User:ElNando888/Blog/Conformational 4

From Eterna Wiki

(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="" /> SwitchDotPlot6.png  <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="" /> SwitchDotPlot 280.png <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="" /> SwitchDotPlot 290.png <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="" /> SwitchDotPlot 310.png <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="" /> SwitchDotPlot 320.png <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="" /> SwitchDotPlot7.png <img style="background-color: dimgrey;" src="/wiki/images/Stst2_t5.png" alt="" />
  As a reminder:
  Stst2 target.png
this was the target, ...
 there was no FMN molecules in the solution, ...

Stst2 estim.png
and this was the result 

 

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 

 

 

Conformational 5