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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509

Anastasia A. Anashkina¹, Vladimir O. Chekhov², Ivan Yu. Torshin³, Leonid A. Uroshlev⁴, Natalia G. Esipova⁵, Vladimir G. Tumanyan^6
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.