Here we describe a detailed protocol for both data collection and interpretation with respect to ion mobility-mass spectrometry analysis of large protein assemblies. Ion mobility is a technique that can separate gaseous ions based on their size and shape. Specifically, within this protocol, we cover general approaches to data interpretation, methods of predicting whether specific model structures for a given protein assembly can be separated by ion mobility, and generalized strategies for data normalization and modeling. The protocol also covers basic instrument settings and best practices for both observation and detection of large noncovalent protein complexes by ion mobility-mass spectrometry.

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Ion mobility-mass spectrometry analysis of large protein complexes.

Previous studies have established that the folding, structure and function of membrane proteins are influenced by their lipid environments and that lipids can bind to specific sites, for example, in potassium channels. Fundamental questions remain however regarding the extent of membrane protein selectivity towards lipids. Here we report a mass spectrometry approach designed to determine the selectivity of lipid binding to membrane protein complexes. We investigate the mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis and aquaporin Z (AqpZ) and the ammonia channel (AmtB) from Escherichia coli, using ion mobility mass spectrometry (IM-MS), which reports gas-phase collision cross-sections. We demonstrate that folded conformations of membrane protein complexes can exist in the gas phase. By resolving lipid-bound states, we then rank bound lipids on the basis of their ability to resist gas phase unfolding and thereby stabilize membrane protein structure. Lipids bind non-selectively and with high avidity to MscL, all imparting comparable stability; however, the highest-ranking lipid is phosphatidylinositol phosphate, in line with its proposed functional role in mechanosensation. AqpZ is also stabilized by many lipids, with cardiolipin imparting the most significant resistance to unfolding. Subsequently, through functional assays we show that cardiolipin modulates AqpZ function. Similar experiments identify AmtB as being highly selective for phosphatidylglycerol, prompting us to obtain an X-ray structure in this lipid membrane-like environment. The 2.3 A resolution structure, when compared with others obtained without lipid bound, reveals distinct conformational changes that re-position AmtB residues to interact with the lipid bilayer. Our results demonstrate that resistance to unfolding correlates with specific lipid-binding events, enabling a distinction to be made between lipids that merely bind from those that modulate membrane protein structure and/or function. We anticipate that these findings will be important not only for defining the selectivity of membrane proteins towards lipids, but also for understanding the role of lipids in modulating protein function or drug binding.

Membrane proteins bind lipids selectively to modulate their structure and function

We have examined the architecture of a protein complex in the absence of bulk water. By determining collision cross sections of assemblies of the trp RNA binding protein, TRAP, we established that the 11-membered ring topology of the complex can be maintained within a mass spectrometer. We also found that the binding of tryptophan enhances the stability of the ring structure and that addition of a specific RNA molecule increases the size of the complex and prevents structural collapse. These results provide definitive evidence that protein quaternary structure can be maintained in the absence of bulk water and highlight the potential of ion mobility separation for defining shapes of heterogeneous macromolecular assemblies.

https://science.sciencemag.org/content/sci/310/5754/1658.full.pdf

Evidence for macromolecular protein rings in the absence of bulk water.

Silicon is the most important semiconducting material in the microelectronics industry. If current miniaturization trends continue, minimum device features will soon approach the size of atomic clusters. In this size regime, the structure and properties of materials often differ dramatically from those of the bulk. An enormous effort has been devoted to determining the structures of free silicon clusters1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22. Although progress has been made for Sin with n < 8, theoretical predictions for larger clusters are contradictory2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 and none enjoy any compelling experimental support. Here we report geometries calculated for medium-sized silicon clusters using an unbiased global search with a genetic algorithm. Ion mobilities23 determined for these geometries by trajectory calculations are in excellent agreement with the values that we measure experimentally. The cluster geometries that we obtain do not correspond to fragments of the bulk. For n = 12–18 they are built on a structural motif consisting of a stack of Si9 tricapped trigonal prisms. For n ⩾ 19, our calculations predict that near-spherical cage structures become the most stable. The transition to these more spherical geometries occurs in the measured mobilities for slightly larger clusters than in the calculations, possibly because of entropic effects.

Structures of medium-sized silicon clusters

Although nonnative protein conformations, including intermediates along the folding pathway and kinetically trapped misfolded species that disfavor the native state, are rarely isolated in the solution phase, they are often stable in the gas phase, where macromolecular ions from electrospray ionization can exist in varying charge states. Differences in the structures of nonnative conformations in the gas phase are often large enough to allow different shapes and charge states to be separated because of differences in their mobilities through a gas. Moreover, gentle collisional activation can be used to induce structural transformations. These new structures often have different mobilities. Thus, there is the possibility of developing a multidimensional separation that takes advantage of structural differences of multiple stable states. This review discusses how nonnative states differ in the gas phase compared with solution and presents an overview of early attempts to utilize and manipulate structures in...

Biomolecule Analysis by Ion Mobility Spectrometry

In a number of recent studies, information about the structure of large polyatomic ions has been deduced from gas phase ion mobility measurements by comparing mobilities measured in helium to those estimated for assumed geometries using a hard sphere projection approximation. To examine the validity of this approach, we have compared mobilities calculated using the hard sphere projection approximation for a range of fullerenes (C20−C240) to those determined from trajectory calculations with a more realistic He−fullerene potential. The He−fullerene potential we have employed, a sum of two-body 6-12 interactions plus a sum of ion-induced dipole interactions, was calibrated using the measured mobility of C60+ in helium over an 80−380 K temperature range. For the systems studied, the long-range interactions between the ion and buffer gas have a small, less than 10%, effect on the calculated mobility at room temperature. However, the effects are not insignificant, and in many cases it will be necessary to cons...

and G. C. Schatz

Papers

Structural Information from Ion Mobility Measurements: Effects of the Long-Range Potential