Sequence Analysis of Holins by Reduced Amino Acid Alphabet Model and Permutation Approaches

Sequence Analysis of Holins by Reduced Amino Acid Alphabet Model and Permutation Approaches

Objective: Holins are small proteins which perform many important functions in the cytoplasmic membrane of the cell. There is no crystal structure of holins reported in Protein Data Bank and hence computational sequence analysis is the only alternative to understand structure and functional consequences of these proteins. In the present work, we engaged several careful computational procedures to explore the important amino acid residues responsible for functioning of holins on membranes. Methods: To explore role of amino acid residues in holins, we used reduced amino acid alphabet model by reducing twenty amino acids to fifteen. Transmembrane regions in holin sequences are extracted and subjected to multiple sequence alignment to bring out the role of conserved amino acid residues. Further transmembrane regions in holins are permutated to different possible positions by keeping loops as static to understand the role of transmembrane and non transmembrane regions. Results: We found that the reduced amino acid alphabet model is successful, when no relationship is established between the proteins belonging to similar families. Also, the important physico-chemical properties conserved in the non-redundant holin sequences is explored in detail by computing correlation coefficients. Permutation of transmembrane regions in holins and database search showed that the holin sequence composition and arrangement is unique to perform its specific function. Conclusion: Analysis presented in this paper reveal the vital role of each and every amino acid residue in the holin and this may help to accurately model the structure to understand the sequence-structure-function relationship of holins on the membrane.