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 consider the long-range interactions if the correct structural assignments are to be made from measured ion mobilities.

Summary Despite the central role of Nuclear Pore Complexes (NPCs) as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm, their large size and dynamic nature have impeded a full structural and functional elucidation. Here, we have determined a subnanometer precision structure for the entire 552-protein yeast NPC by satisfying diverse data including stoichiometry, a cryo-electron tomography map, and chemical cross-links. The structure reveals the NPC’s functional elements in unprecedented detail. The NPC is built of sturdy diagonal columns to which are attached connector cables, imbuing both strength and flexibility, while tying together all other elements of the NPC, including membrane-interacting regions and RNA processing platforms. Inwardly-directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized in distinct functional units. Taken together, this integrative structure allows us to rationalize the architecture, transport mechanism, and evolutionary origins of the NPC.

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Ion mobility measurements have been used to examine the geometries of naked BPTI (bovine pancreatic trypsin inhibitor) and cytochrome c ions in the gas phase, as a function of charge. For BPTI, the measured cross sections are close to those estimated for the native solution-phase conformation. Furthermore, gas-phase BPTI retains its compact structure when collisionally heated. These results are consistent with the known stability of BPTI, where the three-dimensional structure is partly locked into place by three covalent disulfide bridges. For cytochrome c, geometries with cross sections close to those estimated for the native solution phase structure were observed for the low charge states. For intermediate charge states, the compact geometries are metastable, and when collisionally heated they gradually unfold, through a series of well-defined intermediates. Only extended conformations are observed for the higher charge states, and they become more extended as the charge increases. The gas-phase conformation of a protein ion results from a balance between attractive intramolecular interactions, intramolecular charge “solvation”, and Coulomb repulsion. For the low charge states, compact folded conformations have the lowest energy because they maximize intramolecular interactions. For intermediate charge states, elongated conformations, which minimize Coulomb repulsion while maximizing intramolecular interactions and intramolecular charge “solvation”, become favored. For the high charge states, the elongated conformations unravel to an extended string as Coulomb repulsion dominates.

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