Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations

Abstract

Secondary-structure forming tendencies are examined for six well-known protein force fields: AMBER94, AMBER96, AMBER99, CHARMM22, OPLS-AA/L, and GROMOS96. We performed generalized-ensemble molecular dynamics simulations of two peptides. One of these peptides is C-peptide of ribonuclease A, and the other is the C-terminal fragment from the B1 domain of streptococcal protein G. The former is known to form α-helix structure and the latter β-hairpin structure by experiments. The simulation results revealed significant differences of the secondary-structure forming tendencies among the force fields. Of the six force fields, the results of AMBER99 and CHARMM22 were in accord with experiments for C-peptide. For G-peptide, on the other hand, the results of OPLS-AA/L and GROMOS96 were most consistent with experiments. Therefore, further improvements on the force fields are necessary for studying the protein folding problem from the first principles, in which a single force field can be used for all cases.