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1010: Abeta Binder Redesign
Status: Closed

Summary

Name: 1010: Abeta Binder Redesign
Status: Closed
Created: 11/10/2014
Points: 100
Expired: 11/17/2014 - 23:00
Difficulty: Intermediate
Description: Help us design a binder for the Abeta peptide, a peptide associated with Alzheimer's disease! This starting structure was partially derived from Puzzle 811 results, with two extra β-strands flanking the central β-sheet. In addition, the connectivity of secondary structure elements has been altered, with new loops in several places. This puzzle has two filters: the Residue IE Score filter monitors that all PHE, TYR, and TRP residues are scoring well, and the SS Design filter prohibits GLY in sheets and helices. Remember, you can use the Upload for Scientists button for up to 3 designs that you want us to look at, even if they are not the best-scoring solutions.
Categories: Design, Overall

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Comments

spvincent's picture
User offline. Last seen 5 hours 53 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
Is there a reason segments

Is there a reason segments 1-25 aren't frozen?

bkoep's picture
User offline. Last seen 19 min 47 sec ago. Offline
Joined: 11/15/2012
Groups: None
Good question!

Yes. We wanted Aβ to be able to wiggle with the design.

Unlike larger, highly structured proteins (e.g. the ebolavirus glycoprotein), the Aβ peptide is very flexible, and its structure will be highly influenced by its binding partner. We expect the Aβ peptide to wiggle a bit when it binds, in order to better fit the binding pocket of the designed protein.

Joined: 06/06/2013
Groups: Gargleblasters
goal about binding

is our goal to make this bind in such a way that the AB does not want to bond with cholesterol or lipids? that it is unable to bind with anything else once in the pocket?

bkoep's picture
User offline. Last seen 19 min 47 sec ago. Offline
Joined: 11/15/2012
Groups: None
Yes

The goal is to create a tight-enough binder to the Aβ peptide such that it will not interact with other molecules, and to keep it from aggregating with other Aβ molecules.

Joined: 09/21/2011
Groups: Void Crushers
SS structure filter

Wouldnt it be better if the AB segments would not be included in the filter?

bkoep's picture
User offline. Last seen 19 min 47 sec ago. Offline
Joined: 11/15/2012
Groups: None
Probably

Generally speaking, yes, it would probably be best to keep the target protein in its starting conformation, since we know that it is already capable of binding in this arrangement. Unfortunately, the Fragment Filter code needs some updates before we can implement this feature, but those are forthcoming!

As I've mentioned above, though, the Aβ peptide is very flexible in solution, and is capable of taking many different conformations. Our goal is to create a stable complex between Aβ and the designed protein, which may entail finding a new binding conformation for Aβ. In this line of thinking, we probably want the entire complex to look like an "ideal" protein, in which all components pass the Fragment Filter.

Joined: 10/07/2012
Groups: None
Where's the Binding?

Perhaps a foolish question, but in a normal circumstance what does the binding look like...i.e. where on the AB molecule is the binding occurring, is it just the sheets or is it also the loop connecting the sheets?

bkoep's picture
User offline. Last seen 19 min 48 sec ago. Offline
Joined: 11/15/2012
Groups: None
We don't know!

I'm assuming you're asking about how Aβ binds to itself in the disease state? One of the problems that makes Aβ such a difficult molecule to study is that we don't know exactly how it self-associates!

We do know that Aβ can aggregate as a "cross-beta fibril," in which many Aβ molecules take a β-hairpin conformation and form an extensible β-sheet. However, we don't know how it associates to form smaller, soluble complexes which are thought to be most toxic to neurons.

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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, Amazon, Microsoft, Adobe, RosettaCommons