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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, Onl J Bioinform., 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.