Beta-Bends As An Example Of Conformationally Predetermined Segments Of Protein. Conditions Of Stabilization Of The Structure And Role Of Context

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Anastasia A. Anashkina1, Vladimir O. Chekhov2, Ivan Yu. Torshin3, Leonid A. Uroshlev4, Natalia G. Esipova5, Vladimir G. Tumanyan6
1EIMB RAS, Moscow, Russia, nastya@eimb.ru
2EIMB RAS, Moscow, Russia, bock@eimb.ru
3FIC IU RAS, Moscow, Russia, tiy135@yahoo.com
4IGG RAS, Moscow, Russia, leoniduroshlev@gmail.com
5EIMB RAS, Moscow, Russia, nge@eimb.ru
6EIMB RAS, Moscow, Russia, tuman@eimb.ru

Conformations of the local protein structures is determined by the balance of their own energy characteristics and the context (flanking regions). The conformation of a given fragment becomes predetermined if the contribution of the context is clearly defined. Beta bends were chosen as the object of the study due to availability of formalised classification of this structure, small number of variables that determine the conformation of a segment, as well as the beta bends high prevalence in the three-dimensional structures of proteins. Using the PDB data, a complete cluster analysis of the conformationally predetermined beta-bend segments of the four main types was performed. Statistical data on the conformational parameters, amino acid composition and the amino acid sequences in beta-bends and their flanking regions were summarized. Factors have been established that stabilize the beta bend (additional hydrogen bonds between the residues involved in the bend) and the beta hairpin, flanking the bend (presence of a conformationally stable peptide). The existence of such stabilizing hydrogen bonds is confirmed by quantum chemical calculations of the energy of the fragment including bending. Stabilization of the hairpin neck is achieved by a conformationally stable hexapeptide in the conformation of the beta strand that is included in the structure, which is also confirmed by the method of denaturing molecular dynamics.

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Nikita Ivanisenko
Nikita Ivanisenko
3 years ago

Thank you for interesting study! I have following questions and comments –
Is it possible to estimate individual energetic contribution of type 1-3 hydrogen bonds in the stability of the beta bends from ab initio calculations? In particular from the figure of the slide 3 it looks like type 1 hydrogen bond in the beta bends type II doesn’t have proper geometry, so another question if corresponding position (that is the second residue in the type II beta bends) was enriched with proline in the collected structural dataset, thus leading to disappearance of type 1 HB? Also it would be interesting to find out in which cases there is high impact of specific amino acid side chains on the energetic landscape of beta-bends

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