1
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Furuita K, Kojima C. Improved analysis of NMR chemical shift perturbations through an error estimation method. Biophys Chem 2024; 310:107255. [PMID: 38728808 DOI: 10.1016/j.bpc.2024.107255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/25/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
In solution NMR, chemical shift perturbation (CSP) experiments are widely employed to study intermolecular interactions. However, excluding the nonsignificant peak shift is difficult because little is known about errors in CSP. Here, to address this issue, we introduce a method for estimating errors in CSP based on the noise level. First, we developed a technique that involves line shape fitting to estimate errors in peak position via Monte Carlo simulations. Second, this technique was applied to estimate errors in CSP. In intermolecular interaction analysis of VAP-A with SNX2, error estimation of CSP enabled the evaluation of small but significant changes in peak position and yielded detailed insights that are unattainable with conventional CSP analysis. Third, this technique was successfully applied to estimate errors in residual dipolar couplings. In conclusion, our error estimation method improves CSP analysis by excluding the nonsignificant peak shift.
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Affiliation(s)
- Kyoko Furuita
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Chojiro Kojima
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Engineering Science, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama 240-8501, Japan.
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2
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Specht T, Arweiler J, Stüber J, Münnemann K, Hasse H, Jirasek F. Automated nuclear magnetic resonance fingerprinting of mixtures. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:286-297. [PMID: 37515509 DOI: 10.1002/mrc.5381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/31/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for qualitative and quantitative analysis. However, for complex mixtures, determining the speciation from NMR spectra can be tedious and sometimes even unfeasible. On the other hand, identifying and quantifying structural groups in a mixture from NMR spectra is much easier than doing the same for components. We call this group-based approach "NMR fingerprinting." In this work, we show that NMR fingerprinting can even be performed in an automated way, without expert knowledge, based only on standard NMR spectra, namely, 13C, 1H, and 13C DEPT NMR spectra. Our approach is based on the machine-learning method of support vector classification (SVC), which was trained here on thousands of labeled pure-component NMR spectra from open-source data banks. We demonstrate the applicability of the automated NMR fingerprinting using test mixtures, of which spectra were taken using a simple benchtop NMR spectrometer. The results from the NMR fingerprinting agree remarkably well with the ground truth, which was known from the gravimetric preparation of the samples. To facilitate the application of the method, we provide an interactive website (https://nmr-fingerprinting.de), where spectral information can be uploaded and which returns the NMR fingerprint. The NMR fingerprinting can be used in many ways, for example, for process monitoring or thermodynamic modeling using group-contribution methods-or simply as a first step in species analysis.
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Affiliation(s)
- Thomas Specht
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, Kaiserslautern, Germany
| | - Justus Arweiler
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, Kaiserslautern, Germany
| | - Johannes Stüber
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, Kaiserslautern, Germany
| | - Kerstin Münnemann
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, Kaiserslautern, Germany
| | - Hans Hasse
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, Kaiserslautern, Germany
| | - Fabian Jirasek
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, Kaiserslautern, Germany
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3
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Zumpfe K, Berbon M, Habenstein B, Loquet A, Smith AA. Analytical Framework to Understand the Origins of Methyl Side-Chain Dynamics in Protein Assemblies. J Am Chem Soc 2024; 146:8164-8178. [PMID: 38476076 PMCID: PMC10979401 DOI: 10.1021/jacs.3c12620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
Side-chain motions play an important role in understanding protein structure, dynamics, protein-protein, and protein-ligand interactions. However, our understanding of protein side-chain dynamics is currently limited by the lack of analytical tools. Here, we present a novel analytical framework employing experimental nuclear magnetic resonance (NMR) relaxation measurements at atomic resolution combined with molecular dynamics (MD) simulation to characterize with a high level of detail the methyl side-chain dynamics in insoluble protein assemblies, using amyloid fibrils formed by the prion HET-s. We use MD simulation to interpret experimental results, where rotameric hops, including methyl group rotation and χ1/χ2 rotations, cannot be completely described with a single correlation time but rather sample a broad distribution of correlation times, resulting from continuously changing local structure in the fibril. Backbone motion similarly samples a broad range of correlation times, from ∼100 ps to μs, although resulting from mostly different dynamic processes; nonetheless, we find that the backbone is not fully decoupled from the side-chain motion, where changes in side-chain dynamics influence backbone motion and vice versa. While the complexity of side-chain motion in protein assemblies makes it very challenging to obtain perfect agreement between experiment and simulation, our analytical framework improves the interpretation of experimental dynamics measurements for complex protein assemblies.
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Affiliation(s)
- Kai Zumpfe
- Institute
for Medical Physics and Biophysics, Leipzig
University, Härtelstraße
16-18, 04107 Leipzig, Germany
| | - Mélanie Berbon
- University
of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 33600 Pessac, France
| | - Birgit Habenstein
- University
of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 33600 Pessac, France
| | - Antoine Loquet
- University
of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 33600 Pessac, France
| | - Albert A. Smith
- Institute
for Medical Physics and Biophysics, Leipzig
University, Härtelstraße
16-18, 04107 Leipzig, Germany
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4
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Callon M, Luder D, Malär AA, Wiegand T, Římal V, Lecoq L, Böckmann A, Samoson A, Meier BH. High and fast: NMR protein-proton side-chain assignments at 160 kHz and 1.2 GHz. Chem Sci 2023; 14:10824-10834. [PMID: 37829013 PMCID: PMC10566471 DOI: 10.1039/d3sc03539e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/16/2023] [Indexed: 10/14/2023] Open
Abstract
The NMR spectra of side-chain protons in proteins provide important information, not only about their structure and dynamics, but also about the mechanisms that regulate interactions between macromolecules. However, in the solid-state, these resonances are particularly difficult to resolve, even in relatively small proteins. We show that magic-angle-spinning (MAS) frequencies of 160 kHz, combined with a high magnetic field of 1200 MHz proton Larmor frequency, significantly improve their spectral resolution. We investigate in detail the gain for MAS frequencies between 110 and 160 kHz MAS for a model sample as well as for the hepatitis B viral capsid assembled from 120 core-protein (Cp) dimers. For both systems, we found a significantly improved spectral resolution of the side-chain region in the 1H-13C 2D spectra. The combination of 160 kHz MAS frequency with a magnetic field of 1200 MHz, allowed us to assign 61% of the aliphatic protons of Cp. The side-chain proton assignment opens up new possibilities for structural studies and further characterization of protein-protein or protein-nucleic acid interactions.
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Affiliation(s)
| | | | | | | | - Václav Římal
- Physical Chemistry, ETH Zürich 8093 Zürich Switzerland
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry (MMSB) UMR 5086, CNRS, Université de Lyon, Labex Ecofect 7 passage du Vercors 69367 Lyon France
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry (MMSB) UMR 5086, CNRS, Université de Lyon, Labex Ecofect 7 passage du Vercors 69367 Lyon France
| | - Ago Samoson
- Institute of Cybernetics, Spin Design Laboratory, Tallinn University of Technology Tallinn Estonia
| | - Beat H Meier
- Physical Chemistry, ETH Zürich 8093 Zürich Switzerland
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5
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Fandrei F, Havrišák T, Opálka L, Engberg O, Smith A, Pullmannová P, Kučerka N, Ondrejčeková V, Demé B, Nováková L, Steinhart M, Vávrová K, Huster D. The Intriguing Molecular Dynamics of Cer[EOS] in Rigid Skin Barrier Lipid Layers Requires Improvement of the Model. J Lipid Res 2023; 64:100356. [PMID: 36948272 PMCID: PMC10154977 DOI: 10.1016/j.jlr.2023.100356] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/24/2023] Open
Abstract
Omega-O-acyl ceramides such as 32-linoleoyloxydotriacontanoyl sphingosine (Cer[EOS]) are essential components of the lipid skin barrier, which protects our body from excessive water loss and the penetration of unwanted substances. These ceramides drive the lipid assembly to epidermal-specific long periodicity phase (LPP), structurally much different than conventional lipid bilayers. Here, we synthesized Cer[EOS] with selectively deuterated segments of the ultralong N-acyl chain or deuterated or 13C-labeled linoleic acid and studied their molecular behavior in a skin lipid model. Solid-state 2H NMR data revealed surprising molecular dynamics for the ultralong N-acyl chain of Cer[EOS] with increased isotropic motion towards the isotropic ester-bound linoleate. The sphingosine moiety of Cer[EOS] is also highly mobile at skin temperature, in stark contrast to the other LPP components, N-lignoceroyl sphingosine acyl, lignoceric acid and cholesterol, which are predominantly rigid. The dynamics of the linoleic chain is quantitatively described by distributions of correlation times and using dynamic detector analysis. These NMR results along with neutron diffraction data suggest an LPP structure with alternating fluid (sphingosine chain-rich), rigid (acyl chain-rich), isotropic (linoleate-rich), rigid (acyl-chain rich), and fluid layers (sphingosine chain-rich). Such an arrangement of the skin barrier lipids with rigid layers separated with two different dynamic "fillings" i) agrees well with ultrastructural data, ii) satisfies the need for simultaneous rigidity (to ensure low permeability) and fluidity (to ensure elasticity, accommodate enzymes or antimicrobial peptides), and iii) offers a straightforward way to remodel the lamellar body lipids into the final lipid barrier.
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Affiliation(s)
- Ferdinand Fandrei
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, 04275 Leipzig, Germany
| | - Tomáš Havrišák
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Lukáš Opálka
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Oskar Engberg
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, 04275 Leipzig, Germany
| | - AlbertA Smith
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, 04275 Leipzig, Germany
| | - Petra Pullmannová
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Norbert Kučerka
- Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, 832 32 Bratislava, Slovakia
| | - Veronika Ondrejčeková
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Bruno Demé
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, CEDEX 9, France
| | - Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Miloš Steinhart
- Institute of Macromolecular Chemistry, Czech Academy of Science in Prague, Heyrovského nám. 2, 162 06 Prague, Czech Republic
| | - Kateřina Vávrová
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, 04275 Leipzig, Germany
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6
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Li DW, Bruschweiler-Li L, Hansen A, Brüschweiler R. DEEP Picker1D and Voigt Fitter1D: a versatile tool set for the automated quantitative spectral deconvolution of complex 1D-NMR spectra. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2023; 4:19-26. [PMID: 37904796 PMCID: PMC10539790 DOI: 10.5194/mr-4-19-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/16/2022] [Indexed: 11/01/2023]
Abstract
The quantitative deconvolution of 1D-NMR spectra into individual resonances or peaks is a key step in many modern NMR workflows as it critically affects downstream analysis and interpretation. Depending on the complexity of the NMR spectrum, spectral deconvolution can be a notable challenge. Based on the recent deep neural network DEEP Picker and Voigt Fitter for 2D NMR spectral deconvolution, we present here an accurate, fully automated solution for 1D-NMR spectral analysis, including peak picking, fitting, and reconstruction. The method is demonstrated for complex 1D solution NMR spectra showing excellent performance also for spectral regions with multiple strong overlaps and a large dynamic range whose analysis is challenging for current computational methods. The new tool will help streamline 1D-NMR spectral analysis for a wide range of applications and expand their reach toward ever more complex molecular systems and their mixtures.
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Affiliation(s)
- Da-Wei Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Alexandar L. Hansen
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Rafael Brüschweiler
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA
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7
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Molecular elucidation of drug-induced abnormal assemblies of the hepatitis B virus capsid protein by solid-state NMR. Nat Commun 2023; 14:471. [PMID: 36709212 PMCID: PMC9884277 DOI: 10.1038/s41467-023-36219-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/18/2023] [Indexed: 01/29/2023] Open
Abstract
Hepatitis B virus (HBV) capsid assembly modulators (CAMs) represent a recent class of anti-HBV antivirals. CAMs disturb proper nucleocapsid assembly, by inducing formation of either aberrant assemblies (CAM-A) or of apparently normal but genome-less empty capsids (CAM-E). Classical structural approaches have revealed the CAM binding sites on the capsid protein (Cp), but conformational information on the CAM-induced off-path aberrant assemblies is lacking. Here we show that solid-state NMR can provide such information, including for wild-type full-length Cp183, and we find that in these assemblies, the asymmetric unit comprises a single Cp molecule rather than the four quasi-equivalent conformers typical for the icosahedral T = 4 symmetry of the normal HBV capsids. Furthermore, while in contrast to truncated Cp149, full-length Cp183 assemblies appear, on the mesoscopic level, unaffected by CAM-A, NMR reveals that on the molecular level, Cp183 assemblies are equally aberrant. Finally, we use a eukaryotic cell-free system to reveal how CAMs modulate capsid-RNA interactions and capsid phosphorylation. Our results establish a structural view on assembly modulation of the HBV capsid, and they provide a rationale for recently observed differences between in-cell versus in vitro capsid assembly modulation.
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8
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Parameter Visualization of Benchtop Nuclear Magnetic Resonance Spectra toward Food Process Monitoring. Processes (Basel) 2022. [DOI: 10.3390/pr10071264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
Low-cost and user-friendly benchtop low-field nuclear magnetic resonance (NMR) spectrometers are typically used to monitor food processes in the food industry. Because of excessive spectral overlap, it is difficult to characterize food mixtures using low-field NMR spectroscopy. In addition, for standard compounds, low-field benchtop NMR data are typically unavailable compared to high-field NMR data, which have been accumulated and are reusable in public databases. This work focused on NMR parameter visualization of the chemical structure and mobility of mixtures and the use of high-field NMR data to analyze benchtop NMR data to characterize food process samples. We developed a tool to easily process benchtop NMR data and obtain chemical shifts and T2 relaxation times of peaks, as well as transform high-field NMR data into low-field NMR data. Line broadening and time–frequency analysis methods were adopted for data processing. This tool can visualize NMR parameters to characterize changes in the components and mobilities of food process samples using benchtop NMR data. In addition, assignment errors were smaller when the spectra of standard compounds were identified by transferring the high-field NMR data to low-field NMR data rather than directly using experimentally obtained low-field NMR spectra.
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9
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Materials informatics approach using domain modelling for exploring structure-property relationships of polymers. Sci Rep 2022; 12:10558. [PMID: 35732681 PMCID: PMC9217937 DOI: 10.1038/s41598-022-14394-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/06/2022] [Indexed: 11/23/2022] Open
Abstract
In the development of polymer materials, it is an important issue to explore the complex relationships between domain structure and physical properties. In the domain structure analysis of polymer materials, 1H-static solid-state NMR (ssNMR) spectra can provide information on mobile, rigid, and intermediate domains. But estimation of domain structure from its analysis is difficult due to the wide overlap of spectra from multiple domains. Therefore, we have developed a materials informatics approach that combines the domain modeling (http://dmar.riken.jp/matrigica/) and the integrated analysis of meta-information (the elements, functional groups, additives, and physical properties) in polymer materials. Firstly, the 1H-static ssNMR data of 120 polymer materials were subjected to a short-time Fourier transform to obtain frequency, intensity, and T2 relaxation time for domains with different mobility. The average T2 relaxation time of each domain is 0.96 ms for Mobile, 0.55 ms for Intermediate (Mobile), 0.32 ms for Intermediate (Rigid), and 0.11 ms for Rigid. Secondly, the estimated domain proportions were integrated with meta-information such as elements, functional group and thermophysical properties and was analyzed using a self-organization map and market basket analysis. This proposed method can contribute to explore structure–property relationships of polymer materials with multiple domains.
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10
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Li DW, Leggett A, Bruschweiler-Li L, Brüschweiler R. COLMARq: A Web Server for 2D NMR Peak Picking and Quantitative Comparative Analysis of Cohorts of Metabolomics Samples. Anal Chem 2022; 94:8674-8682. [PMID: 35672005 PMCID: PMC9218957 DOI: 10.1021/acs.analchem.2c00891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Highly quantitative metabolomics studies of complex biological mixtures are facilitated by the resolution enhancement afforded by 2D NMR spectra such as 2D 13C-1H HSQC spectra. Here, we describe a new public web server, COLMARq, for the semi-automated analysis of sets of 2D HSQC spectra of cohorts of samples. The workflow of COLMARq includes automated peak picking using the deep neural network DEEP Picker, quantitative cross-peak volume extraction by numerical fitting using Voigt Fitter, the matching of corresponding cross-peaks across cohorts of spectra, peak volume normalization between different spectra, database query for metabolite identification, and basic univariate and multivariate statistical analyses of the results. COLMARq allows the analysis of cross-peaks that belong to both known and unknown metabolites. After a user has uploaded cohorts of 2D 13C-1H HSQC and optionally 2D 1H-1H TOCSY spectra in their preferred format, all subsequent steps on the web server can be performed fully automatically, allowing manual editing if needed and the sessions can be saved for later use. The accuracy, versatility, and interactive nature of COLMARq enables quantitative metabolomics analysis, including biomarker identification, of a broad range of complex biological mixtures as is illustrated for cohorts of samples from bacterial cultures of Pseudomonas aeruginosa in both its biofilm and planktonic states.
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Affiliation(s)
- Da-Wei Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Abigail Leggett
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.,Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Rafael Brüschweiler
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
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11
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London JA, Taylor SL, Barsukov I, Cartmell A, Yates EA. Exploration of expanded carbohydrate chemical space to access biological activity using microwave-induced acid condensation of simple sugars. RSC Adv 2022; 12:11075-11083. [PMID: 35425031 PMCID: PMC8992359 DOI: 10.1039/d2ra01463g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 03/30/2022] [Indexed: 11/30/2022] Open
Abstract
Complex glycans are ubiquitous in nature and essential to life. Despite their diverse roles, however, only a fraction of their potential chemical space has been explored. New regions of this chemical space can, nevertheless, be accessed by generating structures that do not occur in nature or by modifying naturally-occurring polysaccharide structures – collectively, termed new polysaccharides (NPs). Two synthetic routes to NPs are described; the de novo route, directly from monosaccharide starting materials and the functionalization route, involving glycosylation of existing polysaccharides. The reaction involves a simple condensation step under microwave heating, catalysed by environmentally benign organic acids and is illustrated by the generation of structures with biological activities ranging from cell signalling and inhibition of bacterial growth, to mimicking carbohydrate antigens of pathogenic microorganisms. The method is as applicable to fine chemicals as it is to industrial waste, for example, biotechnologically-derived d-allulose (d-psicose), or the waste products of biofermentation. Accessing this chemical space unlocks new functionalities, generating complex glycans with applications in the biological, medical, biotechnological and materials science arenas. Condensation of simple sugars provides new polysaccharides with diverse biological activities, expanding access to carbohydrate chemical space.![]()
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Affiliation(s)
- James Andrew London
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool Liverpool L69 7ZB UK
| | - Sarah Louise Taylor
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool Liverpool L69 7ZB UK
| | - Igor Barsukov
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool Liverpool L69 7ZB UK
| | - Alan Cartmell
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool Liverpool L69 7ZB UK
| | - Edwin Alexander Yates
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool Liverpool L69 7ZB UK
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12
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Malär AA, Callon M, Smith AA, Wang S, Lecoq L, Pérez-Segura C, Hadden-Perilla JA, Böckmann A, Meier BH. Experimental Characterization of the Hepatitis B Virus Capsid Dynamics by Solid-State NMR. Front Mol Biosci 2022; 8:807577. [PMID: 35047563 PMCID: PMC8762115 DOI: 10.3389/fmolb.2021.807577] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/06/2021] [Indexed: 01/14/2023] Open
Abstract
Protein plasticity and dynamics are important aspects of their function. Here we use solid-state NMR to experimentally characterize the dynamics of the 3.5 MDa hepatitis B virus (HBV) capsid, assembled from 240 copies of the Cp149 core protein. We measure both T1 and T1ρ relaxation times, which we use to establish detectors on the nanosecond and microsecond timescale. We compare our results to those from a 1 microsecond all-atom Molecular Dynamics (MD) simulation trajectory for the capsid. We show that, for the constituent residues, nanosecond dynamics are faithfully captured by the MD simulation. The calculated values can be used in good approximation for the NMR-non-detected residues, as well as to extrapolate into the range between the nanosecond and microsecond dynamics, where NMR has a blind spot at the current state of technology. Slower motions on the microsecond timescale are difficult to characterize by all-atom MD simulations owing to computational expense, but are readily accessed by NMR. The two methods are, thus, complementary, and a combination thereof can reliably characterize motions covering correlation times up to a few microseconds.
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Affiliation(s)
| | | | - Albert A Smith
- Institute of Medical Physics and Biophysics, Universität Leipzig, Leipzig, Germany
| | - Shishan Wang
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS-Université de Lyon, Labex Ecofect, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS-Université de Lyon, Labex Ecofect, Lyon, France
| | - Carolina Pérez-Segura
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Jodi A Hadden-Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS-Université de Lyon, Labex Ecofect, Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Zürich, Switzerland
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13
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Smith AA, Vogel A, Engberg O, Hildebrand PW, Huster D. A method to construct the dynamic landscape of a bio-membrane with experiment and simulation. Nat Commun 2022; 13:108. [PMID: 35013165 PMCID: PMC8748619 DOI: 10.1038/s41467-021-27417-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/11/2021] [Indexed: 11/16/2022] Open
Abstract
Biomolecular function is based on a complex hierarchy of molecular motions. While biophysical methods can reveal details of specific motions, a concept for the comprehensive description of molecular dynamics over a wide range of correlation times has been unattainable. Here, we report an approach to construct the dynamic landscape of biomolecules, which describes the aggregate influence of multiple motions acting on various timescales and on multiple positions in the molecule. To this end, we use 13C NMR relaxation and molecular dynamics simulation data for the characterization of fully hydrated palmitoyl-oleoyl-phosphatidylcholine bilayers. We combine dynamics detector methodology with a new frame analysis of motion that yields site-specific amplitudes of motion, separated both by type and timescale of motion. In this study, we show that this separation allows the detailed description of the dynamic landscape, which yields vast differences in motional amplitudes and correlation times depending on molecular position.
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Affiliation(s)
- Albert A Smith
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, 04107, Leipzig, Germany.
| | - Alexander Vogel
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, 04107, Leipzig, Germany
| | - Oskar Engberg
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, 04107, Leipzig, Germany
| | - Peter W Hildebrand
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, 04107, Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, 04107, Leipzig, Germany
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14
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Kikuchi J, Yamada S. The exposome paradigm to predict environmental health in terms of systemic homeostasis and resource balance based on NMR data science. RSC Adv 2021; 11:30426-30447. [PMID: 35480260 PMCID: PMC9041152 DOI: 10.1039/d1ra03008f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 08/31/2021] [Indexed: 12/22/2022] Open
Abstract
The environment, from microbial ecosystems to recycled resources, fluctuates dynamically due to many physical, chemical and biological factors, the profile of which reflects changes in overall state, such as environmental illness caused by a collapse of homeostasis. To evaluate and predict environmental health in terms of systemic homeostasis and resource balance, a comprehensive understanding of these factors requires an approach based on the "exposome paradigm", namely the totality of exposure to all substances. Furthermore, in considering sustainable development to meet global population growth, it is important to gain an understanding of both the circulation of biological resources and waste recycling in human society. From this perspective, natural environment, agriculture, aquaculture, wastewater treatment in industry, biomass degradation and biodegradable materials design are at the forefront of current research. In this respect, nuclear magnetic resonance (NMR) offers tremendous advantages in the analysis of samples of molecular complexity, such as crude bio-extracts, intact cells and tissues, fibres, foods, feeds, fertilizers and environmental samples. Here we outline examples to promote an understanding of recent applications of solution-state, solid-state, time-domain NMR and magnetic resonance imaging (MRI) to the complex evaluation of organisms, materials and the environment. We also describe useful databases and informatics tools, as well as machine learning techniques for NMR analysis, demonstrating that NMR data science can be used to evaluate the exposome in both the natural environment and human society towards a sustainable future.
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Affiliation(s)
- Jun Kikuchi
- Environmental Metabolic Analysis Research Team, RIKEN Center for Sustainable Resource Science 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
- Graduate School of Bioagricultural Sciences, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8601 Japan
- Graduate School of Medical Life Science, Yokohama City University 1-7-29 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
| | - Shunji Yamada
- Environmental Metabolic Analysis Research Team, RIKEN Center for Sustainable Resource Science 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
- Prediction Science Laboratory, RIKEN Cluster for Pioneering Research 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe 650-0047 Japan
- Data Assimilation Research Team, RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe 650-0047 Japan
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15
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Rahimi M, Lee Y, Markley JL, Lee W. iPick: Multiprocessing software for integrated NMR signal detection and validation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 328:106995. [PMID: 34004411 PMCID: PMC8767925 DOI: 10.1016/j.jmr.2021.106995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 05/12/2023]
Abstract
Peak picking is a critical step in biomolecular NMR spectroscopy. The program, iPick, presented here provides a scripting tool and a graphical user interface (GUI), which allow the user to perform interactive and intuitive peak picking and validation. The click-and-run GUI requires no computer programming skills, while the scripting tool can be used by more advanced users to customize the application. If used with a multi-core CPU, the multiprocessing feature of iPick reduces the processing time significantly by invoking parallel computing. The GUI is a plugin, compatible with the popular NMRFAM-SPARKY software package and its newly released successor, the POKY software. Features implemented in iPick include automated noise level detection and threshold setting, cross-validation against multiple spectra, and a method for quantifying peak reliability. The iPick software is cross-platform, open-source, and freely available from https://github.com/pokynmr/ipick.
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Affiliation(s)
- Mehdi Rahimi
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA.
| | - Yeongjoon Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA.
| | - John L Markley
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Woonghee Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA.
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16
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Signal Deconvolution and Generative Topographic Mapping Regression for Solid-State NMR of Multi-Component Materials. Int J Mol Sci 2021; 22:ijms22031086. [PMID: 33499371 PMCID: PMC7865946 DOI: 10.3390/ijms22031086] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/15/2021] [Accepted: 01/17/2021] [Indexed: 01/19/2023] Open
Abstract
Solid-state nuclear magnetic resonance (ssNMR) spectroscopy provides information on native structures and the dynamics for predicting and designing the physical properties of multi-component solid materials. However, such an analysis is difficult because of the broad and overlapping spectra of these materials. Therefore, signal deconvolution and prediction are great challenges for their ssNMR analysis. We examined signal deconvolution methods using a short-time Fourier transform (STFT) and a non-negative tensor/matrix factorization (NTF, NMF), and methods for predicting NMR signals and physical properties using generative topographic mapping regression (GTMR). We demonstrated the applications for macromolecular samples involved in cellulose degradation, plastics, and microalgae such as Euglena gracilis. During cellulose degradation, 13C cross-polarization (CP)-magic angle spinning spectra were separated into signals of cellulose, proteins, and lipids by STFT and NTF. GTMR accurately predicted cellulose degradation for catabolic products such as acetate and CO2. Using these methods, the 1H anisotropic spectrum of poly-ε-caprolactone was separated into the signals of crystalline and amorphous solids. Forward prediction and inverse prediction of GTMR were used to compute STFT-processed NMR signals from the physical properties of polylactic acid. These signal deconvolution and prediction methods for ssNMR spectra of macromolecules can resolve the problem of overlapping spectra and support macromolecular characterization and material design.
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17
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Wiegand T, Malär AA, Cadalbert R, Ernst M, Böckmann A, Meier BH. Asparagine and Glutamine Side-Chains and Ladders in HET-s(218-289) Amyloid Fibrils Studied by Fast Magic-Angle Spinning NMR. Front Mol Biosci 2020; 7:582033. [PMID: 33195425 PMCID: PMC7556116 DOI: 10.3389/fmolb.2020.582033] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
Asparagine and glutamine side-chains can form hydrogen-bonded ladders which contribute significantly to the stability of amyloid fibrils. We show, using the example of HET-s(218–289) fibrils, that the primary amide side-chain proton resonances can be detected in cross-polarization based solid-state NMR spectra at fast magic-angle spinning (MAS). J-coupling based experiments offer the possibility to distinguish them from backbone amide groups if the spin-echo lifetimes are long enough, which turned out to be the case for the glutamine side-chains, but not for the asparagine side-chains forming asparagine ladders. We explore the sensitivity of NMR observables to asparagine ladder formation. One of the two possible asparagine ladders in HET-s(218–289), the one comprising N226 and N262, is assigned by proton-detected 3D experiments at fast MAS and significant de-shielding of one of the NH2 proton resonances indicative of hydrogen-bond formation is observed. Small rotating-frame 15N relaxation-rate constants point to rigidified asparagine side-chains in this ladder. The proton resonances are homogeneously broadened which could indicate chemical exchange, but is presently not fully understood. The second asparagine ladder (N243 and N279) in contrast remains more flexible.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Alexander A Malär
- Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Riccardo Cadalbert
- Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Matthias Ernst
- Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, Lyon, France
| | - Beat H Meier
- Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
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18
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Dudley JA, Park S, MacDonald ME, Fetene E, Smith CA. Resolving overlapped signals with automated FitNMR analytical peak modeling. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 318:106773. [PMID: 32759043 DOI: 10.1016/j.jmr.2020.106773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
Nuclear magnetic resonance (NMR) is a valuable tool for determining the structures of molecules and probing their dynamics. A longstanding problem facing both small-molecule and macromolecular NMR is overlapped signals in crowded spectra. To address this, we have developed a method that extracts peak features by fitting analytically derived models of NMR lineshapes. The approach takes into account the effects of truncation, apodization, and the resulting artifacts, while avoiding systematic errors that have affected other models. Even severely overlapped peaks, beyond the point of coalescence, can be distinguished in both simulated and experimental data. We show that the method can measure unresolved backbone scalar couplings directly from a 2D proton-nitrogen spectrum of a de novo designed mini protein. The algorithm is implemented in the FitNMR open-source R package and can be used to analyze nearly any type of single or multidimensional data from small molecules or biomolecules.
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Affiliation(s)
- Joshua A Dudley
- Department of Chemistry, Wesleyan University, 52 Lawn Avenue, Middleton, CT 06459, USA
| | - Sojeong Park
- Department of Chemistry, Wesleyan University, 52 Lawn Avenue, Middleton, CT 06459, USA
| | - Meagan E MacDonald
- Department of Chemistry, Wesleyan University, 52 Lawn Avenue, Middleton, CT 06459, USA
| | - Emanual Fetene
- Department of Chemistry, Wesleyan University, 52 Lawn Avenue, Middleton, CT 06459, USA
| | - Colin A Smith
- Department of Chemistry, Wesleyan University, 52 Lawn Avenue, Middleton, CT 06459, USA.
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19
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Palhares LC, Brito AS, de Lima MA, Nader HB, London JA, Barsukov IL, Andrade GP, Yates EA, Chavante SF. A further unique chondroitin sulfate from the shrimp Litopenaeus vannamei with antithrombin activity that modulates acute inflammation. Carbohydr Polym 2019; 222:115031. [DOI: 10.1016/j.carbpol.2019.115031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/07/2019] [Accepted: 06/25/2019] [Indexed: 10/26/2022]
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20
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Malär AA, Smith-Penzel S, Camenisch GM, Wiegand T, Samoson A, Böckmann A, Ernst M, Meier BH. Quantifying proton NMR coherent linewidth in proteins under fast MAS conditions: a second moment approach. Phys Chem Chem Phys 2019; 21:18850-18865. [PMID: 31432055 DOI: 10.1039/c9cp03414e] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Proton detected solid-state NMR under fast magic-angle-spinning (MAS) conditions is currently redefining the applications of solid-state NMR, in particular in structural biology. Understanding the contributions to the spectral linewidth is thereby of paramount importance. When disregarding the sample-dependent inhomogeneous contributions, the NMR proton linewidth is defined by homogeneous broadening, which has incoherent and coherent contributions. Understanding and disentangling these different contributions in multi-spin systems like proteins is still an open issue. The coherent contribution is mainly caused by the dipolar interaction under MAS and is determined by the molecular structure and the proton chemical shifts. Numerical simulation approaches based on numerically exact direct integration of the Liouville-von Neumann equation can give valuable information about the lineshape, but are limited to small spin systems (<12 spins). We present an alternative simulation method for the coherent contributions based on the rapid and partially analytic calculation of the second moments of large spin systems. We first validate the method on a simple system by predicting the 19F linewidth in CaF2 under MAS. We compare simulation results to experimental data for microcrystalline ubiquitin (deuterated 100% back-exchanged at 110 kHz and fully-protonated at 125 kHz). Our results quantitatively explain the observed linewidth per-residue basis for the vast majority of residues.
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Affiliation(s)
- Alexander A Malär
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Susanne Smith-Penzel
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Gian-Marco Camenisch
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Thomas Wiegand
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Ago Samoson
- School of Information Technologies, Tallinn University of Technology, Tallinn, Estonia. and NMR Institute MTÜ, Tallinn, Estonia
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367 Lyon, France.
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
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21
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Matviychuk Y, Bostock MJ, Nietlispach D, Holland DJ. Time-domain signal modelling in multidimensional NMR experiments for estimation of relaxation parameters. JOURNAL OF BIOMOLECULAR NMR 2019; 73:93-104. [PMID: 31055682 DOI: 10.1007/s10858-018-00224-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/29/2018] [Indexed: 06/09/2023]
Abstract
We present a model-based method for estimation of relaxation parameters from time-domain NMR data specifically suitable for processing data in popular 2D phase-sensitive experiments. Our model is formulated in terms of commutative bicomplex algebra, which allows us to use the complete information available in an NMR signal acquired with principles of quadrature detection without disregarding any of its dimensions. Compared to the traditional intensity-analysis method, our model-based approach offers an important advantage for the analysis of overlapping peaks and is robust over a wide range of signal-to-noise ratios. We assess its performance with simulated experiments and then apply it for determination of [Formula: see text], [Formula: see text], and [Formula: see text] relaxation rates in datasets of a protein with more than 100 cross peaks.
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Affiliation(s)
- Yevgen Matviychuk
- Department of Chemical and Process Engineering, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Mark J Bostock
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Daniel J Holland
- Department of Chemical and Process Engineering, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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22
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Penzel S, Oss A, Org ML, Samoson A, Böckmann A, Ernst M, Meier BH. Spinning faster: protein NMR at MAS frequencies up to 126 kHz. JOURNAL OF BIOMOLECULAR NMR 2019; 73:19-29. [PMID: 30680507 PMCID: PMC6441448 DOI: 10.1007/s10858-018-0219-9] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 12/05/2018] [Indexed: 05/05/2023]
Abstract
We report linewidth and proton T1, T1ρ and T2' relaxation data of the model protein ubiquitin acquired at MAS frequencies up to 126 kHz. We find a predominantly linear improvement in linewidths and coherence decay times of protons with increasing spinning frequency in the range from 93 to 126 kHz. We further attempt to gain insight into the different contributions to the linewidth at fast MAS using site-specific analysis of proton relaxation parameters and present bulk relaxation times as a function of the MAS frequency. For microcrystalline fully-protonated ubiquitin, inhomogeneous contributions are only a minor part of the proton linewidth, and at 126 kHz MAS coherent effects are still dominating. We furthermore present site-specific proton relaxation rate constants during a spinlock at 126 kHz MAS, as well as MAS-dependent bulk T1ρ (1HN).
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Affiliation(s)
- Susanne Penzel
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Andres Oss
- NMR Instituut, Tartu Teaduspark, Tehnomeedikum, Tallinn University of Technology, Akadeemia tee 15a, 19086, Tallinn, Estonia
| | - Mai-Liis Org
- NMR Instituut, Tartu Teaduspark, Tehnomeedikum, Tallinn University of Technology, Akadeemia tee 15a, 19086, Tallinn, Estonia
| | - Ago Samoson
- NMR Instituut, Tartu Teaduspark, Tehnomeedikum, Tallinn University of Technology, Akadeemia tee 15a, 19086, Tallinn, Estonia.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, Labex ECOFECT, 7, Passage du Vercors, 69367, Lyon, France.
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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23
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Penzel S, Smith AA, Ernst M, Meier BH. Setting the magic angle for fast magic-angle spinning probes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 293:115-122. [PMID: 29929181 DOI: 10.1016/j.jmr.2018.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
Fast magic-angle spinning, coupled with 1H detection is a powerful method to improve spectral resolution and signal to noise in solid-state NMR spectra. Commercial probes now provide spinning frequencies in excess of 100 kHz. Then, one has sufficient resolution in the 1H dimension to directly detect protons, which have a gyromagnetic ratio approximately four times larger than 13C spins. However, the gains in sensitivity can quickly be lost if the rotation angle is not set precisely. The most common method of magic-angle calibration is to optimize the number of rotary echoes, or sideband intensity, observed on a sample of KBr. However, this typically uses relatively low spinning frequencies, where the spinning of fast-MAS probes is often unstable, and detection on the 13C channel, for which fast-MAS probes are typically not optimized. Therefore, we compare the KBr-based optimization of the magic angle with two alternative approaches: optimization of the splitting observed in 13C-labeled glycine-ethylester on the carbonyl due to the Cα-C' J-coupling, or optimization of the H-N J-coupling spin echo in the protein sample itself. The latter method has the particular advantage that no separate sample is necessary for the magic-angle optimization.
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Affiliation(s)
- Susanne Penzel
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Albert A Smith
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Matthias Ernst
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Beat H Meier
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
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24
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Lapin J, Nevzorov AA. Automated assignment of NMR spectra of macroscopically oriented proteins using simulated annealing. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 293:104-114. [PMID: 29920407 DOI: 10.1016/j.jmr.2018.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/06/2018] [Accepted: 06/07/2018] [Indexed: 06/08/2023]
Abstract
An automated technique for the sequential assignment of NMR backbone resonances of oriented protein samples has been developed and tested based on 15N-15N homonuclear exchange and spin-exchanged separated local-field spectra. By treating the experimental spectral intensity as a pseudopotential, the Monte-Carlo Simulated Annealing algorithm has been employed to seek lowest-energy assignment solutions over a large sampling space where direct enumeration would be unfeasible. The determined sequential assignments have been scored based on the positions of the crosspeaks resulting from the possible orders for the main peaks. This approach is versatile in terms of the parameters that can be specified to achieve the best-fit result. At a minimum the algorithm requires a continuous segment of the main-peak chemical shifts obtained from a uniformly labeled sample and a spin-exchanged experimental spectrum represented as a 2D matrix array. With selective labeling experiments, groups of chemical shifts corresponding to specific locations in the protein backbone can be fixed, thereby decreasing the sampling space. The output from the program consists of a list of top-score main peak assignments, which can be subjected to further scoring criteria until a consensus solution is found. The algorithm has first been tested on a synthetic spectrum with randomly generated chemical shifts and dipolar couplings for the main peaks. The original assignments have been successfully recovered for as many as 100 main peaks when residue-type information was used even in the presence of substantial spectral peak overlap. The algorithm was then applied to assigning two sets of experimental spectra to recover and confirm the previously established assignments in an automated fashion. For the 20-residue transmembrane domain of Pf1 coat protein reconstituted in magnetically aligned bicelles, the original assignment by Park et al. (2010) was recovered by the automated algorithm with additional input from 5 selectively labeled amino acid spectra. The second case considered was the 46 residue Pf1 bacteriophage from Thiriot et al. (2005) and Knox et al. (2010), of which 38 residues were fit. Automated fitting resulted in several possible assignments but not exactly the original assignment. By using a post-fitting filtering procedure based on the number of missed cross peaks and Pf1 helical structure, a consensus spectroscopic assignment is proposed covering 84% of the original assignment. While the automated assignment works best in spectra with well-resolved crosspeaks, it also tolerates substantial spectral crowding to yield reasonable assignments in the cases where ambiguity and degeneracy of possible assignment solutions are inevitable.
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Affiliation(s)
- Joel Lapin
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States.
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