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

Abstract

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.

Probing the Flexibility of the Bacterial Reaction Center: The Wild-Type Protein Is More Rigid Than Two Site-Specific Mutants

“…At low frequencies (in the THz, or meV, range), amorphous solids exhibit a pronounced excess of vibrational states over the Debye level, an excess known as the boson peak (44)(45)(46)(47)(48)(49)(50)(51). This boson peak is displayed equivalently here (Figure 3, a-d) for the three proteins around 1-3 meV, as already observed in many enzymes (13,37,(52)(53)(54)(55)(56)(57). This indicates that the presence of soft modes is not affected by the mutations.…”

“…Data for the H subunit are not shown, as the mutation is found to have no effect on the force constants of its residues. between the increase of 〈u 2 〉 fluctuations, defining the dynamical transition, and the harmonic excess modes contained in the vibrational density of states and the boson peak (13).…”

Water soluble chlorophyll binding protein of higher plants: A most suitable model system for basic analyses of pigment–pigment and pigment–protein interactions in chlorophyll protein complexes

“…Therefore, the density of phonon states cannot be gathered from spectral hole burning (SHB) or FLN but is obtained separately by using the complementary method of inelastic neutron scattering (INS) as shown by Pieper et al (2004). INS studies revealed that the density of phonon states appears to be relatively similar for many different proteins (Orecchini et al, 2002;Paciaroni et al, 2003;Pieper et al, 2004;Kurkal-Siebert and Smith, 2006) but the spectral form was shown to vary with protein size (see e.g. Refs.…”

“…Refs. Orecchini et al, 2002;Kurkal-Siebert and Smith 2006) and due to interaction with the solvent (see e.g. Refs.…”

Dynamical Heterogeneity of Specific Amino Acids in Bacteriorhodopsin

“…The combination has proven to be effective for biological systems as shown by numerous studies. MD simulations were used to decompose measured spectra into contributions from different types of motions [14][15][16][17][18][19] and to study the effect of instrument resolution. 20 Previous MD simulations of the purple membrane for comparison with energy-resolved neutron scattering spectra 21,22 showed promising results but did not contain atomic models of the lipid environment and solvating water.…”