Susume's picture
User offline. Last seen 15 hours 43 min ago. Offline
Joined: 10/02/2011
Disulfide bond?

I am confused about the disulfide bonus on 1462. There are 5 cysteines, at positions 66, 106, 119, 121, and 160. If two or four of these are involved in disulfide bonds, I would expect those two or four to be strongly conserved, that is, there would be cysteines in those spots in many related proteins, and a related protein that has one of the cysteines in a disulfide pair would almost always have the other as well.

Jpred finds 936 homologous sequences (related proteins) for our protein. Of those, 608 have a cys in position 66 - so that cys is strongly conserved. However, none of the others are conserved at anything like the same rate. At positions 106, 119, and 121, respectively, there are only 54, 30, and 6 related proteins that also have a cys there. None of those positions can be providing the selection pressure on position 66 to remain cysteine. 160 is more promising, with 234 related proteins having a cys there, but that's still not close to 608. This makes me wonder if there is some other molecule that residue 66 commonly forms a disulfide bond with, that provides the selection pressure to keep a cys in that spot. The other common AAs at that spot are K, G, Q, S, and N, suggesting that residue 66 is on the surface where it could interact with some other molecule.

Does this line of reasoning make any sense? Is it possible the disulfide is not within our protein but with some other molecule? Do you have some other reason to believe there is a disulfide within our protein?

Hanto's picture
User offline. Last seen 4 days 3 hours ago. Offline
Joined: 05/10/2008
Groups: None
I've already seen hints of a

I've already seen hints of a disulfide during game play, possibly not the point tho.

dbuske's picture
User offline. Last seen 5 hours 10 min ago. Offline
Joined: 09/22/2011
Groups: Beta Folders
experiment

I have made a fold just using the rama utility.
I moved the dots to red and green areas into small groups.
running wiggle here and there.
Dots would move to other colors at times which is fine.
Move dots, wiggle move dots, til finished.
I got perfect rama, but not folded up completely.
I doubt this would fold in the lab, but I wanted to
give it a try.

Joined: 05/19/2009
Groups: Contenders
UNMENTIONED HEFTY BONUS FOR DISULFIDE BONDS

The puzzle description does not mention at all that there is a 250 point bonus for making a disulfide bond !
I found out by accident...

Joined: 10/30/2012
Groups: Beta Folders
there are 2 bonds that score

there are 2 bonds that score

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons