Intramolecular Cohesion of Coils Mediated by Phenylalanine–Glycine Motifs in the Natively Unfolded Domain of a Nucleoporin
Figure 1
The yeast nuclear pore complex, some of its FG nucleoporins, and an ensemble of protein structures generated by MD simulations of a Nup116 FG domain.
(A) A simplified diagram of the yeast nuclear pore complex (green), its cytoplasmic fibrils (yellow), its nuclear basket (red) and some of the GLFG-rich domains of nups that line the transport conduit (blue). The GLFG-rich domains are depicted as a doughnut-shaped array of laterally-cohesive, native pre-molten globules. Other FG domains are excluded for simplicity. The nuclear envelope is in gray. (B) GLFG-rich nucleoporins in the yeast NPC transport conduit. The vertical tick marks in the nups mark the location of each FG motif: GLFG motifs are in yellow, FxFG motifs in red, and other variants in different colors. The fragment of Nup116 (AA 348–458) indicated was selected as a representative FG domain for this study. The F>A mutant version lacks the phenylalanine residue in FG motifs, which were replaced by alanine. (C) The AA sequences for the wild-type and mutant Nup116 FG domains used for MD simulations. The phenylalanine (or alanine) in FG motifs is indicated in red. The AA sequences in gray are not part of Nup116; they are affinity-tags used in the purification of the FG domain. The numbers in the black bold font indicate the AA position in the Nup116 sequence. The numbers in gray indicate the AA position in the FG domain fragment analyzed. The protein structures shown are a representative subset of the twenty MD simulation structures generated for each FG domain at 350 K. The Rg values of the representative structures are within the average range for each FG domain (see Figure 2A).