Nuclear pore complexes (NPCs) reside within circular pores of ~100 nm diameter formed where the inner and outer membranes of the nuclear envelope (NE) join. There they function as the only known mediator of nucleocytoplasmic exchange. NPCs are found in all eukaryotic cells and their general morphology appears to be highly conserved between evolutionary divergent phyla. Each NPC is an ~100 MD supramolecular cylindrical assembly with its octagonally symmetric short axis perpendicular to the plane of the NE and an approximate mirror symmetry about that plane. Several different mechanisms of nucleocytoplasmic exchange occur through the NPC. Ions and small molecules can passively diffuse through ~9 nm diameter aqueous channels. By contrast, macromolecules of 20 kD - >100 MD are actively transported by the NPC. These include imported proteins and snRNPs, exported RNPs and 'shuttling' (repeatedly imported and exported) proteins. The largest transported molecules can exceed the size of the NPC itself. Transport is fast, saturable, energy-dependent, regulated and highly selective. All NPCs appear to function both in nuclear import and export. NPCs are thus unique amongst cellular transporters in their large size (~300 times the mass of a gap junction), variety of substrates and number of functions. One might expect this diversity of roles to be reflected in the diversity and number of NPC components; it has been estimated that there may be upwards of 50 distinct polypeptides comprising the NPC. A variety of biochemical, immunological, and genetic approaches have been employed to isolate NPC proteins. We are currently employing our newly developed mass spectrometric protein identification tools (i.e., our MALDI-ITMS instrument together with the program """"""""Pepfrag"""""""" as well as MALDI-TOF-MS with the program """"""""Profound"""""""" to accelerate the identification of as yet unidentified nuclear pore proteins. It is our aim to identify them all. We have analyzed more than 700 protein bands from SDS-PAGE gel fractions of enriched yeast nuclear pore complex preparations. At present, we are testing the various open reading frames that we have identified to ascertain whether any of them are new nucleoporins (or nuclear pore related proteins). A paper describing this work is in preparation.
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