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Translations of Published Articles
On the choice of force fields for studying the molecular dynamics of ion peptides and their dimers
A. V. Danilkovichab, D. A. Tikhonovc, E. V. Sobolevc, T. E. Shadrinaab, I. P. Udovichenkoab a Pushchino State University, Pushchino, Russia
b Pushchino Branch of M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic
Chemistry, RAS, Pushchino, Russia
c Institute of Mathematical Problems of Biology RAS – the Branch of Keldysh Institute of
Applied Mathematics, Russian Academy of Sciences, Pushchino, Russia
Abstract:
The paper presents comparative data on the impact of force-fields AMBER (ff03, ff99SB, and ff96) on the results of molecular dynamics experiments with dimeric molecules formed by ion-peptide $\mathrm{NH_2\text-(RADA)_4\text-COOH}$ in the $\beta$-conformation at two temperatures (300 K and 320 K). It is shown that an MD simulation in explicit water environment is the most informative approach. The use of different force-fields has a significant influence on the stability of the initial molecular conformation of the peptide over time. Finally, the simulation in ff99SB environment provides significant stability of antiparallel $\beta$-structure of the dimer at 300 K, while ff96 not only ensures the highest stability of the initial b-peptide conformation at higher temperatures, but also enhances the retention of antiparallel $\beta$-conformation, which determines the ability of $\mathrm{NH_2\text-(RADA)_4\text-COOH}$ peptides to self-organization.
Key words:
RADA16, forcefields, molecular dynamic, MD, ff03, ff99SB, ff96, AMBER.
Received 24.05.2018, Published 21.06.2018
Citation:
A. V. Danilkovich, D. A. Tikhonov, E. V. Sobolev, T. E. Shadrina, I. P. Udovichenko, “On the choice of force fields for studying the molecular dynamics of ion peptides and their dimers”, Mat. Biolog. Bioinform., 13, Suppl. (2018), t29–t38
Linking options:
https://www.mathnet.ru/eng/mbb361 https://www.mathnet.ru/eng/mbb/v13/i3/p29
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Abstract page: | 162 | Full-text PDF : | 39 | References: | 25 |
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