Pattern Similarity Analysis of Amino Acid Sequences for Peptide Emulsification

Abstract

A new computer program for homology similarity search (HSS) was introduced. Application of the HSS to peptide sequences of short peptides with fewer 32 amino acid residues has explained the underlying mechanism of their emulsifying ability. It was found that certain regularity in the frequency of alternate polar/apolar cycle with high hydrophobic similarity density was required to obtain good emulsion. To supplement this required regularity, charge distribution, molecular flexibility, and a structural torsion caused by a proline residue might also play roles. Keywords: Homology similarity search; peptide emulsion; pattern similarity; amino acid sequence; QSAR; hydrophobicity distribution