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
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Affiliations:
- Branch of Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, RAS
- 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
- Issue: Vol 49, No 3 (2023)
- Pages: 306-318
- Section: Articles
- URL: https://journals.rcsi.science/0132-3423/article/view/139154
- DOI: https://doi.org/10.31857/S0132342323030107
- EDN: https://elibrary.ru/PDPGKU
- ID: 139154
Cite item
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
About the authors
A. V. Danilkovich
Branch of Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, RAS
Author for correspondence.
Email: danilkovich@bibch.ru
Russia, 142290, Pushchino, prosp. Nauki 6
D. A. 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. M. Lipkin
Branch of Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, RAS
Email: danilkovich@bibch.ru
Russia, 142290, Pushchino, prosp. Nauki 6
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