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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Rizzo D, Cerofolini L, Giuntini S, Iozzino L, Pergola C, Sacco F, Palmese A, Ravera E, Luchinat C, Baroni F, Fragai M. Epitope Mapping and Binding Assessment by Solid-State NMR Provide a Way for the Development of Biologics under the Quality by Design Paradigm. J Am Chem Soc 2022; 144:10006-10016. [PMID: 35617699 PMCID: PMC9185746 DOI: 10.1021/jacs.2c03232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Multispecific biologics
are an emerging class of drugs, in which
antibodies and/or proteins designed to bind pharmacological targets
are covalently linked or expressed as fusion proteins to increase
both therapeutic efficacy and safety. Epitope mapping on the target
proteins provides key information to improve the affinity and also
to monitor the manufacturing process and drug stability. Solid-state
NMR has been here used to identify the pattern of the residues of
the programmed cell death ligand 1 (PD-L1) ectodomain that are involved
in the interaction with a new multispecific biological drug. This
is possible because the large size and the intrinsic flexibility of
the complexes are not limiting factors for solid-state NMR.
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Affiliation(s)
- Domenico Rizzo
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Luisa Iozzino
- Analytical Development Biotech Department, Merck Serono S.p.a, Via Luigi Einaudi, 11, 00012 Guidonia, RM, Italy
| | - Carlo Pergola
- Analytical Development Biotech Department, Merck Serono S.p.a, Via Luigi Einaudi, 11, 00012 Guidonia, RM, Italy
| | - Francesca Sacco
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Analytical Development Biotech Department, Merck Serono S.p.a, Via Luigi Einaudi, 11, 00012 Guidonia, RM, Italy
| | - Angelo Palmese
- Analytical Development Biotech Department, Merck Serono S.p.a, Via Luigi Einaudi, 11, 00012 Guidonia, RM, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Fabio Baroni
- Analytical Development Biotech Department, Merck Serono S.p.a, Via Luigi Einaudi, 11, 00012 Guidonia, RM, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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3
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Yang W, Liang W, O’Dell LA, Toop HD, Maddigan N, Zhang X, Kochubei A, Doonan CJ, Jiang Y, Huang J. Insights into the Interaction between Immobilized Biocatalysts and Metal-Organic Frameworks: A Case Study of PCN-333. JACS AU 2021; 1:2172-2181. [PMID: 34977888 PMCID: PMC8715483 DOI: 10.1021/jacsau.1c00226] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Indexed: 05/05/2023]
Abstract
The immobilization of enzymes in metal-organic frameworks (MOFs) with preserved biofunctionality paves a promising way to solve problems regarding the stability and reusability of enzymes. However, the rational design of MOF-based biocomposites remains a considerable challenge as very little is known about the state of the enzyme, the MOF support, and their host-guest interactions upon immobilization. In this study, we elucidate the detailed host-guest interaction for MOF immobilized enzymes in the biointerface. Two enzymes with different sizes, lipase and insulin, have been immobilized in a mesoporous PCN-333(Al) MOF. The dynamic changes of local structures of the MOF host and enzyme guests have been experimentally revealed for the existence of the confinement effect to enzymes and van der Waals interaction in the biointerface between the aluminum oxo-cluster of the PCN-333 and the -NH2 species of enzymes. This kind of host-guest interaction renders the immobilization of enzymes in PCN-333 with high affinity and highly preserved enzymatic bioactivity.
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Affiliation(s)
- Wenjie Yang
- Laboratory
for Catalysis Engineering, School of Chemical and Biomolecular Engineering,
Sydney Nano Institute, the University of
Sydney, Sydney, NSW 2006, Australia
- School
of Engineering, Macquarie University, Sydney, NSW 2109, Australia
| | - Weibin Liang
- Laboratory
for Catalysis Engineering, School of Chemical and Biomolecular Engineering,
Sydney Nano Institute, the University of
Sydney, Sydney, NSW 2006, Australia
| | - Luke A. O’Dell
- Institute
for Frontier Materials, Deakin University, Geelong, VIC 3220, Australia
| | - Hamish D. Toop
- Department
of Chemistry and the Centre for Advanced Nanomaterials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Natasha Maddigan
- Department
of Chemistry and the Centre for Advanced Nanomaterials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Xingmo Zhang
- Laboratory
for Catalysis Engineering, School of Chemical and Biomolecular Engineering,
Sydney Nano Institute, the University of
Sydney, Sydney, NSW 2006, Australia
| | - Alena Kochubei
- School
of Engineering, Macquarie University, Sydney, NSW 2109, Australia
| | - Christian J. Doonan
- Department
of Chemistry and the Centre for Advanced Nanomaterials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Yijiao Jiang
- School
of Engineering, Macquarie University, Sydney, NSW 2109, Australia
| | - Jun Huang
- Laboratory
for Catalysis Engineering, School of Chemical and Biomolecular Engineering,
Sydney Nano Institute, the University of
Sydney, Sydney, NSW 2006, Australia
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4
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Rizzo D, Cerofolini L, Pérez-Ràfols A, Giuntini S, Baroni F, Ravera E, Luchinat C, Fragai M. Evaluation of the Higher Order Structure of Biotherapeutics Embedded in Hydrogels for Bioprinting and Drug Release. Anal Chem 2021; 93:11208-11214. [PMID: 34339178 PMCID: PMC8382223 DOI: 10.1021/acs.analchem.1c01850] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/20/2021] [Indexed: 01/16/2023]
Abstract
Biocompatible hydrogels for tissue regeneration/replacement and drug release with specific architectures can be obtained by three-dimensional bioprinting techniques. The preservation of the higher order structure of the proteins embedded in the hydrogels as drugs or modulators is critical for their biological activity. Solution nuclear magnetic resonance (NMR) experiments are currently used to investigate the higher order structure of biotherapeutics in comparability, similarity, and stability studies. However, the size of pores in the gel, protein-matrix interactions, and the size of the embedded proteins often prevent the use of this methodology. The recent advancements of solid-state NMR allow for the comparison of the higher order structure of the matrix-embedded and free isotopically enriched proteins, allowing for the evaluation of the functionality of the material in several steps of hydrogel development. Moreover, the structural information at atomic detail on the matrix-protein interactions paves the way for a structure-based design of these biomaterials.
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Affiliation(s)
- Domenico Rizzo
- Magnetic
Resonance Center (CERM), University of Florence,
and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine
(CIRMMP), Via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Linda Cerofolini
- Magnetic
Resonance Center (CERM), University of Florence,
and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine
(CIRMMP), Via L. Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Anna Pérez-Ràfols
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
- Giotto
Biotech, S.R.L, Via Madonna
del piano 6, Sesto Fiorentino, Florence 50019, Italy
| | - Stefano Giuntini
- Magnetic
Resonance Center (CERM), University of Florence,
and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine
(CIRMMP), Via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Fabio Baroni
- Analytical
Development Biotech Department, Merck Serono
S.p.a, Merck KGaA, Guidonia, Rome 00012, Italy
| | - Enrico Ravera
- Magnetic
Resonance Center (CERM), University of Florence,
and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine
(CIRMMP), Via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Claudio Luchinat
- Magnetic
Resonance Center (CERM), University of Florence,
and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine
(CIRMMP), Via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Marco Fragai
- Magnetic
Resonance Center (CERM), University of Florence,
and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine
(CIRMMP), Via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
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5
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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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6
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Cerofolini L, Fragai M, Luchinat C, Ravera E. Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes. Biophys Chem 2020; 265:106441. [PMID: 32745829 PMCID: PMC7387289 DOI: 10.1016/j.bpc.2020.106441] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/24/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022]
Abstract
The possibility of immobilizing a protein with antigenic properties on a solid support offers significant possibilities in the development of immunosensors and vaccine formulations. For both applications, the orientation of the antigen should ensure ready accessibility of the antibodies to the epitope. However, an experimental assessment of the orientational preferences necessarily proceeds through the preparation/isolation of the antigen, the immobilization on different surfaces and one or more biophysical characterization steps. To predict a priori whether favorable orientations can be achieved or not would allow one to select the most promising experimental routes, partly mitigating the time cost towards the final product. In this manuscript, we apply a simple computational model, based on united-residue modelling, to the prediction of the orientation of the receptor binding domain of the SARS-CoV-2 spike protein on surfaces commonly used in lateral-flow devices. These calculations can account for the experimental observation that direct immobilization on gold gives sufficient exposure of the epitope to obtain a response in immunochemical assays.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (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
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (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) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (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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7
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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: 11] [Impact Index Per Article: 2.8] [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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8
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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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9
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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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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, Carlon A, Ravera E, Calderone V, Fragai M, Parigi G, Luchinat C. Characterization of PEGylated Asparaginase: New Opportunities from NMR Analysis of Large PEGylated Therapeutics. Chemistry 2019; 25:1984-1991. [DOI: 10.1002/chem.201804488] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/09/2018] [Indexed: 11/12/2022]
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
| | - Stefano Giuntini
- 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 ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Azzurra Carlon
- 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
- 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 ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Vito Calderone
- 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 ChemistryUniversity of Florence Via della Lastruccia 3 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 ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Giacomo Parigi
- 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 ChemistryUniversity of Florence Via della Lastruccia 3 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 ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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12
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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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13
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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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14
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Sprenger KG, Prakash A, Drobny G, Pfaendtner J. Investigating the Role of Phosphorylation in the Binding of Silaffin Peptide R5 to Silica with Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1199-1207. [PMID: 28981294 DOI: 10.1021/acs.langmuir.7b02868] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Biomimetic silica formation, a process that is largely driven by proteins, has garnered considerable interest in recent years due to its role in the development of new biotechnologies. However, much remains unknown of the molecular-scale mechanisms underlying the binding of proteins to biomineral surfaces such as silica, or even of the key residue-level interactions between such proteins and surfaces. In this study, we employ molecular dynamics (MD) simulations to study the binding of R5-a 19-residue segment of a native silaffin peptide used for in vitro silica formation-to a silica surface. The metadynamics enhanced sampling method is used to converge the binding behavior of R5 on silica at both neutral (pH 7.5) and acidic (pH 5) conditions. The results show fundamental differences in the mechanism of binding between the two cases, providing unique insight into the pH-dependent ability of R5 and native silaffin to precipitate silica. We also study the effect of phosphorylation of serine residues in R5 on both the binding free energy to silica and the interfacial conformation of the peptide. Results indicate that phosphorylation drastically decreases the binding free energy and changes the structure of silica-adsorbed R5 through the introduction of charge and steric repulsion. New mechanistic insights from this work could inform rational design of new biomaterials and biotechnologies.
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Affiliation(s)
- K G Sprenger
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98105, United States
| | - Arushi Prakash
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98105, United States
| | - Gary Drobny
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98105, United States
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15
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Quinn CM, Wang M, Polenova T. NMR of Macromolecular Assemblies and Machines at 1 GHz and Beyond: New Transformative Opportunities for Molecular Structural Biology. Methods Mol Biol 2018; 1688:1-35. [PMID: 29151202 PMCID: PMC6217836 DOI: 10.1007/978-1-4939-7386-6_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
As a result of profound gains in sensitivity and resolution afforded by ultrahigh magnetic fields, transformative applications in the fields of structural biology and materials science are being realized. The development of dual low temperature superconducting (LTS)/high-temperature superconducting (HTS) magnets has enabled the achievement of magnetic fields above 1 GHz (23.5 T), which will open doors to an unprecedented new range of applications. In this contribution, we discuss the promise of ultrahigh field magnetic resonance. We highlight several methodological developments pertinent at high-magnetic fields including measurement of 1H-1H distances and 1H chemical shift anisotropy in the solid state as well as studies of quadrupolar nuclei such as 17O. Higher magnetic fields have advanced heteronuclear detection in solution NMR, valuable for applications including metabolomics and disordered proteins, as well as expanded use of proton detection in the solid state in conjunction with ultrafast magic angle spinning. We also present several recent applications to structural studies of the AP205 bacteriophage, the M2 channel from Influenza A, and biomaterials such as human bone. Gains in sensitivity and resolution from increased field strengths will enable advanced applications of NMR spectroscopy including in vivo studies of whole cells and intact virions.
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Affiliation(s)
- Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA.
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA.
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16
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Atomic structural details of a protein grafted onto gold nanoparticles. Sci Rep 2017; 7:17934. [PMID: 29263419 PMCID: PMC5738368 DOI: 10.1038/s41598-017-18109-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/05/2017] [Indexed: 12/18/2022] Open
Abstract
The development of a methodology for the structural characterization at atomic detail of proteins conjugated to nanoparticles would be a breakthrough in nanotechnology. Solution and solid-state NMR spectroscopies are currently used to investigate molecules and peptides grafted onto nanoparticles, but the strategies used so far fall short in the application to proteins, which represent a thrilling development in theranostics. We here demonstrate the feasibility of highly-resolved multidimensional heteronuclear spectra of a large protein assembly conjugated to PEGylated gold nanoparticles. The spectra have been obtained by direct proton detection under fast MAS and allow for both a fast fingerprinting for the assessment of the preservation of the native fold and for resonance assignment. We thus demonstrate that the structural characterization and the application of the structure-based methodologies to proteins bound to gold nanoparticles is feasible and potentially extensible to other hybrid protein-nanomaterials.
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17
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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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18
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Liu C, Liu J, Xu X, Xiang S, Wang S. Gd 3+-chelated lipid accelerates solid-state NMR spectroscopy of seven-transmembrane proteins. JOURNAL OF BIOMOLECULAR NMR 2017; 68:203-214. [PMID: 28560567 DOI: 10.1007/s10858-017-0120-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/26/2017] [Indexed: 06/07/2023]
Abstract
Solid-state NMR (SSNMR) is an attractive technique for studying large membrane proteins in membrane-mimetic environments. However, SSNMR experiments often suffer from low efficiency, due to the inherent low sensitivity and the long recycle delays needed to recover the magnetization. Here we demonstrate that the incorporation of a small amount of a Gd3+-chelated lipid, Gd3+-DMPE-DTPA, into proteoliposomes greatly shortens the spin-lattice relaxation time (1H-T 1) of lipid-reconstituted membrane proteins and accelerates the data collection. This effect has been evaluated on a 30 kDa, seven-transmembrane protein, Leptosphaeria rhodopsin. With the Gd3+-chelated lipid, we can perform 2D SSNMR experiments 3 times faster than by diamagnetic control. By combining this paramagnetic relaxation-assisted data collection with non-uniform sampling, the 3D experimental times are reduced eightfold with respect to traditional 3D experiments on diamagnetic samples. A comparison between the paramagnetic relaxation enhancement (PRE) effects of Cu2+- and Gd3+-chelated lipids indicates the much higher relaxivity of the latter. Hence, a tenfold lower concentration is needed for Gd3+-chelated lipids to achieve comparable PRE effects to Cu2+-chelated lipids. In addition, Gd3+-chelated lipids neither alter the protein structures nor induce significant line-width broadening of the protein signals. This work is expected to be beneficial for structural and dynamic studies of large membrane proteins by SSNMR.
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Affiliation(s)
- Chang Liu
- College of Chemistry and Molecular Engineering, Peking University, Yiheyuan Rd. 5th, Beijing, China
- Beijing NMR Center, Peking University, Yiheyuan Rd. 5th, Beijing, China
| | - Jing Liu
- College of Chemistry and Molecular Engineering, Peking University, Yiheyuan Rd. 5th, Beijing, China
- Beijing NMR Center, Peking University, Yiheyuan Rd. 5th, Beijing, China
| | - Xiaojun Xu
- College of Chemistry and Molecular Engineering, Peking University, Yiheyuan Rd. 5th, Beijing, China
- Beijing NMR Center, Peking University, Yiheyuan Rd. 5th, Beijing, China
| | - ShengQi Xiang
- Department NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering, Peking University, Yiheyuan Rd. 5th, Beijing, China.
- Beijing NMR Center, Peking University, Yiheyuan Rd. 5th, Beijing, China.
- National Laboratories of Beijing National Laboratory for Molecular Science, Beijing, China.
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19
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Gopinath T, Nelson SED, Soller KJ, Veglia G. Probing the Conformationally Excited States of Membrane Proteins via 1H-Detected MAS Solid-State NMR Spectroscopy. J Phys Chem B 2017; 121:4456-4465. [DOI: 10.1021/acs.jpcb.7b03268] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- T. Gopinath
- Department of Chemistry and ‡Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sarah E. D. Nelson
- Department of Chemistry and ‡Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kailey J. Soller
- Department of Chemistry and ‡Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Gianluigi Veglia
- Department of Chemistry and ‡Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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20
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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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