Placeholder image of a protein
Icon representing a puzzle

2353: Electron Density Reconstruction 57 (with DNA!)

Closed since over 2 years ago

Novice Overall Prediction Electron Density

Summary

Created
September 12, 2023
Expires
Max points
100
Description

This puzzle is a bit different than previous Reconstruction puzzles. Like others, the structure of this protein has already been solved and published, and 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. The difference is that in addition to a protein in this puzzle, the protein is bound to DNA! So we're curious if Foldit players can improve both the protein and the DNA using the electron density. Not every tool that works well with proteins also works with DNA, so this might take a bit more time to figure out strategy.

Sequence
Protein: MATVKFKYKGEEKQVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLAKQKK DNA: GTGATCGC

Top groups

  1. Avatar for VeFold 11. VeFold 1 pt. 23,571
  2. Avatar for HMT heritage 12. HMT heritage 1 pt. 23,361
  3. Avatar for BOINC@Poland 13. BOINC@Poland 1 pt. 21,599
  4. Avatar for AlphaFold 14. AlphaFold 1 pt. 19,062
  5. Avatar for Foldit Staff 15. Foldit Staff 1 pt. 16,476
  1. Avatar for Galaxie
    1. Galaxie Lv 1
    100 pts. 24,858
  2. Avatar for LociOiling 2. LociOiling Lv 1 63 pts. 24,848
  3. Avatar for MicElephant 3. MicElephant Lv 1 37 pts. 24,834
  4. Avatar for phi16 4. phi16 Lv 1 21 pts. 24,833
  5. Avatar for jeff101 5. jeff101 Lv 1 11 pts. 24,827
  6. Avatar for guineapig 6. guineapig Lv 1 5 pts. 24,827
  7. Avatar for Bruno Kestemont 7. Bruno Kestemont Lv 1 2 pts. 24,827
  8. Avatar for gmn 8. gmn Lv 1 1 pt. 24,821
  9. Avatar for alcor29 9. alcor29 Lv 1 1 pt. 24,817
  10. Avatar for Gonegirl 10. Gonegirl Lv 1 1 pt. 24,770

Comments

Artoria2e5 Lv 1

PDB-REDO entry says that the rotamers are probably very bad; we can shake that out. The handful of rama issues are probably best idealized or remixed out. Clashes (bumps) are not too bad.

rosie4loop Lv 1

For a high resolution structure like this, water densities are visible. Those perfect spherical densities in the map could be a water oxygen. Some of them are within hbond distance that could contribute to protein structure stability or DNA interaction.

Probably challenging at this stage for Foldit to handle this, though.

rmoretti Staff Lv 1

How best to handle waters in these electron density puzzles is something we're currently discussing. For best results, they need to get added back in. We may eventually implement tools to allow players to add/remove waters, but you're correct that it's challenging to get Foldit to handle waters properly. Right now I believe the approach is to add them back in with a post-processing step.