The heme protein low frequency vibrational motions by self consistent normal mode analysis
Abstract
Vibrational dynamics of iron active sites in heme proteins and heme model compounds have been studied by normal mode analysis (NMA) and self consistent normal mode analysis (SCNMA). NMA is first used to identify and characterize the iron vibrational modes of the heme model Iron (II)octaethylporphyrin Fe(OEP), and the heme c type cytochrome f. The NMA, in conjunction with NRVS data, provides a good set of refined low temperature force constants. Then, SCNMA is applied to heme c type cytochrome f to study temperature dependent protein motion. Classical NMA assumes harmonic behavior and the protein mean square displacement (MSD) has a linear dependence on temperature. This is only consistent with low temperature experimental results. To connect the protein vibrational motions between low temperature and physiological temperature, we have incorporated a fitted set of anharmonic potentials into SCNMA. In addition, Quantum Harmonic Oscillator (QHO) 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 it may be the cause of the non-Gaussian behavior of the protein motions probed by Elastic Incoherent Neutron Scattering (EINS). The combined theory displays a dynamical transition caused by the softening of few ”torsional” modes in the low frequency regime (< 50cm-1 or < 6meV or > 0.6ps). 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.
Degree
Ph.D.
Advisors
Prohofsky, Purdue University.
Subject Area
Theoretical physics|Biophysics
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