4 - Central Institute of Brackishwater Aquaculture

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etter crystallographic R-factor and less E-value with the related family was aligned and used as a reference structure to build a 3D model for target protein. The model was constructed by using the program Modellergv2 under Windows. Modeller is a comparative protein structure modeling software. It is based on spatial restraints derived from the alignment and Probability Density Functions (PDFs) [Sali et al. 19931. The 3D model of a protein is obtained by optimization of the molecular PDFs such that the model violates the input restraints as little as possible. After building the protein 3D structure, in order to assess the overall stereo chemical quality of the modeled protein, Ramachandran plot analysis was performed using the program PROCHECK [Laskowski et al., 1993 ; Morris et al., 1992; Ramachandran et al., 19631. Further evaluation of modeled structure was done by VERIFY3D [Eisenberg et a/., 19971, Errat [Colovos and Yeates, 19931, Prove [Pontius et al., 19961 and WHAT-IF [Vriend, 19901 through SAVS: structure analysis and verification server (htt~://nihserver.mbi.ucla.edu/SAVS/). 2.2 Active Site Identification: Sites of activity in proteins usually lie in cavities. The size and shape of protein cavities dictates the three-dimensional geometry of ligands that must fit like a hand in glove. The binding of a substrate typically serves as a mechanism for chemical modification or conformational change of protein [Binkowski et al., 20031. Binding sites are often targeted by various llgands in attempts to interrupt related molecular processes. Active sites of a protein are a key factor for the flexible docking. Active sites of the target protein (Holliday junction DNA helicase RuvB) were predicted by using tool CASTp (computed atlas of surface topography of proteins) [Binkowski et al., 20031. CASTp provides resources for locating, delineating and measuring concave surface regions on three-dimensional structures of proteins. These include pockets located on protein surfaces and voids buried in the interior of proteins that are frequently associated with binding events. In addition, it measures the size of mouth openings of individual pockets for better accessibility of binding sites to various ligands and substrates. 3.1 Results and discussion Whole genome sequences of the human pathogen C. pneumoniae were analyzed to identify drug targets. Strain wise distribution of genes is summarized in Figure 2. A total number of 4388 protein coding genes from four strains were studied. Out of which 3948 genes having more than 100 amino acids in their coding sequence were selected. This was on the assumption that proteins more than 100 amino acids long are known to be able to affect the catalytic activity of proteins and participate in protein complex formation which affect their enzyme activity [Yang et al., 19991.
National Workshop-cum-Tralnlng on Bioinformaticr and Informalion Management in Aquaculture m Total number of proteln ~odlng gclics Gcncs where protcln are > IOOam~no ac~dscquc'ncc r Essential genes of C oneunionlac rn Csscnt~al non-hunian Iioniologues C P-AR33 C P.CWL029 C P-1138 C P TW183 I Figure 2: Gene distribution of four stra~ns of Chlamydoph~la pneumonlae After screening against the DEG database 1382 genes were identified as essential genes for four strains of C. pneumoniae. These genes are essential for survival of C, pneumoniae. Comparison of the screened essential genes with human genome resulted in identification of 147 genes which are essential and non-human homologous genes among four strains of C, pneumoniae. It was observed that though strains C.P-AR39, C.P-3138, C.P-TW183 show almost similar number of essential and non human homologous genes, the strain C.P-CWLO29 shows a marked increase in number of respective genes.
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4 - Central Institute of Brackishwater Aquaculture

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