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Matematicheskaya Biologiya i Bioinformatika, 2022, Volume 17, Issue 2, Pages 441–451
DOI: https://doi.org/10.17537/2022.17.441
(Mi mbb498)
 

Bioinformatics

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

E. V. Brazhnikov, A. V. Efimov

Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
References:
Abstract: 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.
Key words: OB-fold, $\beta$-strand, $\alpha$-helix, structural motif, folding, handedness.
Funding agency Grant number
Russian Foundation for Basic Research 20-04-00453
Received 29.09.2022, 24.11.2022, Published 06.12.2022
Bibliographic databases:
Document Type: Article
Language: Russian
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
Citation in format AMSBIB
\Bibitem{BraEfi22}
\by E.~V.~Brazhnikov, A.~V.~Efimov
\paper Structure and features of amino acid sequences of $\Pi$-modules in $\mathrm{OB}$-folds
\jour Mat. Biolog. Bioinform.
\yr 2022
\vol 17
\issue 2
\pages 441--451
\mathnet{http://mi.mathnet.ru/mbb498}
\crossref{https://doi.org/10.17537/2022.17.441}
\elib{https://elibrary.ru/item.asp?id=50158442}
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