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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 Institute of Science and Technology.Chennai-600 119 TN, India. 3Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599 USA.

 

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.


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