4 - Central Institute of Brackishwater Aquaculture

Natlonal Workshop-cum-Tralnlng on BioinfonnaUco and Intomution Management in Aqwcultum
Table 2: The predicted active sites of Holliday junction DNA helicase RuvB
protein.
S. No. / Cavity Area 1 Cavitv
Volume
1333.5
4. Conclusion
Seven common non-human homologous essential genes were identified among
C, pneumoniae strains. Out of the identified targets Holliday junction DNA
helicase RuvB plays important role in DNA recombination and repair. Inhibition of
this protein stops genomic stability such as to protect genomes from doublestrand
breakage or inter-strand cross-linkage [Tuteja et al., 2006; Frick, 20031.
The non homogeneity of the sequence with the human genome rules out the
cross interference of the drugs designed specifically against it with the host
metabolom. A homology model of Holliday junction DNA helicase RuvB was built
by homology modeling. The model was validated using Ramachandran's plot,
VERIFY3D, ERRAT and PROCHECK and WHAT-IF programs to arrive at a reliable
and stable model for structure based drug design. Validation programs showed
that the homology model scores are similar to crystal structure of the template.
Acknowledgement
We are also thankful to The Department of Biotechnology, Government of India
for the funds to set up a bioinformatics infrastructure facility at our Department
of Biotechnology and Medical Engineering, at National Institute of Technology,
Rourkela where this work has been ~erformed.
References
Binkowski, T.A., Naghibzadeh, S. and Liang, I. (2003). CASTp: Computed Atlas
of Surface Topography of proteins. Nucleic Acids Research, 31, 3352-3355.
Bowman, G.D., ODonnell, M. and Kuriyan, 3. (2004) Structural analysis of a
eukaryotic sliding DNA clamp-clamp loader complex. Nature , 429, 724-730.
Cazzola, M.A., Matera, M.G.B. and Blasi, F. (2004). Macrolide and occult infection
in asthma. Current Opinion in Pulmonary Medicine, 10, 7-14.
Colovos, C. and Yeates, T.O. (1993). Verification of protein structures: patterns
of non-bonded atomic interactions. Protein Science, 2, 1511-1519.
Davies, I.M., Brunger, A.T. and Weis, W.I. (2008). Improved structures of fulllength
p97, an AAA ATPase: implications for mechanisms of nucleotidedependent
conformational change. Structure, 16, 715-726.