Nuclear localization signals (NLSs) facilitate the transport of proteins into the nucleus.
Monopartite interaction with alternative conformations, which were observed (simultaneously) at specificity-determining subsites
of V40 NLS and the N-terminal portion in the minor binding site (staggering one position N-terminally). The structures show the
SV40 NLS binds in a very similar manner as mammalian NLS (residues 127-130).
Sequences flanking the basic clusters modulate recognition of the NLS. Proline residues in the flanking regions often appear
to have a positive effect on NLS activity, likely by reducing the energetic cost of binding by restraining the NLS sequences in
the extended conformation. The more stringent sequence requirements of the basic cluster of the monopartite NLSs are
relaxed in the bipartite NLSs, by the second basic cluster compensating for the reduction of favorable contacts in the major
The autoinhibitory sequence comprising residues 44-54 of importin-α binds to the major NLS binding site, resembling NLS
binding. The path of the main chain of residues 47-53 is identical with the path of SV40 and nucleoplasmin NLS residues in
the major binding site. Only residues 44-46 bind in a different mode than the analogous nucleoplasmin residues; however, in
either case, few favorable interactions are formed in these regions with the protein, and the chains are poorly ordered.
Specificity determining factors:
Polar interactions through conserved asparagine sidechains to NLS backbone to determine chain (NLS) direction.
Hydrophobic interactions to conserved tryptophanes in shallow grooves.
Interactions between basic NLS motifs and the negative charges of importin α.
Phosphorylation of the T antigen NLS facilitates transport, but does not involve direct interaction with importin-α.
Fuzzy linker modulates specificities of different importin-α isoforms for different cargo proteins.
Alternative binding modes may account for diverse NLS binding by the same receptor and effective competition with