Mapping protein interfaces by chemical cross-linking and Fourier transform ion cyclotron resonance mass spectrometry: application to a calmodulin/adenylyl cyclase 8 peptide complex

Chemical cross-linking-an established technique in protein chemistry-has re-emerged, in combination with mass spectrometric analysis of the reaction products, as a valuable tool to identify interacting amino acid sequences in protein complexes. In the present study, we are mapping the interface of the calcium-dependent complex between calmodulin (CaM) and a peptide derived from the C-terminal region of adenylyl cyclase 8 (AC 8). Cross-linking reactions are performed using the two amine-reactive, isotope-labeled (d(0) and d(4)) cross-linkers BS3 (bis[sulfosuccinimidyl]suberate) and BS(2)G (bis[sulfosuccinimidyl]glutarate) as well as the "zero-length" cross-linker (EDC, ethyl-3-[3-dimethylaminopropyl] carbodiimide hydrochloride). After separation of the cross-linking reaction mixtures by one-dimensional gel electrophoresis (sodium dodecyl sulphate polyacrylamide gel) and in-gel digestion of the cross-linked complexes, the resulting peptide mixtures are analyzed by nano-high-performance liquid chromatography/nano-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. The identified intermolecular cross-linking products will give further insight into calmodulin/adenylyl cyclase 8 interaction.