Conference publications


XXVI conference

Characteristics and Role of Conformationally Predetermined Segments of aPpolypeptide Chain in Proteins

Anashkina A.A., Uroshlev L.A.1, Torshin I.Y.2, Esipova N.G., Tumanyan V.G.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Vavilova 32, Russia,

1Vavilov Institute of General Genetics of the Russian Academy of Sciences, 119991 Moscow, Gubkina, 3, Russia

2Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Leninskie Gory 1/3, Russia

1 pp. (accepted)

A beta-hairpin that includes a beta-bend can be viewed as an example of a composite local structure whose components play a different structural, energetic, and geometric role. In accordance with our concept, a fragment of an antiparallel beta-structure characterized by increased stability imposes a specific set of conformations on the linker. At the same time, the number of independent conformational variables decreases due to the formation of a pseudocycle of hydrogen bonds. As a result, the total number of conformations in this system does not exceed two for the main types of beta turns. Thus, the conformation of the beta-turn is determined by the context. It should be emphasized that beta-turn is in a certain conformation, regardless of the sequence, even if this conformation is sterically unprofitable (the so-called “forbidden” conformations). In this study, we studied the amino acid sequences and three-dimensional structures of beta turns of four types: I, I ’, II, and II’. Based on a representative dataset, we found that the sequence and structure together ensure the stability of the context part. In spite to predetermined character of the beta-bend some peculiarities in amino acid composition rather than in sequence take place. Contacts within beta­hairpin and its part as well as long­distance contacts were estimated by Voronoi­Delaunay tessellation. Degree of residues conservation in beta­structural part and in beta­bend separately was determined by the position-weight matrices. Possible biological implementations are discussed.

This work was supported by the Russian Foundation for Basic Research (projects No. 17-04-02105 and 18-54-00037).


1. Torshin, I. Y., Batyanovskii, A. V., Uroshlev, L. A., Esipova, N. G., & Tumanyan, V. G. Noncanonical and Strongly Disallowed Conformations of the Backbone in Polypeptide Chains of Globular Proteins // Biophysics 63(2), 2018. Pp. 149-153.

2. Torshin, I. Y., Batyanovskii, A. V., Uroshlev, L. A., Esipova, N. G., & Tumanyan, V. G. The relationship between the sign of the polypeptide backbone angle omega and the type of the side chain radical of amino-acid residues // Biophysics 62(3), 2017. Pp. 342-347.

3. Torshin, I. Y., Uroshlev, L. A., Esipova, N. G., & Tumanyan, V. G. Descriptive statistics of disallowed regions and various protein secondary structures in the context of studying twisted β-hairpins // Biophysics 61(1), 2016. Pp. 6-12.

4. Uroshlev, L. A., Torshin, I. Y., Batyanovskii, A. V., Esipova, N. G., & Tumanyan, V. G. Disallowed conformations of a polypeptide chain as exemplified by the β-turn of the β-hairpin in the α-spectrin SH3 domain // Biophysics 60(1), 2015. Pp. 1-9.

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