Cross-Linkers Target Acidic Amino Acids

By chemically cross-linking proteins, digesting them with enzymes, and analyzing the resulting peptides with mass spectrometry, scientists generate distance information they can use in protein structure modeling. Most cross-linking chemistries currently target the primary amine in lysine’s side chain. Linking other amino acid side chains might provide additional data that improve structural models. Ruedi Aebersold and Alexander Leitner of ETH Zurich and coworkers report new dihydrazide-based chemical cross-linkers that target carboxyl groups in aspartic acid and glutamic acid (Proc. Natl. Acad. Sci. USA 2014, DOI: 10.1073/pnas.1320298111). The researchers used adipic acid dihydrazide or pimelic acid dihydrazide to cross-link eight model proteins and two multisubunit protein complexes: the TRiC chaperonin, an almost 1-megadalton complex with 16 subunits, and the 26S proteasome, a 2.5-megadalton complex with more than 60 subunits. Pimelic acid dihydrazide—the longer of the two cross-linkers—provided more extensive cross-linking coverage than did adipic acid ­dihydrazide.