title: Zinc cysteine active sites of metalloproteins: a density functional theory and x-ray absorption fine structure study.
abstract: Density functional theory (DFT) and x-ray absorption fine structure (XAFS) spectroscopy are complementary tools for the biophysical study of active sites in metalloproteins. DFT is used to compute XAFS multiple scattering Debye Waller factors, which are then employed in genetic algorithm-based fitting process to obtain a global fit to the XAFS in the space of fitting parameters. Zn-Cys sites, which serve important functions as transcriptional switches in Zn finger proteins and matrix metalloproteinases, previously have proven intractable by this method; here these limitations are removed. In this work we evaluate optimal DFT nonlocal functionals and basis sets for determining optimal geometries and vibrational densities of states of mixed ligation Zn(His)(4-n)(Cys)(n) sites. Theoretical results are compared to experimental XAFS measurements and Raman spectra from the literature and tabulated for use.
authors: Department of Physics and Geology, University of Texas-Pan American, Edinburg, TX 78539, USA. ndimakis@gmail.com
authors: Nicholas
authors: N
authors: Dimakis
authors: Mohammed Junaid
authors: MJ
authors: Farooqi
authors: Emily Sofia
authors: ES
authors: Garza
authors: Grant
authors: G
authors: Bunker
mesh_terms: D015502:Absorptiometry, Photon; D000465:Algorithms; D001665:Binding Sites; D055592:Biophysical Phenomena; D001703:Biophysics; D003545:Cysteine / Q000737:chemistry* / Q000378:metabolism; D008667:Metalloproteins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D013059:Spectrum Analysis, Raman; D014961:X-Ray Diffraction; D015032:Zinc / Q000737:chemistry* / Q000378:metabolism
chemical_list: D008667:Metalloproteins; D015032:Zinc; D003545:Cysteine