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

Genes

Sathishkumar Natarajan¹  Senthil Kumar Thamilarasan¹  Jong-In Park¹  Mi-Young Chung²  Ill-Sup Nou¹ 

[1] Department of Horticulture, Sunchon National University, Suncheon 57922, Korea; E-Mails:;Department of Agricultural Education, Sunchon National University, Suncheon 540-950, Korea; E-Mail:

关键词: myrosinase;    sinigrin;    Brassica oleracea;    homology modeling;    docking and dynamics;   

DOI  :  10.3390/genes6041315

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2015 by the authors; licensee MDPI, Basel, Switzerland.