Adoption of quaternary protein structure involves ordered aggregation of separate polypeptide chains into multi-subunit complexes. Consequently, each monomer assumes a specific set of noncovalent contacts with neighboring subunits. The structure of these protein-protein interfaces confers binding specificity and characteristic multimer stability. The distinct binding affinities of different interfaces can be exploited in solution to disassemble complexes in a stepwise fashion and thus obtain subcomplexes informative of overall topology. The nature of a given protein-protein interface is also likely to impart a particular dissociation signature during gas phase disassembly via MS/MS. To further the applicability of MS/MS to analytical problems in structural biology, we seek a better understanding of the interplay between complex structures, interfacial contacts, and fragmentation behaviors.
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