Bioinformatics Analysis of Evolution of Secondary Structures of Protein Trypsin Beta

Abstract

Impact of divergence of amino acid sequences of protein during evolution on the secondary structures of polypeptide and phylogenetic significance of different secondary structures such as alpha helix, beta sheet and random coil in evolution are not known . Due to conservation of conformationally identifiable regions through evolution, in closely related species, the amino acid sequence will show close similarity, thereby giving rise to similar structural motifs after folding the proteins. To understand the most conserved secondary structure element of a protein, we have conducted a bioinformatics work for molecular evolution of protein trypsin beta as a sample in order to analysis the phylogeny of secondary strucutres (alpha helix, beta sheet and random coil) of proteins Trypsin Beta among 25 species. In this method we retrieved amino acid sequences of these proteins from 25 species from protein data bank then folded each individually into 3-D structure using the software J-Pred. From the folded sequence it was possible to identify sequences in regions forming alpha helix, Beta sheet, random coil, which we retrieved and individually ligated end-end to obtain peptides made up of sequence in the random coil, alpha helix and beta sheet conformations ( final functional shape).Then examined the phylogentic trees built after aligning the sequence using four different multiple alignment protocols. The result has assumed that random coil of Trypisn beta was phylogentically most conserved .This project plays significant role in understanding the role of molecular evolution of proteins and their phylogenic significance.