Proteomics systems for integrative structural biology

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We present a program of research designed to provide new tools for characterizing and modeling the structure of complex protein systems. Our strategy for generating structure-rich biophysical data involves condensed-phase protein chemistries that code protein properties into quantities measurable by mass spectrometry, at all organizational scales (structural proteomics). There are four interrelated themes in the proposed program. First, we will investigate new protein bioconjugation strategies that involve fast-acting, light-triggered chemical reactions, and develop next-generation reagents for both covalent labeling mass spectrometry (CL-MS) and crosslinking mass spectrometry (XL-MS). We propose that separating the equilibrium protein solvation properties of these reagents from the photolytic process will provide unprecedented opportunities to increase the structural value of modeling restraints derived from both CL-MS (topographical mapping) and XL-MS (distance measurements). Second, we present concepts for implementing protein bioconjugation methods in complex mixtures and cells, to avoid reconstituting protein complexes. Reconstitution is a laborious and failure-prone process, thus overcoming this current requirement is critical step towards extending structural methods into a cellular context. The work in this theme will involve the production fast-isolation methods for removing complexes from