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Perras FA. Elimination of homogeneous broadening in 1H solid-state NMR. Chem Commun (Camb) 2024; 60:6552-6555. [PMID: 38842442 DOI: 10.1039/d4cc02191f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
1H solid-state NMR spectra are plagued by low resolution, necessitating the use of complex pulse sequences or specialized equipment. We introduce a new resolution enhancement method, inspired by super-resolution microscopy, that uses a 2D Hahn-echo experiment to constrain deconvolution. The result is an effective doubling of the MAS frequency.
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Affiliation(s)
- Frédéric A Perras
- Chemical and Biological Sciences Division, Ames National Laboratory, Ames, IA 50011, USA.
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
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2
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Karabanov A, Kryukov E, Langlais D, Iuga D, Good J. Post-acquisition correction of NMR spectra distorted by dynamic and static field inhomogeneity of cryogen-free magnets. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 353:107494. [PMID: 37348258 DOI: 10.1016/j.jmr.2023.107494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/26/2023] [Accepted: 05/27/2023] [Indexed: 06/24/2023]
Abstract
Post-acquisition correction of NMR spectra is an important part of NMR spectroscopy that enables refined NMR spectra to be obtained, clean from undesirable out-phasing, broadening and noising. We describe analytical and numerical mathematical methods for post-acquisition correction of NMR spectra distorted by static and dynamic magnetic field inhomogeneity caused by imperfections of main superconducting coils and the cold head operation, typical for cryogen-free magnets. For the dynamic inhomogeneity, we apply a variant of the general reference deconvolution method, complemented with our mathematical analysis of spectral parameters. For the static inhomogeneity, we apply the method of a delayed Fourier transform, also supported with our analytical calculations. We verify our approach by correction processing of high-field experimental liquid-state 1H NMR spectra of water and ethanol as well as solid-state 13C MAS NMR spectra of adamantane and obtain good results for both static and dynamic field distortions. This work complements our previous work on instrumental suppression of dynamic distortions caused by the cold head operation. The results presented contribute well to the general field of processing NMR spectra and serve towards a more extensive use of cryogen-free magnets in high-resolution NMR spectroscopy.
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Affiliation(s)
| | | | | | - Dinu Iuga
- The University of Warwick, Coventry, UK
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3
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Osetrina DA, Kusova AM, Bikmullin AG, Klochkova EA, Yulmetov AR, Semenova EA, Mukhametzyanov TA, Usachev KS, Klochkov VV, Blokhin DS. Extent of N-Terminus Folding of Semenogelin 1 Cleavage Product Determines Tendency to Amyloid Formation. Int J Mol Sci 2023; 24:ijms24108949. [PMID: 37240295 DOI: 10.3390/ijms24108949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
It is known that four peptide fragments of predominant protein in human semen Semenogelin 1 (SEM1) (SEM1(86-107), SEM1(68-107), SEM1(49-107) and SEM1(45-107)) are involved in fertilization and amyloid formation processes. In this work, the structure and dynamic behavior of SEM1(45-107) and SEM1(49-107) peptides and their N-domains were described. According to ThT fluorescence spectroscopy data, it was shown that the amyloid formation of SEM1(45-107) starts immediately after purification, which is not observed for SEM1(49-107). Seeing that the peptide amino acid sequence of SEM1(45-107) differs from SEM1(49-107) only by the presence of four additional amino acid residues in the N domain, these domains of both peptides were obtained via solid-phase synthesis and the difference in their dynamics and structure was investigated. SEM1(45-67) and SEM1(49-67) showed no principal difference in dynamic behavior in water solution. Furthermore, we obtained mostly disordered structures of SEM1(45-67) and SEM1(49-67). However, SEM1(45-67) contains a helix (E58-K60) and helix-like (S49-Q51) fragments. These helical fragments may rearrange into β-strands during amyloid formation process. Thus, the difference in full-length peptides' (SEM1(45-107) and SEM1(49-107)) amyloid-forming behavior may be explained by the presence of a structured helix at the SEM1(45-107) N-terminus, which contributes to an increased rate of amyloid formation.
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Affiliation(s)
- Daria A Osetrina
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Aleksandra M Kusova
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan 420111, Russia
| | - Aydar G Bikmullin
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420021, Russia
| | - Evelina A Klochkova
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420021, Russia
| | - Aydar R Yulmetov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Evgenia A Semenova
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Timur A Mukhametzyanov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Konstantin S Usachev
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420021, Russia
- Laboratory for Structural Analysis of Biomacromolecules, Federal Research Center "Kazan Scientific Center of Russian Academy of Sciences", Kazan 420111, Russia
| | - Vladimir V Klochkov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Dmitriy S Blokhin
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
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Qiu T, Jahangiri A, Han X, Lesovoy D, Agback T, Agback P, Achour A, Qu X, Orekhov V. Resolution enhancement of NMR by decoupling with the low-rank Hankel model. Chem Commun (Camb) 2023; 59:5475-5478. [PMID: 37070867 PMCID: PMC10152455 DOI: 10.1039/d2cc06682c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/13/2023] [Indexed: 04/19/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy has become a formidable tool for biochemistry and medicine. Although J-coupling carries essential structural information it may also limit the spectral resolution. Homonuclear decoupling remains a challenging problem. In this work, we introduce a new approach that uses a specific coupling value as prior knowledge, and the Hankel property of the exponential NMR signal to achieve broadband heteronuclear decoupling using the low-rank method. Our results on synthetic and realistic HMQC spectra demonstrate that the proposed method not only effectively enhances resolution by decoupling, but also maintains sensitivity and suppresses spectral artefacts. The approach can be combined with non-uniform sampling, which means that the resolution can be further improved without any extra acquisition time.
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Affiliation(s)
- Tianyu Qiu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Biomedical Intelligent Cloud Research and Development Centre, Xiamen University, Xiamen, 361005, China.
- Department of Chemistry and Molecular Biology, and Swedish NMR Centre, University of Gothenburg, Box 465, Gothenburg, 40530, Sweden.
| | - Amir Jahangiri
- Department of Chemistry and Molecular Biology, and Swedish NMR Centre, University of Gothenburg, Box 465, Gothenburg, 40530, Sweden.
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, 17176, Sweden
| | - Dmitry Lesovoy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RA, Moscow, 117997, Russia
| | - Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, Uppsala, 75007, Sweden
| | - Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, Uppsala, 75007, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, 17176, Sweden
| | - Xiaobo Qu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Biomedical Intelligent Cloud Research and Development Centre, Xiamen University, Xiamen, 361005, China.
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology, and Swedish NMR Centre, University of Gothenburg, Box 465, Gothenburg, 40530, Sweden.
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Jahangiri A, Han X, Lesovoy D, Agback T, Agback P, Achour A, Orekhov V. NMR spectrum reconstruction as a pattern recognition problem. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 346:107342. [PMID: 36459916 DOI: 10.1016/j.jmr.2022.107342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/15/2022] [Accepted: 11/19/2022] [Indexed: 06/17/2023]
Abstract
A new deep neural network based on the WaveNet architecture (WNN) is presented, which is designed to grasp specific patterns in the NMR spectra. When trained at a fixed non-uniform sampling (NUS) schedule, the WNN benefits from pattern recognition of the corresponding point spread function (PSF) pattern produced by each spectral peak resulting in the highest quality and robust reconstruction of the NUS spectra as demonstrated in simulations and exemplified in this work on 2D 1H-15N correlation spectra of three representative globular proteins with different sizes: Ubiquitin (8.6 kDa), Azurin (14 kDa), and Malt1 (44 kDa). The pattern recognition by WNN is also demonstrated for successful virtual homo-decoupling in a 2D methyl 1H-13C - HMQC spectrum of MALT1. We demonstrate using WNN that prior knowledge about the NUS schedule, which so far was not been fully exploited, can be used for designing new powerful NMR processing techniques that surpass the existing algorithmic methods.
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Affiliation(s)
- Amir Jahangiri
- Department of Chemistry and Molecular Biology, Swedish NMR Centre, University of Gothenburg, Box 465, Gothenburg 40530, Sweden
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Dmitry Lesovoy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RA, Moscow 117997, Russia
| | - Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, Uppsala 75007, Sweden
| | - Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, Uppsala 75007, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology, Swedish NMR Centre, University of Gothenburg, Box 465, Gothenburg 40530, Sweden.
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6
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Conformational ensemble of amyloid-forming semenogelin 1 peptide SEM1(68-107) by NMR spectroscopy and MD simulations. J Struct Biol 2022; 214:107900. [PMID: 36191746 DOI: 10.1016/j.jsb.2022.107900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/15/2022] [Accepted: 09/26/2022] [Indexed: 12/30/2022]
Abstract
SEM1(68-107) is a peptide corresponding to the region of semenogelin 1 protein from 68 to 107 amino acid position. SEM1(68-107) is an abundant component of semen, which participates in HIV infection enhanced by amyloid fibrils forming. To understand the causes influencing amyloid fibril formation, it is necessary to determine the spatial structure of SEM1(68-107). It was shown that the determination of SEM1(68-107) structure is complicated by the non-informative NMR spectra due to the high intramolecular mobility of peptides. The complementary approach based on the geometric restrictions of individual peptide fragments and molecular modeling was used for the determination of the spatial structure of SEM1(68-107). The N- (SEM1(68-85)) and C-terminuses (SEM1(86-107)) of SEM1(68-107) were chosen as two individual peptide fragments. SEM1(68-85) and SEM1(86-107) structures were established with NMR and circular dichroism CD spectroscopies. These regions were used as geometric restraints for the SEM1(68-107) structure modeling. Even though most of the SEM1(68-107) peptide is unstructured, our detailed analysis revealed the following structured elements: N-terminus (70His-84Gln) forms an α-helix, (86Asp-94Thr) and (101Gly-103Ser) regions fold into 310-helixes. The absence of a SEM1(68-107) rigid conformation leads to instability of these secondary structure regions. The calculated SEM1(68-107) structure is in good agreement with experimental values of hydrodynamic radius and dihedral angles obtained by NMR spectroscopy. This testifies the adequacy of a combined approach based on the use of peptide fragment structures for the molecular modeling formation of full-size peptide spatial structure.
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7
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Han X, Levkovets M, Lesovoy D, Sun R, Wallerstein J, Sandalova T, Agback T, Achour A, Agback P, Orekhov VY. Assignment of IVL-Methyl side chain of the ligand-free monomeric human MALT1 paracaspase-IgL 3 domain in solution. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:363-371. [PMID: 36094731 PMCID: PMC9510110 DOI: 10.1007/s12104-022-10105-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Mucosa-associated lymphoid tissue protein 1 (MALT1) plays a key role in adaptive immune responses by modulating specific intracellular signalling pathways that control the development and proliferation of both T and B cells. Dysfunction of these pathways is coupled to the progress of highly aggressive lymphoma as well as to potential development of an array of different immune disorders. In contrast to other signalling mediators, MALT1 is not only activated through the formation of the CBM complex together with the proteins CARMA1 and Bcl10, but also by acting as a protease that cleaves multiple substrates to promote lymphocyte proliferation and survival via the NF-κB signalling pathway. Herein, we present the partial 1H, 13C Ile/Val/Leu-Methyl resonance assignment of the monomeric apo form of the paracaspase-IgL3 domain of human MALT1. Our results provide a solid ground for future elucidation of both the three-dimensional structure and the dynamics of MALT1, key for adequate development of inhibitors, and a thorough molecular understanding of its function(s).
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Affiliation(s)
- Xiao Han
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and, Division of Infectious Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Maria Levkovets
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden
| | - Dmitry Lesovoy
- Department of Structural Biology, Shemyakin-Ovchinnikov, Institute of Bioorganic Chemistry RAS, Moscow, Russia, 117997
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and, Division of Infectious Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Johan Wallerstein
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and, Division of Infectious Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07, Uppsala, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and, Division of Infectious Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07, Uppsala, Sweden.
| | - Vladislav Yu Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden.
- Swedish NMR Centre, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden.
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8
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Kusova A, Abramova M, Skvortsova P, Yulmetov A, Mukhametzyanov T, Klochkov V, Blokhin D. Structure of amyloidogenic PAP(85-120) peptide by high-resolution NMR spectroscopy. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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9
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Agback P, Lesovoy DM, Han X, Sun R, Sandalova T, Agback T, Achour A, Orekhov VY. 1H, 13C and 15N resonance assignment of backbone and IVL-methyl side chain of the S135A mutant NS3pro/NS2B protein of Dengue II virus reveals unique secondary structure features in solution. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:135-145. [PMID: 35149939 PMCID: PMC9068680 DOI: 10.1007/s12104-022-10071-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
The serotype II Dengue (DENV 2) virus is the most prevalent of all four known serotypes. Herein, we present nearly complete 1H, 15N, and 13C backbone and 1H, 13C isoleucine, valine, and leucine methyl resonance assignment of the apo S135A catalytically inactive variant of the DENV 2 protease enzyme folded as a tandem formed between the serine protease domain NS3pro and the cofactor NS2B, as well as the secondary structure prediction of this complex based on the assigned chemical shifts using the TALOS-N software. Our results provide a solid ground for future elucidation of the structure and dynamic of the apo NS3pro/NS2B complex, key for adequate development of inhibitors, and a thorough molecular understanding of their function(s).
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Affiliation(s)
- Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, 750 07, Uppsala, Sweden.
| | - Dmitry M Lesovoy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RA, 117997, Moscow, Russia
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, 750 07, Uppsala, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Vladislav Yu Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden
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Kasprzak P, Urbańczyk M, Kazimierczuk K. Clustered sparsity and Poisson-gap sampling. JOURNAL OF BIOMOLECULAR NMR 2021; 75:401-416. [PMID: 34739685 PMCID: PMC8642362 DOI: 10.1007/s10858-021-00385-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/24/2021] [Indexed: 05/11/2023]
Abstract
Non-uniform sampling (NUS) is a popular way of reducing the amount of time taken by multidimensional NMR experiments. Among the various non-uniform sampling schemes that exist, the Poisson-gap (PG) schedules are particularly popular, especially when combined with compressed-sensing (CS) reconstruction of missing data points. However, the use of PG is based mainly on practical experience and has not, as yet, been explained in terms of CS theory. Moreover, an apparent contradiction exists between the reported effectiveness of PG and CS theory, which states that a "flat" pseudo-random generator is the best way to generate sampling schedules in order to reconstruct sparse spectra. In this paper we explain how, and in what situations, PG reveals its superior features in NMR spectroscopy. We support our theoretical considerations with simulations and analyses of experimental data from the Biological Magnetic Resonance Bank (BMRB). Our analyses reveal a previously unnoticed feature of many NMR spectra that explains the success of "blue-noise" schedules, such as PG. We call this feature "clustered sparsity". This refers to the fact that the peaks in NMR spectra are not just sparse but often form clusters in the indirect dimension, and PG is particularly suited to deal with such situations. Additionally, we discuss why denser sampling in the initial and final parts of the clustered signal may be useful.
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Affiliation(s)
- Paweł Kasprzak
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Mateusz Urbańczyk
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
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Karunanithy G, Hansen DF. FID-Net: A versatile deep neural network architecture for NMR spectral reconstruction and virtual decoupling. JOURNAL OF BIOMOLECULAR NMR 2021; 75:179-191. [PMID: 33870472 PMCID: PMC8131344 DOI: 10.1007/s10858-021-00366-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/24/2021] [Indexed: 05/25/2023]
Abstract
In recent years, the transformative potential of deep neural networks (DNNs) for analysing and interpreting NMR data has clearly been recognised. However, most applications of DNNs in NMR to date either struggle to outperform existing methodologies or are limited in scope to a narrow range of data that closely resemble the data that the network was trained on. These limitations have prevented a widescale uptake of DNNs in NMR. Addressing this, we introduce FID-Net, a deep neural network architecture inspired by WaveNet, for performing analyses on time domain NMR data. We first demonstrate the effectiveness of this architecture in reconstructing non-uniformly sampled (NUS) biomolecular NMR spectra. It is shown that a single network is able to reconstruct a diverse range of 2D NUS spectra that have been obtained with arbitrary sampling schedules, with a range of sweep widths, and a variety of other acquisition parameters. The performance of the trained FID-Net in this case exceeds or matches existing methods currently used for the reconstruction of NUS NMR spectra. Secondly, we present a network based on the FID-Net architecture that can efficiently virtually decouple 13Cα-13Cβ couplings in HNCA protein NMR spectra in a single shot analysis, while at the same time leaving glycine residues unmodulated. The ability for these DNNs to work effectively in a wide range of scenarios, without retraining, paves the way for their widespread usage in analysing NMR data.
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Affiliation(s)
- Gogulan Karunanithy
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - D Flemming Hansen
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK.
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