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Bioinformatics
Structure and features of amino acid sequences of Π-modules in OB-folds
E. V. Brazhnikov, A. V. Efimov Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
Abstract:
Stereochemical analysis has been performed for Π-modules from the large set of non-homologous protein structures containing the OB-fold. That module consists of two β-strands connected by a loop and placed in different sheets in such a way which looks as Greek letter Π. Total 70 non-homologous proteins at resolution not less than 2.5A˚ 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.
Key words:
OB-fold, \beta-strand, \alpha-helix, structural motif, folding, handedness.
Received 29.09.2022, 24.11.2022, Published 06.12.2022
Citation:
E. V. Brazhnikov, A. V. Efimov, “Structure and features of amino acid sequences of \Pi-modules in \mathrm{OB}-folds”, Mat. Biolog. Bioinform., 17:2 (2022), 441–451
Linking options:
https://www.mathnet.ru/eng/mbb498 https://www.mathnet.ru/eng/mbb/v17/i2/p441
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Abstract page: | 49 | Full-text PDF : | 13 | References: | 22 |
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