A novel 2D graphical representation of protein sequence based on individual amino acid

Abstract

AbstractThe primary structure, i.e., the amino acids sequence, plays determinant roles in dynamical folding process and stable structure of protein molecules, then how to put forward sequences based approaches to demonstrate the biological information of the primary sequence will facilitate correlative researches. In this article, we outline a novel 2D graphical representation on the basis of a selected pair of physiochemical properties of amino acids, which integrates both the electric and hydrophobic factors to demonstrate the characteristic features of proteins. This novel representation transforms protein into a zigzag curve uniquely and allows direct inspection of similarities/dissimilarities among different protein sequences with higher resolution than previous methods. From this representation, some efficient numerical descriptors are derived, by which we quantitatively analyze the evolutionary distances among the ND6 (NADH dehydrogenase subunit 6) protein sequences of eight species, the results are coincident with the actual evolutions, which illustrate the efficiencies of the present approach. This representation can also provide convenient tools and alternative studying strategies for protein sequences and structures analysis. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011