Structural analysis of XXXX using synchrotron protein footprinting.

@entity3787 @entity141 @entity19330
Protein footprinting provides detailed structural information on protein structure in solution by directly identifying accessible and @entity3787 radical-reactive side chain residues. Radiolytic generation of @entity3787 radicals using millisecond pulses of a synchrotron "white" beam results in the formation of stable side chain oxidation products, which can be digested with proteases for mass spectrometry (MS) analysis. Liquid chromatography-coupled MS and tandem MS methods allow for the quantitation of the ratio of modified and unmodified peptides and identify the specific side chain probes that are oxidized, respectively. The ability to monitor the changes in accessibility of multiple side chain probes by monitoring increases or decreases in their oxidation rates as a function of ligand binding provides an efficient and powerful tool for analyzing protein structure and dynamics. In this study, we probe the detailed structural features of @entity19330 in its "inactive" and @entity141 -activated state. Oxidation rate data for 81 peptides derived from the trypsin digestion of @entity19330 are presented; 60 of these peptides were observed not to be oxidized, and 21 had detectable oxidation rates. We also report the @entity141 -dependent changes in oxidation for all 81 peptides. Fifty-nine remained unoxidized, five increased their oxidation rate, and two experienced protections. Tandem mass spectrometry was used to identify the specific side chain probes responsible for the @entity141 -insensitive and @entity141 -dependent responses. These data are consistent with crystallographic data for the inactive form of @entity19330 in terms of the surface accessibility of reactive residues within the protein. The results demonstrate that radiolytic protein footprinting can provide detailed structural information on the conformational dynamics of ligand-induced structural changes, and the data provide a detailed model for @entity19330 activation.
