BootsMcGraw Lv 1
This can't be a real protein. Why did we spend months learning how to build good cores, only to be given this?
2359: Electron Density Reconstruction 59
Closed since over 2 years ago
Novice Overall Prediction Electron DensitySummary
- Created
- September 25, 2023
- Expires
- Max points
- 100
The structure of this protein has already been solved and published, but close inspection suggests that there are some problems with the published solution. We'd like to see if Foldit players can use the same electron density data to reconstruct a better model. This one is small, so should be able to fine tune it to a pretty high degree.
- Sequence
- LAAKEAKLRDLEDSLARERDTSWRLLAEKEREMAEMRARMQQQLDEYQELLDIKLALDMEIHAYRKLLEGEEER
Top groups
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100 pts. 16,265
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Comments
Artoria2e5 Lv 1
It's… well, a real expressed molecule 3V4Q, but a very small part of a real gene consisting of entirely too much helices. Intermediate filaments are naughty like that.
rmoretti Staff Lv 1
It's a real protein – as mentioned in the description, this puzzle is a re-refinement of an actual structure that has been experimentally determined by X-ray crystallography.
However, the protein at issue is a lamin, a structural protein, rather than the globular proteins you're more likely to have experience with. Structural proteins often function as "supermolecular assemblies" of multiple chains, rather than the single, compact chain that globular proteins have. As such, individual chains may have extended structures which only form "cores" when bound to other chains. (Indeed, the primary function of structural proteins is often interacting with other proteins.)
For this puzzle we have the electron density, which theoretically should contain all the information needed to properly refine the structure. That said, it could well be that in order for Foldit to accurately capture the structure proper, you'll also need the interacting chains. Depending on the results of this puzzle, we may do a follow-up where the interacting chains are provided. But that would make the puzzle larger and more complicated, so it's worth checking if the current Foldit tools are adequate in the single-chain case first.
Artoria2e5 Lv 1
The C-terminal seems to give quite a few points upon DRW. Not all of these better-scoring solutions retain the expected helix… One looks real enough though!
horowsah Staff Lv 1
One other note is that in crystallography, these sorts of proteins are not uncommon to look like this, when in reality it will have other copies of itself to bind to in the crystal that will make it obey the rules we think of better. But when we model them, we just look at the one copy, since they typically will all be the same.