Presentations

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, nastya@eimb.ru

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

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).

References

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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