title: Cloning, in silico characterization and prediction of three dimensional structure of SbDof1, SbDof19, SbDof23 and SbDof24 proteins from Sorghum [Sorghum bicolor (L.) Moench].
abstract: In the present study, four full-length Dof (DNA-binding with one finger) genes from Sorghum bicolor namely SbDof1, SbDof19, SbDof23, and SbDof24 were PCR amplified, gel eluted, cloned, and sequenced (accession number HQ540084, HQ540085, HQ540086, and HQ540087, respectively). These sequences were further characterized in silico by subjecting them to homology search, multiple sequence alignment, phylogenetic tree construction, and protein functional analysis, revealing their identity to Dof like proteins. Phylogenetic analysis of cloned SbDof genes along with other reported Dof proteins revealed existence of two major groups A and B, while group A was further bifurcated into two sub-groups (viz., I and II). Motif scan analysis of SbDof proteins revealed the presence of glycine- and alanine-rich profiles in SbDof1, while proline-rich profile was observed in SbDof23. Asparagines, methionine, and serine-rich profiles were common in case of both SbDof19 and SbDof24 proteins. The three dimensional structures of SbDof proteins were predicted by I-TASSER server based on multiple threading method. The modeled structures were refined by energy minimization and their stereo chemical qualities were validated by PROCHECK and QMEAN server indicating the acceptability of the predicted models. The final models were submitted to PMDB database with assigned PMDB IDs, i.e., PM0077395, PM0077396, PM0077397, PM0077398, and PM0076448 for SbDof1, SbDof19, SbDof23, SbDof24, and Dof domain, respectively. Based on gene ontology (GO) terms in I-TASSER server putative functions of modeled SbDof proteins were also predicted.
authors.affiliation: Department of Biotechnology, Integral University, Lucknow 226026, Uttar Pradesh, India.
authors.forename: Hariom
authors.initials: H
authors.lastname: Kushwaha
authors.forename: Shubhra
authors.initials: S
authors.lastname: Gupta
authors.forename: Vinay Kumar
authors.initials: VK
authors.lastname: Singh
authors.forename: Naveen C
authors.initials: NC
authors.lastname: Bisht
authors.forename: Bijaya K
authors.initials: BK
authors.lastname: Sarangi
authors.forename: Dinesh
authors.initials: D
authors.lastname: Yadav
mesh_terms: D000595:Amino Acid Sequence; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics; D020134:Catalytic Domain; D003001:Cloning, Molecular; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics; D017434:Protein Structure, Tertiary; D045868:Sorghum / Q000737:chemistry / Q000235:genetics; D013059:Spectrum Analysis, Raman; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; C407526:DAG1 protein, Arabidopsis; D004268:DNA-Binding Proteins; D010940:Plant Proteins; D014157:Transcription Factors