1155: gp120 Design: V3 Hairpin

Summary

Name:

Status:

Closed

Created:

11/04/2015

Points:

100

Expired:

11/09/2015 - 23:00

Difficulty:

Intermediate

Description:

This protein is a portion of the HIV-1 envelope glycoprotein. The HIV-1 Env protein is a trimer of heterodimers--gp120 (the receptor binding domain) and gp41 (the transmembrane and fusion domain)--and is found on the surface of the HIV-1 virus. The HIV-1 Env complex is responsible for recognizing and binding to a human immune cell through its receptors. When gp120 binds to the human receptors (CD4 and CXCR4 or CXCR5), dramatic conformational changes occur in gp120 and gp41 that cause the virus to fuse with and infect the human cell. This structure of gp120, in a pre-fusion conformation, was recently obtained by x-ray crystallography. However, we know that the V3 loop of gp120 (which exists as a beta-hairpin here) can move in solution, allowing binding of antibodies that will clash with this pre-fusion conformation.

We're asking Foldit players to redesign the V3 hairpin to stabilize it in this pre-fusion conformation! Note that this protein exists as a trimer; stabilization of the hairpin may also be achieved through intermolecular contacts! See the puzzle comments for more details.

Categories:

Design, Overall, Symmetry

Rank

Group

Score

Points

Contenders

10,713

100

Beta Folders

10,692

L'Alliance Francophone

10,670

Go Science

10,664

Anthropic Dreams

10,652

Rank

Player

Group

Score

Points

gitwut 46 1458

Contenders

10,713

100

10,711

10,708

10,707

retiredmichael 46 1458

Beta Folders

10,692

Rank

Player

Group

Score

Points

retiredmichael 46 1458

Beta Folders

10,688

100

Museka 46 1458

L'Alliance Francophone

10,670

10,663

10,663

10,656

Wed, 11/04/2015 - 21:59

bkoep 46 251

Offline

Joined: 11/15/2012

Groups: Foldit Staff

Constraints on the hairpin

This puzzle includes no extra filters, but we have enabled some constraints to keep the V3 hairpin close to its starting conformation. The rest of the gp120 protein has a fixed backbone.

Players may only mutate residues on the V3 hairpin.

Wed, 11/04/2015 - 23:37

jamiexq 16 36

Offline

Joined: 07/31/2011

Groups: Anthropic Dreams

Cysteine bonds

Cysteines on hairpin will not bond with cysteines on backbone (frozen part)

Sat, 11/07/2015 - 16:53

stomjoh 46 92

Offline

Joined: 11/18/2012

Groups: None

Scoring Bug?

I asked on the forums, but I'll also ask here: If there is a scoring bug going on with this puzzle, shouldn't it be taken down/restarted with the bug fixed? Or, will the bug be fixed before the puzzle finishes?

Tue, 11/10/2015 - 14:37

inkycatz 46 1458

Offline

Joined: 04/24/2014

Groups: None

Please see

http://fold.it/portal/node/2001423 Please see this post for updates. Thanks!

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