3.3 In silico analysis of the partial similarity of amino
acid sequence
Using the Property-Based Peptide Similarity Index PD for Two Sequences
tool, we
detected
24 peptide sets between αs1- and β-CN and 14 sets between αs1- and κ-CN
that showed PD values lower than 10 (Table 1). The lowestPD value, 5.30, was detected between amino acid sequences of
αs1-CN (E61–E70) and β-CN (I12–E21). On the other hand, the lowestPD value between αs1-CN and κ-CN was 8.47. Furthermore, we found
38 peptide sets with PD values lower than 10 between αs1- and
αs2-CN, 34 sets between αs2- and β-CN, 19 sets between αs2- and κ-CN,
and 18 sets between β- and κ-CN (Table S2).
In the above results, the domains where PD values were low
existed between αs- and β-CN. The peptide sets with the lowest PDvalues between each CN component are shown in Table 2. As a result,
αs1-CN had a particularly lowPD value against β- and κ-CN and the amino acid compositions in
these peptides were identical in 7/10 and 3/10 residues, respectively.
On the other hand, identical amino acid compositions of αs2-CN against
αs1- and β-CN were 6/10 and 7/10 residues, respectively. Of note, these
peptides included the particular ”SSSEE” amino acid sequence.