355: CASP is over... BOOM! TNT Design Puzzle

Closed since over 15 years ago

Summary

• Created: August 19, 2010
• Expires: August 27, 2010 at 23:00 UTC
• Max points: 100

Description

Is that...?! Yes, it is! It's TNT! We've got a very energetic, high profile molecule for you guys to bind. Sure, we already have antibodies that bind TNT, but they're very expensive to make. Wouldn't it be better if we just designed an easy to express protein that bound TNT? We could use it to make cheap detectors and sensors so we can look for TNT contamination or explosives! Brilliant! Remember, there is more than one way to play these design puzzles since we look at all the designs and the best scoring design may not necessarily be the most useful/promising. Check out the puzzle comments for hints!

Top groups

• 1. Contenders 100 pts. 11,079
• 2. Anthropic Dreams 84 pts. 11,063
• 3. Void Crushers 70 pts. 11,035
• 4. Mojo Risin' 57 pts. 11,028
• 5. Russian team 47 pts. 11,015
• 6. SETI.Germany 38 pts. 11,010
• 7. Richard Dawkins Foundation 30 pts. 11,009
• 8. Go Science 24 pts. 11,009
• 9. Deleted group pts. 11,006
• 10. Deleted group pts. 11,000

Top soloists

• 1. Bletchley Park 100 pts. 11,079
• 2. CharlieFortsConscience 99 pts. 11,071
• 3. marie_s 98 pts. 11,056
• 4. Mark- 97 pts. 11,044
• 5. mat747 96 pts. 11,035
• 6. jakyl 95 pts. 11,033
• 7. TheGUmmer 94 pts. 11,030
• 8. steveB 93 pts. 11,029
• 9. sandir 92 pts. 11,028
• 10. chansuke 91 pts. 11,026

Comments

[beta_helix]

Here are some tips you can follow to increase your chance of us selecting and testing your design:

1) Don't bury the TNT ligand too deeply, this may disrupt the overall protein structure.

2) Avoid using charged residues (ASP, GLU, ARG, LYS, HIS) to make hydrogen bonds when possible (although one or two may be fine).

3) Make sure that the tail of the ligand has a way to get out of the binding site. The tail is the end of the ligand that is directed away from the center of the protein initially. (The linker isn't modeled in, but that tail is connected to more atoms, so make sure it can get out!)

[Dj-P]

Everyone who joins the group Go Science?

[steveB]

So when this is finished, you plan to get a protein that one of us crazy non scientists has designed, take it to the wet lab, and then see what happens when you throw it at a piece of TNT.

Brave. Very brave :)

[xiando]

Thank you both for your comments in the puzzle description and in the comments down below here. The both offer some helpful information.

If I could vote more than once there'd be yet another thumbs up.

[beta_helix]

Thanks to austinday for providing us with such detailed descriptions!

[xiando]

This is the first design puzzle I've attempted, and I'm not quite sure of the goal (aside from ftw points)

From the descriptive, it's seems* that the tail (at least) needs a way out of the protein. What's not quite so clear about the ligands in general is in regards to deformations in the ligand structure during the "adjustment" of the design (since presumably this is truly a refinement rather than a redesign puzzle at least in the ?polypeptide? (backbone) layout.

Specifically, is one of the goals to maintain the initial structural conformation of the ligand? As opened, the ligand is very monoplanar (aside from the "Y" structures on the head end.

Some adjustments result in the tail end curling slightly, but it would be very useful to understand if this is an indication of bad judgement with respect to "adjustments"…grrr tweaks, I mean tweaks! (not the foldit function, the common-english action of slightly modifying something) or just a necessary result of the transformations?

*having said that, by getting out of the binding site, I'm not exactly sure if that means literally getting out of the protein or just to another part of the protein. My assumption is/was that it means "a clear path to the outside", but it would be helpful to understand that statement in slightly more detail.
Perhaps it has to do with what a binding site is. Maybe a brief parenthetical ( a short description enclosed by parenthesis) after the use of something like "binding site", which for noviats and non protein scientists might be a bit opaque otherwise…

Also on a side note, I'm not quite clear on the "mutate side chains" function. Is that essentially an automatic version of "manually changing a single side chain into another" function from design mode that acts on the whole protein? I accidentally hit it instead of something else and noticed my score jumped a few points. (16 points to be exact)

thanks

[austinday]

Hi there!

I'll try to take you through the thinking process used to make this puzzle. I think that will hopefully answer the questions you had. So the overall goal is to make a physical protein, in the real world, that will bind TNT. Before we start designing the protein in the computer, we needed to figure out how to even test the designs. What we're going to be using is a yeast display system which requires that whatever molecule we are attempting to bind (TNT, in this case) be biotinylated (has an attached biotin group at one end). Also, if we just coupled a biotin directly to the TNT molecule, the biotin would most likely interfere with the way TNT binds. To reduce that possibility, there is a long linker (a long chain of carbon atoms, more or less) that is made in between the TNT and the biotin molecules. In the design puzzle, you only see the TNT molecule and part of that linker (since it would be cumbersome to include the entire linker and biotin in the puzzle).

As for the goal of the puzzle, there is usually a gap between what the score says and what we actually hope to get out of the puzzle. The puzzle setup requires quite a bit of refinement in order for the score to directly relate to what we would consider a good design. Because of that, I included those "hints" in the description such as making sure the tail has an exit, try to use fewer charged residues, etc… Since it's difficult to get the score to directly reflect that in a proper way. We do, however, log every move that is made, so even if you don't get the highest score and those tasty points, if your design is good, we'll find it.

Okay, so that's what I've been thinking. I'll try to answer some of the specific questions you had now:

The ligand should only be allowed to "bend" at certain joints. (ie. the aromatic ring in TNT has a resonance going on which favors their being planar with respect to the nitro groups). However, the two nitro groups near the linker have been found to be rotated out of plane in some instances. I believe the current version of foldit supports "joint" minimization instead of using a predefined library, which may be problematic (we'll find out after the puzzle is done). So basically, if you can bend the ligand into a conformation, the energy should reflect how good that new conformation is. In the real world, everything will be moving around and that tail will be flopping around and bending every whichaway that it can, so if you can find a minimum energy state (highest score state), that will most likely be the structure that the protein/ligand will take. (But there are also other considerations like enthalpy vs entropy which we aren't able to model very well…it's a hard problem)

An exit for the tail just means that if you imagine extending the "tail" portion of the ligand out further, the carbon that makes up the tail would be able to get clear of the protein without running into the backbone. (We can trim back the side chains if they're in the way)

The mutate side chain function (which can be used on all side chains at once, or on a subset) just uses the rosetta energy function to choose the side chain that gives the lowest energy at that position. Of course, if you make a selection of multiple side chains, it can become a huge non-linear optimization problem, so the algorithm may not find a global optimum, but it'll at least find a local one. (you can also check out the tutorials for more information on how to use that function) So we're hoping that's where the foldit players will come in. You guys are able to do a more efficient search of the possible sequence space and may have a better chance of finding a global optimum, or at least a better local optimum than rosetta would alone. Also, when you allow the mutate algorithm to "run free" on your protein, it will tend to favor charged residues where we wouldn't like them. (A problem with the energy function which is constantly being improved)

Oh! And some more hints:

1. It would be desirable if when you move the entire ligand away from the protein and repack, that the side chains which were making the ligand interactions don't move much. A less stringent test would be to just to repack with the ligand still there and make sure that the hydrogen bonding residues don't move away.

2. Also, If you can "back up" residues that interact with the ligand, that would help to "glue" them into place (which is desirable). When I say "back up", I mean you want to be making good hydrogen bonds not only to the ligand, but to the residues which interact with the ligand.

I hope that answers your questions! I think I wrote a little too much, but if you need any more clarification, don't hesitate to ask!

-Austin

[xiando]

Austin,

thanks for the detailed reply. That was exactly what was looking for. When I first got into this program, (well before my posted start date for this simulacrum me) I established a set of beliefs based partially on inchat discussion, partially on a wide range of preconceptions, about what was and wasn't the right way to think about how the protein needs to be "modified" for best purposes of the actual design/refinement/fold in the lab, some I think on target, some way off base. Posts like the ones you just made, I believe (if people read it thoroughly) will benefit the overall conceptualization about what needs to be done to make a good effort, whether high or low scoring… At least people like me, who can become fuddled by the various paradigms others are using to succeed (whatever that means).

I also really appreciate the comment about viewing all the solutions. It has concerned me that perhaps only top scores were evaluated. That goes a long way to remedying some or perhaps most of my worry about "productive time spent".

Thanks again. Very very helpful to me, and hopefully to others as well.

[saksoft2]

Why can we not mutate any residue?

I mean, if the goal here is to design a better binder for TNT and if the basic shape you gave us is to be used as a starting point, why can we not modify all of the positions?

What if (for example) we wanted to improve the rigidity (cross bonding) between the inner sheets and the outer helices?

What if we wanted to replace the outer helices with sheets in some places?

If we could modify the outer shell, we may be able to build a better cage that would allow us to push the ligand binding sites closer to the edge. With our detectors nearer to the surface, we would need a shorter "tail" and we would be more likely to catch the target molecule.

Am I just dreaming?

[infjamc]

The main reason that we might not want to mutate the outer shell is that the structure could change considerably. In this puzzle, the backbone is held rigid– but when the mutated folding actually folds, the rigidity doesn't actually apply… which means that you risk changing the structure too much by modifying the outer shell. In fact, even mutating only the inner residues is a risk because sometimes a difference of a single residue is enough to prevent it from functioning properly. (Example: the Delta F508 mutation, which results in the removal of a single residue from a human protein, is a common cause of cystic fibrosis.) This is part of the reason the resulting structure has to be re-checked with actual experimentation.

==> That being said, redesigning the outer shell is something that can be considered if necessary. Ultimately, it boils down to the issue of efficiency– namely, whether the increase of complexity (larger search space) is worth the extra effort of coming up with an outer structure from scratch.