User:ElNando888/Blog/Mimic: Difference between revisions

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<p>This entry won't develop much to a blog post. I'm just throwing ideas in the context of a discussion I'm having with [[User:Brourd|Brourd]] about [[mimic]]s.</p>
<p>This entry won't develop much into a blog post. I'm just throwing ideas in the context of a discussion I'm having with [[User:Brourd|Brourd]] about [[mimic]]s.</p>
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<p>These are not perfect, but at least, the EteRNA model thinks these folds are even money...</p>
<p>These are not perfect, but at least, the EteRNA model thinks these folds are even money...</p>
<p>The idea is to compare the stability of the unbound FMN binding site against various sarcin-ricin loops. If the model is correct, the 16-21 and 28-33 segments should display roughly the same SHAPE protection signal, something around 50%. If the hypothesis that the sarcin-loop is nearly as stable as a <span style="text-decoration: underline;">bound</span> FMN site is correct, a strong difference should be visible between those 2 segments.</p>
<p>The idea is to compare the stability of the unbound FMN binding site against various sarcin-ricin loops. If the model is correct, the 16-21 and 28-33 segments should display roughly the same SHAPE protection signal, something around 50%. If the hypothesis that the sarcin-loop is nearly as stable as a <span style="text-decoration: underline;">bound</span> FMN site is correct, a strong difference should be visible between those 2 segments.</p>
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<p>[[File:FMN-Sarcin mimic project 3.png|1000px]]</p>
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<p>It seems easier to stabilize the design when using 5 nts long stems, instead of 6.</p>

Revision as of 06:33, 18 February 2014

 

This entry won't develop much into a blog post. I'm just throwing ideas in the context of a discussion I'm having with Brourd about mimics.

 

<tbody> </tbody>
1FMN stacking pattern.png Sarcin-ricin stacking pattern.png
FMN Sarcin-ricin (15 nts)

 

The top half is structurally quite similar, but the bottom differs a bit. Specifically, it is undeniable that the FMN molecule offers a much larger stacking area than the A+A platform in motif IL_85647.3

 

<tbody> </tbody>
1FMN stacking pattern.png Sarcin-ricin (reduced) stacking pattern.png
FMN Sarcin-ricin (13 nts)

 

A possible way to compensate the difference would be to use a reduced form of the loop, with an additional cWW pair, like in motif IL_49493.4

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By the way, this canonical pairs mimic...

<tbody> </tbody>
Mimic 1.png Mimic 2.png

I'm counting -11.9 kcal, much more than the -4.9 that we're supposed to mimic...

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Based on Brourd's constructs, a few tests we could run:

FMN-Sarcin mimic project 1.png

 

FMN-Sarcin mimic project 2.png

 

These are not perfect, but at least, the EteRNA model thinks these folds are even money...

The idea is to compare the stability of the unbound FMN binding site against various sarcin-ricin loops. If the model is correct, the 16-21 and 28-33 segments should display roughly the same SHAPE protection signal, something around 50%. If the hypothesis that the sarcin-loop is nearly as stable as a bound FMN site is correct, a strong difference should be visible between those 2 segments.

 

FMN-Sarcin mimic project 3.png

 

It seems easier to stabilize the design when using 5 nts long stems, instead of 6.