Aflatoxin Challenge Update

Foldit Community, we are ready for an Aflatoxin update! Thank you for all your efforts in designing the first round of designs to combat aflatoxin. To date we have had hundreds of players design >400,000 structures! There is a lot to choose from and it has been a fantastic way to start off this effort. Players have been incredibly creative, and have engineered exciting new molecular interactions that truly have the potential to stabilize the aflatoxin hydrolysis transition state we provided in the models. Two examples are below: the first is a pi-pi stacking interaction between a tryptophan and the conjugated ring system of aflatoxin AFB1 (left, Figure 1). If the designed protein is stable enough in this state to provide this interaction in the physical world it would almost certainly position aflatoxin in a manner poised for enzymatic hydrolysis. The second interaction is a classical hydrogen bond with a ketone group (right, Figure 1). Again, these energetically favorable and strong interactions will provide the physical properties needed to stabilize aflatoxin AFB1 in a manner ready for hydrolysis by the naturally occurring catalytic core of the enzymes. We look forward to seeing more of these interactions in subsequent rounds!


Figure 1. AFB1 interactions in Foldit player designs. In both images the white structure is the native enzyme (starting structure), and the green is a Foldit player design. Left, a double mutation accommodated by some backbone movement enabled a pi-stacking interaction between tryptophan and AFB1. Right, a single mutation and backbone change introduce a hydrogen bond with the ketone group on AFB1. Keep making changes! And remember that it is not only important to interact with AFB1, but also to stabilize the new protein structure to reinforce the AFB1 interactions!

Experimental Charactization

On the experimental front we are excited to announce that we have transferred all methods into a microtiter plate format and have tested the first 100 GeneStrings from ThermoFisher designed by players (Figure 2). These were selected on a variety of factors (~30 of the top scoring based on overall score; ~30 based on top AFB1 energy with above average overall score; best score of 20 players sorted on best scoring designs; all of the player Scientist Shares). While the process from design to data was seamless, unfortunately all of the data was negative (i.e. none of the designs degraded aflatoxin). We are going back to this first round and re-evaluating how we picked designs, as well as going back and refining some of the designs we thought were most interesting ourselves, however in the meantime we want to get another round of puzzles going. Don’t lose hope! We expect this will require several rounds of design as we optimize the puzzle and solution selection parameters, as well as start to prepare a few new scaffold proteins to try. But we are confident we will find something in the next few rounds and we appreciate your diligence and efforts in helping solve this global issue!


Figure 2. Workflow from Foldit to experimental data

Next Puzzles

There was great feedback from the community about the original puzzles and we plan to adjust the next puzzles based on this feedback. Most importantly, we plan to trim some of the frozen protein regions, so you can deal with a smaller puzzle and focus on the regions of interest. We may also upweight the ligand scoring, to encourage more interactions with the ligand. Although some players have requested the ability to move the ligand around the binding pocket, we will continue to keep the ligand fixed in place; the ligand's orientation with respect to the catalytic residues is critical if we want the reaction to occur!

We will continue to update you as we go, but we're off to a strong start! Check out Puzzle 1497: Aflatoxin Challenge: Round 5 now!

( Posted by 73 1891  |  Wed, 03/14/2018 - 23:04  |  6 comments )
2
spvincent's picture
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How was that figure of

How was that figure of 400,000 arrived at?

bkoep's picture
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"Works-in-progress" included

If you're playing Foldit online, then the Foldit client regularly uploads your latest solution to the Foldit server, once every 2-5 minutes. Each of the two-week aflatoxin puzzles garnered a little over 100,000 solutions this way.

In design puzzles, we're usually most interested in Foldit players' final top-scoring designs, but we do also analyze these bulk models to some degree. Sometimes we can pick out interesting designs that don't score well, but still might be worth following up on. These bulk solutions also help us understand the breadth of different structures that Foldit players are exploring, and can even give us a rough idea of players' folding techniques.

In structure prediction puzzles, these "work-in-progress" solutions are especially important, because they help to inform the entire energy landscape of the target sequence. That is, while it's important that the native structure scores well, it's equally important that non-native structures score poorly.

spvincent's picture
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It sounds then as if

It sounds then as if scientist-shared solutions are redundant for this puzzle.

rmoretti's picture
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Not necessarily

Share-with-scientist solutions are still relevant for these puzzles, even though we're looking at more than just the top results.

The biggest reason is that sharing with scientists highlights those particular structures you think are interesting. If you don't highlight it with a scientist share, it's mixed in with the rest of the work-in-progress structures, and may or may not be pulled out from the rest by the post-analysis. A scientist share indicates that there's something "special" about this structure, and worth a closer look during result processing. At the very least, it may help highlight differences between what players think is important/interesting and what the scientists think is important/interesting.

Also, the work-in-progress sampling doesn't capture every structure you create. There's a chance that a structure you think is interesting (and would scientist-share) isn't captured by the automatic sampling. By scientist-sharing, you ensure that it ends up being collected.

jeff101's picture
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Are you mining our results?

Are you analyzing more than the usual # of solutions per player? Don't you usually analyze only 7 solutions from each player (5 shared w/scientists + best solo + best evo) per puzzle even though every few minutes that we play, each Foldit client sends its latest results to the server?

S0ckrates's picture
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Pretty sure they are.

Since this is a big collaboration they said there's more resources to test more solutions outside the usual viable window.

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