Study of the interaction of the oxidoreductase laccase of Pleurotus ostreatus with gold nanoparticles and phenolic compounds through empirical and in silico techniques

Maestría en ingeniería química enfocada en bioprocesos, metodos computacionales, experimentales, bioinformática y diseño de experimentos con análisis probabilísticos

Autores:: Monsalve Villamil, Daniel Andrés

Tipo de recurso:

Fecha de publicación:: 2021

Institución:: Universidad de los Andes

Repositorio:: Séneca: repositorio Uniandes

Idioma:: eng

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dc.title.none.fl_str_mv	Study of the interaction of the oxidoreductase laccase of Pleurotus ostreatus with gold nanoparticles and phenolic compounds through empirical and in silico techniques
title	Study of the interaction of the oxidoreductase laccase of Pleurotus ostreatus with gold nanoparticles and phenolic compounds through empirical and in silico techniques
spellingShingle	Study of the interaction of the oxidoreductase laccase of Pleurotus ostreatus with gold nanoparticles and phenolic compounds through empirical and in silico techniques Gold nanoparticle synthesis Laccase Active site Interaction Oxidation Stability Nanopartículas Oxidorreductasas Lacasas Ingeniería
title_short	Study of the interaction of the oxidoreductase laccase of Pleurotus ostreatus with gold nanoparticles and phenolic compounds through empirical and in silico techniques
title_full	Study of the interaction of the oxidoreductase laccase of Pleurotus ostreatus with gold nanoparticles and phenolic compounds through empirical and in silico techniques
title_fullStr	Study of the interaction of the oxidoreductase laccase of Pleurotus ostreatus with gold nanoparticles and phenolic compounds through empirical and in silico techniques
title_full_unstemmed	Study of the interaction of the oxidoreductase laccase of Pleurotus ostreatus with gold nanoparticles and phenolic compounds through empirical and in silico techniques
title_sort	Study of the interaction of the oxidoreductase laccase of Pleurotus ostreatus with gold nanoparticles and phenolic compounds through empirical and in silico techniques
dc.creator.fl_str_mv	Monsalve Villamil, Daniel Andrés
dc.contributor.advisor.none.fl_str_mv	Sierra Ramírez, Rocio
dc.contributor.author.none.fl_str_mv	Monsalve Villamil, Daniel Andrés
dc.contributor.jury.none.fl_str_mv	Salcedo Galán, Felipe Contreras, Lydia M.
dc.contributor.researchgroup.es_CO.fl_str_mv	Grupo de Diseño de Productos y Procesos (GDPP) Rocio Sierra Ramirez. Línea de Investigación: Ingeniería Biológica
dc.subject.keyword.none.fl_str_mv	Gold nanoparticle synthesis Laccase Active site Interaction Oxidation Stability
topic	Gold nanoparticle synthesis Laccase Active site Interaction Oxidation Stability Nanopartículas Oxidorreductasas Lacasas Ingeniería
dc.subject.armarc.none.fl_str_mv	Nanopartículas Oxidorreductasas Lacasas
dc.subject.themes.es_CO.fl_str_mv	Ingeniería
description	Maestría en ingeniería química enfocada en bioprocesos, metodos computacionales, experimentales, bioinformática y diseño de experimentos con análisis probabilísticos
publishDate	2021
dc.date.issued.none.fl_str_mv	2021-08-03
dc.date.accessioned.none.fl_str_mv	2022-03-04T13:23:03Z
dc.date.available.none.fl_str_mv	2022-03-04T13:23:03Z
dc.type.spa.fl_str_mv	Trabajo de grado - Maestría
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dc.type.driver.spa.fl_str_mv	info:eu-repo/semantics/masterThesis
dc.type.content.spa.fl_str_mv	Text
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dc.identifier.uri.none.fl_str_mv	http://hdl.handle.net/1992/56101
dc.identifier.instname.spa.fl_str_mv	instname:Universidad de los Andes
dc.identifier.reponame.spa.fl_str_mv	reponame:Repositorio Institucional Séneca
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url	http://hdl.handle.net/1992/56101
identifier_str_mv	instname:Universidad de los Andes reponame:Repositorio Institucional Séneca repourl:https://repositorio.uniandes.edu.co/
dc.language.iso.es_CO.fl_str_mv	eng
language	eng
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Muddapur, «Biosynthesis of Metal Nanoparticles: A Review», Journal of Nanotechnology, vol. 2014, p. e510246, may 2014, doi: 10.1155/2014/510246. A. A. Yaqoob et al., «Recent Advances in Metal Decorated Nanomaterials and Their Various Biological Applications: A Review», Front. Chem., vol. 0, 2020, doi: 10.3389/fchem.2020.00341. K. Saha, S. S. Agasti, C. Kim, X. Li, y V. M. Rotello, «Gold Nanoparticles in Chemical and Biological Sensing», Chem. Rev., vol. 112, n.o 5, pp. 2739-2779, may 2012, doi: 10.1021/cr2001178 S. J. Amina y B. Guo, «A Review on the Synthesis and Functionalization of Gold Nanoparticles as a Drug Delivery Vehicle», IJN, vol. Volume 15, pp. 9823-9857, dic. 2020, doi: 10.2147/IJN.S279094. Y. Long, S. Wang, Y. Wang, F. Deng, y T. Ding, «Light-Directed Growth/Etching of Gold Nanoparticles via Plasmonic Hot Carriers», J. Phys. Chem. C, vol. 124, n.o 35, pp. 19212-19218, sep. 2020, doi: 10.1021/acs.jpcc.0c04672. F. d'Acunzo, C. Galli, y B. 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Claus, «Laccase: A Review of Its Past and Its Future in Bioremediation», Critical Reviews in Environmental Science and Technology, vol. 41, n.o 4, pp. 373-434, ene. 2011, doi: 10.1080/10643380902945706 K. Agrawal, V. Chaturvedi, y P. Verma, «Fungal laccase discovered but yet undiscovered», Bioresources and Bioprocessing, vol. 5, n.o 1, p. 4, ene. 2018, doi: 10.1186/s40643-018-0190-z. J. L. Cole, G. O. Tan, E. K. Yang, K. O. Hodgson, y E. I. Solomon, «Reactivity of the laccase trinuclear copper active site with dioxygen: an x-ray absorption edge study», J. Am. Chem. Soc., vol. 112, n.o 6, pp. 2243-2249, mar. 1990, doi: 10.1021/ja00162a025. S. M. Jones y E. I. Solomon, «Electron Transfer and Reaction Mechanism of Laccases», Cell Mol Life Sci, vol. 72, n.o 5, pp. 869-883, mar. 2015, doi: 10.1007/s00018- 38 014-1826-6. T. V. Tikhonova et al., «Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase», Proc Natl Acad Sci USA, vol. 117, n.o 10, pp. 5280-5290, mar. 2020, doi: 10.1073/pnas.1922133117. R. Dasgupta et al., «Chemical Exchange at the Trinuclear Copper Center of Small Laccase from Streptomyces coelicolor», Biophysical Journal, vol. 119, n.o 1, pp. 9-14, jul. 2020, doi: 10.1016/j.bpj.2020.05.022. M. Dagys, K. Haberska, S. Shleev, T. Arnebrant, J. Kulys, y T. Ruzgas, «Laccase' gold nanoparticle assisted bioelectrocatalytic reduction of oxygen», Electrochemistry Communications, vol. 12, n.o 7, pp. 933-935, jul. 2010, doi: 10.1016/j.elecom.2010.04.024. X. Yu, F. Zou, P. Yao, X. Huang, y Y. Qu, «Gold nanoparticles tune the activity of laccase in anionic reverse micelles», Soft Matter, vol. 10, n.o 34, p. 6425, jun. 2014, doi: 10.1039/C4SM01127A. R. G. Rayavarapu, W. Petersen, C. Ungureanu, J. N. Post, T. G. van Leeuwen, y S. Manohar, «Synthesis and Bioconjugation of Gold Nanoparticles as Potential Molecular Probes for Light-Based Imaging Techniques», International Journal of Biomedical Imaging, vol. 2007, p. e29817, ago. 2007, doi: 10.1155/2007/29817. M. Peixoto de Almeida et al., «Measurement of adsorption constants of laccase on gold nanoparticles to evaluate the enhancement in enzyme activity of adsorbed laccase», Phys. Chem. Chem. Phys., vol. 20, n.o 24, pp. 16761-16769, 2018, doi: 10.1039/C8CP03116A. F. Li, Z. Li, C. Zeng, y Y. Hu, «Laccase-Assisted Rapid Synthesis of Colloidal Gold Nanoparticles for the Catalytic Reduction of 4-Nitrophenol», J. Braz. Chem. Soc., 2016, doi: 10.21577/0103-5053.20160246. R. Sanghi, P. Verma, y S. Puri, «Enzymatic Formation of Gold Nanoparticles Using <i>Phanerochaete Chrysosporium</i&gt»;, ACES, vol. 01, n.o 03, pp. 154- 162, 2011, doi: 10.4236/aces.2011.13023. M. A. Faramarzi y H. Forootanfar, «Biosynthesis and characterization of gold nanoparticles produced by laccase from Paraconiothyrium variabile», Colloids and Surfaces B: Biointerfaces, vol. 87, n.o 1, pp. 23-27, oct. 2011, doi: 10.1016/j.colsurfb.2011.04.022. R. C. Susana y T. H. L., «Inhibitors of Laccases: A Review», Current Enzyme Inhibition, vol. 2, n.o 4, pp. 343-352, oct. 2006. M. Alfaro et al., «Comparative and transcriptional analysis of the predicted secretome in the lignocellulose-degrading basidiomycete fungus Pleurotus ostreatus: Functional study of P. ostreatus bioinfosecretome», Environmental Microbiology, vol. 18, n.o 12, pp. 4710-4726, dic. 2016, doi: 10.1111/1462-2920.13360. R. Castanera et al., «Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles», PLoS Genet, vol. 12, n.o 6, p. e1006108, jun. 2016, doi: 10.1371/journal.pgen.1006108. L. Kupski, G. M. Salcedo, S. S. Caldas, T. D. de Souza, E. B. Furlong, y E. G. 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Theory Comput., vol. 15, n.o 3, pp. 2022-2032, mar. 2019, doi: 10.1021/acs.jctc.8b01304. W. Tian, C. Chen, X. Lei, J. Zhao, y J. Liang, «CASTp 3.0: computed atlas of surface topography of proteins», Nucleic Acids Research, vol. 46, n.o W1, pp. W363- W367, jul. 2018, doi: 10.1093/nar/gky473. C. J. Williams et al., «MolProbity: More and better reference data for improved all-atom structure validation», Protein Sci, vol. 27, n.o 1, pp. 293-315, ene. 2018, doi: 10.1002/pro.3330. C. Colovos y T. O. Yeates, «Verification of protein structures: Patterns of nonbonded atomic interactions», Protein Sci., vol. 2, n.o 9, pp. 1511-1519, sep. 1993, doi: 10.1002/pro.5560020916. M. Wiederstein y M. J. Sippl, «ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins», Nucleic Acids Res, vol. 35, n.o Web Server issue, pp. W407-W410, jul. 2007, doi: 10.1093/nar/gkm290. R. Lüthy, J. U. Bowie, y D. 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Govindwar, «Enzymatic analysis, structural study and molecular docking of laccase and catalase from B. subtilis SK1 after textile dye exposure», Ecological Informatics, vol. 48, pp. 269-280, nov. 2018, doi: 10.1016/j.ecoinf.2018.10.003. M. A. Tadesse, A. D'Annibale, C. Galli, P. Gentili, y F. Sergi, «An assessment of the relative contributions of redox and steric issues to laccase specificity towards putative substrates», Org. Biomol. Chem., vol. 6, n.o 5, pp. 868-878, feb. 2008, doi: 10.1039/B716002J. L. Santagostini et al., «Probing the location of the substrate binding site of ascorbate oxidase near type 1 copper: an investigation through spectroscopic, inhibition and docking studies», The International Journal of Biochemistry & Cell Biology, vol. 36, n.o 5, pp. 881-892, may 2004, doi: 10.1016/j.biocel.2003.10.003. «Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase \| PNAS». https://www.pnas.org/content/117/10/5280 (accedido jul. 23, 2021). «Laccase», Structure-function studies of proteins, ene. 11, 2019. https://slavazaitsev914078364.wordpress.com/laccase/ (accedido jul. 23, 2021).
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dc.format.extent.es_CO.fl_str_mv	95 páginas
dc.publisher.es_CO.fl_str_mv	Universidad de los Andes
dc.publisher.program.es_CO.fl_str_mv	Maestría en Ingeniería Química
dc.publisher.faculty.es_CO.fl_str_mv	Facultad de Ingeniería
dc.publisher.department.es_CO.fl_str_mv	Departamento de Ingeniería Química y de Alimentos
institution	Universidad de los Andes
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spelling	Al consultar y hacer uso de este recurso, está aceptando las condiciones de uso establecidas por los autores.http://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Sierra Ramírez, Rociovirtual::5281-1Monsalve Villamil, Daniel Andrés018a0126-d928-4fe3-b7e7-47f70fcde54d600Salcedo Galán, FelipeContreras, Lydia M.Grupo de Diseño de Productos y Procesos (GDPP) Rocio Sierra Ramirez. Línea de Investigación: Ingeniería Biológica2022-03-04T13:23:03Z2022-03-04T13:23:03Z2021-08-03http://hdl.handle.net/1992/56101instname:Universidad de los Andesreponame:Repositorio Institucional Sénecarepourl:https://repositorio.uniandes.edu.co/Maestría en ingeniería química enfocada en bioprocesos, metodos computacionales, experimentales, bioinformática y diseño de experimentos con análisis probabilísticosThe evaluation of the interaction of gold nanoparticles and the phenolic compound chlorogenic acid with laccase isoforms produced by the white root fungus P. ostreatus was performed. Key interactions were evaluated both through in silico techniques and laboratory measurements. In the computational study, the stability of chlorogenic acid in the laccase active site in the presence of a gold nanoparticle was analyzed using molecular dockings and molecular dynamics. Parametrization of the non-standard 4 copper center active site of the enzyme was performed. Distances between copper ions and residues were close enough to those reported in the literature for laccases and multicopper oxidases. Chlorogenic acid was most stable near the three nuclear copper center, which is surprising because it is different from the expected kinetic configuration. Stable configurations near the mononuclear copper center were rarely found and the ligand showed a preference for histidines 143 and 145 in the enzyme active site. Presence of gold nanoparticle near the trinuclear center access of the catalytic pocket retained the ligand for longer inside the active site. Stabilization of chlorogenic acid in the laccase catalytic pocket can be related to higher activity during the oxidation processes, gold nanoparticle interference in ligand leaving active site could inhibit such oxidation as seen in the experimental work. The in silico study led to conclude that the laccase isoforms 2 and 10 share homology, 3D configuration and are 99% identical prior the translation processes. For all experiments, an enzyme extract was used where the presence of the laccase isoforms 2 and 10 was ensured. Furthermore, the experimental work was aimed to determine the influence of gold nanoparticles on chlorogenic acid oxidation and vice versa, that is, the influence of chlorogenic acid on the synthesis of gold nanoparticles. Using a central composite experimental design with temperature, amount of chlorogenic acid, and enzymatic activity as factors, it was found that the best reaction conditions for gold nanoparticle synthesis were 75,2°C and enzyme activity of 113 UL-1 in the presence of chlorogenic acid. Also, below 50°C and 80 UL-1 chlorogenic acid might inhibit nanoparticle synthesis. On the other hand, low chlorogenic acid oxidation rates were found when gold nanoparticles were present. Nanoparticle characterization was done though SEM and EDX analysis. Spherical 20 nm to 48 nm nanoparticles that agglomerate in 200 nm structures were found. Characterization suggests that a bionanoconjugate of laccase and gold nanoparticles may have formed. 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Study of the interaction of the oxidoreductase laccase of Pleurotus ostreatus with gold nanoparticles and phenolic compounds through empirical and in silico techniques

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