Low-temperature protein dynamics: a simulation analysis of interprotein vibrations and the boson peak at 150 k.
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 approximately 2-2.5 meV, originates from approximately 10(2) 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.
Kurkal-Siebert
Vandana
V
Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany. vandana.kurkal@iwr.uni-heidelberg.de
Smith
Jeremy C
JC
D003080:Cold Temperature; D003198:Computer Simulation; D009211:Myoglobin / Q000737:chemistry*; D009502:Neutrons; D025341:Principal Component Analysis; D012542:Scattering, Radiation; D013816:Thermodynamics
D009211:Myoglobin