One of the things proteomic researchers want to figure out is how proteins interact with one another to form complexes. Chemical crosslinking combined with mass spectrometry is one way to understand these processes. But the problem is that most of the current crosslinking methods can only tackle simple protein mixtures and can’t handle large protein complexes or networks of proteins. To address these issues, a team led by Jeffrey Ranish at the Institute for Systems Biology developed a new crosslinker, Biotin-Aspartate-Rink-Glycine (also referred to as BDRG, where D stands for aspartate), which was recently described in Molecular & Cellular Proteomics. BDRG “is the only crosslinker that contains an affinity handle along with a single mass spectrometric-labile bond,” which is the Rink moiety, explains Ranish. The biotin group is the affinity handle that allows researchers to enrich for crosslinked peptides in a sample on an avidin affinity column. For the subsequent mass spectrometric analysis of the crosslinked peptides, the labile bond in the Rink moiety reduces the number of fragmentation products generated, which makes it easier for researchers to identify fragments in a spectrum. As proof of principle, Ranish’s team used BDRG to study the architecture of a partially purified preparation of the 12-subunit RNA polymerase II complex that contained 90 copurifying proteins. Ranish says while the work “represents a major advance in the structural characterization of large protein complexes,” he cautions that BDRG is quite hydrophobic. The group is currently working on designing crosslinkers that are more hydrophilic with different affinity handles.
Rajendrani Mukhopadhyay (firstname.lastname@example.org) is the senior science writer for ASBMB Today and the technical editor for the Journal of Biological Chemistry.