Protein Design Critique: IL-7R Binder Redesign
You’re doing great so far! I've looked at your solutions from first 4 puzzle rounds, and I think a lot of your designs are going to work! I just wanted to remind everyone that, in addition to the Foldit score you get on each puzzle, in the end you'll also get a binding score based on our testing of these designs in the lab!
Designing a protein to fold precisely is a difficult problem! When we test your protein, we are testing whether the sequence you chose folds into the shape of your solution. In Foldit, you can change your solution into whatever shape you want, but in the lab your sequence might not fold into the shape you wanted. It took scientists decades to figure out the shape a given protein sequence folds into (they call this the Protein Folding Problem). The good news for you though is that the Protein Folding Problem has a really simple answer:
I want to emphasize a few guidelines you can use to ensure your designed fold is the most favorable state:
· Secondary structure - use lots of alpha-helices or beta sheets
· Puzzle score - try to have the best score for your chosen fold
· Short loops - you'll need to use loops, but keep them as short as possible
Next I’ll show some examples and give my thoughts on a few designs from Foldit players. Please note that all of these designs have been chosen because they showcase a single weakness in an otherwise excellent design. We don't mean to disparage anyone's designs—on the contrary, the solutions highlighted in this critique are among our favorites!
A study of two 3-helix bundles
While both of these structures emphasize secondary structure and well-packed cores, design A is more likely to fold because of its shorter loops.
The reason we prefer secondary structure to loops is that loops typically have many alternate conformations (decoys) that score the same or even better than the design model. Shorter loops mean fewer decoys and a better chance of folding as intended. For instance, one can imagine how the loop of design B could misfold so that the third helix is on the wrong side of the bundle.
Bad beta-sheet, better beta-sheet, best beta-sheet
Beta sheets are a tricky secondary structure, because they require distant parts of the protein chain to come together. The point I want to highlight here again is that shorter loops are almost always better. In design C, there are too many loop residues between the helices and sheets. These loop residues are likely to rearrange themselves in real life.
Design D has shorter loops, but I still see a few backbone H-bond pairs that are unsatisfied here. (Also, I'm not so sure about that ARG / GLU zipper there. ARG / GLU like to form helices, so I'd probably go with HIS / THR...)
Design E is an optimized Baker Lab design (not from the IL-7R series), but I wanted to include it to demonstrate my point. Look at how short those loops are! This is a difficult fold to master, but FoldIt players like challenges, right?
4-helix bundles, the good, the bad, and the ugly
When it comes to 4-helical bundles (and really all designed proteins), the name of the game is compact. You want your design to resemble a ball with all portions stabilized by at least 2 other secondary structures. Design H fails just that; it's too long and unsupported. This structure will almost certainly fold into something more compact in real life.
Design G also fails this rule, as it's leaving a large portion of the structure thin and unsupported. Those two helices would have been better on top of the protein like the good example is doing here.
Yes, design F would be better if the helices were longer, but we didn't give players enough residues for that (unfortunately, we're limited to small proteins for our lab experiment). If you run out of residues for good helix packing, you can try beta-sheets. Although, previous experiments have shown that helices are more robust than beta-sheets. So if the choice is between an okay beta-sheet and an okay helix, I'd go for the helix.
Don't try to make additional target contacts
First let me say that these designs are very interesting in that they make additional contacts with the target. Especially in design I, I'm not even sure I could design that with all the tools I have! But, I want to remind everyone that in this design challenge, folding is more important than binding.
You've already been given two helices that are guaranteed to bind the IL-7R. If you can just fold the rest of the protein into a stable fold then you'll have a binder!
Great 3-helix bundle, but that long loop isn't going to fly
Finally, one more design to really hammer home the message of shorter loops. Design K looks great with three well packed helices, but look a little closer and you'll see that a long loop is required to stretch back and meet the third helix. I'll admit, this protein has a chance to work, but with a loop that long, who knows where the final helix will actually fold...
Posted by bcov 118 5892 |
Fri, 08/16/2019 - 17:57 |
We have a lot more puzzles planned for this series, and we look forward to seeing more designs from Foldit players! Round 5 just closed, and we'll get started on the analysis of those solutions right away. In the mean time, check out the Round 6 puzzle, which is online now!