I'm deep into the literature on type four pili. (They're variously abbreviated as Tfp or T4P - I'm going to go with Tfp* because a Google search for Tfp pilin finds over 10,000 hits, whereas a search for T4P pilin finds only 273.)
I was thinking that the USS-specific interaction between pilin subunits and the DNA sequence flanking the core USS would be mediated by the positively charged regions of the pilin that are exposed on the sides of the pilus, but it could instead be a region that is exposed only at the pilus tip.
When Tfp cause adhesion or twitching motility by sticking to surfaces, it's the tip of the pilus that does the sticking. Because of the way the subunits assemble, the top and part of the sides of each non-tip subunit are covered by the subunits above them, but the tops and parts of the sides of the subunits at the tip are exposed, and can interact with their environment.
If the side of the pilus was interacting with the USS outside of the pore, when the pilus retracted the pore would need to accommodate the pilus plus the two sides of the DNA loop. But the pores that have been studied aren't big enough for this; they are about 6-7nm across when open, and can fit a pilus (5-5nm), or two filaments of double-stranded DNA (2nm each), but not them all, and maybe not even the pilus plus one filament of DNA.
Thus continuing uptake may require that the pilus stay in the periplasm, and reel the DNA in through the pore (as I drew it in this post). But when uptake is being initiated the pilus must protrude through the pore to form the initial attachment to the DNA. Pulling the DNA in through the pore would be a lot easier if the DNA was attached to the pilus tip rather than to its side.
I have an initiation figure that shows the DNA binding to the side of the pilus; I'll modify it and add it to this post later.
* Except of course when corresponding with someone who prefers T4P, such as the author of a recent helpful review.
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