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Open AccessArticle

Molecular Modeling of Epithiospecifier and Nitrile-Specifier Proteins of Broccoli and Their Interaction with Aglycones

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Departamento de Ingeniería Química, Universidad de Santiago de Chile, Avenida Libertador Bernardo O’Higgins 3363, Estación Central, Santiago 9170019, Chile
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Departamento de Ingeniería Informática, Universidad de Santiago de Chile, Avenida Libertador Bernardo O’Higgins 3363, Estación Central, Santiago 9170019, Chile
*
Author to whom correspondence should be addressed.
Molecules 2020, 25(4), 772; https://doi.org/10.3390/molecules25040772 (registering DOI)
Received: 23 December 2019 / Revised: 31 January 2020 / Accepted: 3 February 2020 / Published: 11 February 2020
(This article belongs to the Special Issue Computational Methods in Drug Design and Food Chemistry)
Glucosinolates are secondary plant metabolites of Brassicaceae. They exert their effect after enzymatic hydrolysis to yield aglycones, which become nitriles and epithionitriles through the action of epithiospecifier (ESP) and nitrile-specifier proteins (NSP). The mechanism of action of broccoli ESP and NSP is poorly understood mainly because ESP and NSP structures have not been completely characterized and because aglycones are unstable, thus hindering experimental measurements. The aim of this work was to investigate the interaction of broccoli ESP and NSP with the aglycones derived from broccoli glucosinolates using molecular simulations. The three-dimensional structure of broccoli ESP was built based on its amino-acid sequence, and the NSP structure was constructed based on a consensus amino-acid sequence. The models obtained using Iterative Threading ASSEmbly Refinement (I-TASSER) were refined with the OPLS-AA/L all atom force field of GROMACS 5.0.7 and were validated by Veryfy3D and ERRAT. The structures were selected based on molecular dynamics simulations. Interactions between the proteins and aglycones were simulated with Autodock Vina at different pH. It was concluded that pH determines the stability of the complexes and that the aglycone derived from glucoraphanin has the highest affinity to both ESP and NSP. This agrees with the fact that glucoraphanin is the most abundant glucosinolate in broccoli florets. View Full-Text
Keywords: broccoli; epithiospecifier protein; nitrile-specifier protein; aglycones; molecular docking broccoli; epithiospecifier protein; nitrile-specifier protein; aglycones; molecular docking
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MDPI and ACS Style

Román, J.; González, D.; Inostroza, M.; Mahn, A. Molecular Modeling of Epithiospecifier and Nitrile-Specifier Proteins of Broccoli and Their Interaction with Aglycones. Molecules 2020, 25, 772.

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