<em>In silico</em> identification, phylogenetic analysis and protein modeling of EREBP-1 genes of <em>Phaseolus vulgaris</em>, <em>Arabidopsis thaliana</em> and<em> Cucumis sativus</em>

Abstract

Transcription factors (TFs) are proteins that bind to DNA and activate or repress gene expression at the transcriptional level. Ethylene-Responsive Element Binding Protein (EREBP) represents one such class of DNA binding proteins/TFs. In the present study, EREBP-1 gene of <em>Glycine max</em> was selected to find out similar genes in<em> Phaseolus vulgaris</em>, <em>Arabidopsis thaliana </em>and <em>Cucumis sativus</em> dicot plants by taking their protein sequences. A combined phylogenetic tree was constructed, which yielded four EREBP subgroups. From each subgroup, one protein sequence was evaluated, which had highest Bits (score) and lowest E-value. Consequently, two EREBPs of <em>P. vulgaris</em> and two of <em>C. sativus</em> were chosen from the four subgroups of the phylogenetic tree. Four EREBP structures were then modelled using <em>ab initio</em> based approach and were energy minimized. They were validated on the basis of Ramachandran plot analysis, where residues were in most favored region ranging from 75.80-87.70%. Further, intrinsically disordered regions were found out representing the ethylene-responsive nucleotide binding regions. All of the four modelled EREBP structures have been reported in this study with elaborate analysis and stability evaluation using a number of computational techniques.