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.