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1667: "Too Much Density!" Freestyle puzzle

Closed since almost 7 years ago

Overall Prediction Electron Density

Summary

Created
April 25, 2019
Expires
Max points
100
Description

This Electron Density puzzle is different than anything we've ever posted before! The extended chain is 187 residues long, but we are giving you a lot more density than that. You'll need to find where to fit this chain in the giant blob of density. (The "Trim Density" tool will be your friend)

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Comments

jeff101 Lv 1

It looks like this puzzle starts with an extended chain with all residues having loop as their secondary structure.
If there is a reliable secondary structure prediction for this puzzle, please post it here.

Thanks!

Bruno Kestemont Lv 1

lrpalstfiflllitggvypllttvlgqwwfpwqangsliregdtvrgsaligqnftgngyfhgrpsat
aempynpqasggsnlavsnpeldkliaarvaalraanpdasasvpvelvtasasgldnnitpq
aaawqiprvakarnlsveqltqliakysqqplvkyigqpvvnivelnlaldklde

Bruno Kestemont Lv 1

LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLEEEEELLEEEEEEELLLLLLLL
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHLLLLLLLLLHHHHHLL
LLLLLLLLLHHHHHHHHHHHHHHLLLLHHHHHHHHHHHLLLLLLLLLLLLLLLHHHHHH

but there are not so many helices in the cloud …

Anfinsen_slept_here Lv 1

What do you mean by "a lot more density"? I would love to know more. Does what we are given correspond to more than 1 asymmetric unit?
What do we expect to find there? 2 monomers, 3 monomers, another different peptide? Where does this density come from? X-ray diffraction, cryo-EM?
Resolution? I think some stuff like that would help us know what we are looking at. Thanks

jeff101 Lv 1

Is it possible that a section of the protein, say segments 1-30,
appears in the displayed ED cloud more than once? Could the
ED cloud be showing more than one conformation of the protein
simultaneously? Could the ED cloud be showing the average
of a distribution of conformations so that some regions of the
cloud look fatter than others? Is some part of the ED cloud
from proteins, ligands, or solvent molecules distinct from the
187-segment amino acid sequence you've given us? Should
we expect one continuous copy of our 187-segment chain to
be in the ED cloud, or should we expect one or more partial
copies of the chain to appear? Several partial copies would
seem to have multiple NH2 and COO termini, which would
be confusing.

Is this ED puzzle different from previous ones because usually
you trim the extra density before posting the puzzle, but here you
give us a very raw un-trimmed ED cloud? Is there some other key
difference between this ED puzzle and previous ones? Should we
expect unusually large Density subscores when we Tab on residues
in this puzzle?

Is the ED cloud here from a crystal or from a sample in solution?
At what temperature was the ED data taken?

When we use the Trim Density tool, do we just alter the appearance
of the ED cloud, or do we directly affect the scoring as well?

The pages below might be helpful:
https://foldit.fandom.com/wiki/Electron_Density_Puzzles
https://foldit.fandom.com/wiki/Electron_density_(tool)
https://fold.it/portal/node/995580 (Electron Density Trim)

Thanks!

toshiue Lv 1

RaptorX LLHHHHHHHHHHHHHHLHHHHHHHHHHHHHLLLLLLLLEEEELLEEEE
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHH
LLLLLLLLLLLHHLLLLLLLLLLLLHHHHHLLHHHHHHHHLLLHHHHHHHHHHHLLLLLLLLLLLLLLLHHHHHHHHLLLLL 187
bruno psipred LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLEEEEELLEEEEEEE
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHH
LLLLLLLLLHHHHHLLLLLLLLLLLHHHHHHHHHHHHHHLLLLHHHHHHHHHHHLLLLLLLLLLLLLLLHHHHHH 180
PsiPred LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLEEEEELLEEEEEEEE
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHH
LLLLLLLLLHHHHHLLLLLLLLLLLHHHHHHHHHHHHHHLLLLHHHHHHHHHHHLLLLLLLLLLLLLHHHHHHHHHHHHLLL 187
Jpred4 LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLEEEEELLEEEEEEEE
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHH
LLLLLLLLLHHHHHLLLLLLLLLLLHHHHHHHHHHHHHHLLLLHHHHHHHHHHHLLLLLLLLLLLLLHHHHHHHHHHHHLLL 187

toshiue Lv 1

one other secondary currently in play…

phyx17870 LLLLEELLLLLLLLLLLHHHHHHHHHHLLLLLLLLLLLLEELLLLLLLLL
HHHHHHHHHHHHHLLLLLLLLLLLLLLHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
LLLLLLLLLLLLLLLLHHHHELLLLHHHHHHHLLLLLLLLLLLHHHLLHHHHHLLLLELLLLLLLLLLLLLLL 187

Bautho Lv 1

The structure is actually known: look at PDB entry 5MRW
But it does not seem easy to build…

Bruno Kestemont Lv 1

For my computer, density cloud is toooo slooow (video card limitation I suppose). Almost impossible to play (hand fold). More time would be needed.