Closed since about 10 years ago
Intermediate Overall PredictionThis is a throwback puzzle to the early days of Foldit. This small protein, from the venom of the saw-scaled viper, interferes with the cellular adhesion machinery that allows blood clotting. This protein contains eight cysteine residues that oxidize to form four disulfide bonds. We are revisiting old Foldit puzzles so we can see how useful the recent additions to the game have been.
Sequence:
I'd be interested in knowing what that pro-x-x-pro-x-x-pro, x hydrophilic forms when the puzzle closes. As a helix it makes a nice stripe. A polyproline helix that moved to the surface? The prolines could form a highly specific interaction zone, but hydrophillics keep it facing inward. A true alpha helix with full h-bonds would be preferred, so why are the prolines conserved?
I suppose it's probably just a disordered loop but the pattern is very suggestive.
Very interesting question, brow42! As you say, proline is unfavored for alpha helices and beta sheets, because its amino group cannot make the hydrogen bonds that stabilize those secondary structures. Indeed, the proline regions of this protein do not form any regular secondary structure.
I dug a little deeper into this particular protein. While proline is not strictly conserved at these sites in related proteins, these proteins do tend to be proline-rich. And in fact, these proteins adopt—not disordered loops—but surprisingly ordered loops. In fact, some of these "secondary structure-less" proteins have even been crystallized!
My guess is that the prolines actually serve to disfavor alternate conformations of this protein. By destabilizing alpha helices and beta sheets, the prolines can make this loopy structure the most stable option.
