Structural genomics is ultimately concerned with determining high-resolution structures of all the functional macromolecules within living cells and tissues. While high-detail structural information can be obtained directly from protein complexes using technologies such as X-ray crystallography or nuclear magnetic resonance spectroscopy, these technologies have significant limitations in terms of sample quantity and homogeneity, and are therefore currently applicable to only a relatively small portion of the known proteome. Consequently, there is a need to develop and apply new, more universal technologies capable of determining the structural details of large multiprotein complexes.
Over the past several years, we have been developing ion mobility-mass spectrometry (IM-MS) methods for the analysis of intact large protein assemblies. IM separates ions in the gas phase based on their ability to traverse a chamber filled with inert neutral molecules under the influence of a weak electric field. Ions that are large undergo a greater number of collisions with neutrals and thus take more time to elute from the chamber than smaller, more compact proteins. Ion size is, therefore, the primary information content of IM separation and computational approaches can be used in conjunction with this information and MS data to assign the overall composition, stoichiometry, shape, topology and structure of the assembly. Critically, the IM-MS method has the ability to generate this information in the context of heterogeneity, complex mixtures, and at relatively low protein concentrations. This presentation will focus a number of heteromeric and homomeric protein complexes currently under investigation to illustrate our approach.