Communication between the nucleus and cytoplams of an eukaryotic cell is mediated by the nuclear pore complexes (NPCs), which act as selective molecular gateways. Through these gateways, RNAs and proteins are exported into the nucleus. Each NPC consists of ~30 distinct proteins termed nucleoporins, each present in at least eight copies, reflecting the octagonal symmetry of the complex. The following nucleoporins share an ~150-residue C-terminal domain responsible for NPC targeting [1,2]:

• Vertebrate Nup98, a component of the nuclear pore that plays its primary role in the export of RNAs.
• Yeast Nup100, plays an important role in several nuclear export and import pathways including poly(A)+ RNA and protein transport.
• Yeast Nup116, which is involved in mRNA export and protein transport.
• Yeast Nup145, involved in nuclear poly(A)+ RNA and tRNA export.

The NUP C-terminal domains of Nup98 and Nup145 possess peptidase S59 autoproteolytic activity [E1]. The autoproteolytic sites of Nup98 and Nup145 each occur immediately C-terminal to the NUP C-terminal domain. Thus, although this domain occurs in the middle of each precursor polypeptide, it winds up at the C-terminal end of the N-terminal cleavage product. Cleavage of the peptide chains are necessary for the proper targeting to the nuclear pore [1,2].

The NUP C-terminal domain adopts a predominantly β-strand structure (see <PDB:2AIV>). The molecule consists of a six-stranded β-sheet sandwiched against a two-stranded β-sheet and flanked by α-helical regions. The N-terminal helical region consists of two short helices, whereas the stretch on the opposite side of molecule consists of a single, longer helix [1,2].

The profile we developed covers the entire NUP C-terminal domain.