Comparison of two force fields in MD-simulations of alpha-helical structures in keratins

Molecular dynamic (MD) simulations based on two different force fields, CVFF and CFF91, were carried out in order to check their feasibility for the structural investigation of the wool intermediate filament (IF) monomeric unit. Selecting an ideal alpha-helix as start conformation, all MD-simulations with CVFF in vacuum show the alpha-helix to be unstable. Independently of the amino acid sequence of the alpha-helix, a new helical structure with a larger diameter arises during the MD-simulation, due to a shift of the intrahelical hydrogen bonds. However in simulations with surrounding water the alpha-helix remains stable throughout the simulations with the CVFF force field. In contrast to this, MD-simulations in vacuum based on the CFF91 force field are able to determine different stabilities for the alpha-helical start conformation of various IF-segments, that agree well with secondary structure predictions. The simulation results obtained with CFF91 in vacuum can likewise be verified using an explicit water environment. We found that higher partial charges attributed to the atoms of the amide groups that form the intrahelical hydrogen bonds are the reason for the superiority of the CFF91 force field.