Zeitschrift für Informatik und Systembiologie

Modeling Calcium Dependent Protein Kinase Isoform 1 from Cicer arietinum (chick pea)

Abstract

Lakshmi Pillai and K. R. Pardasani

The homology based 3-Dimensional structure prediction of calcium dependent protein kinase Isoform 1 From Cicer arietinum (chick pea) was carried out using bioinformatics tools. The CPK1 sequence on Protein BLAST analysis for homology search revealed 100 hits and Out which a few had significant E score (E <0.005) and better sequence similarity. Multiple sequence alignment analysis of CPK1 using MultAlin and HHpred showed above 90% similarities with protein sequences of Thermotoga petriphila (Hypothetical protein), Geobacillus stereothermophilus (1w91; 99.5%; E score=1.2 E-11), Thermoanaerobacterium saccharolyticum (1uhv; 99.4%; E score=2.9 E-11) and Bacillus stereothermophilus (1qw9; 98.5%; E score=4.9 E-6) from the PDB database. The secondary structure of CPK1 using PSIPRED VIEW revealed many helices, strands and coils in the protein structure. The tertiary structure prediction of CPK1 by MODELLER 8v2 showed a (ß/á) 8 fold. The program VERIFY 3D assessed the quality of the predicted structure of CPK1 with acceptable scores.