Characteristics and Role of Conformationally Predetermined Segments of aPpolypeptide Chain in Proteins
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Vavilova 32, Russia, firstname.lastname@example.org
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).
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