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.
Published in:
Physical Review E 82,4 (2010)
Link to original published article:
http://dx.doi.org/10.1103/PhysRevE.82.041917
Date of Version
October 2010
Recommended Citation
Guo, J. G.; Budarz, T.; Ward, J. M.; and Prohofsky, E. W., "Dynamical transition in proteins and non-Gaussian behavior of low-frequency modes in
self-consistent normal mode analysis" (2010). Department of Physics and Astronomy Faculty Publications. Paper 1238.
https://docs.lib.purdue.edu/physics_articles/1238