1463: Classroom Puzzle: HIV RNA

Summary

Name:

Status:

Closed

Created:

12/25/2017

Points:

100

Expired:

01/03/2018 - 18:00

Difficulty:

Intermediate

Description:

In this Classroom puzzle, students will learn about RNA structure and dynamics, as well as the ongoing debate between conformational capture and induced fit models of biomolecular binding. The RNA molecule of choice here, HIV TAR, is provided in one of its many possible folded conformations. However, we know the RNA is flexible, and it is still unclear what fold is most favorable for this molecule. See if you can find other stable folds for this RNA molecule! University of Denver students will be asked to read two articles alongside this Foldit puzzle. The first is a 2007 article by Zhang et al., which demonstrates an innovative experimental technique for probing the structure and dynamics of this RNA molecule. The second article is a 2009 report by Bardaro et al., in which the authors use more traditional techniques to examine how the structure of this RNA might respond to the presence of binding partners.

Categories:

Pilot

Rank

Group

Score

Points

Go Science

8,310

100

Beta Folders

8,308

Anthropic Dreams

8,296

Gargleblasters

8,279

Another Hour Another Point

8,278

Rank

Player

Group

Score

Points

toshiue 8 168

Go Science

8,310

100

8,310

8,308

8,307

8,303

Rank

Player

Group

Score

Points

tokens 87 2553

Anthropic Dreams

8,296

100

8,294

8,292

retiredmichael 87 1584

Beta Folders

8,284

Galaxie 5 9

Anthropic Dreams

8,284

Sat, 12/30/2017 - 01:48

Susume 86 184

Offline

Joined: 10/02/2011

Groups: Anthropic Dreams

nucleotide sequence

The sequence of nucleotides (sidechains) for this puzzle is:
GGCAGAUCUGAGCCUGGGAGCUCUCUGCC

Sat, 12/30/2017 - 01:53

Susume 86 184

Offline

Joined: 10/02/2011

Groups: Anthropic Dreams

random stuff for players

To see hydrogen bonds, turn on show bonds (non-protein) in view menu.

In lua, when using structure.GetAminoAcid(n) on an RNA molecule, foldit returns a 2-letter abbreviation for base n ("ra", "rc", "rg", or "ru").

Wikipedia has a page on secondary structure of RNA, with a few pictures of shapes that RNA can make:
https://en.wikipedia.org/wiki/Nucleic_acid_secondary_structure

More pics of shapes RNA can make - scroll down to the "secondary structure" section: http://www.sivabio.50webs.com/nucleicacidstructure.htm

Sat, 12/30/2017 - 19:43

Susume 86 184

Offline

Joined: 10/02/2011

Groups: Anthropic Dreams

Need more tools

We really need a way to straighten out the backbone when it gets twisted (wiggle twists it a LOT when we use bands to move things around). No tweak, no remix, no rebuild, no cutting - it's very hard to recover from twisting!

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