N Dimakis et al 2009 J. Phys.: Conf. Ser. 190 012198 doi:10.1088/1742-6596/190/1/012198
N Dimakis1,3, T Mion1, C Ramirez1 and G Bunker2
Show affiliationsWe present an efficient and accurate method for calculating XAFS Debye-Waller factors for deformed active sites of hemoproteins and metal substituted hemes. Based on the Normal Coordinate Structural Decomposition scheme, the deformation of the porphyrin macrocycle is expressed as a linear combination of the normal modes of the planar species. In our approach, we identify the modes that contribute most to the deformation. Small metal-porphyrin structures which match the macrocycle structural deformation of the deformed hemoprotein site are used to calculate the Debye-Waller parameters at sample's temperature. The Debye-Waller factors are directly obtained by calculating the normal mode spectrum of the corresponding metal-porphyrin structure using Density Functional Theory. Our method is tested on Ni-tetraadamantyl porphyrin and cytochrome c structures with more than 500 available scattering paths.
87.15.M- Spectra of biomolecules
87.15.La Mechanical properties
87.15.B- Structure of biomolecules
87.80.-y Biophysical techniques (research methods)
87.64.-t Spectroscopic and microscopic techniques in biophysics and medical physics
Issue 1 (2009)
N Dimakis et al 2009 J. Phys.: Conf. Ser. 190 012198
K Amemiya et al 2009 J. Phys.: Conf. Ser. 190 012108
D de Ligny et al 2009 J. Phys.: Conf. Ser. 190 012178
Hidekazu Ikeno et al 2009 J. Phys.: Conf. Ser. 190 012005
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