Dynamics of 24 Self-Assembling H-(RADA) 4 -OH Peptides Complexed in Bi-Layered Structure with Layers in  syn  and  anti  Orientation

A. V. Danilkovich; Данилкович А. В.; D. A. Tikhonov; Тихонов Д. А.; V. M. Lipkin; Липкин В. М.

doi:10.31857/S0132342323030107

Dynamics of 24 Self-Assembling H-(RADA)₄-OH Peptides Complexed in Bi-Layered Structure with Layers in syn and anti Orientation

Authors: Danilkovich A.V.¹, Tikhonov D.A.²^,3, Lipkin V.M.¹
Affiliations:
1. Branch of Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, RAS
2. Institute of Mathematical Problems of Biology – the Branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences
3. Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences
Issue: Vol 49, No 3 (2023)
Pages: 306-318
Section: Articles
URL: https://rjmseer.com/0132-3423/article/view/670623
DOI: https://doi.org/10.31857/S0132342323030107
EDN: https://elibrary.ru/PDPGKU
ID: 670623

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Abstract

H-(RADA)₄-OH peptide in water tends to form biolgels at physiological conditions. Thusly made scaffold is formed of fibrils resulted from peptides self-assembling. Fibrils have two external hydrophilic layers, while hydrophobic one is situated between of them. Bio gels by the H-(RADA)₄-OH peptides are considered to be a prominent source for designed extra cellular matrix aimed to cell cultures of different types. Little is known about detailed structure the filament structure and β-sheets peptide composition. We have designed and studied molecular dynamics of bi-layered protofilament structures with β-sheets formed of parallel or anti-parallel peptide chains. Method of molecular dynamics was used to study H-(RADA)₄-OH peptide complexes at 80 and 300 K. While the most stable peptide complex was found to consist of anti-parallel peptides, had the lowest free energy and the least deviation of atom coordinates, yet another stable structure of the peptide complex was identified as 24-mer of parallel peptides with two β-sheets placed in syn orientation. These results underlined the importance of factors, directing the initial stages of the H-(RADA)₄-OH peptide self-assembling in solution.

Keywords

self-assembly, scaffold, filament structure, polar peptides, H-(RADA)₄-OH

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