Joshua Ward - Dynamical transition in proteins and non-Gaussian behavior of low-frequency modes in self-consistent normal mode analysis

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      Publication Details (including relevant citation   information):

      Jianguang Guo, Timo Budarz, Joshua M. Ward, and Earl W.   Prohofsky; Phys. Rev. E, 2010,   82, 041917

      Abstract:

        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