Classifi cation of Protein Structural Classes using Isoluecine and Lysine Amino Acids

Abstract

Exploration of the structural organisation of proteins is essential for understanding of the mechanisms of protein folding and function, and for insights into protein evolution. Protein structure comparison can provide useful information on the biological function of a protein and can imply evolutionary relationships between proteins with low sequence similarity. Structural biology and structural genomics are expected to produce many three-dimensional protein structures in the near future. Each new structure raises questions about its function and evolution. Correct functional and evolutionary classifi cation of a new structure is diffi cult for distantly related proteins and error-prone using simple statistical scores based on sequence or structure similarity. The objective of this study is to classifying the protein structural classes using key amino acid residues as Isoluecine (I) and Lysine (K), which is without any complicated mathematical or statistical representations. The classifi cation of structural class is based on, grouping of 20 different amino acids with the comparison of isoluecine and lysine amino acid residues only. The combination of grouping of amino acids with the individual amino acid comparison will represent structural classes of the given protein sequences. This technique is tested over 40801 (inclusive of side chains, i.e., chain A, B, 1, 2, etc) proteins belonging to 67 different families randomly selected from All Alpha, All Beta, Alpha plus Beta and Alpha by Beta protein classes with the fl at protein primary structure only. The classifi cation rate is achieved with an accuracy of 52%. This method is alternative for experimental determination of structural classifi cation from X-ray crystallography or NMR spectroscopy etc.

A Comprehensive Assessment and Perception of Genetically Modified Foods

“…Genetically modified corn has been approved as an animal feed in several countries, but information about the fate of genetically modified DNA [39,40] and protein in vivo is insufficient. Genetically modified corn Bt11 is developed by inserting a recombinant DNA [41,42] sequence encoding insecticidal Cry1Ab protein from Bacillus thuringiensis. The Genetic modification involves the insertion or deletion of genes [43].…”

Secondary Structural Analysis of Families of Protein Sequences using Chaos Game Representation

“…[2] Converted CGR pattern of DNA sequences into structures and used the distances between them to find out phylogenetic proximity. [10][11][12][13][14][15] analyzed different proteome and genome sequences.…”