The myriad events that occur in living cells (replication, organellar assembly, transport, genome
organization, transcription etc.) are to a large extent carried out through dynamic associations and
assemblies of macromolecules. I will describe our efforts to develop and integrate sets of tools
that are designed to throw light on the evolution, structure and function of these macromolecular
machines.
At the very earliest stage of analysis, we define the precise ensembles of macromolecular players
that make up the assemblies of interest. Mass spectrometry has become an increasingly enabling
tool for this task, owing to its sensitivity and its ability to characterize the primary structures of
endogenous proteins along with any modifications that may be present. At the next stage of
analysis, we apply combined proteomic-biochemical approaches to gain insights into the
architectures of protein complexes, especially those that are too large or too poorly behaved for
traditional X-ray crystallographic diffraction or NMR spectroscopic analyses. Finally, we integrate
data from all these sources to generate models that can provide insights into the evolution,
structure and function of these remarkable macromolecular machines. I will to discuss current
capabilities and limits of this approach as well as prospects for the future.