation by sampling only a small fraction of the data, but requires sophisticated algorithms to reconstruct omitted data points. A significant group of such algorithms known as compressed sensing (CS) is based on the assumption of sparsity of a reconstructed spectrum. Several papers on the application of CS in multidimensional NMR have been published in the last years, and the developed methods have been implemented in most spectral processing software. However, the publications rarely show the cases when NUS reconstruction does not work perfectly or explain how to solve the problem. On the other hand, every-day users of NUS develop their rules-of-thumb, which help to set up the processing in an optimal way, but often without a deeper insight. In this paper, we discuss several sources of problems faced in CS reconstructions: low sampling level, missassumption of spectral sparsity, wrong stopping criterion and attempts to extrapolate the signal too much. As an appendix, we provide MATLAB codes of several CS algorithms used in NMR. We hope that this work will explain the mechanism of NUS reconstructions and help readers to set up acquisition and processing parameters. Also, we believe that it might be helpful for algorithm developers.
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Affiliation(s)
- Alexandra Shchukina
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
- Institute for Spectroscopy, Russian Academy of Sciences, Fizicheskaya 5, Troitsk, Moscow, Russia, 108840
| | - Paweł Kasprzak
- Department of Mathematical Methods in Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, Poland
| | - Rupashree Dass
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Michał Nowakowski
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
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24
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Chong M, Jayaraman A, Marin S, Selivanov V, de Atauri Carulla PR, Tennant DA, Cascante M, Günther UL, Ludwig C. Combined Analysis of NMR and MS Spectra (CANMS). Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Mei Chong
- Institute of Cancer and Genome Sciences; University of Birmingham; UK
| | - Anusha Jayaraman
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | - Silvia Marin
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | - Vitaly Selivanov
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | | | - Daniel A. Tennant
- Institute of Metabolism and Systems Research; University of Birmingham; IBR West Tower Birmingham UK B15 2TT
| | - Marta Cascante
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | - Ulrich L. Günther
- Institute of Cancer and Genome Sciences; University of Birmingham; UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research; University of Birmingham; IBR West Tower Birmingham UK B15 2TT
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25
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Chong M, Jayaraman A, Marin S, Selivanov V, de Atauri Carulla PR, Tennant DA, Cascante M, Günther UL, Ludwig C. Combined Analysis of NMR and MS Spectra (CANMS). Angew Chem Int Ed Engl 2017; 56:4140-4144. [DOI: 10.1002/anie.201611634] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Mei Chong
- Institute of Cancer and Genome Sciences; University of Birmingham; UK
| | - Anusha Jayaraman
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | - Silvia Marin
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | - Vitaly Selivanov
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | | | - Daniel A. Tennant
- Institute of Metabolism and Systems Research; University of Birmingham; IBR West Tower Birmingham, B15 2TT UK
| | - Marta Cascante
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | - Ulrich L. Günther
- Institute of Cancer and Genome Sciences; University of Birmingham; UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research; University of Birmingham; IBR West Tower Birmingham, B15 2TT UK
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26
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Hansen AL, Brüschweiler R. Absolute Minimal Sampling in High-Dimensional NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:14169-14172. [PMID: 27723193 PMCID: PMC5663440 DOI: 10.1002/anie.201608048] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Indexed: 11/05/2022]
Abstract
Standard three-dimensional Fourier transform (FT) NMR experiments of molecular systems often involve prolonged measurement times due to extensive sampling required along the indirect time domains to obtain adequate spectral resolution. In recent years, a wealth of alternative sampling methods has been proposed to ease this bottleneck. However, due to their algorithmic complexity, for a given sample and experiment it is often hard to determine the minimal sampling requirement, and hence the maximal achievable experimental speed up. Herein we introduce an absolute minimal sampling (AMS) method that can be applied to common 3D NMR experiments. We show for the proteins ubiquitin and arginine kinase that for widely used experiments, such as 3D HNCO, accurate carbon frequencies can be obtained with a single time increment, while for others, such as 3D HN(CA)CO, all relevant information is obtained with as few as 6 increments amounting to a speed up of a factor 7-50.
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Affiliation(s)
- Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA.
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA.
- Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Road, Columbus, OH, 43210, USA.
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27
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Hansen AL, Brüschweiler R. Absolut minimales Sampling in der hochdimensionalen NMR-Spektroskopie. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alexandar L. Hansen
- Campus Chemical Instrument Center; The Ohio State University; 460 W. 12th Avenue Columbus OH 43210 USA
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
- Campus Chemical Instrument Center; The Ohio State University; 460 W. 12th Avenue Columbus OH 43210 USA
- Department of Biological Chemistry and Pharmacology; The Ohio State University; 1645 Neil Avenue Columbus OH 43210 USA
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28
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Ndukwe IE, Shchukina A, Kazimierczuk K, Cobas C, Butts CP. EXtended ACquisition Time (EXACT) NMR-A Case for ′Burst′ Non-Uniform Sampling. Chemphyschem 2016; 17:2799-803. [DOI: 10.1002/cphc.201600541] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Ikenna E. Ndukwe
- School of Chemistry; University of Bristol; Cantocks Close Bristol BS8 1TS UK
| | - Alexandra Shchukina
- Centre of New Technologies; University of Warsaw; Banacha 2C 02089 Warszawa Poland
- Institute for Spectroscopy; Russian Academy of Sciences; Fizicheskaya 5 142190 Moscow Troitsk Russia
| | | | - Carlos Cobas
- Mestrelab Research S.L.; Feliciano Barrera 9B-Bajo 15706 Santiago de Compostela Spain
| | - Craig P. Butts
- School of Chemistry; University of Bristol; Cantocks Close Bristol BS8 1TS UK
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29
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Kakita VMR, Hosur RV. Non-Uniform-Sampling Ultrahigh Resolution TOCSY NMR: Analysis of Complex Mixtures at Microgram Levels. Chemphyschem 2016; 17:2304-8. [DOI: 10.1002/cphc.201600255] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Veera M. R. Kakita
- UM-DAE Centre for Excellence in Basic Sciences; Mumbai University Campus, Kalina, Santa Cruz Mumbai 400 098 India
| | - Ramakrishna V. Hosur
- UM-DAE Centre for Excellence in Basic Sciences; Mumbai University Campus, Kalina, Santa Cruz Mumbai 400 098 India
- Department of Chemical Sciences; Tata Institute of Fundamental Research (TIFR); 1-Homi Bhabha Road, Colaba Mumbai 400 005 India
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30
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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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Dass R, Kasprzak P, Koźmiński W, Kazimierczuk K. Artifacts in time-resolved NUS: A case study of NOE build-up curves from 2D NOESY. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 265:108-116. [PMID: 26896866 DOI: 10.1016/j.jmr.2016.01.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/13/2016] [Accepted: 01/19/2016] [Indexed: 06/05/2023]
Abstract
Multidimensional NMR spectroscopy requires time-consuming sampling of indirect dimensions and so is usually used to study stable samples. However, dynamically changing compounds or their mixtures commonly occur in problems of natural science. Monitoring them requires the use multidimensional NMR in a time-resolved manner - in other words, a series of quick spectra must be acquired at different points in time. Among the many solutions that have been proposed to achieve this goal, time-resolved non-uniform sampling (TR-NUS) is one of the simplest. In a TR-NUS experiment, the signal is sampled using a shuffled random schedule and then divided into overlapping subsets. These subsets are then processed using one of the NUS reconstruction methods, for example compressed sensing (CS). The resulting stack of spectra forms a temporal "pseudo-dimension" that shows the changes caused by the process occurring in the sample. CS enables the use of small subsets of data, which minimizes the averaging of the effects studied. Yet, even within these limited timeframes, the sample undergoes certain changes. In this paper we discuss the effect of varying signal amplitude in a TR-NUS experiment. Our theoretical calculations show that the variations within the subsets lead to t1-noise, which is dependent on the rate of change of the signal amplitude. We verify these predictions experimentally. As a model case we choose a novel 2D TR-NOESY experiment in which mixing time is varied in parallel with shuffled NUS in the indirect dimension. The experiment, performed on a sample of strychnine, provides a near-continuous NOE build-up curve, whose shape closely reflects the t1-noise level. 2D TR-NOESY reduces the measurement time compared to the conventional approach and makes it possible to verify the theoretical predictions about signal variations during TR-NUS.
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Affiliation(s)
- Rupashree Dass
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Paweł Kasprzak
- Department of Mathematical Methods in Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
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Lesot P, Kazimierczuk K, Trébosc J, Amoureux JP, Lafon O. Fast acquisition of multidimensional NMR spectra of solids and mesophases using alternative sampling methods. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:927-939. [PMID: 26332109 DOI: 10.1002/mrc.4290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/09/2015] [Accepted: 06/12/2015] [Indexed: 06/05/2023]
Abstract
Unique information about the atom-level structure and dynamics of solids and mesophases can be obtained by the use of multidimensional nuclear magnetic resonance (NMR) experiments. Nevertheless, the acquisition of these experiments often requires long acquisition times. We review here alternative sampling methods, which have been proposed to circumvent this issue in the case of solids and mesophases. Compared to the spectra of solutions, those of solids and mesophases present some specificities because they usually display lower signal-to-noise ratios, non-Lorentzian line shapes, lower spectral resolutions and wider spectral widths. We highlight herein the advantages and limitations of these alternative sampling methods. A first route to accelerate the acquisition time of multidimensional NMR spectra consists in the use of sparse sampling schemes, such as truncated, radial or random sampling ones. These sparsely sampled datasets are generally processed by reconstruction methods differing from the Discrete Fourier Transform (DFT). A host of non-DFT methods have been applied for solids and mesophases, including the G-matrix Fourier transform, the linear least-square procedures, the covariance transform, the maximum entropy and the compressed sensing. A second class of alternative sampling consists in departing from the Jeener paradigm for multidimensional NMR experiments. These non-Jeener methods include Hadamard spectroscopy as well as spatial or orientational encoding of the evolution frequencies. The increasing number of high field NMR magnets and the development of techniques to enhance NMR sensitivity will contribute to widen the use of these alternative sampling methods for the study of solids and mesophases in the coming years.
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Affiliation(s)
- Philippe Lesot
- RMN en Milieu Orienté, ICMMO, UMR-CNRS 8182, Université de Paris-Sud, Orsay, F-91405, Cedex Orsay, France
| | | | - Julien Trébosc
- Univ. Lille Nord de France, Unité de Catalyse et de Chimie du Solide (UCCS), CNRS UMR 8181, Univ. Lille, 59652, Villeneuve d'Ascq, France
| | - Jean-Paul Amoureux
- Univ. Lille Nord de France, Unité de Catalyse et de Chimie du Solide (UCCS), CNRS UMR 8181, Univ. Lille, 59652, Villeneuve d'Ascq, France
- Physics Department and Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai, 200062, China
| | - Olivier Lafon
- Univ. Lille Nord de France, Unité de Catalyse et de Chimie du Solide (UCCS), CNRS UMR 8181, Univ. Lille, 59652, Villeneuve d'Ascq, France
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Didenko T, Proudfoot A, Dutta SK, Serrano P, Wüthrich K. Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination. Chemistry 2015; 21:12363-9. [PMID: 26227870 PMCID: PMC4576834 DOI: 10.1002/chem.201502544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 11/10/2022]
Abstract
High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [(1)H,(1)H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data.
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Affiliation(s)
- Tatiana Didenko
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA) http://www.jcsg.org
- Joint Center for Structural Genomics, La Jolla, CA 92037 (USA), Fax: (+1) 858-784-8014
- GPCR-Network, 3430 S. Vermont Ave., TRF 105, Los Angeles, CA 90089-3301 (USA), Fax: (+1) 858-784-8014 http://gpcr.usc.edu
| | - Andrew Proudfoot
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA) http://www.jcsg.org
- Joint Center for Structural Genomics, La Jolla, CA 92037 (USA), Fax: (+1) 858-784-8014
| | - Samit Kumar Dutta
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA) http://www.jcsg.org
- Joint Center for Structural Genomics, La Jolla, CA 92037 (USA), Fax: (+1) 858-784-8014
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA) http://www.jcsg.org
- Joint Center for Structural Genomics, La Jolla, CA 92037 (USA), Fax: (+1) 858-784-8014
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA) http://www.jcsg.org. , ,
- Joint Center for Structural Genomics, La Jolla, CA 92037 (USA), Fax: (+1) 858-784-8014. , ,
- GPCR-Network, 3430 S. Vermont Ave., TRF 105, Los Angeles, CA 90089-3301 (USA), Fax: (+1) 858-784-8014 http://gpcr.usc.edu. , ,
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA), Fax: (+1) 858-784-8014. , ,
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34
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Qu X, Mayzel M, Cai JF, Chen Z, Orekhov V. Accelerated NMR Spectroscopy with Low-Rank Reconstruction. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409291] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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Qu X, Mayzel M, Cai JF, Chen Z, Orekhov V. Accelerated NMR spectroscopy with low-rank reconstruction. Angew Chem Int Ed Engl 2014; 54:852-4. [PMID: 25389060 DOI: 10.1002/anie.201409291] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 11/09/2022]
Abstract
Accelerated multi-dimensional NMR spectroscopy is a prerequisite for high-throughput applications, studying short-lived molecular systems and monitoring chemical reactions in real time. Non-uniform sampling is a common approach to reduce the measurement time. Here, a new method for high-quality spectra reconstruction from non-uniformly sampled data is introduced, which is based on recent developments in the field of signal processing theory and uses the so far unexploited general property of the NMR signal, its low rank. Using experimental and simulated data, we demonstrate that the low-rank reconstruction is a viable alternative to the current state-of-the-art technique compressed sensing. In particular, the low-rank approach is good in preserving of low-intensity broad peaks, and thus increases the effective sensitivity in the reconstructed spectra.
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Affiliation(s)
- Xiaobo Qu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, P.O. Box 979, Xiamen 361005 (China).
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36
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Holland DJ, Gladden LF. Weniger ist mehr: Neue Messkonzepte in der Chemie durch Compressed Sensing. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400535] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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Holland DJ, Gladden LF. Less is More: How Compressed Sensing is Transforming Metrology in Chemistry. Angew Chem Int Ed Engl 2014; 53:13330-40. [DOI: 10.1002/anie.201400535] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 06/02/2014] [Indexed: 11/08/2022]
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38
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Bermel W, Dass R, Neidig KP, Kazimierczuk K. Two-Dimensional NMR Spectroscopy with Temperature-Sweep. Chemphyschem 2014; 15:2217-20. [DOI: 10.1002/cphc.201402191] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Indexed: 11/11/2022]
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Kazimierczuk K, Stanek J, Zawadzka-Kazimierczuk A, Koźmiński W. High-Dimensional NMR Spectra for Structural Studies of Biomolecules. Chemphyschem 2013; 14:3015-25. [DOI: 10.1002/cphc.201300277] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Indexed: 11/06/2022]
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40
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Amata I, Maffei M, Igea A, Gay M, Vilaseca M, Nebreda AR, Pons M. Multi-phosphorylation of the intrinsically disordered unique domain of c-Src studied by in-cell and real-time NMR spectroscopy. Chembiochem 2013; 14:1820-7. [PMID: 23744817 DOI: 10.1002/cbic.201300139] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Indexed: 12/28/2022]
Abstract
Intrinsically disordered regions (IDRs) are preferred sites for post-translational modifications essential for regulating protein function. The enhanced local mobility of IDRs facilitates their observation by NMR spectroscopy in vivo. Phosphorylation events can occur at multiple sites and respond dynamically to changes in kinase-phosphatase networks. Here we used real-time NMR spectroscopy to study the effect of kinases and phosphatases present in Xenopus oocytes and egg extracts on the phosphorylation state of the "unique domain" of c-Src. We followed the phosphorylation of S17 in oocytes, and of S17, S69, and S75 in egg extracts by NMR spectroscopy, MS, and western blotting. Addition of specific kinase inhibitors showed that S75 and S69 are phosphorylated by CDKs (cyclin-dependent kinases) differently from Cdk1. Moreover, although PKA (cAMP-dependent protein kinase) can phosphorylate S17 in vitro, this was not the major S17 kinase in egg extracts. Changes in PKA activity affected the phosphorylation levels of CDK-dependent sites, thus suggesting indirect effects of kinase-phosphatase networks. This study provides a proof-of-concept of the use of real-time in vivo NMR spectroscopy to characterize kinase/phosphatase effects on intrinsically disordered regulatory domains.
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Affiliation(s)
- Irene Amata
- Biomolecular NMR Laboratory, Department of Organic Chemistry, University of Barcelona, Baldiri Reixac, 10-12, 08028 Barcelona (Spain); Signaling and Cell Cycle Laboratory, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona (Spain)
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