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

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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.

作者简介

A. Danilkovich

Branch of Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, RAS

编辑信件的主要联系方式.
Email: danilkovich@bibch.ru
Russia, 142290, Pushchino, prosp. Nauki 6

D. Tikhonov

Institute of Mathematical Problems of Biology – the Branch of Keldysh Institute of Applied Mathematics,
Russian Academy of Sciences; Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences

Email: danilkovich@bibch.ru
Russia, 142290, Pushchino, ul. Vitkevicha 1; Russia, 142290, Pushchino, ul. Institutskaya 3

V. Lipkin

Branch of Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, RAS

Email: danilkovich@bibch.ru
Russia, 142290, Pushchino, prosp. Nauki 6

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版权所有 © А.В. Данилкович, Д.А. Тихонов, В.М. Липкин, 2023

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