Low-Temperature Protein Physics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K.

An understanding of low-frequency, collective protein dynamics at low temperatures can furnish valuable information on functional protein energy landscapes, on the origins of the protein glass transition and on protein−protein interactions. Here, molecular dynamics (MD) simulations and normal-mode analyses are performed on various models of crystalline myoglobin in order to characterize intra- and interprotein vibrations at 150 K. Principal component analysis of the MD trajectories indicates that the Boson peak, a broad peak in the dynamic structure factor centered at about 2−2.5 meV, originates from 102 collective, harmonic vibrations. An accurate description of the environment is found to be essential in reproducing the experimental Boson peak form and position. At lower energies other strong peaks are found in the calculated dynamic structure factor. Characterization of these peaks shows that they arise from harmonic vibrations of proteins relative to each other. These vibrations are likely to furnish valuable information on the physical nature of protein−protein interactions.