[gmx-users] Simulation of slow folding proteins

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Mar 22 02:02:36 CET 2011

Dear Bharat:

I hope that this doesn't impede others giving you advice about how to  
go about doing what you want to do, but here's my two cents for what  
it's worth:

My suggestion is to forget about trying to do that. 3-ns simulations  
are not going to give you equilibrium populations of conformational  
basins (and neither would 3-us simulations, I suspect). Not every  
question is amenable to MD on the currently available timescales.

If you really want to try to do it, I would find out what  
conformations lead to flourescence and see if you get more drift away  
from those conformations in some models with longer loops. But again,  
I think it's probably going to be a waste of time.


-- original message --


I simulated a protein (GFP) with one of its loop replaced with a longer loop
. After simulating for some 5 to 10 models with different loop sequences , I
decided to carry out wet-lab experiments for one model on the basis of
simulation result. The analysis of simulation was done in the following way

1) Comparison of RMSD values of backbone - for both GFP wild type and loop
replaced (mutated GFP)
2) Comparison of RMSF of the residues common to both the proteins.
3) Visual Inspection of entry of water into GFP.

The simulation was carried out for 3ns for both the proteins.

After that I did the wet-lab experiment for the modeled structure and I
found the fluorescence to be 50% of the wild type.

Now I want to investigate the reason for this reduction in fluorescence
??... How can this be quantified using MD.

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