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2454: Electron Density Reconstruction 90

Closed since almost 2 years ago

Novice Overall Prediction Electron Density

Summary

Created
May 02, 2024
Expires
Max points
100
Description

The structure of this protein-DNA complex 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. You may notice that there’s a base pair in here that doesn’t look normal; it’s a Hoogsteen base pair (as opposed to Watson-Crick). Later on, we’ll ask you to play another version of this puzzle where it’s been put in as Watson-Crick instead of Hoogsteen as we’d like to see which works better. Also, a useful note from Bletchley Park for working with DNA: DNA sidechains can be turned relative to their blue arms with bands.

Sequence
MGNLSYADLITRAIESSPDKRLTLSQIYEWMVRCVPYFKDKGDSNSSAGWKNSIRHNLSLHSRFMRVQNEGTGKSSWWIINPDGGKSGKAPRRRAVS. CTATGTAAACAAC. GTTGTTTACATAG

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Comments

LociOiling Lv 1

I didn't go hunting for the Hoogsteen base pair until after the puzzle expired, but it's there.

On the left, adenine in a Watson-Crick base pair. On the right, at segment 224, the adenine is in a Hoogsteen base pair.

There are two hydrogen bonds in both cases. The thymine side of the pair is in the same orientation in both.

There's also a Hoogsteen pairing for guanine and cytosine, but there wasn't one in this puzzle. The Hoogsteen G-C pairing has two hydrogen bonds, where Watston-Crick has three.

The Hoogsteen base pair article on Wikipedia has a good illustration that shows the differences between Hoogsteen and Watson-Crick.

LociOiling Lv 1

Just to complete the set, here's what the density looked like for those two pairs. The adenine in the Hoogsteen pair has a slightly better density score, but a lower overall score.