More Fun with Catalysts
Widespread use of clean-burning hydrogen for fuel would be an amazing step forward for society. Have we mentioned recently how amazing? Oh that’s right, we have.
To recap: molecular hydrogen (H2) produces water when it’s burned, and can be re-made from water plus a bit of energy. Well, a LOT of energy, but that’s where hydrogenase catalysts come in: if we can reduce the cost of producing hydrogen from water, we can power everything with clean, near-unlimited hydrogen that we can make cheaply at our power plants or in-home plug-in hydrogen makers. If we get a good enough hydrogenase catalyst working, the future becomes really exciting.
We’ve shown you a hydrogenase catalyst before (Puzzle 644: http://fold.it/portal/node/993779 ). Now we’ll be working with a different catalyst with proven activity; a nickel-phosphine dimer inspired by the active sites of some natural enzymes. We can watch hydrogen bubble off it when we apply a small current to feed it electrons. This catalyst was developed at PNNL (Pacific Northwest National Labs, in south-central Washington State) by a group led by Daniel DuBois. It’s a really neat molecule, and more information can be found at the PNNL website here: http://www.pnl.gov/news/release.aspx?id=883
The good news is that we’ve already proven we can attach peptides to this catalyst without making it worse. (This is a bigger hurdle than you might realize!) With peptide attachments –specifically, with YOUR help building good peptide attachments – we can make this a much better catalyst.
So, how do we make this catalyst a game-changer? For starters, we’re just looking for interesting, compact designs. Just putting this catalyst into a protein-like environment and determining its structure would be a huge step forward. But this isn’t just about making our catalyst a cozy little apartment out of protein. We need to feed protons (hydrogen atoms) to the active site so we can assemble hydrogen faster.
We also need to hold the catalyst in place so that it can’t wiggle. The catalyst is more flexible than it appears in our puzzle. It can bend into other conformations where it stops working as a catalyst. But with a strong, compact protein support, we’ll be able to hold it in the working conformation so that it stays active more of the time.
Many natural enzymes do exactly this sort of thing: they encase their active site in a protein machine that keeps it stable, and “feed” it protons or other molecules it needs. If we can get a Borg-like hybrid protein/small-molecule catalyst working, we won’t just make a big step towards a hydrogen energy economy, we’ll also have a unique hybrid bio-machine to brag about. :)
Future puzzles will provide bonuses for reaching either the central metal or nearby nitrogen with polar hydrogen atoms. But for this first puzzle (#675: https://fold.it/portal/node/994490) just have fun building up peptide scaffolding to wrap around the catalyst.
Technical advice (for puzzle #675 and those like it):
Feel free to look to previous two-chain symmetric design puzzles for inspiration, but don’t limit yourself to what’s worked before, since this big central molecule linking your two chains provides new opportunities and new challenges. Specifically, the two chains are now permanently stuck together, so you don’t have to worry about two separate chains finding each other; they count as one chain now, so they don’t have to be able to fold up on their own. On the other hand, the bulky molecule in the middle means that the available geometries for packing the chains are more limited, and to get a good score you’ll probably have to include at least part of that big molecule in your core.
Even more technical: be warned that it’s going to be trickier than normal to wiggle and rebuild segments near the N-termini of the two chains, since they’re locked together at the catalyst.( Posted by DrLemming 136 3772 | Fri, 02/08/2013 - 08:51 | 3 comments )