User:ElNando888/Blog/Conformational 4
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< User:ElNando888 | Blog
(back to Conformational 3)
In FMN switches, the "bonus" given by the presence of the ligand in the solution is itself a function of the concentration of the FMN species (see this GetSat thread for details). Using the "hack" I talked about in Conformational 1, I simulated a few contexts with variable bonuses for JR's design.
| MFE | Pairing probabilities | Centroid | |
| 0.0 (unbound) |
<img style="background-color: dimgrey;" src="/wiki/images/Stst2_t1.png" alt="" /> |  |
<img style="background-color: dimgrey;" src="/wiki/images/Stst2_t1.png" alt="" /> |
| -2.8 | <img style="background-color: dimgrey;" src="/wiki/images/Stst2_t1.png" alt="" /> |  |
<img style="background-color: dimgrey;" src="/wiki/images/Stst2_t2.png" alt="" /> |
| -2.9 | <img style="background-color: dimgrey;" src="/wiki/images/Stst2_t1.png" alt="" /> |  |
<img style="background-color: dimgrey;" src="/wiki/images/Stst2_t3.png" alt="" /> |
| -3.1 | <img style="background-color: dimgrey;" src="/wiki/images/Stst2_t1.png" alt="" /> |  |
<img style="background-color: dimgrey;" src="/wiki/images/Stst2_t3.png" alt="" /> |
| -3.2 | <img style="background-color: dimgrey;" src="/wiki/images/Stst2_t4.png" alt="" /> |  |
<img style="background-color: dimgrey;" src="/wiki/images/Stst2_t3.png" alt="" /> |
| -4.86 (bound) |
<img style="background-color: dimgrey;" src="/wiki/images/Stst2_t4.png" alt="" /> |  |
<img style="background-color: dimgrey;" src="/wiki/images/Stst2_t5.png" alt="" /> |
| As a reminder: | |||
 this was the target, ... |
there was no FMN molecules in the solution, ... |
|
|
Observations:
- the centroid structure switches from an unbound-like structure to a bound-like one at a ΔG = -2.9 kcal.mol-1
- the MFE structure change occurs at ΔG -3.2 kcal.mol-1
