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OJBTM
Online Journal of Bioinformatics ©
Volume 8 (1):1-7, 2007
In silico tools for
evaluating conservation homology among interleukins
Krupanidhi S1*, Madhukar SS2, Doughman
SD1,3
1Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthinilayam
- 515 134 AP, 2Department of Bioinformatics, Sathyabama
ABSTRACT
Krupanidhi S, Madhukar
SS, Doughman SD, In Silico
Tools for evaluating conservation homology amongst interleukins, Online J
Bioinformatics, 8 (1) : 1-7, 2007. Interleukins (IL) of the hematopoietin
family of cytokines were analysed to evaluate the
consensus homology in relation to their sequence alignments and biological
functions. An interspecies IL-2 protein comparison among a few chosen
members of the Class Eutherians (true placental
mammals) confirmed the homology between humans and chimps as the closest related
class members. Macaca constituted an early
offshoot of the primary cluster. Related sequences of IL-2 through IL-9
of Homo sapiens were obtained by NCBI and /or BLAST search
Upon submitting these related IL sequences on-line to the ClustalW programme, a rooted
tree, viz., cladogram, appeared with two primary IL
clusters, and a multiple sequence alignment. Each primary cluster pair had
redundant biological functions. Tthe derived phylogenetic tree suggested a hypothetical ancestral
origin, an early period of gene duplication, and an extended period of
divergence and specialization among all the interleukins analyzed. In the
amino acid sequence alignment, a residue analyses among chosen IL family
members in humans revealed that there was relatively limited homology; however,
there was hydrophobic residue conservation and preserved secondary structure
consensus. Finally, a protein data base (PDB) search of ILs allowed a three dimensional analysis of IL-6 using Rasmol, which revealed 5 α-helices with predicted amphipathic faces.
Key words:
In Silico, Conservation, Homology, proteins, ClustalW, Rasmol, interleukins, Hematopoietin family.