Structure and features of amino acid sequences of $\Pi$-modules in $\mathrm{OB}$-folds

E. V. Brazhnikov ; A. V. Efimov

Matematičeskaâ biologiâ i bioinformatika, Tome 17 (2022) no. 2, pp. 441-451.

Résumé

Stereochemical analysis has been performed for $\Pi$-modules from the large set of non-homologous protein structures containing the $\mathrm{OB}$-fold. That module consists of two $\beta$-strands connected by a loop and placed in different sheets in such a way which looks as Greek letter $\Pi$. Total $70$ non-homologous proteins at resolution not less than $2.5\mathring{\mathrm{A}}$ have been selected for the analysis from $265$ suitable structures belonging to sixteen $\mathrm{OB}$-fold super families. We have disclosed two types of $\Pi$-modules: the fist with the connecting loop containing $\alpha$-helix, and second one without helix. Entrance of protein chain into second $\beta$-sheet is carried out by the same arch with conformation $\beta\beta\beta\alpha_{\mathrm{L}}\beta_{\mathrm{p}}$. In most cases, $85\%$ of total, $\alpha$-positions are occupied by glycine residue, while at entrance in the loop such residues are absent. Occupancy frequency of $\Pi$-modules has been obtained in dependence on the loop length. Spatial pathway of structures of all modules are superimposed very well. Structural alignment of amino acid for $\Pi$-module sequences allows us to determine the key positions of the hydrophobic, hydrophilic, and glycine residues.

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