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Volume 6   Issue 1   Year 2011
On The Choice of Force Fields for Studying the Molecular Dynamics of Ion Peptides and Their Dimers

Danilkovich A.V., Tikhonov D.A., Sobolev E.V., Shadrina T.E., Udovichenko I.P.

 Branch of Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
 Pushchino State University, Pushchino, Moscow Region, 142290, Russia
 Institute of Mathematical Problems of Biology, Russian Academy of Science, Pushchino, Moscow Region, 142290, Russia

danilkovich@fibkh.serpukhov.su

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 NH2-(RADA)4-COOH in the β-conformation at two temperatures (300K and 320K). 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 β-structure of the dimer at 300K, while ff96 not only ensures the highest stability of the initial b-peptide conformation at higher temperatures, but also enhances the retention of antiparallel β-conformation, which determines the ability of NH2-(RADA)4-COOH peptides to self-organization.

Key words: RADA16, forcefields, molecular dynamic, MD, ff03, ff99SB, ff96, AMBER.


 

Table of Contents Original Article
Math. Biol. Bioinf.
2011;6(1):53-62
doi: 10.17537/2011.6.53
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References Translation into English
Math. Biol. Bioinf.
2018;13(Suppl.):t29-t38
doi: 10.17537/2018.13.t29

Full text (eng., pdf)

 

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