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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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2
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Aubrecht J, Pospelova V, Kikhtyanin O, Veselý M, Kubička D. Critical evaluation of parameters affecting Cu nanoparticles formation and their activity in dimethyl adipate hydrogenolysis. Catal Today 2022. [DOI: 10.1016/j.cattod.2021.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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3
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Adiram-Filiba N, Ohaion E, Verner G, Schremer A, Nadav-Tsubery M, Lublin-Tennenbaum T, Keinan-Adamsky K, Lucci M, Luchinat C, Ravera E, Goobes G. Structure and Dynamics Perturbations in Ubiquitin Adsorbed or Entrapped in Silica Materials Are Related to Disparate Surface Chemistries Resolved by Solid-State NMR Spectroscopy. Biomacromolecules 2021; 22:3718-3730. [PMID: 34333966 DOI: 10.1021/acs.biomac.1c00495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein immobilization on material surfaces is emerging as a powerful tool in the design of devices and active materials for biomedical and pharmaceutical applications as well as for catalysis. Preservation of the protein's biological functionality is crucial to the design process and is dependent on the ability to maintain its structural and dynamical integrity while removed from the natural surroundings. The scientific techniques to validate the structure of immobilized proteins are scarce and usually provide limited information as a result of poor resolution. In this work, we benchmarked the ability of standard solid-state NMR techniques to resolve the effects of binding to dissimilar silica materials on a model protein. In particular, the interactions between ubiquitin and the surfaces of MCM41, SBA15, and silica formed in situ were tested for their influence on the structure and dynamics of the protein. It is shown that the protein's globular fold in the free state is only slightly perturbed in the three silica materials. Local motions on a residue level that are quenched by immobilization or, conversely, that arise from the process are also detailed. NMR measurements show that these perturbations are unique to each silica material and can serve as reporters of the characteristic surface chemistry.
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Affiliation(s)
| | - Eli Ohaion
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Gilit Verner
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Avital Schremer
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | | | | | | | - Massimo Lucci
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Gil Goobes
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
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Al Dmour H, Kooli F, Mohmoud A, Liu Y, Popoola SA. Al and Zr Porous Clay Heterostructures as Removal Agents of Basic Blue-41 Dye from an Artificially Polluted Solution: Regeneration Properties and Batch Design. MATERIALS (BASEL, SWITZERLAND) 2021; 14:2528. [PMID: 34068006 PMCID: PMC8152262 DOI: 10.3390/ma14102528] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 11/17/2022]
Abstract
The removal of Basic Blue-41 dye molecules was carried out by using two doped porous clay heterostructures by aluminum (Al) or zirconium (Zr) species. The proposed method of synthesis showed its efficiency, starting from Al or Zr intercalated hydrolyzed species, prior to its reaction with dodecylamine (C12 amine) and tetraethyl orthosilicate (TEOS) as a silica source. The intercalated precursors and their porous clay heterostructures (PCH) derivatives were characterized by different techniques. Solid NMR technique proved the presence of Al species into the intercalated silica between the clay sheets, and in addition to Si in different environments within the PCH materials. The Zr-PCH material exhibited a higher surface area and pore volume compared to its Al-PCH counterpart, with a mesoporous character for both materials. A maximum removed amount of 279 and 332 mg/g was achieved and deduced from the Langmuir equation. The regeneration tests revealed that the removal efficiency of Zr-PCH was retained after five regeneration runs, with a loss of 15% of the original value; meanwhile, the Al-PCH lost 45% of its efficiency after only three cycles. A single-stage batch design was proposed based on the Langmuir isotherm parameters. The increase of the removal capacity of Zr-PCH led to the reduction of the required amounts for the target removal of BB-41 dye compared to Al-PCH.
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Affiliation(s)
- Hmoud Al Dmour
- Department of Physics, Faculty of Science, Mu’tah University, Mu’tah 61710, Jordan;
| | - Fethi Kooli
- Department of Chemistry, Faculty of Science, Islamic University of Madinah, Al-Madinah Al-Munawwarah 42351, Saudi Arabia;
| | - Ahmed Mohmoud
- Petroleum Technology, Operated Offshore Oil Field Development, Qatar Petroleum, Doha 3212, Qatar;
| | - Yan Liu
- Institute of Chemicals and Engineering Sciences, 1 Pesek Road, Jurong Island, Singapore 627833, Singapore;
| | - Saheed A. Popoola
- Department of Chemistry, Faculty of Science, Islamic University of Madinah, Al-Madinah Al-Munawwarah 42351, Saudi Arabia;
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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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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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7
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Hollow silica microspheres as robust immobilization carriers. Bioorg Chem 2019; 93:102813. [DOI: 10.1016/j.bioorg.2019.02.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 11/17/2022]
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8
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How does osteocalcin lacking γ-glutamic groups affect biomimetic apatite formation and what can we say about its structure in mineral-bound form? J Struct Biol 2019; 207:104-114. [DOI: 10.1016/j.jsb.2019.04.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 04/11/2019] [Accepted: 04/17/2019] [Indexed: 12/20/2022]
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9
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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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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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