X-ray Absorption Spectroscopy and Coherent X-ray Diffraction Imaging for Time-Resolved Investigation of the Biological Complexes: Computer Modelling towards the XFEL Experiment

16th International Conference on X-ray Absorption Fine Structure

Bugaev, A.L.^1,2 ; Guda, A.A.^1 ; Yefanov, O.M.^3,4 ; Lorenz, U.^3,5 ; Soldatov, A.V.^1 ; Vartanyants, I.A.^3,6

International Research Centre Smart Materials, Southern Federal University, Zorge street 5, Rostov-on-Don

344090, Russia^1

Department of Chemistry, University of Turin, Via P. Giuria 7, Turin

10125, Italy^2

Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg

D-22607, Germany^3

Center for Free-Electron Laser Science, DESY, Notkestraße 85, Hamburg

D-22607, Germany^4

Institute of Chemistry, University of Potsdam, Potsdam

D-14476, Germany^5

National Research Nuclear University, MEPhI (Moscow Engineering Physics Institute), Kashirskoe shosse 31, Moscow

115409, Russia^6

关键词: Coherent x-ray diffraction;    Coherent X-ray diffraction imaging;    Conformational state;    Molecular dynamics computer simulations;    Phosphoglycerate kinase;    Quantum chemistry calculations;    Synchrotron radiation source;    Time resolved experiments;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/712/1/012024/pdf
DOI  :  10.1088/1742-6596/712/1/012024

来源: IOP

【 摘 要 】

The development of the next generation synchrotron radiation sources - free electron lasers - is approaching to become an effective tool for the time-resolved experiments aimed to solve actual problems in various fields such as chemistry' biology' medicine' etc. In order to demonstrate' how these experiments may be performed for the real systems to obtain information at the atomic and macromolecular levels' we have performed a molecular dynamics computer simulation combined with quantum chemistry calculations for the human phosphoglycerate kinase enzyme with Mg containing substrate. The simulated structures were used to calculate coherent X-ray diffraction patterns' reflecting the conformational state of the enzyme, and Mg K-edge X-ray absorption spectra, which depend on the local structure of the substrate. These two techniques give complementary information making such an approach highly effective for time-resolved investigation of various biological complexes, such as metalloproteins or enzymes with metal-containing substrate, to obtain information about both metal-containing active site or substrate and the atomic structure of each conformation.