Amino acid composition
For all available sequences of bacterial ribosomal S1 proteins, we collected and calculated the percentage of amino acid residues for each group (in accordance with the number of structural domains) (Analysis Amino acid composition,http://oka.protres.ru:4200). The data are presented in Table 2.
As mentioned above, the basic structural unit of ribosomal S1 proteins is the S1 domain, which is represented by a β-barrel with an additional α-helix between the third and fourth β-strands 47. Detailed analysis of the position-specific tendencies of amino acids in β-strands 48,49 revealed a predominance of large aromatic residues (Y, F, W) and β-branched amino acids (T, V, I). As can be seen from Table 2, V, I, F and T are specific for structural β-strands in ribosomal proteins S1. A and L are characteristics of an additional α-helix in the structure of the S1 domain. The predominance of ‘disorder-promoting’ residues E and K is explained by flexible linkers and terminus, as well as a flexible region in the S1 structural domain 7. As a rule, for the most representative phyla of S1 proteins containing four and six domains, the percentage of different amino acid residues is almost the same, which is associated with the conservatism of the S1 domain. Note that the alignment of the sequences between the individual domains in each group reveals a rather low percentage of identity, indicating that the structure scaffold (S1 domain) is obviously more important for the overall functioning of these proteins 9.