Placeholder image of a protein
Icon representing a puzzle

1431: Unsolved De-novo Freestyle 117

Closed since over 8 years ago

Intermediate Overall Prediction

Summary

Created
September 16, 2017
Expires
Max points
100
Description

Note: In response to some player feedback related to the excessive size of this protein, we're extending the puzzle deadline by two weeks! The puzzle will expire on October 9 at 23:00 UTC.



Chikungunya (CHIK-un-goon-ya) virus (also known as CHIKV) is a mosquito-transmitted alphavirus that has spread around the world and is currently infecting people in about 60 countries globally. CHIKV is rarely fatal, but causes severe joint pain for months to years that can debilitate affected patients for long periods of time. There are currently no known drugs to treat CHIKV infection, primarily due to a lack of understanding of the structure of CHIKV proteins involved in viral genome replication. The Geiss lab has worked on developing drug targeting the membrane bound CHIKV nsP1 protein, which is the anchor for the viral genome replication complex on cellular membranes and a multifunctional enzyme that forms a 5’ RNA cap structure on the end of the CHIKV RNA genome. Solving the structure of the CHIKV nsP1 protein would provide critical information for designing drugs that inhibit nsP1 function and abort viral genome replication.


The structure of this protein is still unknown. Secondary structure predictions (from PSIPRED) are marked on the starting structure, and provide clues about where the protein might form helices and sheets!


Note: Since the protein is huge for Foldit, we have divided the protein into two puzzles. This is the first puzzle.


Sequence:

MDPVYVDIDADSAFLKALQRAYPMFEVEPRQVTPNDHANARAFSHLAIKLIEQEIDPDSTILDIGSAPARRMMSDRKYHCVCPMRSAEDPERLANYARKLASAAGKVLDRNISGKIGDLQAVMAVPDTETPTFCLHTDVSCRQRADVAIYQDVYAVHAPTSLYHQAIKGVRVAYWVGFDTTPFMYNAMAGAYPSYSTNWADEQVLKAKNIGLCSTDLTEGRRGKLSIMRGKKLKPCDRVLFSV

Top groups

  1. Avatar for xkcd 11. xkcd 13 pts. 8,432
  2. Avatar for HMT heritage 12. HMT heritage 10 pts. 8,313
  3. Avatar for :) 13. :) 7 pts. 7,885
  4. Avatar for freefolder 14. freefolder 6 pts. 7,522
  5. Avatar for Natural Abilities 15. Natural Abilities 4 pts. 6,943
  6. Avatar for Herobrine's Army 16. Herobrine's Army 3 pts. 6,813
  7. Avatar for Italiani Al Lavoro 17. Italiani Al Lavoro 2 pts. 6,614
  8. Avatar for Eὕρηκα! Heureka! 18. Eὕρηκα! Heureka! 2 pts. 6,398
  9. Avatar for Richard Dawkins Foundation 19. Richard Dawkins Foundation 1 pt. 6,300
  10. Avatar for Alpha Rays 20. Alpha Rays 1 pt. 5,855
  1. Avatar for Susume
    1. Susume Lv 1
    100 pts. 10,200
  2. Avatar for markm457 2. markm457 Lv 1 99 pts. 10,084
  3. Avatar for Enzyme 3. Enzyme Lv 1 97 pts. 10,060
  4. Avatar for nicobul 4. nicobul Lv 1 95 pts. 10,017
  5. Avatar for retiredmichael 5. retiredmichael Lv 1 94 pts. 10,009
  6. Avatar for Galaxie 6. Galaxie Lv 1 92 pts. 9,956
  7. Avatar for Bruno Kestemont 7. Bruno Kestemont Lv 1 90 pts. 9,891
  8. Avatar for frood66 8. frood66 Lv 1 89 pts. 9,887
  9. Avatar for Timo van der Laan 9. Timo van der Laan Lv 1 87 pts. 9,882
  10. Avatar for actiasluna 10. actiasluna Lv 1 86 pts. 9,874

Comments

Timo van der Laan Lv 1

On such a big puzzle, it might be an idea to give us a few templates to work with. That might give us a chance to get to a structure that might be close.

Skippysk8s Lv 1

Just a note. I'd love to work this, but was out two days and don't have time to pull this together. sorry not to have more time, but little machine can't do this size puzzle in regular time period.
Maybe a little extra time for the next large puzzle would help
Skippy

Susume Lv 1

There are a few homolog (related) sequences that form real proteins but that match only segments 49-175 of our target protein, with one or both ends of our protein missing. I'm pretty sure that means segments 49-175 should be able to fold into a realistic protein shape without the ends being present. The ends would then add on without disrupting the shape of the middle section (and without depending on each other, since either end can be present while the other is absent). I have tried a couple of tracks where I fold 49-175 first, then add the ends on, and they seem to be working out well.

Bruno Kestemont Lv 1

Then for a following round, researchers could provide us with several templates for seg 49-175 (as suggested by Timo). It would help focusing.

lamoille Lv 1

Just asking, but is there an issue in scoring this puzzle ? It expired 12 hours ago and still no scores have been posted. Thanks for any feedback.