Consequences of intramolecular dityrosine formation on a DNA–protein complex: a molecular modeling study

Structure and conformational studies on dityrosine formation in the DNA binding domain of RFX5

The DNA binding protein RFX5 is a subunit of RFX complex involved in transcription regulation of MHCII molecules. The RFX complex binds to the X-box DNA through the DNA binding domain of RFX5. We have examined the formation of intramolecular tyrosine cross linking, dityrosine, in RFX5DBD under oxidative stress, through UV irradiation and enzymatic action of H(2)O(2)/peroxidase by fluorescence spectroscopic studies. Dityrosine (DT) was formed predominantly in alkaline condition showing its intense characteristic fluorescence emission. Homology modeling indicated Y(39) and Y(42) could be the potential tyrosine residues undergoing oxidative cross-linking. Conformational changes in RFX5DBD under oxidative stress were observed by CD measurements. The in vitro association of X-box DNA with RFX5DBD increased DT fluorescence significantly and protected RFX5DBD from UV irradiation as observed in SDS-PAGE followed by mass spectrometric analysis. Results indicate cross protection in both RFX5DBD and DNA under oxidative stress playing important role in protein modification.

Radiation-induced oxidative damage to the DNA-binding domain of the lactose repressor

Understanding the cellular effects of radiation-induced oxidation requires the unravelling of key molecular events, particularly damage to proteins with important cellular functions. The Escherichia coli lactose operon is a classical model of gene regulation systems. Its functional mechanism involves the specific binding of a protein, the repressor, to a specific DNA sequence, the operator. We have shown previously that upon irradiation with gamma-rays in solution, the repressor loses its ability to bind the operator. Water radiolysis generates hydroxyl radicals (OH* radicals) which attack the protein. Damage of the repressor DNA-binding domain, called the headpiece, is most likely to be responsible of this loss of function. Using CD, fluorescence spectroscopy and a combination of proteolytic cleavage with MS, we have examined the state of the irradiated headpiece. CD measurements revealed a dose-dependent conformational change involving metastable intermediate states. Fluorescence measurements showed a gradual degradation of tyrosine residues. MS was used to count the number of oxidations in different regions of the headpiece and to narrow down the parts of the sequence bearing oxidized residues. By calculating the relative probabilities of reaction of each amino acid with OH. radicals, we can predict the most probable oxidation targets. By comparing the experimental results with the predictions we conclude that Tyr7, Tyr12, Tyr17, Met42 and Tyr47 are the most likely hotspots of oxidation. The loss of repressor function is thus correlated with chemical modifications and conformational changes of the headpiece.