Comparison of SecondaryStructure Formation Using10 Different Force Fields in Microsecond Molecular Dynamics Simulations

摘要

We have compared molecular dynamics (MD) simulations of a β-hairpin forming peptide derived from the protein Nrf2 with 10 biomolecular force fields using trajectories of at least 1 μs. The total simulation time was 37.2 μs. Previous studies have shown that different force fields, water models, simulation methods, and parameters can affect simulation outcomes. The MD simulations were done in explicit solvent with a 16-mer Nrf2 β-hairpin forming peptide using Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amber ff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, GROMOS96 53a6, CHARMM27, and OPLS-AA/L force fields. The effects of charge-groups, terminal capping, and phosphorylation on the peptide folding were also examined. Despite using identical starting structures and simulation parameters, we observed clear differences among the various force fields and even between replicates using the same force field. Our simulations show that the uncapped peptide folds into a native-like β-hairpin structure at 310 K when Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amberff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, orGROMOS96 53a6 were used. The CHARMM27 simulations were able to formnative hairpins in some of the elevated temperature simulations, whilethe OPLS-AA/L simulations did not yield native hairpin structuresat any temperatures tested. Simulations that used charge-groups orpeptide capping groups were not largely different from their uncappedcounterparts with single atom charge-groups. On the other hand, phosphorylationof the threonine residue located at the β-turn significantlyaffected the hairpin formation. To our knowledge, this is the firststudy comparing such a large set of force fields with respect to β-hairpinfolding. Such a comprehensive comparison will offer useful guidanceto others conducting similar types of simulations.