A group of Novosibirsk State University scientists, together with colleagues from the Institute of Cytology and Genetics SB RAS and the Institute of Chemical Biology and Fundamental Medicine SB RAS, have expanded on existing X-ray analysis of evolutionary information to better understand how proteins work. Their work was published in the international journal “DNA Repair”.
In the study of proteins, scientists often use the X-ray diffraction analysis method to determine the structure of the molecule with atomic accuracy. It provides a snapshot, but it is only a static image of the protein molecule. Similar to the challenges in perceiving the movement in a jump from a photograph of a person sitting down, it is not possible to fully understand the process of a biological molecule from a photograph.
Dmitry Zharkov, research leader and Head of NSU Protein Engineering Laboratory, described their work in more detail,
We added evolutionary information to the X-ray analysis. For millions of years amino acid residues in proteins slowly changed. These random mutations involve substitutions to preserve the working capacity of the molecule. We calculated which amino acids change, and superimposed the map of changes on the protein’s structure. We were able to establish which interactions inside the protein molecule are important to its function and which cannot be understood from one structure.
The scientists applied a new approach to the analysis of the structure of the E. coli enzyme, which is called formamidopyrimidine-DNA glycosylase (Fpg). This enzyme is involved in protecting DNA from oxidation and prevents mutations. As a result of the teams expansion to X-ray structural analysis, it was possible to detect two previously unknown regions critical for the enzyme. One is responsible for changing its structure when oxidized DNA binds, and the second is necessary so the protein molecule does not unfold at the human body temperature necessary for E. coli to live.
The Novosibirsk scientists selected protein from E. coli because the human cell has three proteins like Fpg that protect our genome. Mutations in them increase the risk of cancer and neurodegenerative diseases. The new data will allow us to refine personalized risk predictions for people with different variants of these genes.