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Cerofolini L, Ramberg KO, Padilla LC, Antonik P, Ravera E, Luchinat C, Fragai M, Crowley PB. Solid-state NMR - a complementary technique for protein framework characterization. Chem Commun (Camb) 2023; 59:776-779. [PMID: 36546612 DOI: 10.1039/d2cc05725e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein frameworks are an emerging class of biomaterial with medical and technological applications. Frameworks are studied mainly by X-ray diffraction or scattering techniques. Complementary strategies are required. Here, we report solid-state NMR analyses of a microcrystalline protein-macrocycle framework and the rehydrated freeze-dried protein. This methodology may aid the characterization of low-crystallinity frameworks.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy. .,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Kiefer O Ramberg
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland.
| | - Luis C Padilla
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy. .,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Paweł Antonik
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland.
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy. .,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, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy. .,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, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy. .,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
| | - Peter B Crowley
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland.
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2
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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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3
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Bruno F, Gigli L, Ferraro G, Cavallo A, Michaelis VK, Goobes G, Fratini E, Ravera E. Lysozyme is Sterically Trapped Within the Silica Cage in Bioinspired Silica-Lysozyme Composites: A Multi-Technique Understanding of Elusive Protein-Material Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8030-8037. [PMID: 35738569 PMCID: PMC9261187 DOI: 10.1021/acs.langmuir.2c00836] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Lysozyme is widely known to promote the formation of condensed silica networks from solutions containing silicic acid, in a reproducible and cost-effective way. However, little is known about the fate of the protein after the formation of the silica particles. Also, the relative arrangement of the different components in the resulting material is a matter of debate. In this study, we investigate the nature of the protein-silica interactions by means of solid-state nuclear magnetic resonance spectroscopy, small-angle X-ray scattering, and electron microscopy. We find that lysozyme and silica are in intimate contact and strongly interacting, but their interaction is neither covalent nor electrostatic: lysozyme is mostly trapped inside the silica by steric effects.
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Affiliation(s)
- Francesco Bruno
- Magnetic
Resonance Center (CERM), University of Florence, via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Lucia Gigli
- Magnetic
Resonance Center (CERM), University of Florence, via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Giovanni Ferraro
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
- Consorzio
per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia, 3, Sesto Fiorentino 50019, Italy
| | - Andrea Cavallo
- CERTEMA
S.c.a.r.l., S.P. Del
Cipressino Km 10, Cinigiano 58044, Italy
| | | | - Gil Goobes
- Department
of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Emiliano Fratini
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
- Consorzio
per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia, 3, Sesto Fiorentino 50019, Italy
| | - Enrico Ravera
- Magnetic
Resonance Center (CERM), University of Florence, via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, Sesto Fiorentino 50019, Italy
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Mandal A, Boatz JC, Wheeler TB, van der Wel PCA. On the use of ultracentrifugal devices for routine sample preparation in biomolecular magic-angle-spinning NMR. JOURNAL OF BIOMOLECULAR NMR 2017; 67:165-178. [PMID: 28229262 PMCID: PMC5445385 DOI: 10.1007/s10858-017-0089-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/19/2017] [Indexed: 05/07/2023]
Abstract
A number of recent advances in the field of magic-angle-spinning (MAS) solid-state NMR have enabled its application to a range of biological systems of ever increasing complexity. To retain biological relevance, these samples are increasingly studied in a hydrated state. At the same time, experimental feasibility requires the sample preparation process to attain a high sample concentration within the final MAS rotor. We discuss these considerations, and how they have led to a number of different approaches to MAS NMR sample preparation. We describe our experience of how custom-made (or commercially available) ultracentrifugal devices can facilitate a simple, fast and reliable sample preparation process. A number of groups have since adopted such tools, in some cases to prepare samples for sedimentation-style MAS NMR experiments. Here we argue for a more widespread adoption of their use for routine MAS NMR sample preparation.
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Affiliation(s)
- Abhishek Mandal
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Jennifer C Boatz
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Travis B Wheeler
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15260, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA.
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Hackel C, Zinkevich T, Belton P, Achilles A, Reichert D, Krushelnitsky A. The trehalose coating effect on the internal protein dynamics. Phys Chem Chem Phys 2012; 14:2727-34. [DOI: 10.1039/c2cp23098d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Krushelnitsky A, Zinkevich T, Mukhametshina N, Tarasova N, Gogolev Y, Gnezdilov O, Fedotov V, Belton P, Reichert D. 13C and 15N NMR study of the hydration response of T4 lysozyme and alphaB-crystallin internal dynamics. J Phys Chem B 2009; 113:10022-34. [PMID: 19603846 DOI: 10.1021/jp900337x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The response to hydration of the internal protein dynamics was studied by the means of solid state NMR relaxation and magic angle spinning exchange techniques. Two proteins, lysozyme from bacteriophage T4 and human alphaB-crystallin were used as exemplars. The relaxation rates R1 and R1rho of 13C and 15N nuclei were measured as a function of a hydration level of the proteins in the range 0-0.6 g of water/g of protein. Both proteins were totally 15N-enriched with natural 13C abundance. The relaxation rates were measured for different spectral bands (peaks) that enabled the characterization of the dynamics separately for the backbone, side chains, and CH3 and NH3+ groups. The data obtained allowed a comparative analysis of the hydration response of the protein dynamics in different frequency ranges and different sites in the protein for two different proteins and two magnetic nuclei. The most important result is a demonstration of a qualitatively different response to hydration of the internal dynamics in different frequency ranges. The amplitude of the fast (nanosecond time scale) motion gradually increases with increasing hydration, whereas that of the slow (microsecond time scale) motion increases only until the hydration level 0.2-0.3 g of water/g of protein and then shows almost no hydration dependence. The reason for such a difference is discussed in terms of the different physical natures of these two dynamic processes. Backbone and side chain nuclei show the same features of the response of dynamics with hydration despite the fact that the backbone motional amplitudes are much smaller than those of side chains. Although T4 lysozyme and alphaB-crystallin possess rather different structural and biochemical properties, both proteins show qualitatively very similar hydration responses. In addition to the internal motions, exchange NMR data enabled the identification of one more type of motion in the millisecond to second time scale that appears only at high hydration levels. This motion was attributed to the restricted librations of the protein as a whole.
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Affiliation(s)
- A Krushelnitsky
- Kazan Institute of Biochemistry and Biophysics, Kazan, Russia.
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