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A New Perspective for Sequence Analysis – Carbon Content

Parul Johri, Mrunal Gokhale

Abstract


The sequence alignment of proteins is an approach which relies on measuring the changes in protein sequences in terms of the differences in the alignment of amino acids in the sequences. It is a technique in bioinformatics which is used for the alignment of protein sequences to identify the regions of similarity whose presence is attributed to the existence of structural, functional and evolutionary relationships between the sequences. The elemental composition of proteins signifies the basic level of biological organization. The key elements in all amino acids are hydrogen, carbon, oxygen, nitrogen and sulphur. These elements are responsible for giving the amino acids the properties of hydrophobicity/hydrophilicity which play an important role in protein interactions. The hydrophobic amino acids characteristically have greater number of carbon atoms as carbon is the main element which contributes to hydrophobic interactions in proteins. On the basis of the hydrophobic/hydrophilic properties of the side chains, each amino acid is assigned a hydropathy index. The higher the index, the more hydrophobic the amino acid is. The presence of carbon contributes to a higher hydropathy index. Thus the overall distribution of carbon in a protein contributes to its hydrophobicity. For analyzing protein sequence, their alignment is done which relies on measuring the changes in protein sequences in terms of the differences in amino acids. This difference cannot be felt merely by comparing the amino acid sequences but also the atomic content of those sequences. Carbon is the prime element which contributes majorly towards the dogmatic force in all chemical reactions-hydrophobic interaction. Carbon being the major atom and the main atom that contributes towards the hydrophobicity of the protein is analyzed in the current studies. By going one step further down at atomic level, much extensive analysis of the peptide sequences can be done. In the current work the authors have tried to analyze peptide sequences at atomic level taking mainly carbon atoms into consideration. During the analysis, it was found that the carbon distribution pattern of a peptide shows similarities with hydropathy profile, indicating that carbon distribution is an important factor contributing towards hydrophobicity. This was further utilized for studying certain proteins from both higher and lower organisms to find out whether they show a specific threshold of carbon content. The results indicate that there is a specific threshold of carbon content in all proteins either at species level or at their functional level. Thus the importance of carbon invoked the study analysis of proteins at the atomic level.

 


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