Examination of ethanol interactions with Trp‐cage peptide through MD simulations and intermolecular nuclear Overhauser effects

Abstract

AbstractMolecular dynamic (MD) simulations of the model protein Trp‐cage dissolved in 35% ethanol‐water at 298 K have been carried out using conventional force fields. The goal was to develop a better understanding of experimental intermolecular nuclear Overhauser effects (NOEs) that arise from interactions of ethanol methyl groups with hydrogens of the peptide. Cross‐relaxation terms ( ) for peptide N‐H hydrogens and several side chain groups were calculated from the MD trajectories. The simulations indicate that water preferentially solvates hydrogens at the peptide termini while ethanol preferentially accumulates at the other hydrogens of the peptide. Most of a calculated NOE arises from interaction of ethanol molecules in the first solvent layer with a peptide hydrogen. Calculated are qualitatively consistent with experimental values but are not in quantitative agreement. Results from MD trajectories calculated by using modified force fields for ethanol intended to reduce peptide‐methyl group interactions do not lead to better agreement between observed and calculated . Possible reasons for the poor predictions of from the MD trajectories are discussed.