User talk:ElNando888/Blog/Models
< User talk:ElNando888 | Blog
Interesting post there ElNando, the eterna screen shot still leaves me with questions - why for instance is the base 77 dark blue ? Edward Lane (talk) 19:25, 6 November 2013 (UTC)
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Hi Edward, I'm not really sure why it turned out that way in this design. All I can say is that the pattern seems relatively consistent with the majority of UUCG tetraloops we collected in SHAPE results over the months and years. Typically, the first Uracil is quite mobile and unprotected, while the rest of the loop usually shows protection, to a degree or another. When you think about it, these facts are also consistent with the prediction that the UUCG tetraloop is a (somewhat surprisingly) very stable structure, and this cannot happen without a fair amount of hydrogen bonds and stacking interactions, which necessarily are going to reduce mobility and reactivity, don't you think?
-- ElNando888 (talk) 00:14, 7 November 2013 (UTC)
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Why is residue 31 in the GAAA tetraloop exposed?
Brourd
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Hi Brourd,
I'm intrigued. Supposedly, this base is in a loop, so it is normally expected to be unpaired and thus, exposed. So I wonder, why not?
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In theory, a GAAA tetraloop, based on experimental data that we have received previously for this motif, should have a pattern of Protected, Exposed, Protected, Protected. The question is, why in this case was residue 31 exposed? Experimental error? Or perhaps there is something deeper within the results...
Brourd
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In fact, I would tend to believe in your last alternative. This goes a little off from the topic of the page, so I'll try to be brief. Plus, I know you don't need long explanations ;)
Protection signal arises from pairing+stacking, essentially. And nothing says what a protected base was paired with. UUCG is known to be very stable, without external help. On the other hand, GNRA loops are known to be quite stable, but also to be a little more flexible (see http://www.ncbr.muni.cz/NMR/hairpin_dynamics.html for instance), which is what allows them to easily engage in tertiary interactions. And often, those interactions can't be inferred from a signal at another point of the sequence, because it involves motifs like the A-motif. And all we're left with are blueish shadows in GNRA tetraloops... Maybe in this particular design, the position of the loop relative to the global 3D shape of the folded molecule, made it difficult for it to interact with anything, be it locally, or by dimerization. Which could have resulted in a rather clean reactivity signal for the 3' stacked bases of the motif.
Just offering an hypothesis here :)
-- ElNando888 (talk) 19:04, 8 November 2013 (UTC)
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