Homology Modeling and in silico Characterization of a Hypothetical Protein of Arabidopsis lyrata ssp. Lyrata

Abstract

Arabidopsis lyrata, a plant belonging to brassicaceae, is a model organism for studying evolutionary and ecological genetics. Most of the proteins of this plant have remained uncharacterized and their functional roles are still to be elucidated. In this investigation, we have attempted to characterize one such hypothetical protein in terms of its physico-chemical properties, secondary and tertiary structure features by in silico study. The protein was classified under glycoside hydrolase family 28 having parallel beta helix repeat and pectin lyase fold based on CDD-BLAST and INTERPROSCAN analyses. The protein consisted of 404 amino acid residues with molecular weight 44278.5. Computed isoelectric point revealed the protein to be alkaline in nature and high value of aliphatic index indicated its thermostability. Low-range negative GRAVY index showed hydrophilic nature of the protein. Dominance of coil regions among secondary structural features revealed its stability. Further, tertiary structure of the protein was modeled and quality of the model was checked using Verify3D. The compatibility scores above zero showed acceptable side chain environments indicating its good packing quality. Stereo-chemical properties of the protein were studied by Ramachandran plot. The value of Z score assessed through ProSA-web server was found to be negative showing the correctness of the generated model. 

Keywords: Arabidopsis lyrata, hypothetical protein, homology modeling, in silico characterization