Publication Details (including relevant citation information):
Jianguang Guo, Timo Budarz, Joshua M. Ward, and Earl W. Prohofsky; Phys. Rev. E, 2010, 82, 041917
Self-consistent normal mode analysis (SCNMA) is applied to heme c type cytochrome f to study temperature-dependent protein motion. Classical normal mode analysis assumes harmonic behavior and the protein mean-square displacement has a linear dependence on temperature. This is only consistent with low-temperature experimental results. To connect the protein vibrational motions between low and physiological temperatures, we have incorporated a fitted set of anharmonic potentials into SCNMA. In addition, quantum harmonic-oscillator theory has been used to calculate the displacement distribution for individual vibrational modes. We find that the modes involving soft bonds exhibit significant non-Gaussian dynamics at physiological temperature, which suggests that it may be the cause of the non-Gaussian behavior of the protein motions probed by elastic incoherent neutron scattering. The combined theory displays a dynamical transition caused by the softening of few “torsional” modes in the low-frequency regime (<50 cm−1 or <6 meV or >0.6 ps). These modes change from Gaussian to a classical distribution upon heating. Our theory provides an alternative way to understand the microscopic origin of the protein dynamical transition.
Address (URL): http://link.aps.org/doi/10.1103/PhysRevE.82.041917