| Abstract
| - An understanding of low-frequency, collective protein dynamics at low temperatures can furnishvaluable information on functional protein energy landscapes, on the origins of the protein glass transitionand on protein−protein interactions. Here, molecular dynamics (MD) simulations and normal-mode analysesare performed on various models of crystalline myoglobin in order to characterize intra- and interproteinvibrations at 150 K. Principal component analysis of the MD trajectories indicates that the Boson peak, abroad 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 theexperimental Boson peak form and position. At lower energies other strong peaks are found in the calculateddynamic structure factor. Characterization of these peaks shows that they arise from harmonic vibrationsof proteins relative to each other. These vibrations are likely to furnish valuable information on the physicalnature of protein−protein interactions.
|
