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Gigli L, Silva JM, Cerofolini L, Macedo AL, Geraldes CFGC, Suturina EA, Calderone V, Fragai M, Parigi G, Ravera E, Luchinat C. Machine Learning-Enhanced Quantum Chemistry-Assisted Refinement of the Active Site Structure of Metalloproteins. Inorg Chem 2024; 63:10713-10725. [PMID: 38805564 DOI: 10.1021/acs.inorgchem.4c01274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Understanding the fine structural details of inhibitor binding at the active site of metalloenzymes can have a profound impact on the rational drug design targeted to this broad class of biomolecules. Structural techniques such as NMR, cryo-EM, and X-ray crystallography can provide bond lengths and angles, but the uncertainties in these measurements can be as large as the range of values that have been observed for these quantities in all the published structures. This uncertainty is far too large to allow for reliable calculations at the quantum chemical (QC) levels for developing precise structure-activity relationships or for improving the energetic considerations in protein-inhibitor studies. Therefore, the need arises to rely upon computational methods to refine the active site structures well beyond the resolution obtained with routine application of structural methods. In a recent paper, we have shown that it is possible to refine the active site of cobalt(II)-substituted MMP12, a metalloprotein that is a relevant drug target, by matching to the experimental pseudocontact shifts (PCS) those calculated using multireference ab initio QC methods. The computational cost of this methodology becomes a significant bottleneck when the starting structure is not sufficiently close to the final one, which is often the case with biomolecular structures. To tackle this problem, we have developed an approach based on a neural network (NN) and a support vector regression (SVR) and applied it to the refinement of the active site structure of oxalate-inhibited human carbonic anhydrase 2 (hCAII), another prototypical metalloprotein target. The refined structure gives a remarkably good agreement between the QC-calculated and the experimental PCS. This study not only contributes to the knowledge of CAII but also demonstrates the utility of combining machine learning (ML) algorithms with QC calculations, offering a promising avenue for investigating other drug targets and complex biological systems in general.
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Affiliation(s)
- Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - José Malanho Silva
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Anjos L Macedo
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- Associate Laboratory i4HB─Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Carlos F G C Geraldes
- Department of Life Sciences, Faculty of Science and Technology, 3000-393 Coimbra, Portugal
- Coimbra Chemistry Center─Institute of Molecular Sciences (CCC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
| | | | - Vito Calderone
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
- Florence Data Science, University of Florence, Florence 50134, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
- Giotto Biotech, S.R.L., Sesto Fiorentino 50019, Italy
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Aguion PI, Marchanka A, Carlomagno T. Nucleic acid-protein interfaces studied by MAS solid-state NMR spectroscopy. J Struct Biol X 2022; 6:100072. [PMID: 36090770 PMCID: PMC9449856 DOI: 10.1016/j.yjsbx.2022.100072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Solid-state NMR (ssNMR) has become a well-established technique to study large and insoluble protein assemblies. However, its application to nucleic acid-protein complexes has remained scarce, mainly due to the challenges presented by overlapping nucleic acid signals. In the past decade, several efforts have led to the first structure determination of an RNA molecule by ssNMR. With the establishment of these tools, it has become possible to address the problem of structure determination of nucleic acid-protein complexes by ssNMR. Here we review first and more recent ssNMR methodologies that study nucleic acid-protein interfaces by means of chemical shift and peak intensity perturbations, direct distance measurements and paramagnetic effects. At the end, we review the first structure of an RNA-protein complex that has been determined from ssNMR-derived intermolecular restraints.
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Affiliation(s)
- Philipp Innig Aguion
- Institute for Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Alexander Marchanka
- Institute for Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Teresa Carlomagno
- School of Biosciences/College of Life and Enviromental Sciences, Institute of Cancer and Genomic Sciences/College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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3
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Ahmed M, Marchanka A, Carlomagno T. Structure of a Protein–RNA Complex by Solid‐State NMR Spectroscopy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mumdooh Ahmed
- Centre for Biomolecular Drug Research and Institute of Organic ChemistryLeibniz University Hannover Schneiderberg 38 30167 Hannover Germany
| | - Alexander Marchanka
- Centre for Biomolecular Drug Research and Institute of Organic ChemistryLeibniz University Hannover Schneiderberg 38 30167 Hannover Germany
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research and Institute of Organic ChemistryLeibniz University Hannover Schneiderberg 38 30167 Hannover Germany
- Group of NMR-based Structural ChemistryHelmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany
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Ahmed M, Marchanka A, Carlomagno T. Structure of a Protein-RNA Complex by Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2020; 59:6866-6873. [PMID: 32023357 PMCID: PMC7187219 DOI: 10.1002/anie.201915465] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Indexed: 12/17/2022]
Abstract
Solid‐state NMR (ssNMR) is applicable to high molecular‐weight (MW) protein assemblies in a non‐amorphous precipitate. The technique yields atomic resolution structural information on both soluble and insoluble particles without limitations of MW or requirement of crystals. Herein, we propose and demonstrate an approach that yields the structure of protein–RNA complexes (RNP) solely from ssNMR data. Instead of using low‐sensitivity magnetization transfer steps between heteronuclei of the protein and the RNA, we measure paramagnetic relaxation enhancement effects elicited on the RNA by a paramagnetic tag coupled to the protein. We demonstrate that this data, together with chemical‐shift‐perturbation data, yields an accurate structure of an RNP complex, starting from the bound structures of its components. The possibility of characterizing protein–RNA interactions by ssNMR may enable applications to large RNP complexes, whose structures are not accessible by other methods.
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Affiliation(s)
- Mumdooh Ahmed
- Centre for Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Alexander Marchanka
- Centre for Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany.,Group of NMR-based Structural Chemistry, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
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Cerofolini L, Ravera E, Fragai M, Luchinat C. NMR of Immobilized Enzymes. Methods Mol Biol 2020; 2100:363-383. [PMID: 31939136 DOI: 10.1007/978-1-0716-0215-7_24] [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] [Indexed: 06/10/2023]
Abstract
Solid-state NMR has become the method of choice for the assessment of protein structure for insoluble objects lacking long-range order. In this context, it is apparent that solid-state NMR is also perfectly poised toward the characterization of immobilized proteins. For these systems, it is possible to understand at the atomic level which perturbations, if any, are occurring as a result of the functionalization. Here we describe how it is possible to accomplish the NMR characterization of enzymes that have been immobilized through different approaches, and we introduce the reader to the choice of the experimental strategy that can be useful in different cases. An outlook on the level of information that can be attained is also given, in view of recent methodological advancements.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario, Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario, Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy.
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy.
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario, Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario, Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
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Cerofolini L, Fragai M, Luchinat C. Mechanism and Inhibition of Matrix Metalloproteinases. Curr Med Chem 2019; 26:2609-2633. [PMID: 29589527 DOI: 10.2174/0929867325666180326163523] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 01/02/2023]
Abstract
Matrix metalloproteinases hydrolyze proteins and glycoproteins forming the extracellular matrix, cytokines and growth factors released in the extracellular space, and membrane-bound receptors on the outer cell membrane. The pathological relevance of MMPs has prompted the structural and functional characterization of these enzymes and the development of synthetic inhibitors as possible drug candidates. Recent studies have provided a better understanding of the substrate preference of the different members of the family, and structural data on the mechanism by which these enzymes hydrolyze the substrates. Here, we report the recent advancements in the understanding of the mechanism of collagenolysis and elastolysis, and we discuss the perspectives of new therapeutic strategies for targeting MMPs.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
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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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8
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Giuntini S, Balducci E, Cerofolini L, Ravera E, Fragai M, Berti F, Luchinat C. Characterization of the Conjugation Pattern in Large Polysaccharide-Protein Conjugates by NMR Spectroscopy. Angew Chem Int Ed Engl 2017; 56:14997-15001. [PMID: 29024352 PMCID: PMC5813213 DOI: 10.1002/anie.201709274] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Indexed: 11/08/2022]
Abstract
Carbohydrate-based vaccines are among the safest and most effective vaccines and represent potent tools for prevention of life-threatening bacterial infectious diseases, like meningitis and pneumonia. The chemical conjugation of a weak antigen to protein as a source of T-cell epitopes generates a glycoconjugate vaccine that results more immunogenic. Several methods have been used so far to characterize the resulting polysaccharide-protein conjugates. However, a reduced number of methodologies has been proposed for measuring the degree of saccharide conjugation at the possible protein sites. Here we show that detailed information on large proteins conjugated with large polysaccharides can be achieved by a combination of solution and solid-state NMR spectroscopy. As a test case, a large protein assembly, l-asparaginase II, has been conjugated with Neisseria meningitidis serogroup C capsular polysaccharide and the pattern and degree of conjugation were determined.
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Affiliation(s)
- Stefano Giuntini
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto FiorentinoItaly
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)Via L. Sacconi 650019Sesto FiorentinoItaly
| | - Evita Balducci
- GSK VaccinesPreclinical R&DVia Fiorentina 153100SienaItaly
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)Via L. Sacconi 650019Sesto FiorentinoItaly
| | - Enrico Ravera
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto FiorentinoItaly
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)Via L. Sacconi 650019Sesto FiorentinoItaly
| | - Marco Fragai
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto FiorentinoItaly
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)Via L. Sacconi 650019Sesto FiorentinoItaly
| | | | - Claudio Luchinat
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto FiorentinoItaly
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)Via L. Sacconi 650019Sesto FiorentinoItaly
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Giuntini S, Balducci E, Cerofolini L, Ravera E, Fragai M, Berti F, Luchinat C. Characterization of the Conjugation Pattern in Large Polysaccharide-Protein Conjugates by NMR Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Stefano Giuntini
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
- Magnetic Resonance Center (CERM); University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Evita Balducci
- GSK Vaccines; Preclinical R&D; Via Fiorentina 1 53100 Siena Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM); University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Enrico Ravera
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
- Magnetic Resonance Center (CERM); University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Marco Fragai
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
- Magnetic Resonance Center (CERM); University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Francesco Berti
- GSK Vaccines; Preclinical R&D; Via Fiorentina 1 53100 Siena Italy
| | - Claudio Luchinat
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
- 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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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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Ravera E, Ciambellotti S, Cerofolini L, Martelli T, Kozyreva T, Bernacchioni C, Giuntini S, Fragai M, Turano P, Luchinat C. Solid-State NMR of PEGylated Proteins. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510148] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
| | - Silvia Ciambellotti
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
| | - Tommaso Martelli
- Giotto Biotech S.r.l. Via Madonna del Piano 6; 50019 Sesto Fiorentino FI Italy
| | - Tatiana Kozyreva
- Giotto Biotech S.r.l. Via Madonna del Piano 6; 50019 Sesto Fiorentino FI Italy
| | - Caterina Bernacchioni
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
- Giotto Biotech S.r.l. Via Madonna del Piano 6; 50019 Sesto Fiorentino FI Italy
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Ravera E, Ciambellotti S, Cerofolini L, Martelli T, Kozyreva T, Bernacchioni C, Giuntini S, Fragai M, Turano P, Luchinat C. Solid-State NMR of PEGylated Proteins. Angew Chem Int Ed Engl 2016; 55:2446-9. [PMID: 26756539 DOI: 10.1002/anie.201510148] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Indexed: 11/10/2022]
Abstract
PEGylated proteins are widely used in biomedicine but, in spite of their importance, no atomic-level information is available since they are generally resistant to structural characterization approaches. PEGylated proteins are shown here to yield highly resolved solid-state NMR spectra, which allows assessment of the structural integrity of proteins when PEGylated for therapeutic or diagnostic use.
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Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Silvia Ciambellotti
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Tommaso Martelli
- Giotto Biotech S.r.l. Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Tatiana Kozyreva
- Giotto Biotech S.r.l. Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Caterina Bernacchioni
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy. .,Giotto Biotech S.r.l. Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy.
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13
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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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14
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Ravera E, Fragai M, Parigi G, Luchinat C. Differences in Dynamics between Crosslinked and Non-Crosslinked Hyaluronates Measured by using Fast Field-Cycling Relaxometry. Chemphyschem 2015; 16:2803-2809. [PMID: 26263906 DOI: 10.1002/cphc.201500446] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Indexed: 11/11/2022]
Abstract
The dynamic properties of water molecules in gels containing linear and crosslinked hyaluronic acid polymers are investigated by using an integrated approach that includes relaxometry, solid-state NMR spectroscopy, and scanning electron microscopy. A model-free analysis of field-dependent nuclear relaxation is applied to obtain information on mobility and the population of different pools of water molecules in the gels. Differences between linear and crosslinked hyaluronic acid polymers are observed, indicating that crosslinking increases both the fraction and the correlation time of water molecules with slow dynamics.
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Affiliation(s)
- Enrico Ravera
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
| | - Marco Fragai
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
| | - Giacomo Parigi
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
| | - Claudio Luchinat
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
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15
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16
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Fragai M, Luchinat C, Martelli T, Ravera E, Sagi I, Solomonov I, Udi Y. SSNMR of biosilica-entrapped enzymes permits an easy assessment of preservation of native conformation in atomic detail. Chem Commun (Camb) 2014; 50:421-3. [DOI: 10.1039/c3cc46896h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Fragai M, Luchinat C, Parigi G, Ravera E. Practical considerations over spectral quality in solid state NMR spectroscopy of soluble proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 57:155-66. [PMID: 23990200 DOI: 10.1007/s10858-013-9776-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 08/23/2013] [Indexed: 05/09/2023]
Abstract
Great theoretical and methodological advances are pushing the limits of resolution and sensitivity in solid state NMR (SSNMR). However, sample preparation remains a critical issue for the success of an experiment. The factors affecting spectral quality in SSNMR samples are discussed, examining cases encountered in the literature and presenting new experimental data. A discussion on resolution and sensitivity in sedimented solutes is framed in this context.
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Affiliation(s)
- Marco Fragai
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
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18
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Varghese S, Yang F, Pacheco V, Wrede K, Medvedev A, Ogata H, Knipp M, Heise H. Expression, purification, and solid-state NMR characterization of the membrane binding heme protein nitrophorin 7 in two electronic spin states. Biochemistry 2013; 52:7031-40. [PMID: 24033104 DOI: 10.1021/bi401020t] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nitrophorins (NPs) comprise a group of NO transporting ferriheme b proteins found in the saliva of the blood sucking insect Rhodnius prolixus . In contrast to other nitrophorins (NP1-4), the recently identified membrane binding isoform NP7 tends to form oligomers and precipitates at higher concentrations in solution. Hence, solid-state NMR (ssNMR) was employed as an alternative method to gain structural insights on the precipitated protein. We report the expression and purification of (13)C,(15)N isotopically labeled protein together with the first ssNMR characterization of NP7. Because the size of NP7 (21 kDa) still provides a challenge for ssNMR, the samples were reverse labeled with Lys and Val to reduce the number of crosspeaks in two-dimensional spectra. The two electronic spin states with S = 1/2 and S = 0 at the ferriheme iron were generated by the complexation with imidazole and NO, respectively. ssNMR spectra of both forms are well resolved, which allows for sequential resonance assignments of 22 residues. Importantly, the ssNMR spectra demonstrate that aggregation does not affect the protein fold. Comparison of the spectra of the two electronic spin states allows the determination of paramagnetically shifted cross peaks due to pseudocontact shifts, which assists the assignment of residues close to the heme center.
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Affiliation(s)
- Sabu Varghese
- ICS-6 Institute of Complex Systems-Structural Biochemistry, Forschungszentrum Jülich , D-2425 Jülich, Germany
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19
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Carnevale D, Perez Linde A, Bauer G, Bodenhausen G. Solid-state proton NMR of paramagnetic metal complexes: DANTE spin echoes for selective excitation in inhomogeneously broadened lines. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.06.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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20
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21
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Moseley HNB, Sperling LJ, Rienstra CM. Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of β1 immunoglobulin binding domain of protein G (GB1). JOURNAL OF BIOMOLECULAR NMR 2010; 48:123-8. [PMID: 20931264 PMCID: PMC2962796 DOI: 10.1007/s10858-010-9448-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 08/18/2010] [Indexed: 05/11/2023]
Abstract
Magic-angle spinning solid-state NMR (MAS SSNMR) represents a fast developing experimental technique with great potential to provide structural and dynamics information for proteins not amenable to other methods. However, few automated analysis tools are currently available for MAS SSNMR. We present a methodology for automating protein resonance assignments of MAS SSNMR spectral data and its application to experimental peak lists of the β1 immunoglobulin binding domain of protein G (GB1) derived from a uniformly ¹³C- and ¹⁵N-labeled sample. This application to the 56 amino acid GB1 produced an overall 84.1% assignment of the N, CO, CA, and CB resonances with no errors using peak lists from NCACX 3D, CANcoCA 3D, and CANCOCX 4D experiments. This proof of concept demonstrates the tractability of this problem.
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22
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Lange V, Becker-Baldus J, Kunert B, van Rossum BJ, Casagrande F, Engel A, Roske Y, Scheffel FM, Schneider E, Oschkinat H. A MAS NMR study of the bacterial ABC transporter ArtMP. Chembiochem 2010; 11:547-55. [PMID: 20099290 DOI: 10.1002/cbic.200900472] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
ATP-binding cassette (ABC) transport systems facilitate the translocation of substances, like amino acids, across cell membranes energised by ATP hydrolysis. This work describes first structural studies on the ABC transporter ArtMP from Geobacillus stearothermophilus in native lipid environment by magic-angle spinning NMR spectroscopy. The 2D crystals of ArtMP and 3D crystals of isolated ArtP were prepared in different nucleotide-bound or -unbound states. From selectively (13)C,(15)N-labelled ArtP, several sequence-specific assignments were obtained, most of which could be transferred to spectra of ArtMP. Residues Tyr133 and Pro134 protrude directly into the ATP-binding pocket at the interface of the ArtP subunits, and hence, are sensitive monitors for structural changes during nucleotide binding and hydrolysis. Distinct sets of NMR shifts were obtained for ArtP with different phosphorylation states of the ligand. Indications were found for an asymmetric or inhomogeneous state of the ArtP dimer bound with triphosphorylated nucleotides. With this investigation, a model system was established for screening all functional states occurring in one ABC transporter in native lipid environment.
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Affiliation(s)
- Vivien Lange
- NMR-Supported Structural Biology, Leibniz-Institut für Molekulare Pharmakologie, R.-Rössle-Strasse 10, 13125 Berlin, Germany
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23
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Sperling LJ, Berthold DA, Sasser TL, Jeisy-Scott V, Rienstra CM. Assignment strategies for large proteins by magic-angle spinning NMR: the 21-kDa disulfide-bond-forming enzyme DsbA. J Mol Biol 2010; 399:268-82. [PMID: 20394752 PMCID: PMC2880403 DOI: 10.1016/j.jmb.2010.04.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 04/04/2010] [Indexed: 01/08/2023]
Abstract
We present strategies for chemical shift assignments of large proteins by magic-angle spinning solid-state NMR, using the 21-kDa disulfide-bond-forming enzyme DsbA as prototype. Previous studies have demonstrated that complete de novo assignments are possible for proteins up to approximately 17 kDa, and partial assignments have been performed for several larger proteins. Here we show that combinations of isotopic labeling strategies, high field correlation spectroscopy, and three-dimensional (3D) and four-dimensional (4D) backbone correlation experiments yield highly confident assignments for more than 90% of backbone resonances in DsbA. Samples were prepared as nanocrystalline precipitates by a dialysis procedure, resulting in heterogeneous linewidths below 0.2 ppm. Thus, high magnetic fields, selective decoupling pulse sequences, and sparse isotopic labeling all improved spectral resolution. Assignments by amino acid type were facilitated by particular combinations of pulse sequences and isotopic labeling; for example, transferred echo double resonance experiments enhanced sensitivity for Pro and Gly residues; [2-(13)C]glycerol labeling clarified Val, Ile, and Leu assignments; in-phase anti-phase correlation spectra enabled interpretation of otherwise crowded Glx/Asx side-chain regions; and 3D NCACX experiments on [2-(13)C]glycerol samples provided unique sets of aromatic (Phe, Tyr, and Trp) correlations. Together with high-sensitivity CANCOCA 4D experiments and CANCOCX 3D experiments, unambiguous backbone walks could be performed throughout the majority of the sequence. At 189 residues, DsbA represents the largest monomeric unit for which essentially complete solid-state NMR assignments have so far been achieved. These results will facilitate studies of nanocrystalline DsbA structure and dynamics and will enable analysis of its 41-kDa covalent complex with the membrane protein DsbB, for which we demonstrate a high-resolution two-dimensional (13)C-(13)C spectrum.
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Affiliation(s)
- Lindsay J. Sperling
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Deborah A. Berthold
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Terry L. Sasser
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Victoria Jeisy-Scott
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
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24
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Bertini I, Emsley L, Lelli M, Luchinat C, Mao J, Pintacuda G. Ultrafast MAS Solid-State NMR Permits Extensive 13C and 1H Detection in Paramagnetic Metalloproteins. J Am Chem Soc 2010; 132:5558-9. [DOI: 10.1021/ja100398q] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center, CERM, University of Florence, Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Sesto Fiorentino, Italy, and Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1), 69100 Villeurbanne, France
| | - Lyndon Emsley
- Magnetic Resonance Center, CERM, University of Florence, Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Sesto Fiorentino, Italy, and Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1), 69100 Villeurbanne, France
| | - Moreno Lelli
- Magnetic Resonance Center, CERM, University of Florence, Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Sesto Fiorentino, Italy, and Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1), 69100 Villeurbanne, France
| | - Claudio Luchinat
- Magnetic Resonance Center, CERM, University of Florence, Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Sesto Fiorentino, Italy, and Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1), 69100 Villeurbanne, France
| | - Jiafei Mao
- Magnetic Resonance Center, CERM, University of Florence, Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Sesto Fiorentino, Italy, and Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1), 69100 Villeurbanne, France
| | - Guido Pintacuda
- Magnetic Resonance Center, CERM, University of Florence, Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Sesto Fiorentino, Italy, and Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1), 69100 Villeurbanne, France
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25
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Bertini I, Bhaumik A, De Paëpe G, Griffin RG, Lelli M, Lewandowski JR, Luchinat C. High-resolution solid-state NMR structure of a 17.6 kDa protein. J Am Chem Soc 2010; 132:1032-40. [PMID: 20041641 DOI: 10.1021/ja906426p] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The use of pseudocontact shifts arising from paramagnetic metal ions in a microcrystalline protein sample is proposed as a strategy to obtain unambiguous signal assignments in solid-state NMR spectra enabling distance extraction for protein structure calculation. With this strategy, 777 unambiguous (281 sequential, 217 medium-range, and 279 long-range) distance restraints could be obtained from PDSD, DARR, CHHC, and the recently introduced PAR and PAIN-CP solid-state experiments for the cobalt(II)-substituted catalytic domain of matrix metalloproteinase 12 (159 amino acids, 17.6 kDa). The obtained structure is a high resolution one, with backbone rmsd of 1.0 +/- 0.2 A, and is in good agreement with the X-ray structure (rmsd to X-ray 1.3 A). The proposed strategy, which may be generalized for nonmetalloproteins with the use of paramagnetic tags, represents a significant step ahead in protein structure determination using solid-state NMR.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center, CERM, University of Florence, Via L. Sacconi, 6-50019 Sesto Fiorentino, Italy.
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26
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Bermel W, Bertini I, Felli IC, Peruzzini R, Pierattelli R. Exclusively Heteronuclear NMR Experiments to Obtain Structural and Dynamic Information on Proteins. Chemphyschem 2010; 11:689-95. [DOI: 10.1002/cphc.200900772] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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McDermott A. Structure and dynamics of membrane proteins by magic angle spinning solid-state NMR. Annu Rev Biophys 2009; 38:385-403. [PMID: 19245337 DOI: 10.1146/annurev.biophys.050708.133719] [Citation(s) in RCA: 288] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Membrane proteins remain difficult to study by traditional methods. Magic angle spinning solid-state NMR (MAS SSNMR) methods present an important approach for studying membrane proteins of moderate size. Emerging MAS SSNMR methods are based on extensive assignments of the nuclei as a basis for structure determination and characterization of function. These methods have already been used to characterize fibrils and globular proteins and are being increasingly used to study membrane proteins embedded in lipids. This review highlights recent applications to intrinsic membrane proteins and summarizes recent technical advances that will enable these methods to be utilized for more complex membrane protein systems in the near future.
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Affiliation(s)
- Ann McDermott
- Department of Chemistry, Columbia University, New York, NY 10027, USA.
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28
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Krabben L, van Rossum BJ, Jehle S, Bocharov E, Lyukmanova EN, Schulga AA, Arseniev A, Hucho F, Oschkinat H. Loop 3 of Short Neurotoxin II is an Additional Interaction Site with Membrane-bound Nicotinic Acetylcholine Receptor as Detected by Solid-state NMR Spectroscopy. J Mol Biol 2009; 390:662-71. [DOI: 10.1016/j.jmb.2009.05.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 04/23/2009] [Accepted: 05/12/2009] [Indexed: 11/30/2022]
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29
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Kervern G, D'Aléo A, Toupet L, Maury O, Emsley L, Pintacuda G. Crystal-Structure Determination of Powdered Paramagnetic Lanthanide Complexes by Proton NMR Spectroscopy. Angew Chem Int Ed Engl 2009; 48:3082-6. [DOI: 10.1002/anie.200805302] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Kervern G, D'Aléo A, Toupet L, Maury O, Emsley L, Pintacuda G. Crystal-Structure Determination of Powdered Paramagnetic Lanthanide Complexes by Proton NMR Spectroscopy. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Jehle S, van Rossum B, Stout JR, Noguchi SM, Falber K, Rehbein K, Oschkinat H, Klevit RE, Rajagopal P. alphaB-crystallin: a hybrid solid-state/solution-state NMR investigation reveals structural aspects of the heterogeneous oligomer. J Mol Biol 2008; 385:1481-97. [PMID: 19041879 DOI: 10.1016/j.jmb.2008.10.097] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Revised: 09/24/2008] [Accepted: 10/29/2008] [Indexed: 10/21/2022]
Abstract
Atomic-level structural information on alphaB-Crystallin (alphaB), a prominent member of the small heat-shock protein family, has been a challenge to obtain due its polydisperse oligomeric nature. We show that magic-angle spinning solid-state NMR can be used to obtain high-resolution information on an approximately 580-kDa human alphaB assembled from 175-residue 20-kDa subunits. An approximately 100-residue alpha-crystallin domain is common to all small heat-shock proteins, and solution-state NMR was performed on two different alpha-crystallin domain constructs isolated from alphaB. In vitro, the chaperone-like activities of full-length alphaB and the isolated alpha-crystallin domain are identical. Chemical shifts of the backbone and C(beta) resonances have been obtained for residues 64-162 (alpha-crystallin domain plus part of the C-terminus) in alphaB and the isolated alpha-crystallin domain by solid-state and solution-state NMR, respectively. Both sets of data strongly predict six beta-strands in the alpha-crystallin domain. A majority of residues in the alpha-crystallin domain have similar chemical shifts in both solid-state and solution-state, indicating similar structures for the domain in its isolated and oligomeric forms. Sites of intersubunit interaction are identified from chemical shift differences that cluster to specific regions of the alpha-crystallin domain. Multiple signals are observed for the resonances of M68 in the oligomer, identifying the region containing this residue as existing in heterogeneous environments within alphaB. Evidence for a novel dimerization motif in the human alpha-crystallin domain is obtained by a comparison of (i) solid-state and solution-state chemical shift data and (ii) (1)H-(15)N heteronuclear single quantum coherence spectra as a function of pH. The isolated alpha-crystallin domain undergoes a dimer-monomer transition over the pH range 7.5-6.8. This steep pH-dependent switch may be important for alphaB to function optimally (e.g., to preserve the filament integrity of cardiac muscle proteins such as actin and desmin during cardiac ischemia, which is accompanied by acidosis).
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32
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Paramagnetic shifts in solid-state NMR of proteins to elicit structural information. Proc Natl Acad Sci U S A 2008; 105:17284-9. [PMID: 18988744 DOI: 10.1073/pnas.0708460105] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recent observation of pseudocontact shifts (pcs) in (13)C high-resolution solid-state NMR of paramagnetic proteins opens the way to their application as structural restraints. Here, by investigating a microcrystalline sample of cobalt(II)-substituted matrix metalloproteinase 12 [CoMMP-12 (159 AA, 17.5 kDa)], it is shown that a combined strategy of protein labeling and dilution of the paramagnetic species (i.e., (13)C-,(15)N-labeled CoMMP-12 diluted in unlabeled ZnMMP-12, and (13)C-,(15)N-labeled ZnMMP-12 diluted in unlabeled CoMMP-12) allows one to easily separate the pcs contributions originated from the protein internal metal (intramolecular pcs) from those due to the metals in neighboring proteins in the crystal lattice (intermolecular pcs) and that both can be used for structural purposes. It is demonstrated that intramolecular pcs are significant structural restraints helpful in increasing both precision and accuracy of the structure, which is a need in solid-state structural biology nowadays. Furthermore, intermolecular pcs provide unique information on positions and orientations of neighboring protein molecules in the solid phase.
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33
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Bertini I, Luchinat C, Parigi G, Pierattelli R. Perspectives in paramagnetic NMR of metalloproteins. Dalton Trans 2008:3782-90. [PMID: 18629397 DOI: 10.1039/b719526e] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
NMR experiments and tools for the characterization of the structure and dynamics of paramagnetic proteins are presented here. The focus is on the importance of (13)C direct-detection NMR for the assignment of paramagnetic systems in solution, on the information contained in paramagnetic effects observed both in solution and in the solid state, and on novel paramagnetism-based tools for the investigation of conformational heterogeneity in protein-protein complexes or in multi-domain proteins.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, (FI), Italy.
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