Force Field Effects on a β-Sheet Protein Domain Structure in Thermal Unfolding Simulations.

Abstract

The secondary structure propensities observed in protein simulations depend heavily on the force field parameters used. The existing empirical force fields often have difficulty in balancing the relative stabilities of helical and extended conformations. The resultant secondary structure bias may not be apparent in short simulations at room temperature starting from the native folded states. However, it can manifest itself dramatically at high temperatures and lead to large deviations from experimentally observed secondary structure propensities. Motivated by thermal unfolding simulations of several WW domains, which have a three-stranded β-sheet structure, we chose the FBP28 WW domain as a well-characterized system to investigate several AMBER force fields as well as parametrization of the NPSA (Neutralized, Polarized ionizable side chains with a solvent-accessible Surface Area-dependent term) implicit solvent model. The ff94 force field and two variants with altered parameters for the backbone torsion term were found to convert the native β-sheet structure directly to a single helix at high temperatures, whereas the ff96 force field produced significant non-native β-sheet content at high temperatures. The ff03 force field was able to reproduce the β-sheet-coil transition and experimentally observed unfolding pathways with both an explicit water solvent and the NPSA implicit solvent model at relatively low temperatures. However, the protein domain became predominantly helical after unfolding. Modification of the solvation parameter in the NPSA implicit solvent model was not sufficient to remedy this problem. The results imply that the intrinsic secondary structure bias in a force field cannot easily be solved by modifying a single parameter such as backbone torsion potential or a solvation parameter of a solvent model. Nevertheless, the results show that the AMBER ff03 force field together with an explicit solvent model or the NPSA implicit solvent model is a useful tool for studying the unfolding of both α- and β-sheet structure protein domains, and an integrative consideration of all force field parameters is likely to be necessary for a complete solution.