A Comparative Study of Two Different Force Fields on Structural and Thermodynamics Character of H1 Peptide via Molecular Dynamics Simulations

Abstract

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 a-helix and β-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 Ca atoms and all heavy atoms, formation of β-turn, the stability of folded β-hairpin structure and the favorite conformations of different force fields. The simulation using GROMOS 43A1 force field starting from a-helix structure sampled the conformation cluster which Ca RMSD was 0.05 nm from β-sheet structure and the cluster contains 39% of all conformations. The simulation using OPLS-AA force field produced more sampling in PII region than in GROMOS 43A1 force field. The both force field simulations produced some sampling in the a region, but the probabilities of the conformations including any helical content were only 1–2%. Under the both force fields, the β-turn structures exhibited higher stability than a-helix structures and the folded β-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 β-peptides (not the H1 peptide) and the other molecular dynamics simulations of H1 peptide. However, the folded β-hairpin structure was more destabilized in the OPLS-AA force field than in the GROMOS 43A1 force field and experiments.