[gmx-users] How to calculate the free energy difference of solvation for a Tyr-Phe mutation!

Yang Ye leafyoung81-group at yahoo.com
Tue Jun 27 14:08:36 CEST 2006

Hi, Mikko

700AA is too much a dinosaur for MD. Perhaps you can focus on the chain 
which contains that mutation.
Also, for solvation energy, you may check GBSA model available in AMBER 

Yang Ye

Mikko Hellgren wrote:
> Hi all,
> I would like to get some advice on how to calculate the free energy 
> difference of solvation between two proteins, a native (about 700AA) 
> and one with a single mutation of a Tyr to Phe. 
> The Tyr residue is located in the exterior of the protein structure 
> and involved in two hydrogen bonds from the hydroxyl group to two 
> other residues in the protein.
> From CD spectra we know that the spectra is unchanged by this mutation 
> and this indicate a conserved secondary structure. The structure of 
> the native protein is known but not for the mutant - can one from 
> these background data get support that there is only minor changes in 
> the structure between the native and the mutant and that these 
> changes could be modeled well with a "long" MD simulation?
> Could the Linear response theory be used for calculation of the free 
> energy difference of solvation for the single mutation or do I have to 
> do something a bit more fancy? Or could one perhaps use experimental 
> data for solvation free energy differences between amino 
> acids?....Anyhow I would like to get a suggestion on how this can be 
> calculated.
> I would also be great-full for any suggestions of a suitable MD 
> tutorial or review article on the subject. 
> Thanks for any advice or comments on these not so specific questions - 
> sry about that!
> Mikko Hellgren - Graduate Student
> mikko.hellgren at ki.se
> ____________________________________________________
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