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Molecular Modeling of Myrosinase from Brassica oleracea: A Structural Investigation of Sinigrin Interaction

1
Department of Horticulture, Sunchon National University, Suncheon 57922, Korea
2
Department of Agricultural Education, Sunchon National University, Suncheon 540-950, Korea
*
Author to whom correspondence should be addressed.
Academic Editor: Nora Nock
Genes 2015, 6(4), 1315-1329; https://doi.org/10.3390/genes6041315
Received: 1 October 2015 / Revised: 2 December 2015 / Accepted: 15 December 2015 / Published: 21 December 2015
Myrosinase, which is present in cruciferous plant species, plays an important role in the hydrolysis of glycosides such as glucosinolates and is involved in plant defense. Brassicaceae myrosinases are diverse although they share common ancestry, and structural knowledge about myrosinases from cabbage (Brassica oleracea) was needed. To address this, we constructed a three-dimensional model structure of myrosinase based on Sinapis alba structures using Iterative Threading ASSEmbly Refinement server (I-TASSER) webserver, and refined model coordinates were evaluated with ProQ and Verify3D. The resulting model was predicted with β/α fold, ten conserved N-glycosylation sites, and three disulfide bridges. In addition, this model shared features with the known Sinapis alba myrosinase structure. To obtain a better understanding of myrosinase–sinigrin interaction, the refined model was docked using Autodock Vina with crucial key amino acids. The key nucleophile residues GLN207 and GLU427 were found to interact with sinigrin to form a hydrogen bond. Further, 20-ns molecular dynamics simulation was performed to examine myrosinase–sinigrin complex stability, revealing that residue GLU207 maintained its hydrogen bond stability throughout the entire simulation and structural orientation was similar to that of the docked state. This conceptual model should be useful for understanding the structural features of myrosinase and their binding orientation with sinigrin. View Full-Text
Keywords: myrosinase; sinigrin; Brassica oleracea; homology modeling; docking and dynamics myrosinase; sinigrin; Brassica oleracea; homology modeling; docking and dynamics
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MDPI and ACS Style

Natarajan, S.; Thamilarasan, S.K.; Park, J.-I.; Chung, M.-Y.; Nou, I.-S. Molecular Modeling of Myrosinase from Brassica oleracea: A Structural Investigation of Sinigrin Interaction. Genes 2015, 6, 1315-1329. https://doi.org/10.3390/genes6041315

AMA Style

Natarajan S, Thamilarasan SK, Park J-I, Chung M-Y, Nou I-S. Molecular Modeling of Myrosinase from Brassica oleracea: A Structural Investigation of Sinigrin Interaction. Genes. 2015; 6(4):1315-1329. https://doi.org/10.3390/genes6041315

Chicago/Turabian Style

Natarajan, Sathishkumar, Senthil K. Thamilarasan, Jong-In Park, Mi-Young Chung, and Ill-Sup Nou. 2015. "Molecular Modeling of Myrosinase from Brassica oleracea: A Structural Investigation of Sinigrin Interaction" Genes 6, no. 4: 1315-1329. https://doi.org/10.3390/genes6041315

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