Figure 4

An identified coiled-coil motif in EIAV Rev is predicted to mediate dimerization. A. Domain organization and secondary structure prediction for EIAV Rev165, showing the location of the predicted coiled-coil motif in the central region (residues 82–109). The coiled-coil motif is within a predicted extended alpha helix. Amino acid residues of the coiled-coil motif heptad repeats are shown in upper case. The register (abcdefg) of each residue is shown in lower case, and ‘a’ and ‘d’ registers, which are critical for interfacial interactions [56],[57], are underlined. B: Helical wheel representation [58] of predicted intermolecular interactions mediated by ‘a’ and ‘d’ registers of the coiled-coil motif. Diamonds represent hydrophobic residues; + denotes positively charged polar residues, − denotes negatively charged polar residues; open circles represent uncharged polar residues. Dashed lines connect pairs of hydrophobic residues predicted to make interfacial contacts. Filled diamonds are Trp residues that could participate in oligomerization. C. Cartoon illustrating head-to-tail dimeric structure generated by ClusPro docking of two EIAV Rev fragments corresponding to the coiled-coil motif. Side chains of ‘a’ and ‘d’ residues predicted to make interhelical contacts in (B) are shown as black sticks. Note that Trp residues (W97) that could potentiate oligomerization are exposed on opposite faces of the docked structure. D. Sequence conservation in the coiled-coil motif. The sequence logo of residues 82–109 of EIAV Rev was generated from a multiple sequence alignment of 200 EIAV Rev isolates from US, Ireland, and China using WebLogo [59]. Stacks of letters at each position indicate the relative frequency of an amino acid in the multiple sequence alignment. Six of the 8 residues in the ‘a’ and ‘d’ positions are invariant while the Ile in the first ‘a’ position accommodates only Val, a closely related hydrophobic residue.