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      Room-temperature dynamic nuclear polarization enhanced NMR spectroscopy of small biological molecules in water

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          Abstract

          Nuclear magnetic resonance (NMR) spectroscopy is a powerful and popular technique for probing the molecular structures, dynamics and chemical properties. However the conventional NMR spectroscopy is bottlenecked by its low sensitivity. Dynamic nuclear polarization (DNP) boosts NMR sensitivity by orders of magnitude and resolves this limitation. In liquid-state this revolutionizing technique has been restricted to a few specific non-biological model molecules in organic solvents. Here we show that the carbon polarization in small biological molecules, including carbohydrates and amino acids, can be enhanced sizably by in situ Overhauser DNP (ODNP) in water at room temperature and at high magnetic field. An observed connection between ODNP 13C enhancement factor and paramagnetic 13C NMR shift has led to the exploration of biologically relevant heterocyclic compound indole. The QM/MM MD simulation underscores the dynamics of intermolecular hydrogen bonds as the driving force for the scalar ODNP in a long-living radical-substrate complex. Our work reconciles results obtained by DNP spectroscopy, paramagnetic NMR and computational chemistry and provides new mechanistic insights into the high-field scalar ODNP.

          Abstract

          Dynamic nuclear polarization (DNP) greatly improves the NMR sensitivity, but its implementation in aqueous solutions is challenging. Here the authors demonstrate carbon polarization enhancement via in situ Overhauser DNP in small biomolecules in water at room temperature and high magnetic field.

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          • Record: found
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          Circos: an information aesthetic for comparative genomics.

          We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.
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            Development and testing of a general amber force field.

            We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 A, which is comparable to that of the Tripos 5.2 force field (0.25 A) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 A, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 A and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 A and 1.18 kcal/mol, respectively), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching. Copyright 2004 Wiley Periodicals, Inc.
              Bookmark
              • Record: found
              • Abstract: not found
              • Article: not found

              The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals

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                Author and article information

                Contributors
                xiaohe@phy.ecnu.edu.cn
                j.mao@em.uni-frankfurt.de
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                25 November 2021
                25 November 2021
                2021
                : 12
                : 6880
                Affiliations
                [1 ]GRID grid.7839.5, ISNI 0000 0004 1936 9721, Institute of Physical and Theoretical Chemistry, , Goethe University Frankfurt, ; 60438 Frankfurt am Main, Germany
                [2 ]GRID grid.7839.5, ISNI 0000 0004 1936 9721, Center for Biomolecular Magnetic Resonance, , Goethe University Frankfurt, ; 60438 Frankfurt am Main, Germany
                [3 ]GRID grid.22069.3f, ISNI 0000 0004 0369 6365, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, , East China Normal University, ; Shanghai, 200062 China
                [4 ]GRID grid.469325.f, ISNI 0000 0004 1761 325X, College of Science, , Zhejiang University of Technology, ; Hangzhou, Zhejiang 310023 China
                [5 ]GRID grid.41156.37, ISNI 0000 0001 2314 964X, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, , Nanjing University, ; Nanjing, 210023 China
                [6 ]GRID grid.41156.37, ISNI 0000 0001 2314 964X, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, , Nanjing University, ; Nanjing, 210023 China
                [7 ]GRID grid.7839.5, ISNI 0000 0004 1936 9721, Institute of Biophysical Chemistry, , Goethe University Frankfurt, ; 60438 Frankfurt am Main, Germany
                [8 ]GRID grid.449457.f, ISNI 0000 0004 5376 0118, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, ; Shanghai, 200062 China
                Author information
                http://orcid.org/0000-0003-4471-426X
                http://orcid.org/0000-0002-8812-6163
                http://orcid.org/0000-0002-3554-6586
                http://orcid.org/0000-0002-4199-8175
                http://orcid.org/0000-0003-2850-9573
                http://orcid.org/0000-0003-1547-325X
                Article
                27067
                10.1038/s41467-021-27067-0
                8616939
                34824218
                8fb41cc6-cb24-4421-a763-98eb515b23fe
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 3 March 2021
                : 1 November 2021
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100004543, China Scholarship Council (CSC);
                Funded by: FundRef https://doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft (German Research Foundation);
                Award ID: GL 307/12-1
                Award ID: 405972957
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100001809, National Natural Science Foundation of China (National Science Foundation of China);
                Award ID: 21922301
                Award ID: 21673074
                Award Recipient :
                Categories
                Article
                Custom metadata
                © The Author(s) 2021

                Uncategorized
                biophysical chemistry,analytical chemistry,theoretical chemistry
                Uncategorized
                biophysical chemistry, analytical chemistry, theoretical chemistry

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