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Chow WY, De Paëpe G, Hediger S. Biomolecular and Biological Applications of Solid-State NMR with Dynamic Nuclear Polarization Enhancement. Chem Rev 2022; 122:9795-9847. [PMID: 35446555 DOI: 10.1021/acs.chemrev.1c01043] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Solid-state NMR spectroscopy (ssNMR) with magic-angle spinning (MAS) enables the investigation of biological systems within their native context, such as lipid membranes, viral capsid assemblies, and cells. However, such ambitious investigations often suffer from low sensitivity due to the presence of significant amounts of other molecular species, which reduces the effective concentration of the biomolecule or interaction of interest. Certain investigations requiring the detection of very low concentration species remain unfeasible even with increasing experimental time for signal averaging. By applying dynamic nuclear polarization (DNP) to overcome the sensitivity challenge, the experimental time required can be reduced by orders of magnitude, broadening the feasible scope of applications for biological solid-state NMR. In this review, we outline strategies commonly adopted for biological applications of DNP, indicate ongoing challenges, and present a comprehensive overview of biological investigations where MAS-DNP has led to unique insights.
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Affiliation(s)
- Wing Ying Chow
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France.,Univ. Grenoble Alpes, CEA, CNRS, Inst. Biol. Struct. IBS, 38044 Grenoble, France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
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Fleckenstein M, Herr K, Theiß F, Knecht S, Wienands L, Brodrecht M, Reggelin M, Buntkowsky G. A disintegrin derivative as a case study for PHIP labeling of disulfide bridged biomolecules. Sci Rep 2022; 12:2337. [PMID: 35149768 PMCID: PMC8837631 DOI: 10.1038/s41598-022-06327-z] [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] [Received: 11/01/2021] [Accepted: 01/25/2022] [Indexed: 01/08/2023] Open
Abstract
A specific labeling strategy for bioactive molecules is presented for eptifibatide (integrilin) an antiplatelet aggregation inhibitor, which derives from the disintegrin protein barbourin in the venom of certain rattlesnakes. By specifically labeling the disulfide bridge this molecule becomes accessible for the nuclear spin hyperpolarization method of parahydrogen induced polarization (PHIP). The PHIP-label was synthesized and inserted into the disulfide bridge of eptifibatide via reduction of the peptide and insertion by a double Michael addition under physiological conditions. This procedure is universally applicable for disulfide-containing biomolecules and preserves their tertiary structure with a minimum of change. HPLC and MS spectra prove the successful insertion of the label. 1H-PHIP-NMR experiments yield a factor of over 1000 as lower limit for the enhancement factor. These results demonstrate the high potential of the labeling strategy for the introduction of site selective PHIP-labels into biomolecules’ disulfide bonds.
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Affiliation(s)
- Max Fleckenstein
- Institute of Organic Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Kevin Herr
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Franziska Theiß
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Stephan Knecht
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Laura Wienands
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Martin Brodrecht
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Michael Reggelin
- Institute of Organic Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany.
| | - Gerd Buntkowsky
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany.
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Herr K, Fleckenstein M, Brodrecht M, Höfler MV, Heise H, Aussenac F, Gutmann T, Reggelin M, Buntkowsky G. A novel strategy for site selective spin-labeling to investigate bioactive entities by DNP and EPR spectroscopy. Sci Rep 2021; 11:13714. [PMID: 34211027 PMCID: PMC8249612 DOI: 10.1038/s41598-021-92975-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/18/2021] [Indexed: 11/09/2022] Open
Abstract
A novel specific spin-labeling strategy for bioactive molecules is presented for eptifibatide (integrilin) an antiplatelet aggregation inhibitor, which derives from the venom of certain rattlesnakes. By specifically labeling the disulfide bridge this molecule becomes accessible for analytical techniques such as Electron Paramagnetic Resonance (EPR) and solid state Dynamic Nuclear Polarization (DNP). The necessary spin-label was synthesized and inserted into the disulfide bridge of eptifibatide via reductive followed by insertion by a double Michael addition under physiological conditions. This procedure is universally applicable for disulfide containing biomolecules and is expected to preserve their tertiary structure with minimal change due to the small size of the label and restoring of the previous disulfide connection. HPLC and MS analysis show the successful introduction of the spin label and EPR spectroscopy confirms its activity. DNP-enhanced solid state NMR experiments show signal enhancement factors of up to 19 in 13C CP MAS experiments which corresponds to time saving factors of up to 361. This clearly shows the high potential of our new spin labeling strategy for the introduction of site selective radical spin labels into biomolecules and biosolids without compromising its conformational integrity for structural investigations employing solid-state DNP or advanced EPR techniques.
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Affiliation(s)
- Kevin Herr
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Max Fleckenstein
- Institute of Organic Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Martin Brodrecht
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Mark V Höfler
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Henrike Heise
- Structural Biochemistry (ICS-6), Institute of Complex Systems, Forschungszentrum Jülich, 52425, Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Fabien Aussenac
- Bruker France SAS, 34 rue de l'industrie, 67160, Wissembourg, France
| | - Torsten Gutmann
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Michael Reggelin
- Institute of Organic Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany.
| | - Gerd Buntkowsky
- Institute of Physical Chemistry, Technical University Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany.
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Gauto D, Dakhlaoui O, Marin-Montesinos I, Hediger S, De Paëpe G. Targeted DNP for biomolecular solid-state NMR. Chem Sci 2021; 12:6223-6237. [PMID: 34084422 PMCID: PMC8115112 DOI: 10.1039/d0sc06959k] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/18/2021] [Indexed: 12/23/2022] Open
Abstract
High-field dynamic nuclear polarization is revolutionizing the scope of solid-state NMR with new applications in surface chemistry, materials science and structural biology. In this perspective article, we focus on a specific DNP approach, called targeted DNP, in which the paramagnets introduced to polarize are not uniformly distributed in the sample but site-specifically located on the biomolecular system. After reviewing the various targeting strategies reported to date, including a bio-orthogonal chemistry-based approach, we discuss the potential of targeted DNP to improve the overall NMR sensitivity while avoiding the use of glass-forming DNP matrix. This is especially relevant to the study of diluted biomolecular systems such as, for instance, membrane proteins within their lipidic environment. We also discuss routes towards extracting structural information from paramagnetic relaxation enhancement (PRE) induced by targeted DNP at cryogenic temperature, and the possibility to recover site-specific information in the vicinity of the paramagnetic moieties using high-resolution selective DNP spectra. Finally, we review the potential of targeted DNP for in-cell NMR studies and how it can be used to extract a given protein NMR signal from a complex cellular background.
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Affiliation(s)
- Diego Gauto
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
| | - Ons Dakhlaoui
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
- Univ. Grenoble Alpes, CNRS, CERMAV Grenoble France
| | - Ildefonso Marin-Montesinos
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
- University of Aveiro, CICECO Chem. Dept. Aveiro Portugal
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
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Buntkowsky G, Vogel M. Small Molecules, Non-Covalent Interactions, and Confinement. Molecules 2020; 25:E3311. [PMID: 32708283 PMCID: PMC7397022 DOI: 10.3390/molecules25143311] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/07/2020] [Accepted: 07/15/2020] [Indexed: 11/27/2022] Open
Abstract
This review gives an overview of current trends in the investigation of small guest molecules, confined in neat and functionalized mesoporous silica materials by a combination of solid-state NMR and relaxometry with other physico-chemical techniques. The reported guest molecules are water, small alcohols, and carbonic acids, small aromatic and heteroaromatic molecules, ionic liquids, and surfactants. They are taken as characteristic role-models, which are representatives for the typical classes of organic molecules. It is shown that this combination delivers unique insights into the structure, arrangement, dynamics, guest-host interactions, and the binding sites in these confined systems, and is probably the most powerful analytical technique to probe these systems.
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Affiliation(s)
- Gerd Buntkowsky
- Institut für Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Michael Vogel
- Institut für Festkörperphysik, Technische Universität Darmstadt, 64295 Darmstadt, Germany
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Vuong W, Mosquera-Guagua F, Sanichar R, McDonald TR, Ernst OP, Wang L, Vederas JC. Synthesis of Chiral Spin-Labeled Amino Acids. Org Lett 2019; 21:10149-10153. [DOI: 10.1021/acs.orglett.9b04216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wayne Vuong
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | | | - Randy Sanichar
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Tyler R. McDonald
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Oliver P. Ernst
- Departments of Biochemistry & Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Lei Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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