Journal de protéomique et bioinformatique
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Classification of Protein Structural Classes using Isoluecine and Lysine Amino Acids

K. Manikandakumar, K. Gokul Raj, R. Srikumar and S. Muthukumaran

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 classification of a new structure is difficult 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 classification 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 flat protein primary structure only. The classification rate is achieved with an accuracy of 52%. This method is alternative for experimental determination of structural classification from X-ray crystallography or NMR spectroscopy etc.