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Awad ME, Borrego-Sánchez A, Escamilla-Roa E, Hernández-Laguna A, Sainz-Díaz CI. Modeling of the adsorption of a protein-fragment on kaolinite with potential antiviral activity. APPLIED CLAY SCIENCE 2020; 199:105865. [PMID: 33078035 PMCID: PMC7556793 DOI: 10.1016/j.clay.2020.105865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 09/02/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
This work aimed at studying the potentiality of interactions between kaolinite surfaces and a protein-fragment (350-370 amino acid units) extracted from the glycoprotein E1 in the transmembrane domain (TMD) of hepatitis C virus capsid. A computational work was performed for locating the potential electrostatic interaction sites between kaolinite aluminol and siloxane surfaces and the residues of this protein-fragment ligand, monitoring the possible conformational changes. This hydrated neutralized kaolinite/protein-fragment system was simulated by means of molecular modeling based on atomistic force fields based on empirical interatomic potentials and molecular dynamic (MD) simulations. The MD calculations indicated that the studied protein-fragment interacted with the kaolinite surfaces with an exothermic process and structural distortions were observed, particularly with the hydrophilic aluminol surface by favorable adsorption energy. The viral units isolation or trapping by the adsorption on the kaolinite nanoparticles producing structural distortion of the peptide ligands could lead to the blockage of the entry on the receptor and hence a lack of viral activity would be produced. Therefore, these findings with the proposed insights could be an useful information for the next experimental and development studies in the area of discovering inhibitors of the global challenged hepatitis and other pathogenic viruses based on the phyllosilicate surface activity. These MD studies can be extended to other viruses like the COVID-19 interacting with silicate minerals surfaces.
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Affiliation(s)
- Mahmoud E Awad
- Department of Geology, Faculty of Science, Al-Azhar University, Nasr City, 11884 Cairo, Egypt
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
- Instituto Andaluz de Ciencias de la Tierra, CSIC-UGR, Av. de las Palmeras 4, 18100 Armilla, Granada, Spain
| | - Ana Borrego-Sánchez
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
- Instituto Andaluz de Ciencias de la Tierra, CSIC-UGR, Av. de las Palmeras 4, 18100 Armilla, Granada, Spain
| | - Elizabeth Escamilla-Roa
- Instituto Andaluz de Ciencias de la Tierra, CSIC-UGR, Av. de las Palmeras 4, 18100 Armilla, Granada, Spain
- Department of Computer Science, Electrical and Space Engineering, Luleå University of Technology, 97187 Luleå, Sweden
| | - Alfonso Hernández-Laguna
- Instituto Andaluz de Ciencias de la Tierra, CSIC-UGR, Av. de las Palmeras 4, 18100 Armilla, Granada, Spain
| | - C Ignacio Sainz-Díaz
- Instituto Andaluz de Ciencias de la Tierra, CSIC-UGR, Av. de las Palmeras 4, 18100 Armilla, Granada, Spain
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Wu M, Zhao S, Tang M, Jing R, Shao Y, Liu X, Dong Y, Li M, Liao Q, Lv G, Zhang Q, Meng Z, Liu A. Adsorption of sulfamethoxazole and tetracycline on montmorillonite in single and binary systems. Colloids Surf A Physicochem Eng Asp 2019. [DOI: 10.1016/j.colsurfa.2019.05.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Ranieri A, Di Rocco G, Millo D, Battistuzzi G, Bortolotti CA, Lancellotti L, Borsari M, Sola M. Thermodynamics and kinetics of reduction and species conversion at a hydrophobic surface for mitochondrial cytochromes c and their cardiolipin adducts. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.07.065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Hristova SH, Zhivkov AM. Adsorption of cytochrome c on montmorillonite nanoplates: Protein concentration dependence. J Colloid Interface Sci 2015; 446:252-62. [DOI: 10.1016/j.jcis.2015.01.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 01/05/2015] [Accepted: 01/13/2015] [Indexed: 11/25/2022]
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Effect of amine substituted at ortho and para positions on the electrochemical and electrocatalytic properties of cobalt porphyrins self-assembled on glassy carbon surface. Electrochim Acta 2014. [DOI: 10.1016/j.electacta.2013.10.157] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Castellini E, Bortolotti CA, Di Rocco G, Bernini F, Ranieri A. Enhancing Biocatalysis: The Case of Unfolded Cytochrome cImmobilized on Kaolinite. ChemCatChem 2013. [DOI: 10.1002/cctc.201200876] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Águila S, Vidal-Limón A, Alderete J, Sosa-Torres M, Vázquez-Duhalt R. Unusual activation during peroxidase reaction of a cytochrome c variant. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Ranieri A, Bernini F, Bortolotti CA, Castellini E. The Met80Ala point mutation enhances the peroxidase activity of immobilized cytochrome c. Catal Sci Technol 2012. [DOI: 10.1039/c2cy20347b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ranieri A, Bernini F, Bortolotti CA, Bonifacio A, Sergo V, Castellini E. pH-Dependent peroxidase activity of yeast cytochrome c and its triple mutant adsorbed on kaolinite. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:10683-10690. [PMID: 21776978 DOI: 10.1021/la201876k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The peroxidase activity of wild-type yeast cytochrome c and its triple mutant K72AK73AK79A adsorbed onto kaolinite was investigated as a function of pH and temperature. Both adsorbed proteins displayed an appreciable catalytic activity, which remained constant from pH 7 to pH 10, decreased below pH 7, and showed a remarkable increase at pH values lower than 4. In the whole pH range investigated the catalytic activity of the adsorbed wild-type cytochrome c was higher than that of the mutant. Both diffuse-reflectance UV-vis and resonance Raman spectroscopies applied on solid samples were used to probe the structural features responsible for the catalytic activity of the immobilized proteins. At neutral and alkaline pH values a six-coordinate low-spin form of cytochrome c was observed, while at pH < 7 the formation of a high-spin species occurred whose population increased at decreasing pH. The orientation and exposure of the heme to the substrate-strictly dependent on adsorption-was found to affect the peroxidase activity.
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Affiliation(s)
- Antonio Ranieri
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, I-41125 Modena, Italy
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Monari S, Ranieri A, Bortolotti CA, Peressini S, Tavagnacco C, Borsari M. Unfolding of cytochrome c immobilized on self-assembled monolayers. An electrochemical study. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.06.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Águila S, Vazquez-Duhalt R, Covarrubias C, Pecchi G, Alderete JB. Enhancing oxidation activity and stability of iso-1-cytochrome c and chloroperoxidase by immobilization in nanostructured supports. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2011.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Hung A, Mwenifumbo S, Mager M, Kuna JJ, Stellacci F, Yarovsky I, Stevens MM. Ordering surfaces on the nanoscale: implications for protein adsorption. J Am Chem Soc 2011; 133:1438-50. [PMID: 21208003 DOI: 10.1021/ja108285u] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Monolayer-protected metal nanoparticles (MPMNs) are a newly discovered class of nanoparticles with an ordered, striped domain structure that can be readily manipulated by altering the ratio of the hydrophobic to hydrophilic ligands. This property makes them uniquely suited to systematic studies of the role of nanostructuring on biomolecule adsorption, a phenomenon of paramount importance in biomaterials design. In this work, we examine the interaction of the simple, globular protein cytochrome C (Cyt C) with MPMN surfaces using experimental protein assays and computational molecular dynamics simulations. Experimental assays revealed that adsorption of Cyt C generally increased with increasing surface polar ligand content, indicative of the dominance of hydrophilic interactions in Cyt C-MPMN binding. Protein-surface adsorption enthalpies calculated from computational simulations employing rigid-backbone coarse-grained Cyt C and MPMN models indicate a monotonic increase in adsorption enthalpy with respect to MPMN surface polarity. These results are in qualitative agreement with experimental results and suggest that Cyt C does not undergo significant structural disruption upon adsorption to MPMN surfaces. Coarse-grained and atomistic simulations furthermore elucidated the important role of lysine in facilitating Cyt C adsorption to MPMN surfaces. The amphipathic character of the lysine side chain enables it to form close contacts with both polar and nonpolar surface ligands simultaneously, rendering it especially important for interactions with surfaces composed of adjacent nanoscale chemical domains. The importance of these structural characteristics of lysine suggests that proteins may be engineered to specifically interact with nanomaterials by targeted incorporation of unnatural amino acids possessing dual affinity to differing chemical motifs.
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Affiliation(s)
- Andrew Hung
- Department of Materials, and Institute for Biomedical Engineering, Imperial College London , London, UK, SW7 2AZ
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