[gmx-users] Re: Simulation of slow folding proteins

bharat gupta bharat.85.monu at gmail.com
Tue Mar 22 01:54:39 CET 2011


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.

Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
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