IDENTIFICATION OF DISTANT STRUCTURAL ORTHOLOG AND A POSSIBLE EVOLUTIONARY LINKAGE OF HSP60 - A FOLD BASED APPROACH

N. PADMADAS¹*, S. CHELLASAMY², S. DURAIRAJ^3
1School of Biotechnology and Bioinformatics, D.Y. Patil University, Navi Mumbai - 400 614, MS, India.
²School of Biotechnology and Bioinformatics, D.Y. Patil University, Navi Mumbai - 400 614, MS, India.
³Department of Advanced Zoology & Biotechnology, Loyola College, Chennai - 600 034, TN, India.
* Corresponding Author : naveenpadmadas@gmail.com

Received : 14-03-2015     Accepted : 04-05-2015     Published : 15-06-2015
Volume : 6     Issue : 1       Pages : 313 - 320
Int J Bioinformatics Res 6.1 (2015):313-320

Keywords : Independent component analysis (ICA), t-test, Support vector machine (SVM), feature selection, classification
Academic Editor : Shine Devaraj, Mrs. P. Rathi Suganya, Er. Neetesh Pandey
Conflict of Interest : None declared
Acknowledgements/Funding : The authors wish to thank D Y Patil University- School of Biotechnology and Bioinformatics for providing lab infrastructure to carry out this research.

Correct folding is imperative for a protein to perform its function. Failing to fold correctly can result in a misfolded or inactive protein. Along with several other factors, molecular chaperones play an integral role in folding. Heat shock proteins (HSPs) are a specialized group of chaperone proteins synthesized in all living organisms in response to stress. Among different Hsps, Hsp60 forms the most conserved chaperone present in eukaryotes and eubacteria. Homology is one of the most important concepts in Evolutionary biology and proteomics. Identifying a distant structural ortholog designates a connection of common descent between entities. It will be great evolutionary significance to explore the distant homologs of this protein. Different biological databases were searched. With no reported valid structural ortholog, Fold based method was used. PGenTHREADER was intensively used to identify different templates sequentially. Hsp60 structure was modeled and validated using various servers. Phylogenetic analysis using ClustalW2 and Mega 5 was carried out to find the most relevant distant homologs from the PGenTHREADER templates. Sub structural comparative study was carried out between Hsp60 structure and the newly found template using UCSF-CHIMERA. The first equatorial, first intermediate and second equatorial regions of Hsp60 and Signal Recognition Particle 54kDa (SRP54) were observed to be much conserved. Some deletions have occurred in the apical and second equatorial region. This study sheds light on the highly conserved nature of the chaperonin which has not got much diversified in the course of evolution and a possible linkage with SRP54 in the light of evolution. Also, the conserved nature of Hsp60 is very much evident from their highly limited homologs reported in databases.