X-ray Absorption Fine Structure Calculations in Combination with QM/MM Methods. Applications to Metalloproteins


Sergio D. Dalosto


X-ray absorption spectroscopy (XAS) is extensively used in physics, materials science, chemistry, biology and geochemistry. It is applied to study crystalline solids, disordered systems, liquids and gaseous molecules. In addition, XAS is element specific and always detectable. The XAS-derived structural information (~ 5 Ň around the absorbing atom) is as precise as X-ray or NMR spectroscopy. In particular, XAS is the only alternative when the crystal structure of a metalloproteins is not available and the metal is silent (e.g. Cu(I) and Zn(II)) to other spectroscopies such as NMR, EPR, ESEEM, and absorption. However, in order to obtain structural information it is necessary to use a model compound and a reliable procedure to calculate amplitudes and phase parameters to fit the XAS experimental findings. We use ab-initio methods in combination with molecular mechanics (QM/MM) to provide a molecular structural model and an ab-initio real-space multiple-scattering code (FEFF) to calculate these parameters. In this work we intended to provide an overview of XAS spectroscopy and QM/MM methods. The procedure is applied to the study of two metalloproteins, one containing Cu(I) and another Zn(II).


1. Cu(I)-Atx1 is a cytosolic yeast copper chaperone that delivers copper to the transport ATPase Ccc2 in the trans-Golgi network. So far the structure of Cu(I)-Atx1 was characterized by NMR and XAS experiments. But these two spectroscopies have shown controversial results about the ligands around the Cu(I) binding site. We show here that the combination of QM/MM methods help to understand the experimental findings and serve as first step towards the characterization of the possible role of surrounding residues for the translocation of copper in metallochaperones.

2. For C-terminal zinc-binding domain of the SecA ATPase, we study the coordination of the 22-residue Zn(II)-binding domain (ZBD) from the coli preprotein translocase subunit SecA using QMMM methods. Recently proposed models based on NMR, XAFS and X-ray studies differ on the coordination geometry around the Zn(II), but we show that can be reconcile using ab-initio methods. ††††


 Author Information

            Name:††††††††††††††††††††††††† Sergio D. Dalosto

            Mentorís name:        ††† Zachary H. Levine

            Division:              †††††††† Electron and Optical Physics Division† †

            Laboratory:              ††† Physics Laboratory

            Building:                  †††† 245

            Room:                      ††† B116

            Mail Stop:                 †† 8411

            Telephone #:            †††† 301-975-8351

            Fax #:                      †††† 301-208-6937

            Email:                    †††††† sergio.dalosto@nist.gov

            Sigma Xi:                 †††† No

            Category:                †††† Physics