Protein Characterization at atomic level: A Novel approach for sequence analysis

Carbon being the most omnipresent element in all the organic compounds is of great importance with regards to its structure and function. The fundamental structure of protein is composed of amino acids arranged in linear chain and folded to a globular form. All twenty amino acids consist of combination of only five different atoms that are Carbon, Nitrogen, Oxygen, Hydrogen and Sulphur. Depending on the property of their side chain the amino acids are classified as hydrophobic and hydrophilic. The allocation of the hydrophobic residue in a protein contributes majorly towards protein folding, protein interaction, active site formation and other biological functions. As carbon is the most important element which contributes to hydrophobic interaction in proteins, the hydrophobic amino acids characteristically have greater number of carbon atoms. In the present study, we have analyzed 4, 306 protein sequences of Escherichia coli, a gram negative, facultative anaerobic, rod shaped bacterium. All the protein sequences of Escherichia coli were scanned to get a profound view on carbon content and its distribution. The sequences were retrieved from proteome section of Uniprot KB (http://www.uniprot.org/uniprot/) database and atomic percentages were calculated with the aid of a dynamic programming algorithm and Microsoft Excel. The analysis of the atomic percentages calculated for the proteins revealed that there is a precise range of carbon percentage for all the Escherichia coli proteins (30%-33% carbon). Also the different categories of protein like transport protein, repressor protein, catalytic protein, inhibitory protein etc have discrete range of carbon percentages which could be further linked to their exact activity