This article is cited in 4 papers

Mathematical Modeling

Considering usage of different force-fields for molecular dynamic studies of the ionic peptides and their dimers

A. V. Danilkovich^ab, D. A. Tikhonov^c, E. V. Sobolev^c, T. E. Shadrina^ab, I. P. Udovichenko<sup>ab

a</sup> Pushchino State University, Pushchino, Moscow Region, Russia
^b Branch of Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
^c Institute of Mathematical Problems of Biology, Russian Academy of Science, Pushchino, Moscow Region, 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.

UDC: 577.112.6/.7+577.13

Received 18.02.2011, Published 04.03.2011