An Anomalous Small-Angle X-Ray Scattering Study of the Formation of Iron Clusters in the Inner Cavity of the Ferritin-Like Protein Dps

• Published in: Moscow University physics bulletin Vol. 77; no. 6; pp. 858 - 867
• Main Authors: Gordienko, A. M., Mozhaev, A. A., Gibizova, V. V., Dadinova, L. A.
• Format: Journal Article
• Language: English
• Published: Moscow Pleiades Publishing 01.12.2022; Springer Nature B.V
• Subjects: Algorithms; Chelating agents; Chelation; Clusters; Computer simulation; E coli; Ferric ions; Ferritin; Ferrous ions; Hydrogen peroxide; Iron; Mathematical analysis; Mathematical and Computational Physics; Molecular structure; Oxidation; Physics; Physics and Astronomy; Proteins; Small angle X ray scattering; Theoretical; mini-ferritin; anomalous small-angle X-ray scattering; Dps protein
• ISSN: 0027-1349; 1934-8460
• DOI: 10.3103/S0027134922060054

The Dps protein (a DNA-binding protein from starving cells) is well known for its ability to protect cells from various negative factors, including oxidative stress. Dps is capable of rapidly oxidizing ferrous ions with hydrogen peroxide and then accumulating ferric ions in its cavity in the form of a ferric mineral. Dps is also able to bind to DNA, forming highly ordered structures and becoming the most abundant stationary-phase nucleoid protein, adding physical protection to chemical protection. In this work, anomalous small-angle X-ray scattering (ASAXS) was used for the first time to study the formation of iron clusters in the cavity of the Dps protein from Escherichia coli . Based on the created software, using a known algorithm, the ASAXS curves were decomposed into resonant, nonresonant, and cross term components, which were subsequently used to calculate the average number of ions per protein molecule and determine the ab initio structure of the protein–iron complex. Using computer simulation methods, detailed information was obtained on the distribution of iron atoms inside the protein cavity at various concentrations of iron in the solution. It has been shown that an increase in the concentration of Fe in the solution has little effect on the morphology of the resulting iron mineral; however, it leads to an increase in its volume, which is in a good agreement with the experimentally determined number of iron ions per Dps molecule. The values we obtained proved to be lower than the calculated values, which may be due to the presence of a chelating agent in the solution.