A seemingly simple aspect of the procedure that provides a major new targets of potential regulatory oxidation events

We have developed a new procedure, PROP, to detect and quantify oxidation of cell proteins, and have used it to detect oxidation and inhibition of the stress-activated p38 Bortezomib Proteasome inhibitor kinase resulting from both H2O2 and from the physiologic mediator of inflammation, prostaglandin J2. The PROP assay is similar in concept to the Jaffrey assay for protein nitrosothiols, in that protein thiols are first blocked with thiol-reactive reagents, and then modified thiols revealed with DTT before recovery using thiol affinity methods. PROP may have some benefit over this prior assay because it involves fewer steps. While the Jaffrey procedure blocks thiols in SDS solutions, we found in pilot studies that the use of guanidine instead of SDS as a denaturant resulted in superior blocking of non-oxidized cysteines. Precipitation of guanidine-denatured protein by methanol is an efficient way of recovering protein while removing small cysteine-modifying chemicals including NEM and DTT. In addition to the Jaffrey method, there are several other approaches for labeling and detecting reversible oxidation of protein targets. Most of these rely on a similar strategy of blocking unmodified cysteines, then reversing the modification and labeling with a thiol reactive reagent that provides a means of detection. Among the available options are fluorescent labels, biotinylated agents, mobility shift, and radioactive compounds. These approaches each have limitations that the PROP procedure obviates. For example, while fluorescent or radioisotopic labeling can enable detection of labeled proteins, these approaches do not purify the labeled proteins away from non-oxidized proteins, that is necessary for proteomics analysis to characterize unidentified proteins. Biotin labeling enables a somewhat efficient purification approach. However, the biotin label on the purified protein can be problematic for mass spectroscopy identification of the modified residue on the oxidized proteins. In the PROP procedure, proteins are released from the thiol beads with reducing agent in an unmodified form, leaving them completely compatible with downstream applications such as mass spectrometry, or for isotopic labeling such as with maleimides containing heavy isotopes. Alternate methods of protein release with ascorbic acid or arsenite, can be used to elute proteins with specific types of cysteine oxidations. Some biotin-switch methods rely on labeling of cell lysates, which introduces the variability of post-lysis oxidation, despite precautions of cell lysate processing in an anaerobic chamber. Our approach uses rapid fixation of cells using 10% trichloroacetic acid, which immediately prevents post-lytic oxidation. As the acid is removed, proteins are continuously in the presence of thiolblocking maleimide.

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