1
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Cerofolini L, Parigi G, Ravera E, Fragai M, Luchinat C. Solid-state NMR methods for the characterization of bioconjugations and protein-material interactions. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101828. [PMID: 36240720 DOI: 10.1016/j.ssnmr.2022.101828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Protein solid-state NMR has evolved dramatically over the last two decades, with the development of new hardware and sample preparation methodologies. This technique is now ripe for complex applications, among which one can count bioconjugation, protein chemistry and functional biomaterials. In this review, we provide our account on this aspect of protein solid-state NMR.
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Affiliation(s)
- Linda Cerofolini
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy; Florence Data Science, Università degli Studi di Firenze, Italy.
| | - Marco Fragai
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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2
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Bruno F, Gigli L, Ferraro G, Cavallo A, Michaelis VK, Goobes G, Fratini E, Ravera E. Lysozyme is Sterically Trapped Within the Silica Cage in Bioinspired Silica-Lysozyme Composites: A Multi-Technique Understanding of Elusive Protein-Material Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8030-8037. [PMID: 35738569 PMCID: PMC9261187 DOI: 10.1021/acs.langmuir.2c00836] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Lysozyme is widely known to promote the formation of condensed silica networks from solutions containing silicic acid, in a reproducible and cost-effective way. However, little is known about the fate of the protein after the formation of the silica particles. Also, the relative arrangement of the different components in the resulting material is a matter of debate. In this study, we investigate the nature of the protein-silica interactions by means of solid-state nuclear magnetic resonance spectroscopy, small-angle X-ray scattering, and electron microscopy. We find that lysozyme and silica are in intimate contact and strongly interacting, but their interaction is neither covalent nor electrostatic: lysozyme is mostly trapped inside the silica by steric effects.
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Affiliation(s)
- Francesco Bruno
- Magnetic
Resonance Center (CERM), University of Florence, via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Lucia Gigli
- Magnetic
Resonance Center (CERM), University of Florence, via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Giovanni Ferraro
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
- Consorzio
per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia, 3, Sesto Fiorentino 50019, Italy
| | - Andrea Cavallo
- CERTEMA
S.c.a.r.l., S.P. Del
Cipressino Km 10, Cinigiano 58044, Italy
| | | | - Gil Goobes
- Department
of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Emiliano Fratini
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
- Consorzio
per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia, 3, Sesto Fiorentino 50019, Italy
| | - Enrico Ravera
- Magnetic
Resonance Center (CERM), University of Florence, via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, Sesto Fiorentino 50019, Italy
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3
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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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4
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Biedenbänder T, Aladin V, Saeidpour S, Corzilius B. Dynamic Nuclear Polarization for Sensitivity Enhancement in Biomolecular Solid-State NMR. Chem Rev 2022; 122:9738-9794. [PMID: 35099939 DOI: 10.1021/acs.chemrev.1c00776] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Solid-state NMR with magic-angle spinning (MAS) is an important method in structural biology. While NMR can provide invaluable information about local geometry on an atomic scale even for large biomolecular assemblies lacking long-range order, it is often limited by low sensitivity due to small nuclear spin polarization in thermal equilibrium. Dynamic nuclear polarization (DNP) has evolved during the last decades to become a powerful method capable of increasing this sensitivity by two to three orders of magnitude, thereby reducing the valuable experimental time from weeks or months to just hours or days; in many cases, this allows experiments that would be otherwise completely unfeasible. In this review, we give an overview of the developments that have opened the field for DNP-enhanced biomolecular solid-state NMR including state-of-the-art applications at fast MAS and high magnetic field. We present DNP mechanisms, polarizing agents, and sample constitution methods suitable for biomolecules. A wide field of biomolecular NMR applications is covered including membrane proteins, amyloid fibrils, large biomolecular assemblies, and biomaterials. Finally, we present perspectives and recent developments that may shape the field of biomolecular DNP in the future.
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Affiliation(s)
- Thomas Biedenbänder
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Victoria Aladin
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Siavash Saeidpour
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Björn Corzilius
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
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5
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Sergeyev IV, Quinn CM, Struppe J, Gronenborn A, Polenova T. Competing Transfer Pathways in Direct and Indirect Dynamic Nuclear Polarization MAS NMR Experiments on HIV-1 Capsid Assemblies: Implications for Sensitivity and Resolution. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:239-249. [PMID: 34136885 PMCID: PMC8203495 DOI: 10.5194/mr-2-239-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/23/2021] [Indexed: 04/25/2023]
Abstract
Dynamic nuclear polarization-enhanced (DNP) magic angle spinning (MAS) NMR of biological systems is a rapidly growing field. Large signal enhancements make the technique particularly attractive for signal-limited cases, such as studies of complex biological assemblies or at natural isotopic abundance. However, spectral resolution is considerably reduced compared to ambient-temperature non-DNP spectra. Herein, we report a systematic investigation into sensitivity and resolution of 1D and 2D 13C-detected DNP MAS NMR experiments on HIV-1 CA tubular assemblies. We show that the magnitude and sign of signal enhancement as well as the homogeneous line width are strongly dependent on the biradical concentration, the dominant polarization transfer pathway, and the enhancement buildup time. Our findings provide guidance for optimal choice of sample preparation and experimental conditions in DNP experiments.
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Affiliation(s)
- Ivan V. Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States
| | - Caitlin M. Quinn
- Department of Chemistry and Biochemistry, University of Delaware,
Newark, DE 19716, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of
Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth
Avenue, Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware,
Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of
Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth
Avenue, Pittsburgh, PA 15261, United States
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6
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Shafiei N, Nasrollahzadeh M, Iravani S. Green Synthesis of Silica and Silicon Nanoparticles and Their Biomedical and Catalytic Applications. COMMENT INORG CHEM 2021. [DOI: 10.1080/02603594.2021.1904912] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Nasrin Shafiei
- Department of Chemistry, Faculty of Science, University of Qom, Qom, Iran
| | | | - Siavash Iravani
- Faculty of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
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7
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Gigli L, Ravera E, Calderone V, Luchinat C. On the Mechanism of Bioinspired Formation of Inorganic Oxides: Structural Evidence of the Electrostatic Nature of the Interaction between a Mononuclear Inorganic Precursor and Lysozyme. Biomolecules 2020; 11:43. [PMID: 33396930 PMCID: PMC7823628 DOI: 10.3390/biom11010043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 12/31/2022] Open
Abstract
Nature has evolved several molecular machineries to promote the formation at physiological conditions of inorganic materials, which would otherwise be formed in extreme conditions. The molecular determinants of this process have been established over the last decade, identifying a strong role of electrostatics in the first steps of the precipitation. However, no conclusive, structure-based evidence has been provided so far. In this manuscript, we test the binding of lysozyme with silica and titania potential precursors. In contrast with the absence of structural information about the interaction with the silica precursor, we observe the interaction with a mononuclear titanium(IV) species, which is found to occur in a region rich of positive charges.
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Affiliation(s)
- Lucia Gigli
- Magnetic Resonance Center (CERM)/Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (L.G.); (C.L.)
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, 50019 Florence, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM)/Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (L.G.); (C.L.)
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, 50019 Florence, Italy
| | - Vito Calderone
- Magnetic Resonance Center (CERM)/Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (L.G.); (C.L.)
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, 50019 Florence, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM)/Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (L.G.); (C.L.)
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, 50019 Florence, Italy
- CNR ICCOM, Sesto Fiorentino, 50019 Florence, Italy
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8
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Montagna M, Brückner SI, Dianat A, Gutierrez R, Daus F, Geyer A, Brunner E, Cuniberti G. Interactions of Long-Chain Polyamines with Silica Studied by Molecular Dynamics Simulations and Solid-State NMR Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:11600-11609. [PMID: 32924496 DOI: 10.1021/acs.langmuir.0c02157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The investigation of molecular interactions between silica phases and organic components is crucial for elucidating the main steps involved in the biosilica mineralization process. In this respect, the structural characterization of the organic/inorganic interface is particularly useful for a deeper understanding of the dominant mechanisms of biomineralization. In this work, we have investigated the interaction of selectively 13C- and 15N-labeled atoms of organic long-chain polyamines (LCPAs) with 29Si-labeled atoms of a silica layer at the molecular level. In particular, silica/LCPA nanocomposites were analyzed by solid-state NMR spectroscopy in combination with all-atom molecular dynamics simulations. Solid-state NMR experiments allow the determination of 29Si-15N and 29Si-13C internuclear distances, providing the parameters for direct verification of atomistic simulations. Our results elucidate the relevant molecular conformations as well as the nature of the interaction between the LCPA and a silica substrate. Specifically, distances and second moments suggest a picture compatible with (i) LCPA completely embedded in the silica phase and (ii) the charged amino groups located in close vicinity of silanol groups.
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Affiliation(s)
- Maria Montagna
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062 Dresden, Germany
| | - Stephan Ingmar Brückner
- Chair of Bioanalytical Chemistry, Faculty of Chemistry and Food Chemistry, TU Dresden, 01062 Dresden, Germany
| | - Arezoo Dianat
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062 Dresden, Germany
| | - Rafael Gutierrez
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062 Dresden, Germany
| | - Fabian Daus
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Armin Geyer
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Eike Brunner
- Chair of Bioanalytical Chemistry, Faculty of Chemistry and Food Chemistry, TU Dresden, 01062 Dresden, Germany
| | - Gianaurelio Cuniberti
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062 Dresden, Germany
- Dresden Center for Computational Materials Science, TU Dresden, 01062 Dresden, Germany
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9
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Bruno F, Francischello R, Bellomo G, Gigli L, Flori A, Menichetti L, Tenori L, Luchinat C, Ravera E. Multivariate Curve Resolution for 2D Solid-State NMR spectra. Anal Chem 2020; 92:4451-4458. [PMID: 32069028 PMCID: PMC7997113 DOI: 10.1021/acs.analchem.9b05420] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We present a processing method, based on the multivariate curve resolution approach (MCR), to denoise 2D solid-state NMR spectra, yielding a substantial S/N ratio increase while preserving the lineshapes and relative signal intensities. These spectral features are particularly important in the quantification of silicon species, where sensitivity is limited by the low natural abundance of the 29Si nuclei and by the dilution of the intrinsic protons of silica, but can be of interest also when dealing with other intermediate-to-low receptivity nuclei. This method also offers the possibility of coprocessing multiple 2D spectra that have the signals at the same frequencies but with different intensities (e.g.: as a result of a variation in the mixing time). The processing can be carried out on the time-domain data, thus preserving the possibility of applying further processing to the data. As a demonstration, we have applied Cadzow denoising on the MCR-processed FIDs, achieving a further increase in the S/N ratio and more effective denoising also on the transients at longer indirect evolution times. We have applied the combined denoising on a set of experimental data from a lysozyme-silica composite.
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Affiliation(s)
- Francesco Bruno
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Roberto Francischello
- Institute of Clinical Physiology, National Research Council, Via G. Moruzzi, 1 56124 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Giovanni Bellomo
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Alessandra Flori
- Fondazione Regione Toscana G. Monasterio, Via G. Moruzzi 1, Pisa 56124, Italy
| | - Luca Menichetti
- Institute of Clinical Physiology, National Research Council, Via G. Moruzzi, 1 56124 Pisa, Italy.,Fondazione Regione Toscana G. Monasterio, Via G. Moruzzi 1, Pisa 56124, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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10
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Papi F, Targetti G, Cerofolini L, Luchinat C, Fragai M, Nativi C. Nanoparticles for the multivalent presentation of a TnThr mimetic and as tool for solid state NMR coating investigation. PURE APPL CHEM 2019. [DOI: 10.1515/pac-2019-0210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Abstract
The fully characterization of tumor associated antigens (TAAs) and of tumor associated carbohydrate antigens (TACAs) have opened the avenue of cancer immunotherapy. The intrinsic poor immunogenicity of TACAs, however, spotlighted the importance of multivalent presentation of the antigen(s) to trigger an immune response. Nanoparticles are excellent scaffolds for this purpose. Here we reported on the easy glycosylation of iron-based and biocompatible dextran-based nanoparticles with 1, a mimetic of the TnThr antigen. The multivalent presentation of 1 induced the induction of TNF-α and IL-6/IL10, respectively. The multivalent glycosylation of silica nanoparticles (GSiNPs) was also performed and saccharide loading qualitative assessed by solid state NMR. Our results offer the proof of concept that biomolecules coating can also be investigated on solid system by NMR.
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Affiliation(s)
- Francesco Papi
- Dipartimento di Chimica , University of Florence , via della Lastruccia , 3,13 – 50019 Sesto F.no (FI) , Italy
| | - Giulia Targetti
- Dipartimento di Chimica , University of Florence , via della Lastruccia , 3,13 – 50019 Sesto F.no (FI) , Italy
| | - Linda Cerofolini
- CERM, University of Florence , via L. Sacconi , 6 – 50019 Sesto F.no (FI) , Italy
| | - Claudio Luchinat
- Dipartimento di Chimica , University of Florence , via della Lastruccia , 3,13 – 50019 Sesto F.no (FI) , Italy
- CERM, University of Florence , via L. Sacconi , 6 – 50019 Sesto F.no (FI) , Italy
| | - Marco Fragai
- Dipartimento di Chimica , University of Florence , via della Lastruccia , 3,13 – 50019 Sesto F.no (FI) , Italy
- CERM, University of Florence , via L. Sacconi , 6 – 50019 Sesto F.no (FI) , Italy
| | - Cristina Nativi
- Dipartimento di Chimica , University of Florence , via della Lastruccia , 3,13 – 50019 Sesto F.no (FI) , Italy
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11
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Cerofolini L, Giuntini S, Ravera E, Luchinat C, Berti F, Fragai M. Structural characterization of a protein adsorbed on aluminum hydroxide adjuvant in vaccine formulation. NPJ Vaccines 2019; 4:20. [PMID: 31149351 PMCID: PMC6538755 DOI: 10.1038/s41541-019-0115-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 05/03/2019] [Indexed: 12/11/2022] Open
Abstract
The heterogeneous composition of vaccine formulations and the relatively low concentration make the characterization of the protein antigens extremely challenging. Aluminum-containing adjuvants have been used to enhance the immune response of several antigens over the last 90 years and still remain the most commonly used. Here, we show that solid-state NMR and isotope labeling methods can be used to characterize the structural features of the protein antigen component of vaccines and to investigate the preservation of the folding state of proteins adsorbed on Alum hydroxide matrix, providing the way to identify the regions of the protein that are mainly affected by the presence of the inorganic matrix. l-Asparaginase from E. coli has been used as a pilot model of protein antigen. This methodology can find application in several steps of the vaccine development pipeline, from the antigen optimization, through the design of vaccine formulation, up to stability studies and manufacturing process.
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Affiliation(s)
- Linda Cerofolini
- 1Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Stefano Giuntini
- 2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- 1Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- 1Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Francesco Berti
- Technical R&D, GSK Vaccines, Via Fiorentina 1, 53100 Siena, Italy
| | - Marco Fragai
- 1Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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12
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Lu M, Wang M, Sergeyev IV, Quinn CM, Struppe J, Rosay M, Maas W, Gronenborn AM, Polenova T. 19F Dynamic Nuclear Polarization at Fast Magic Angle Spinning for NMR of HIV-1 Capsid Protein Assemblies. J Am Chem Soc 2019; 141:5681-5691. [PMID: 30871317 PMCID: PMC6521953 DOI: 10.1021/jacs.8b09216] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report remarkably high, up to 100-fold, signal enhancements in 19F dynamic nuclear polarization (DNP) magic angle spinning (MAS) spectra at 14.1 T on HIV-1 capsid protein (CA) assemblies. These enhancements correspond to absolute sensitivity ratios of 12-29 and are of similar magnitude to those seen for 1H signals in the same samples. At MAS frequencies above 20 kHz, it was possible to record 2D 19F-13C HETCOR spectra, which contain long-range intra- and intermolecular correlations. Such correlations provide unique distance restraints, inaccessible in conventional experiments without DNP, for protein structure determination. Furthermore, systematic quantification of the DNP enhancements as a function of biradical concentration, MAS frequency, temperature, and microwave power is reported. Our work establishes the power of DNP-enhanced 19F MAS NMR spectroscopy for structural characterization of HIV-1 CA assemblies, and this approach is anticipated to be applicable to a wide range of large biomolecular systems.
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Affiliation(s)
- Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Ivan V. Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Caitlin M. Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Melanie Rosay
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Werner Maas
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
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13
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Jaudzems K, Polenova T, Pintacuda G, Oschkinat H, Lesage A. DNP NMR of biomolecular assemblies. J Struct Biol 2018; 206:90-98. [PMID: 30273657 DOI: 10.1016/j.jsb.2018.09.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/13/2018] [Accepted: 09/27/2018] [Indexed: 11/30/2022]
Abstract
Dynamic Nuclear Polarization (DNP) is an effective approach to alleviate the inherently low sensitivity of solid-state NMR (ssNMR) under magic angle spinning (MAS) towards large-sized multi-domain complexes and assemblies. DNP relies on a polarization transfer at cryogenic temperatures from unpaired electrons to adjacent nuclei upon continuous microwave irradiation. This is usually made possible via the addition in the sample of a polarizing agent. The first pioneering experiments on biomolecular assemblies were reported in the early 2000s on bacteriophages and membrane proteins. Since then, DNP has experienced tremendous advances, with the development of extremely efficient polarizing agents or with the introduction of new microwaves sources, suitable for NMR experiments at very high magnetic fields (currently up to 900 MHz). After a brief introduction, several experimental aspects of DNP enhanced NMR spectroscopy applied to biomolecular assemblies are discussed. Recent demonstration experiments of the method on viral capsids, the type III and IV bacterial secretion systems, ribosome and membrane proteins are then described.
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Affiliation(s)
- Kristaps Jaudzems
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, 163 The Green, DE 19716, USA
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Hartmut Oschkinat
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP), Campus Berlin-Buch Robert-Roessle-Str. 10 13125 Berlin, Germany
| | - Anne Lesage
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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14
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Varghese S, Halling PJ, Häussinger D, Wimperis S. Two-dimensional 1H and 1H-detected NMR study of a heterogeneous biocatalyst using fast MAS at high magnetic fields. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2018; 92:7-11. [PMID: 29587153 DOI: 10.1016/j.ssnmr.2018.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/13/2018] [Accepted: 03/13/2018] [Indexed: 05/08/2023]
Abstract
Nuclear magnetic resonance (NMR) is a powerful tool for investigating atomic-scale structure in heterogeneous or composite materials where long-range order is absent. In this work solid-state 1H and 1H-detected NMR experiments were performed with fast magic angle spinning (νR = 75 kHz) and at high magnetic fields (B0 = 20 T) and used to gain structural insight into a heterogeneous biocatalyst consisting of an enzyme, human carbonic anhydrase II (hCA II), covalently immobilized on epoxy-functionalized silica. Two-dimensional 1H-1H NOESY-type correlation experiments were able to provide information on 1H environments in silica, epoxy-silica and the immobilized enzyme. Two distinct signals originating from water protons were observed: water associated with the surface of the silica and the water associated with the immobilized enzyme. Additional two-dimensional 1H-1H double-single quantum (DQ-SQ) correlation experiments suggested that the immobilized enzyme is not in close contact with the silica surface. Most significantly, comparison of two-dimensional 1H-15N spectra of the immobilized enzyme and the solution-state enzyme confirmed that the structural integrity of the protein is well preserved upon covalent immobilization.
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Affiliation(s)
- Sabu Varghese
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK
| | - Peter J Halling
- WestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow, G1 1XL, UK
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, CH-4056, Basel, Switzerland
| | - Stephen Wimperis
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK.
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15
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Louka A, Matlahov I, Giuntini S, Cerofolini L, Cavallo A, Pillozzi S, Ravera E, Fragai M, Arcangeli A, Ramamoorthy A, Goobes G, Luchinat C. Engineering l-asparaginase for spontaneous formation of calcium phosphate bioinspired microreactors. Phys Chem Chem Phys 2018; 20:12719-12726. [PMID: 29697113 DOI: 10.1039/c8cp00419f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Active bioinspired materials are appealing biotechnological targets, and their study is gaining momentum. These materials, which comprise of an inorganic matrix and one or more biomolecules, are extremely variable and therefore may result difficult to characterize in their intimate structure. In this work we have prepared a hydroxyapatite-l-asparaginase composite, with the perspective of using it in acute leukemia treatment. We demonstrate that the use of electron microscopy and powder X-ray diffraction, combined with the atomic-resolution information coming from solid-state NMR, allows us to understand the topology of the material and how the different components interplay to obtain an active composite.
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Affiliation(s)
- Alexandra Louka
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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16
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Kumari B, John D, Hoffmann P, Spende A, Toimil-Molares ME, Trautmann C, Hess C, Ruff P, Schulze M, Stark R, Buntkowsky G, Andrieu-Brunsen A, Gutmann T. Surface Enhanced DNP Assisted Solid-State NMR of Functionalized SiO2 Coated Polycarbonate Membranes. Z PHYS CHEM 2018. [DOI: 10.1515/zpch-2017-1032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Abstract
Surface enhanced solid-state NMR by dynamic nuclear polarization (DNP SENS) enables the characterization of the inner-pore surface functionalization of porous etched ion-track membranes exhibiting low specific surface areas compared to typical SBA- or MCM-type mesoporous silica materials. The membranes were conformally coated with a 5 nm thin SiO2 layer by atomic layer deposition. This layer was subsequently modified by aminopropyl silane linkers that allow further functionalization via the terminal amine group. The results evidence that in principle DNP SENS is a capable tool to analyze more complex porous systems, e.g. bioinspired functional etched ion-track membranes down to the molecular level. These results are relevant also for single nanopore systems, for which a direct analysis of the channel surface functionalization is not feasible by classical characterization methods. The applicability of DNP SENS to complex porous systems requires the optimization of the sample preparation and measurement parameters.
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Affiliation(s)
- Bharti Kumari
- Eduard-Zintl Institute for Inorganic and Physical Chemistry , Technische Universität Darmstadt , Alarich-Weiss-Str. 8 , D-64287 Darmstadt , Germany
| | - Daniel John
- Ernst-Berl Institute for Chemical Engineering and Macromolecular Science , Technische Universität Darmstadt , Alarich-Weiss-Str. 4 , D-64287 Darmstadt , Germany
| | - Paul Hoffmann
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1 , D-64291 Darmstadt , Germany
- Materialwissenschaft, Technische Universität Darmstadt , Alarich-Weiss-Str. 2 , D-64287 Darmstadt , Germany
| | - Anne Spende
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1 , D-64291 Darmstadt , Germany
- Materialwissenschaft, Technische Universität Darmstadt , Alarich-Weiss-Str. 2 , D-64287 Darmstadt , Germany
| | | | - Christina Trautmann
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1 , D-64291 Darmstadt , Germany
- Materialwissenschaft, Technische Universität Darmstadt , Alarich-Weiss-Str. 2 , D-64287 Darmstadt , Germany
| | - Christian Hess
- Eduard-Zintl Institute for Inorganic and Physical Chemistry , Technische Universität Darmstadt , Alarich-Weiss-Str. 8 , D-64287 Darmstadt , Germany
| | - Philip Ruff
- Eduard-Zintl Institute for Inorganic and Physical Chemistry , Technische Universität Darmstadt , Alarich-Weiss-Str. 8 , D-64287 Darmstadt , Germany
| | - Marcus Schulze
- Physics of Surfaces, Institute of Materials Science and Center of Smart Interfaces , Technische Universität Darmstadt , Alarich-Weiss-Str. 16 , D-64287 Darmstadt , Germany
| | - Robert Stark
- Physics of Surfaces, Institute of Materials Science and Center of Smart Interfaces , Technische Universität Darmstadt , Alarich-Weiss-Str. 16 , D-64287 Darmstadt , Germany
| | - Gerd Buntkowsky
- Eduard-Zintl Institute for Inorganic and Physical Chemistry , Technische Universität Darmstadt , Alarich-Weiss-Str. 8 , D-64287 Darmstadt , Germany
| | - Annette Andrieu-Brunsen
- Ernst-Berl Institute for Chemical Engineering and Macromolecular Science , Technische Universität Darmstadt , Alarich-Weiss-Str. 4 , D-64287 Darmstadt , Germany
| | - Torsten Gutmann
- Eduard-Zintl Institute for Inorganic and Physical Chemistry , Technische Universität Darmstadt , Alarich-Weiss-Str. 8 , D-64287 Darmstadt , Germany
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17
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Lilly Thankamony AS, Wittmann JJ, Kaushik M, Corzilius B. Dynamic nuclear polarization for sensitivity enhancement in modern solid-state NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:120-195. [PMID: 29157490 DOI: 10.1016/j.pnmrs.2017.06.002] [Citation(s) in RCA: 268] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/03/2017] [Accepted: 06/08/2017] [Indexed: 05/03/2023]
Abstract
The field of dynamic nuclear polarization has undergone tremendous developments and diversification since its inception more than 6 decades ago. In this review we provide an in-depth overview of the relevant topics involved in DNP-enhanced MAS NMR spectroscopy. This includes the theoretical description of DNP mechanisms as well as of the polarization transfer pathways that can lead to a uniform or selective spreading of polarization between nuclear spins. Furthermore, we cover historical and state-of-the art aspects of dedicated instrumentation, polarizing agents, and optimization techniques for efficient MAS DNP. Finally, we present an extensive overview on applications in the fields of structural biology and materials science, which underlines that MAS DNP has moved far beyond the proof-of-concept stage and has become an important tool for research in these fields.
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Affiliation(s)
- Aany Sofia Lilly Thankamony
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Johannes J Wittmann
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Monu Kaushik
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Björn Corzilius
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany.
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18
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Ravera E, Parigi G, Luchinat C. Perspectives on paramagnetic NMR from a life sciences infrastructure. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 282:154-169. [PMID: 28844254 DOI: 10.1016/j.jmr.2017.07.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 05/17/2023]
Abstract
The effects arising in NMR spectroscopy because of the presence of unpaired electrons, collectively referred to as "paramagnetic NMR" have attracted increasing attention over the last decades. From the standpoint of the structural and mechanistic biology, paramagnetic NMR provides long range restraints that can be used to assess the accuracy of crystal structures in solution and to improve them by simultaneous refinements through NMR and X-ray data. These restraints also provide information on structure rearrangements and conformational variability in biomolecular systems. Theoretical improvements in quantum chemistry calculations can nowadays allow for accurate calculations of the paramagnetic data from a molecular structural model, thus providing a tool to refine the metal coordination environment by matching the paramagnetic effects observed far away from the metal. Furthermore, the availability of an improved technology (higher fields and faster magic angle spinning) has promoted paramagnetic NMR applications in the fast-growing area of biomolecular solid-state NMR. Major improvements in dynamic nuclear polarization have been recently achieved, especially through the exploitation of the Overhauser effect occurring through the contact-driven relaxation mechanism: the very large enhancement of the 13C signal observed in a variety of liquid organic compounds at high fields is expected to open up new perspectives for applications of solution NMR.
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Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy.
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19
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Cerofolini L, Giuntini S, Louka A, Ravera E, Fragai M, Luchinat C. High-Resolution Solid-State NMR Characterization of Ligand Binding to a Protein Immobilized in a Silica Matrix. J Phys Chem B 2017; 121:8094-8101. [PMID: 28762736 DOI: 10.1021/acs.jpcb.7b05679] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Solid-state NMR is becoming a powerful tool to detect atomic-level structural features of biomolecules even when they are bound to (or trapped in) solid systems that lack long-range three-dimensional order. We here demonstrate that it is possible to probe protein-ligand interactions from a protein-based perspective also when the protein is entrapped in silica, thus translating into biomolecular solid-state NMR all of the considerations that are usually made to understand the chemical nature of the interaction of a protein with its ligands. This work provides a proof of concept that also immobilized enzymes can be used for protein-based NMR protein-ligand interactions for drug discovery.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Alexandra Louka
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy.,GiottoBiotech S.R.L. , Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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20
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Adiram-Filiba N, Schremer A, Ohaion E, Nadav-Tsubery M, Lublin-Tennenbaum T, Keinan-Adamsky K, Goobes G. Ubiquitin immobilized on mesoporous MCM41 silica surfaces - Analysis by solid-state NMR with biophysical and surface characterization. Biointerphases 2017; 12:02D414. [PMID: 28565916 PMCID: PMC5451314 DOI: 10.1116/1.4983273] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 12/16/2022] Open
Abstract
Deriving the conformation of adsorbed proteins is important in the assessment of their functional activity when immobilized. This has particularly important bearings on the design of contemporary and new encapsulated enzyme-based drugs, biosensors, and other bioanalytical devices. Solid-state nuclear magnetic resonance (NMR) measurements can expand our molecular view of proteins in this state and of the molecular interactions governing protein immobilization on popular biocompatible surfaces such as silica. Here, the authors study the immobilization of ubiquitin on the mesoporous silica MCM41 by NMR and other techniques. Protein molecules are shown to bind efficiently at pH 5 through electrostatic interactions to individual MCM41 particles, causing their agglutination. The strong attraction of ubiquitin to MCM41 surface is given molecular context through evidence of proximity of basic, carbonyl and polar groups on the protein to groups on the silica surface using NMR measurements. The immobilized protein exhibits broad peaks in two-dimensional 13C dipolar-assisted rotational resonance spectra, an indication of structural multiplicity. At the same time, cross-peaks related to Tyr and Phe sidechains are missing due to motional averaging. Overall, the favorable adsorption of ubiquitin to MCM41 is accompanied by conformational heterogeneity and by a major loss of motional degrees of freedom as inferred from the marked entropy decrease. Nevertheless, local motions of the aromatic rings are retained in the immobilized state.
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Affiliation(s)
| | - Avital Schremer
- Department of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Eli Ohaion
- Department of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
| | | | | | | | - Gil Goobes
- Department of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
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21
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Ravera E, Martelli T, Geiger Y, Fragai M, Goobes G, Luchinat C. Biosilica and bioinspired silica studied by solid-state NMR. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Ravera E, Cerofolini L, Martelli T, Louka A, Fragai M, Luchinat C. (1)H-detected solid-state NMR of proteins entrapped in bioinspired silica: a new tool for biomaterials characterization. Sci Rep 2016; 6:27851. [PMID: 27279168 PMCID: PMC4899708 DOI: 10.1038/srep27851] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/24/2016] [Indexed: 01/16/2023] Open
Abstract
Proton-detection in solid-state NMR, enabled by high magnetic fields (>18 T) and fast magic angle spinning (>50 kHz), allows for the acquisition of traditional (1)H-(15)N experiments on systems that are too big to be observed in solution. Among those, proteins entrapped in a bioinspired silica matrix are an attractive target that is receiving a large share of attention. We demonstrate that (1)H-detected SSNMR provides a novel approach to the rapid assessment of structural integrity in proteins entrapped in bioinspired silica.
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Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Tommaso Martelli
- Giotto Biotech S.R.L., Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Alexandra Louka
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
- Giotto Biotech S.R.L., Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
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23
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Geiger Y, Gottlieb HE, Akbey Ü, Oschkinat H, Goobes G. Studying the Conformation of a Silaffin-Derived Pentalysine Peptide Embedded in Bioinspired Silica using Solution and Dynamic Nuclear Polarization Magic-Angle Spinning NMR. J Am Chem Soc 2016; 138:5561-7. [DOI: 10.1021/jacs.5b07809] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yasmin Geiger
- Department
of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Hugo E. Gottlieb
- Department
of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Ümit Akbey
- Leibniz Institute für Molekulare Pharmakologie (FMP), NMR Supported Structural Biology, Robert-Roessle-Str.
10, Berlin 13125, Germany
| | - Hartmut Oschkinat
- Leibniz Institute für Molekulare Pharmakologie (FMP), NMR Supported Structural Biology, Robert-Roessle-Str.
10, Berlin 13125, Germany
| | - Gil Goobes
- Department
of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
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Sauvée C, Casano G, Abel S, Rockenbauer A, Akhmetzyanov D, Karoui H, Siri D, Aussenac F, Maas W, Weber RT, Prisner T, Rosay M, Tordo P, Ouari O. Tailoring of Polarizing Agents in the bTurea Series for Cross-Effect Dynamic Nuclear Polarization in Aqueous Media. Chemistry 2016; 22:5598-606. [PMID: 26992052 DOI: 10.1002/chem.201504693] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Indexed: 11/10/2022]
Abstract
A series of 18 nitroxide biradicals derived from bTurea has been prepared, and their enhancement factors ɛ ((1)H) in cross-effect dynamic nuclear polarization (CE DNP) NMR experiments at 9.4 and 14.1 T and 100 K in a DNP-optimized glycerol/water matrix ("DNP juice") have been studied. We observe that ɛ ((1)H) is strongly correlated with the substituents on the polarizing agents, and its trend is discussed in terms of different molecular parameters: solubility, average e-e distance, relative orientation of the nitroxide moieties, and electron spin relaxation times. We show that too short an e-e distance or too long a T1e can dramatically limit ɛ ((1)H). Our study also shows that the molecular structure of AMUPol is not optimal and its ɛ ((1)H) could be further improved through stronger interaction with the glassy matrix and a better orientation of the TEMPO moieties. A new AMUPol derivative introduced here provides a better ɛ ((1)H) than AMUPol itself (by a factor of ca. 1.2).
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Affiliation(s)
- Claire Sauvée
- Aix-Marseille Université, CNRS, ICR UMR 7273, 13397, Marseille cedex 20, France
| | - Gilles Casano
- Aix-Marseille Université, CNRS, ICR UMR 7273, 13397, Marseille cedex 20, France
| | - Sébastien Abel
- Aix-Marseille Université, CNRS, ICR UMR 7273, 13397, Marseille cedex 20, France
| | - Antal Rockenbauer
- Institute of Materials and Environmental Chemistry, Hungarian Academy of Sciences, Department of Physics, Budapest University of Technology and Economics and MTA-BME Condensed Matter Research Group, Budafoki ut 8, 1111, Budapest, Hungary
| | - Dimitry Akhmetzyanov
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438, Frankfurt-am-Main, Germany
| | - Hakim Karoui
- Aix-Marseille Université, CNRS, ICR UMR 7273, 13397, Marseille cedex 20, France
| | - Didier Siri
- Aix-Marseille Université, CNRS, ICR UMR 7273, 13397, Marseille cedex 20, France
| | - Fabien Aussenac
- Bruker BioSpin S.A.S., 34 rue de l'industrie, 67166, Wissembourg, France
| | - Werner Maas
- Bruker BioSpin Corporation, 15 Fortune Drive, Billerica, Massachusetts, 01821, USA
| | - Ralph T Weber
- Bruker BioSpin Corporation, 15 Fortune Drive, Billerica, Massachusetts, 01821, USA
| | - Thomas Prisner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438, Frankfurt-am-Main, Germany
| | - Mélanie Rosay
- Bruker BioSpin Corporation, 15 Fortune Drive, Billerica, Massachusetts, 01821, USA
| | - Paul Tordo
- Aix-Marseille Université, CNRS, ICR UMR 7273, 13397, Marseille cedex 20, France.
| | - Olivier Ouari
- Aix-Marseille Université, CNRS, ICR UMR 7273, 13397, Marseille cedex 20, France.
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Martelli T, Ravera E, Louka A, Cerofolini L, Hafner M, Fragai M, Becker CFW, Luchinat C. Atomic-Level Quality Assessment of Enzymes Encapsulated in Bioinspired Silica. Chemistry 2015; 22:425-32. [DOI: 10.1002/chem.201503613] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Indexed: 12/23/2022]
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