A comparative study of two different force fields on structural and thermodynamics character of H1 peptide via molecular dynamics simulations.
The dynamics and thermodynamics character of H1 peptide in aqueous solution has been investigated through temperature replica exchange molecular dynamics (T-REMD) simulations using two different force fields (OPLS-AA and GROMOS 43A1). The two independent T-REMD simulations were completed starting from initial conformations alpha-helix and beta-sheet, respectively. Each replica was run for 300 ns. The performance of each force field was assessed from the parameters such as the distributions of backbone dihedral angles, the number of native hydrogen bond, root mean square deviations (RMSD) of C(alpha) atoms and all heavy atoms, formation of beta-turn, the stability of folded beta-hairpin structure and the favorite conformations of different force fields. The simulation using GROMOS 43A1 force field starting from alpha-helix structure sampled the conformation cluster which C(alpha) RMSD was 0.05 nm from beta-sheet structure and the cluster contains 39% of all conformations. The simulation using OPLS-AA force field produced more sampling in P(II)region than in GROMOS 43A1 force field. The both force field simulations produced some sampling in the alpha region, but the probabilities of the conformations including any helical content were only 1-2%. Under the both force fields, the beta-turn structures exhibited higher stability than alpha-helix structures and the folded beta-hairpin structures. In the GROMOS 43A1 force field, the free energy change from the unfolded state to the hairpin state was in good agreement with the results of several experiments about some beta-peptides (not the H1 peptide) and the other molecular dynamics simulations of H1 peptide. However, the folded beta-hairpin structure was more destabilized in the OPLS-AA force field than in the GROMOS 43A1 force field and experiments.
Cao
Zanxia
Z
Key Lab of Biophysics in universities of Shandong (Dezhou University) Dezhou, China, 253023. jhwyh@yahoo.com.cn.
Wang
Jihua
J
D000818:Animals; D006224:Cricetinae; D006860:Hydrogen Bonding; D008647:Mesocricetus; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D011328:Prions / Q000737:chemistry; D017510:Protein Folding; D055550:Protein Stability; D017433:Protein Structure, Secondary; D012984:Software; D013816:Thermodynamics
D010455:Peptides; D011328:Prions