International Journal of Computational Bioinformatics and In Silico Modeling
ABSTRACT: Shine-Dalgarno (SD) sequence is found just 5' to the translation initiation codon, part or all of a polypurine domain UAAGGAGGU is found in the prokaryotic mRNA ribosome binding site (RBS). The importance of the SD sequence for identification of the translation initiation site on the mRNA by the ribosome is very much clear, and thereby, translational efficiency is strongly affected by the spacing between the SD and the initiation codon. Although, whether there is a unique optimal spacing is not as clear. The definitions of the spacing as well as secondary structures have been complicated and obscured matters. A systematic study installed by the development of a novel modified algorithmic approach to detect the most probable RBS which is located at upstream of any gene of E. coli genome were undertaken by us, and in addition we have also developed an algorithm which picks up the absolute spacers between each RBS and AUG start codon. Moreover, in order to determine their expression rate in E. coli K-12 (MG1655) genomes all genes on the basis of their spacer lengths between RBS and AUG start codons of that gene were classified. A new insight to disclose the actual happening and ambiguity of E. coli K-12 (Mg1655) genome in a more efficient manner might be provided by this global gene analysis.
KeyWords: Shine dalgarno sequence, upstream, codon, ribosome binding site, highly expressed gene.
How to cite: Ahsan JB et. al. Int J Comput Bioinfo In Silico Model. 2(2) 2013: 89-93
ABSTRACT: OsCCCH-Zn-1 (LOC_Os05g45020) is differentially expressed under abiotic stresses as well as developmentally regulated. The aim of present study was to find out the conserved domain and its involvement in gene regulation by interacting with core GCC box motif. For this analysis 1K promoter region of OsCCCH-Zn-1 gene was retrieved from TIGR (v6.1) and core GCC box (GCCGCC) was identified in antisense strand using PLACE database. Presence of conserved domain in OsCCCH-Zn-1 protein was identified by InterProScan. 3D structure prediction of OsCCCH-Zn-1 protein was performed by I-TASSER. Stereochemical quality and accuracy was evaluated by Ramachandran plot analysis. DNA model of 25nt long promoter sequence having core GCCGCC motif was generated by 3D-DART. Interaction of OsCCCH-Zn-1 and GCCGCC motif was studied by HADDOCK server. Zinc finger, CCCH type domain was identified by InterProScan in OsCCCH-Zn-1 protein. While best template used for 3D structure prediction of OsCCCH-Zn-1 protein was lipase protein (PDB Id 1TIC). Ramachandran Plot of OsCCCH-Zn-1 protein shows that cumulatively 94.9% residues are in the allowed region, while 5.1% residues in disallowed region. While in the case of protein-DNA docked model of OsCCCH-Zn-1 lowest HADDOCK score of -41.0 +/- 9.6 and Z-score of -1.6 was observed when interacting with linear DNA segment.
KeyWords: Abiotic stress, CCCH-type Zinc Finger, Oryza sativa, 3D structure, I-TASSER, 3D-DART, HADDOCK
How to cite: Pandey DM and Kumar A. Int J Comput Bioinfo In Silico Model. 2(2) 2013: 94-103