Symmetric Design Results and Guidelines
It’s been a few months since we launched the symmetric design puzzles, and we now have a considerable database of results - your structures - to analyze. Among the designs are many creative, interesting, thought-provoking structural motifs. Unfortunately, the thoughts they typically provoke are: “Wow, this looks amazing! Too bad it probably won’t fold up correctly.” (To be fair, we’ve even made a few of them. No luck getting them to fold so far.)
This is partly our fault - we haven’t really given you a how-to guide; all you’ve had to go on are the energies the game shows you. And in minimizing the total energy, you’ve done well! But designing symmetric, multi-part proteins can be trickier than just looking at the raw energies, which is why we’re working on improving them, and making sure we inform you - the players - about what sorts of designs are most likely to work in real life.
With that in mind, this post will give some insight into what makes a well designed, realistic protein. We don’t want you to see this as a requirement to make ‘boring’ structures; we want to see more than just the same low-energy helical bundles or simple beta sheets that are already common in nature. The structures you’ve come up with so far have been awesome, and if you’re able to get an awesome looking structure that follows these principles, it’s much more likely it will fold up in practice - and we are much more likely to try it out in the lab!
Symmetric Protein Design Guidelines:
Symmetric copies are monomers too!
The first thing is to remember that, while symmetric, each copy of the protein has to fold up reasonably well by itself, as what we call a monomer.
This means that each non-symmetric copy of the protein needs to keep the principals of standard protein design in mind as well.
Each non-symmetric copy still needs a good hydrophobic core, and should try to minimize the surface area interacting with solution. Flat extended sheets are cool looking but have high surface area. If you look at the images below of an existing symmetric protein, you can see that each of the copies is a fairly reasonable looking protein, with a nice hydrophobic core that is highlighted in red in the image on the right. The purple region shows you the hydrophobic residues in the interface between the monomers, which allows these proteins to form a symmetric complex.
You can compare the above designs to something like the following symmetric protein:
This structure looks like it could have a chance to be stable as a complex, but individual copies with a sheet of strands is unlikely to be stable in solution. A lot of designs we saw looked stable as a whole complex but were unstable as an individual chain.
Why do the copies need to fold well by themselves? Well, living cells have quality control machinery to detect and destroy poorly folded proteins. If your monomer has a poor core it will fold more slowly, increasing the chance of being degraded before it can assemble in the complex you are trying to design.
Note that there’s an important exception to this rule: when the subunits are covalently attached to each other. Amino acid chains can be permanently glued together by covalent bonds, either by a disulfide (example: http://fold.it/portal/node/992625) or a small molecule that binds to the N terminus and acts as a “hub” (example: http://fold.it/portal/node/993779). In these cases, the chains don’t have to bump around in solution for a long time before finding each other; they’re stuck with each other for good, and the individual subunits don’t have to fold on their own. So you - the players - are free to interweave the chains any way you’d like; braided sheets, fully “communal” hydrophobic cores, etc. We’ll try to remind you which puzzles will involve these covalent hubs (where you don’t have to worry about independent chains being folded on their own) and which do not (where it’s important to make sure the individual symmetric pieces can fold at least part-way by themselves).
Long loops are too flexible to be controlled and they make your designs have higher chance to fold in unexpected ways. By shortening the loops, you can also make local interaction more likely to happen so that your protein can fold concurrently when it’s being synthesized. The reason for doing that is because free floating flexible loops or random coils get digested by other proteins in cells during protein synthesis. So, if you don’t want your designs to be eaten by other proteins, shorten the loops and make local interactions!
Continuing hydrogen bonds in the helix backbone gives you huge bonus of helix stability. A lot of time you may want to have a helix turn to another direction. In that case, we would recommend you to use a short loop to link two helices instead of building a broken helix with a kink.
Close sequence interactions
Having close sequences interacting with each other can make sure the protein can be partially folded and stabilized during synthesis. What this means is that is better to have beta strands pairing between close pieces of the protein. for example is better to pair strand 1 with 2 than 1 with 8.
Sidechains making hydrogen bonds with the loops.
Having loops forming hydrogen bonds with sidechains on stable strand or helix is a great way to stabilize your loops and the whole subunit so that your design is favored.
Hydrophobics in the interface, but not only hydrophobics.
There are different types of protein interactions but hydrophobic is the main driving force to bring proteins close to each other. However, having only hydrophobics at the interface is not a good strategy because except interaction, you also want specificity. Having only hydrophobics at the interface may allow multiple orientations of subunits that are coming together. Think of the hydrophobic patches as a lock and key - you only want to the correct lock patch to work with the corresponding key patch. A lot of people have experience in assembling foam mat, it gives a perfect example of interlock pattern that you may apply during interface design.
Hydrogen bonds between the subunits
Hydrogen bond can help stabilize interaction between subunits formed by hydrophobic interactions. It can also limit the number of orientation of subunits and increase interaction specificity.