Molecular Modeling and Dynamic Simulation of Arabidopsis Thaliana Carotenoid Cleavage Dioxygenase Gene: A Comparison with Bixa orellana and Crocus Sativus.
Carotenoid cleavage dioxygenase (CCD) gene, ubiquitously found in numerous types of plants, are eminent in synthesizing the various volatile compounds (β-ionone, C13-norisoprenoid, geranylacetone) known as apocarotenoids. These apocarotenoids have various biological functions such as volatile signals, allelopathic interaction and plant defense. In Arabidopsis genome sequence, four potential CCD genes have been identified namely CCD1, CCD4, CCD7, and CCD8. These four genes give rise to diverse biological functions with almost similar sequence identity. In this investigation, an in silico analysis was proposed to study CCD proteins in Arabidopsis thaliana, aiming at constructing three-dimensional (3D) structure for CCD1 proteins of Bixa orellana and Crocus sativus to observe the structural difference among AtCCD (A. thaliana CCD) proteins. The quality of modeled structures was evaluated using RAMPAGE, PSVS protein validation server and Q Mean server. Finally, we utilised molecular dynamics simulation to identify the stability of the predicted CCD protein structures. The molecular dynamic simulation also revealed that AtCCD4 protein showed lesser stability when compared to other CCD proteins. Overall results from molecular dynamics analysis predicted that BoCCD1, CsCCD1, and AtCCD1 show similar structural characteristics. J. Cell. Biochem. 118: 2712-2721, 2017. © 2017 Wiley Periodicals, Inc.
School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India.
R
R
Priya
School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India.
P
P
Sneha
Cenro de Investigacion Cientifica de Yucatan A.C. Calle 43 No. 130, Col. Chuburnade Hidalgo, Merida, 97200, Yucatan, Mexico.
Renata
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Rivera Madrid
School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India.
C George Priya
0000-0002-5971-8290
CGP
Doss
Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, 50603, Malaysia.
Pooja
P
Singh
School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India.
Ramamoorthy
R
Siva
D017360:Arabidopsis / Q000201:enzymology*; D029681:Arabidopsis Proteins / Q000737:chemistry*; D031212:Bixaceae / Q000201:enzymology*; D027622:Crocus / Q000201:enzymology*; D049308:Dioxygenases / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D013045:Species Specificity
D029681:Arabidopsis Proteins; D049308:Dioxygenases; C431939:carotenoid cleavage dioxygenase 1
APOCAROTENOID; CAROTENOID; CAROTENOID CLEAVAGE DIOXYGENASE; MOLECULAR DYNAMIC SIMULATION; MOLECULAR MODELING