Novel MS/MS-Cleavable Cross-Linkers: Synthesis, Evaluation of Fragmentation Behavior, and Application for Protein Structure Analysis

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Chemical cross-linking in combination with mass spectrometry (MS) has evolved into a real alternative strategy for elucidating threedimensional protein structures and for mapping protein interfaces. The joint research grant proposal outlined herein continues our fruitful collaboration in advancing the cross-linking/MS approach, which has previously been funded by the DFG. We will continue to fully explore the superior capabilities of the collision induced dissociation (CID)-labile reagents previously developed for tertiary and quaternary structure elucidation of biologically relevant protein systems and we aim to extend the applicability of the CID-cleavable reagents by further optimization and tuning of reactivity (improved water solubility: sulfonic acid derivatives; C-terminal reactivity: bishydrazide analogues; introduction of a brominated version of our urea-linker for selective detection via accurate ion mass measurements and isotopic pattern evaluation). Additionally, we will intensify our efforts to further refine our customized software tools and algorithms set in place for automated data acquisition and interpretation as bioinformatics has proven to be of vital importance for the success of large scale crosslinking studies (triggered constant neutral loss (CNL) for the detection of cross-linker modified peptides in MS3 experiments). Additionally, a new class of CID-cleavable cross-linkers with a tetrahydro-pyrimidine moiety is proposed for cross-linking purposes that should preferably dissociate via a retro-Diels-Alder (RDA) reaction pathway. All means of tandem MS methods that are available to us will be applied to test its CID characteristics, namely CID, HCD (higher-energy collisioninduced dissociation), electron transfer dissociation (ETD), and electron capture dissociation ECD as well as combinations of different fragmentation techniques (ETciD and EThcD).