A novel high throughput method has been developed that allows the examination of protein dynamics and stability on a proteomic scale. The Marqusee laboratory has challenged the E. coli proteome with extensive proteolysis and identified """"""""survivors"""""""", proteins that are highly resistant to proteolysis. Among the survivors are a subset of proteins with unique function and structure, suggesting that protease resistance within a proteome may be determined by these features rather than by thermodynamic stability. Here we propose to investigate the effects of primary sequence, native fold, function, and stability on protease resistance at a proteomic level. By interrogating proteomes from closely and distantly related thermophilic and mesophilic bacteria, we will be able to compare proteolytic stabilities of proteins that differ to varying degrees in primary sequence, structure, and thermodynamic stability. This will allow us to determine whether differences in protease protection arise from thermodynamic stability, protein dynamics, or functional constraints and to understand how these subtleties are encoded within the amino acid sequence.
