Abstract
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.
Highlights
The development of the 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. 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
Experimental investigation of protein dynamics is a problem of great importance because the conformational changes of the biological complexes in most cases determine their functionality
Calculations were performed at different simulated temperatures from 200 to 450 oK, affecting the kinetic energy per degree of freedom, and indicated that the process is temperature-dependent with phosphoglycerate kinase (PGK) being more stable in close conformation at low temperatures, and remaining in the open conformation when heated above 370 oK
Summary
Experimental investigation of protein dynamics is a problem of great importance because the conformational changes of the biological complexes in most cases determine their functionality The solution of this problem becomes possible with the development of generation synchrotron radiation sources – free electron lasers, providing extremely short pulses with ultrahigh brilliance sufficient for a single molecule imaging. Doi:10.1088/1742-6596/712/1/012024 measurements can provide information on the 3D structure of the sample [1,2,3], e.g. virus, protein or enzyme, the detailed information about a substrate or an active site cannot be obtained These tiny changes in the active site may be a key point in understanding of the chemical processes, as in case of iron oxidation in hemoglobin [4] and changes in Fe-porphyrin geometry [5]. In this work we suggest a complex technique which combines CXDI and XANES study to show how the complementary structural information can be obtained
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