Methyl group dynamics and the onset of anharmonicity in myoglobin.
The role of methyl groups in the onset of low-temperature anharmonic dynamics in a crystalline protein at low temperature is investigated using atomistic molecular dynamics (MD) simulation. Anharmonicity appears at approximately 150 K, far below the much-studied solvent-activated dynamical transition at approximately 220 K. A significant fraction of methyl groups exhibit nanosecond time scale rotational jump diffusion at 150 K. The splitting and shift in peak position of both the librational band (around 100 cm(-1)) and the torsional band (around 270-300 cm(-1)) also differ significantly among methyl groups, depending on the local environment. The simulation results provide no evidence for a correlation between methyl dynamics and solvent exposure, consistent with the hydration-independence of the low-temperature anharmonic dynamics observed in neutron scattering experiments. The calculated proton mean-square fluctuation and methyl NMR order parameters show a systematic nonlinear dependence on the rotational barrier which can be described using model functions. The methyl groups that exhibit many rotational excitations are located near xenon cavities, suggesting that cavities in proteins act as activation centers of anharmonic dynamics. The dynamic heterogeneity and the environmental sensitivity of motional parameters and low-frequency spectral bands of CH(3) groups found here suggest that methyl dynamics may be used as a probe to investigate the relation between low-energy structural fluctuations and packing defects in proteins.
Krishnan
M
M
Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany.
Kurkal-Siebert
V
V
Smith
Jeremy C
JC
D003198:Computer Simulation; D003460:Crystallization; D008745:Methylation; D008954:Models, Biological; D008958:Models, Molecular; D009211:Myoglobin / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D010507:Periodicity; D017434:Protein Structure, Tertiary; D013696:Temperature; D014978:Xenon / Q000737:chemistry
D009211:Myoglobin; D014978:Xenon