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Elena-Real CA, Urbanek A, Imbert L, Morató A, Fournet A, Allemand F, Sibille N, Boisbouvier J, Bernadó P. Site-Specific Introduction of Alanines for the Nuclear Magnetic Resonance Investigation of Low-Complexity Regions and Large Biomolecular Assemblies. ACS Chem Biol 2023; 18:2039-2049. [PMID: 37582223 DOI: 10.1021/acschembio.3c00288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Nuclear magnetic resonance (NMR) studies of large biomolecular machines and highly repetitive proteins remain challenging due to the difficulty of assigning frequencies to individual nuclei. Here, we present an efficient strategy to address this challenge by engineering a Pyrococcus horikoshii tRNA/alanyl-tRNA synthetase pair that enables the incorporation of up to three isotopically labeled alanine residues in a site-specific manner using in vitro protein expression. The general applicability of this approach for NMR assignment has been demonstrated by introducing isotopically labeled alanines into four distinct proteins: huntingtin exon-1, HMA8 ATPase, the 300 kDa molecular chaperone ClpP, and the alanine-rich Phox2B transcription factor. For large protein assemblies, our labeling approach enabled unambiguous assignments while avoiding potential artifacts induced by site-specific mutations. When applied to Phox2B, which contains two poly-alanine tracts of nine and twenty alanines, we observed that the helical stability is strongly dependent on the homorepeat length. The capacity to selectively introduce alanines with distinct labeling patterns is a powerful tool to probe structure and dynamics of challenging biomolecular systems.
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Affiliation(s)
- Carlos A Elena-Real
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Annika Urbanek
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Lionel Imbert
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
| | - Anna Morató
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Aurélie Fournet
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Frédéric Allemand
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Nathalie Sibille
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Jérôme Boisbouvier
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
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2
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Romero JA, Putko P, Urbańczyk M, Kazimierczuk K, Zawadzka-Kazimierczuk A. Linear discriminant analysis reveals hidden patterns in NMR chemical shifts of intrinsically disordered proteins. PLoS Comput Biol 2022; 18:e1010258. [PMID: 36201530 PMCID: PMC9578625 DOI: 10.1371/journal.pcbi.1010258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 10/18/2022] [Accepted: 09/20/2022] [Indexed: 11/27/2022] Open
Abstract
NMR spectroscopy is key in the study of intrinsically disordered proteins (IDPs). Yet, even the first step in such an analysis-the assignment of observed resonances to particular nuclei-is often problematic due to low peak dispersion in the spectra of IDPs. We show that the assignment process can be aided by finding "hidden" chemical shift patterns specific to the amino acid residue types. We find such patterns in the training data from the Biological Magnetic Resonance Bank using linear discriminant analysis, and then use them to classify spin systems in an α-synuclein sample prepared by us. We describe two situations in which the procedure can greatly facilitate the analysis of NMR spectra. The first involves the mapping of spin systems chains onto the protein sequence, which is part of the assignment procedure-a prerequisite for any NMR-based protein analysis. In the second, the method supports assignment transfer between similar samples. We conducted experiments to demonstrate these cases, and both times the majority of spin systems could be unambiguously assigned to the correct residue types.
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Affiliation(s)
- Javier A. Romero
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Paulina Putko
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Mateusz Urbańczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | | | - Anna Zawadzka-Kazimierczuk
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
- * E-mail: (KK); (AZK)
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3
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Lesovoy DM, Georgoulia PS, Diercks T, Matečko‐Burmann I, Burmann BM, Bocharov EV, Bermel W, Orekhov VY. Unambiguous Tracking of Protein Phosphorylation by Fast High‐Resolution FOSY NMR**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dmitry M. Lesovoy
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS 117997 Moscow Russia
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases Moscow Institute of Physics and Technology (State University) 141700 Dolgoprudny Russia
| | - Panagiota S. Georgoulia
- Department of Chemistry and Molecular Biology University of Gothenburg Box 465 40530 Gothenburg Sweden
| | - Tammo Diercks
- NMR Platform CiC bioGUNE Bld. 800, Parque Tecnológico de Bizkaia 48160 Derio Spain
| | - Irena Matečko‐Burmann
- Department of Psychiatry and Neurochemistry University of Gothenburg 40530 Gothenburg Sweden
- Wallenberg Centre for Molecular and Translational Medicine University of Gothenburg 40530 Gothenburg Sweden
| | - Björn M. Burmann
- Department of Chemistry and Molecular Biology University of Gothenburg Box 465 40530 Gothenburg Sweden
- Wallenberg Centre for Molecular and Translational Medicine University of Gothenburg 40530 Gothenburg Sweden
| | - Eduard V. Bocharov
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS 117997 Moscow Russia
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases Moscow Institute of Physics and Technology (State University) 141700 Dolgoprudny Russia
| | - Wolfgang Bermel
- Bruker BioSpin GmbH Silberstreifen 4 76287 Rheinstetten Germany
| | - Vladislav Y. Orekhov
- Department of Chemistry and Molecular Biology University of Gothenburg Box 465 40530 Gothenburg Sweden
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4
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Lesovoy DM, Georgoulia PS, Diercks T, Matečko‐Burmann I, Burmann BM, Bocharov EV, Bermel W, Orekhov VY. Unambiguous Tracking of Protein Phosphorylation by Fast High-Resolution FOSY NMR*. Angew Chem Int Ed Engl 2021; 60:23540-23544. [PMID: 34143912 PMCID: PMC8596425 DOI: 10.1002/anie.202102758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/30/2021] [Indexed: 12/12/2022]
Abstract
Dysregulation of post-translational modifications (PTMs) like phosphorylation is often involved in disease. NMR may elucidate exact loci and time courses of PTMs at atomic resolution and near-physiological conditions but requires signal assignment to individual atoms. Conventional NMR methods for this base on tedious global signal assignment that may often fail, as for large intrinsically disordered proteins (IDPs). We present a sensitive, robust alternative to rapidly obtain only the local assignment near affected signals, based on FOcused SpectroscopY (FOSY) experiments using selective polarisation transfer (SPT). We prove its efficiency by identifying two phosphorylation sites of glycogen synthase kinase 3 beta (GSK3β) in human Tau40, an IDP of 441 residues, where the extreme spectral dispersion in FOSY revealed unprimed phosphorylation also of Ser409. FOSY may broadly benefit NMR studies of PTMs and other hotspots in IDPs, including sites involved in molecular interactions.
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Affiliation(s)
- Dmitry M. Lesovoy
- Department of Structural Biology, Shemyakin-OvchinnikovInstitute of Bioorganic Chemistry RAS117997MoscowRussia
- Research Center for Molecular Mechanisms of Aging and Age-related DiseasesMoscow Institute of Physics and Technology (State University)141700DolgoprudnyRussia
| | - Panagiota S. Georgoulia
- Department of Chemistry and Molecular BiologyUniversity of GothenburgBox 46540530GothenburgSweden
| | - Tammo Diercks
- NMR PlatformCiC bioGUNEBld. 800, Parque Tecnológico de Bizkaia48160DerioSpain
| | - Irena Matečko‐Burmann
- Department of Psychiatry and NeurochemistryUniversity of Gothenburg40530GothenburgSweden
- Wallenberg Centre for Molecular and Translational MedicineUniversity of Gothenburg40530GothenburgSweden
| | - Björn M. Burmann
- Department of Chemistry and Molecular BiologyUniversity of GothenburgBox 46540530GothenburgSweden
- Wallenberg Centre for Molecular and Translational MedicineUniversity of Gothenburg40530GothenburgSweden
| | - Eduard V. Bocharov
- Department of Structural Biology, Shemyakin-OvchinnikovInstitute of Bioorganic Chemistry RAS117997MoscowRussia
- Research Center for Molecular Mechanisms of Aging and Age-related DiseasesMoscow Institute of Physics and Technology (State University)141700DolgoprudnyRussia
| | | | - Vladislav Y. Orekhov
- Department of Chemistry and Molecular BiologyUniversity of GothenburgBox 46540530GothenburgSweden
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5
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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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Pedersen CP, Prestel A, Teilum K. Software for reconstruction of nonuniformly sampled NMR data. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:315-323. [PMID: 32516838 DOI: 10.1002/mrc.5060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Nonuniform sampling (NUS) of multidimensional NMR experiments is a powerful tool to obtain high-resolution spectra with less instrument time. With NUS, only a subset of the points needed for conventional Fourier transformation is recorded, and sophisticated algorithms are needed to reconstruct the missing data points. During the last decade, several software packages implementing the reconstruction algorithms have emerged and been refined and now result in spectra of almost similar quality as spectra from conventionally recorded and processed data. However, from the number of literature references to the reconstruction methods, many more multidimensional NMR spectra could presumably be recorded with NUS. To help researchers considering to start using NUS for their NMR experiments, we here review 13 different reconstruction methods found in five software packages (CambridgeCS, hmsIST, MddNMR, NESTA-NMR, and SMILE). We have compared how the methods run with the provided example scripts for reconstructing a nonuniform sampled three-dimensional 15 N-NOESY-HSQC at sampling densities from 5% to 50%. Overall, the spectra are all of similar quality above 20% sampling density. Thus, without any particular knowledge about the details of the reconstruction algorithms, significant reduction in the experiment time can be achieved. Below 20% sampling density, the intensities of particular weak peaks start being affected. MddNMR's IST with virtual echo and the SMILE algorithms still reproduced the spectra with the highest accuracy of peak intensities.
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Affiliation(s)
- Christian Parsbaek Pedersen
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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7
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Novel NMR Assignment Strategy Reveals Structural Heterogeneity in Solution of the nsP3 HVD Domain of Venezuelan Equine Encephalitis Virus. Molecules 2020; 25:molecules25245824. [PMID: 33321815 PMCID: PMC7763327 DOI: 10.3390/molecules25245824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 11/17/2022] Open
Abstract
In recent years, intrinsically disordered proteins (IDPs) and disordered domains have attracted great attention. Many of them contain linear motifs that mediate interactions with other factors during formation of multicomponent protein complexes. NMR spectrometry is a valuable tool for characterizing this type of interactions on both amino acid (aa) and atomic levels. Alphaviruses encode a nonstructural protein nsP3, which drives viral replication complex assembly. nsP3 proteins contain over 200-aa-long hypervariable domains (HVDs), which exhibits no homology between different alphavirus species, are predicted to be intrinsically disordered and appear to be critical for alphavirus adaptation to different cells. Previously, we have shown that nsP3 HVD of chikungunya virus (CHIKV) is completely disordered with low tendency to form secondary structures in free form. In this new study, we used novel NMR approaches to assign the spectra for the nsP3 HVD of Venezuelan equine encephalitis virus (VEEV). The HVDs of CHIKV and VEEV have no homology but are both involved in replication complex assembly and function. We have found that VEEV nsP3 HVD is also mostly disordered but contains a short stable α-helix in its C-terminal fragment, which mediates interaction with the members of cellular Fragile X syndrome protein family. Our NMR data also suggest that VEEV HVD has several regions with tendency to form secondary structures.
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8
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Roginkin MS, Ndukwe IE, Craft DL, Williamson RT, Reibarkh M, Martin GE, Rovnyak D. Developing nonuniform sampling strategies to improve sensitivity and resolution in 1,1-ADEQUATE experiments. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:625-640. [PMID: 31912914 DOI: 10.1002/mrc.4995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 06/10/2023]
Abstract
Nonuniform sampling (NUS) strategies are developed for acquiring highly resolved 1,1-ADEQUATE spectra, in both conventional and homodecoupled (HD) variants with improved sensitivity. Specifically, the quantile-directed and Poisson gap methods were critically compared for distributing the samples nonuniformly, and the quantile schedules were further optimized for weighting. Both maximum entropy and iterative soft thresholding spectral estimation algorithms were evaluated. All NUS approaches were robust when the degree of data reduction is moderate, on the order of a 50% reduction of sampling points. Further sampling reduction by NUS is facilitated by using weighted schedules designed by the quantile method, which also suppresses sampling noise well. Seed independence and the ability to specify the sample weighting in quantile scheduling are important in optimizing NUS for 1,1-ADEQUATE data acquisition. Using NUS yields an improvement in sensitivity, while also making longer evolution times accessible that would be difficult or impractical to attain by uniform sampling. Theoretical predictions for the sensitivity enhancements in these experiments are in the range of 5-20%; NUS is shown to disambiguate weak signals, reveal some n JCC correlations obscured by noise, and improve signal strength relative to uniform sampling in the same experimental time. This work presents sample schedule development for applying NUS to challenging experiments. The schedules developed here are made available for general use and should facilitate the broader utilization of ADEQUATE experiments (including 1,1-, 1,n-, and HD- variants) for challenging structure elucidation problems.
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Affiliation(s)
- Mark S Roginkin
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | - Ikenna E Ndukwe
- Merck Research Laboratories, Analytical Research and Development, Merck and Co., Inc., Kenilworth, NJ, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - D Levi Craft
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | - R Thomas Williamson
- Merck Research Laboratories, Analytical Research and Development, Merck and Co., Inc., Kenilworth, NJ, USA
- Department of Chemistry, University of North Carolina at Wilmington, Wilmington, NC, USA
| | - Mikhail Reibarkh
- Merck Research Laboratories, Analytical Research and Development, Merck and Co., Inc., Kenilworth, NJ, USA
| | - Gary E Martin
- Merck Research Laboratories, Analytical Research and Development, Merck and Co., Inc., Kenilworth, NJ, USA
- Department of Chemistry & Biochemistry, Seton Hall University, South Orange, NJ, USA
| | - David Rovnyak
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
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9
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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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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; 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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11
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Gołowicz D, Kasprzak P, Orekhov V, Kazimierczuk K. Fast time-resolved NMR with non-uniform sampling. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:40-55. [PMID: 32130958 DOI: 10.1016/j.pnmrs.2019.09.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
NMR spectroscopy is a versatile tool for studying time-dependent processes: chemical reactions, phase transitions or macromolecular structure changes. However, time-resolved NMR is usually based on the simplest among available techniques - one-dimensional spectra serving as "snapshots" of the studied process. One of the reasons is that multidimensional experiments are very time-expensive due to costly sampling of evolution time space. In this review we summarize efforts to alleviate the problem of limited applicability of multidimensional NMR in time-resolved studies. We focus on techniques based on sparse or non-uniform sampling (NUS), which lead to experimental time reduction by omitting a significant part of the data during measurement and reconstructing it mathematically, adopting certain assumptions about the spectrum. NUS spectra are faster to acquire than conventional ones and thus better suited to the role of "snapshots", but still suffer from non-stationarity of the signal i.e. amplitude and frequency variations within a dataset. We discuss in detail how these instabilities affect the spectra, and what are the optimal ways of sampling the non-stationary FID signal. Finally, we discuss related areas of NMR where serial experiments are exploited and how they can benefit from the same NUS-based approaches.
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Affiliation(s)
- Dariusz Gołowicz
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland; Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland.
| | - Paweł Kasprzak
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland; Department of Mathematical Methods in Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | - Vladislav Orekhov
- Department of Chemistry & Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden.
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12
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Hansen DF. Using Deep Neural Networks to Reconstruct Non-uniformly Sampled NMR Spectra. JOURNAL OF BIOMOLECULAR NMR 2019; 73:577-585. [PMID: 31292846 PMCID: PMC6859195 DOI: 10.1007/s10858-019-00265-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/25/2019] [Indexed: 05/27/2023]
Abstract
Non-uniform and sparse sampling of multi-dimensional NMR spectra has over the last decade become an important tool to allow for fast acquisition of multi-dimensional NMR spectra with high resolution. The success of non-uniform sampling NMR hinge on both the development of algorithms to accurately reconstruct the sparsely sampled spectra and the design of sampling schedules that maximise the information contained in the sampled data. Traditionally, the reconstruction tools and algorithms have aimed at reconstructing the full spectrum and thus 'fill out the missing points' in the time-domain spectrum, although other techniques are based on multi-dimensional decomposition and extraction of multi-dimensional shapes. Also over the last decade, machine learning, deep neural networks, and artificial intelligence have seen new applications in an enormous range of sciences, including analysis of MRI spectra. As a proof-of-principle, it is shown here that simple deep neural networks can be trained to reconstruct sparsely sampled NMR spectra. For the reconstruction of two-dimensional NMR spectra, reconstruction using a deep neural network performs as well, if not better than, the currently and widely used techniques. It is therefore anticipated that deep neural networks provide a very valuable tool for the reconstruction of sparsely sampled NMR spectra in the future to come.
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Affiliation(s)
- D Flemming Hansen
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
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13
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Agback P, Dominguez F, Pustovalova Y, Lukash T, Shiliaev N, Orekhov VY, Frolov I, Agback T, Frolova EI. Structural characterization and biological function of bivalent binding of CD2AP to intrinsically disordered domain of chikungunya virus nsP3 protein. Virology 2019; 537:130-142. [PMID: 31493651 DOI: 10.1016/j.virol.2019.08.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 01/17/2023]
Abstract
Alphavirus nsP3 proteins contain long, intrinsically disordered, hypervariable domains, HVD, which serve as hubs for interaction with many cellular proteins. Here, we have deciphered the mechanism and function of HVD interaction with host factors in alphavirus replication. Using NMR spectroscopy, we show that CHIKV HVD contains two SH3 domain-binding sites. Using an innovative chemical shift perturbation signature approach, we demonstrate that CD2AP interaction with HVD is mediated by its SH3-A and SH3-C domains, and this leaves the SH3-B domain available for interaction with other cellular factor(s). This cooperative interaction with two SH3 domains increases binding affinity to CD2AP and possibly induces long-range allosteric effects in HVD. Our data demonstrate that BIN1, CD2AP and SH3KBP1 play redundant roles in initiation of CHIKV replication. Point mutations in both CHIKV HVD binding sites abolish its interaction with all three proteins, CD2AP, BIN1 and SH3KBP1. This results in strong inhibition of viral replication initiation.
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Affiliation(s)
- Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | | | - Yulia Pustovalova
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Tetyana Lukash
- Department of Microbiology, University of Alabama at Birmingham, AL, USA
| | - Nikita Shiliaev
- Department of Microbiology, University of Alabama at Birmingham, AL, USA
| | - Vladislav Yu Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Ilya Frolov
- Department of Microbiology, University of Alabama at Birmingham, AL, USA
| | - Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Elena I Frolova
- Department of Microbiology, University of Alabama at Birmingham, AL, USA.
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14
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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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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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