Protein evolution: The deciphering of latent facets - correlation of synthesis profiles of ribosomally directed proteins and enzyme directed peptides

Key facets pertaining to the evolution of proteins have been probed, using as springboard, the relevant data bases constructed from (i) 60 ribosomally directed proteins, whose 3D structures are known and having 10,000 residue s and (ii) from 73 enzyme directed peptides, comprising of 524 residues. Th e preference profiles, both in terms of the choice of neighbours and the pl acement of the peptide bonds, have been delineated with respect to each of the 20 coded amino acids. By and large, the preference profile from both th e sets are similar, thus giving importance to the nature of the side chains of the coded amino acids. The predictive power of the preference profile h as been tested with good results, thus demonstrating the evidence of common preference pathways for peptide formation during evolution. The ribosomall y directed protein synthesis, controlled by the genome, proceeds by the add ition of single residues at a time. On the other hand, the enzyme directed peptide synthesis largely operates in a more energy conscious block mode, w here each constituent of a large enzyme ensemble is engaged in precisely as sembling the modules and transfering them to the adjacent one, thus realizi ng a sequence specific peptide synthesis. Of significance is the fact that, in spite of such divergence in assembly, predictions for neighbour prefere nces in ribosomally directed protein synthesis work well when applied to en zyme directed peptide synthesis. The findings here are significant since th ey provide (i) a clear picture of directed peptide synthesis in the absence of direct genomic control, (ii) evidence for the preferred formation of pe ptide bonds using protein templates, (iii) they also provide evidence for t he presence of protein like structures, with catalytic activity, prior to t he freezing of the genetic code arising from dominance of the information s ystem and (iv) a logical approach to the evolution of a hierarchical patter n.