In-silico structural modelling of cytochrome complex proteins of white turmeric (Curcuma zedoaria)
DOI:
https://doi.org/10.14719/pst.1436Keywords:
3D-structures, Ramachandran plot, Cytochrome proteins, Structural validationAbstract
Curcuma zedoaria (Christm.) Roscoe (white turmeric) is a perennial herbaceous plant of family Zingiberaceae and mainly found in the wild areas of tropical and subtropical regions worldwide. The cytochrome proteins in plants play important roles in promoting their growth and development, as well as protecting them from stresses and diseases. Cytochrome proteins like psbF, psbE, petB, petD, petN, petG, and ccsA play important roles in degradation of mis-folded proteins, ATP formation, cyclic electron flow and biogenesis of c-type cytochrome of C. zedoaria. However, due to lack of structural availability of these C. zedoaria cytochrome proteins in structural databases, the physiochemical parameters of sequences were estimated using Expasy ProtParam web tool. Self-Optimized Prediction Method with Alignment (SOPMA) server and MODELLER version 9.23 were used for modelling along with Qualitative Model Energy Analysis (QMEAN) and Protein Structure Analysis (ProSA) servers were implemented for validating the secondary and tertiary structures of these proteins. The obtained QMEAN4 values of the modelled cytochrome proteins were -2.04, -1.20, -3.01, -1.57, -2.11, -1.74 and -12.87. The Z-scores obtained from ProSA server were 0.5, -0.83, -1.5, -0.58, -0.02, 0.14 and -3.73. All seven modelled structures have been submitted to protein model database (PMDB). The derived results will be helpful in further investigations towards determining the crystal structure of the hypothetical proteins, structural motifs, physiochemical properties, and also protein-protein interaction studies of various cytochrome proteins.
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Copyright (c) 2022 Chandra Sekhar Tripathy, Bhaskar Chandra Sahoo, Manaswini Dash, Debasis Sahoo, Suprava Sahoo, Basudeba Kar
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