On Fri, May 09, 2003, FyD wrote:
>
> - If we take the AMBER FF equation, is the hydrophobic interaction between 2
> aromatic residues (for instance) taken into account ? Is it through the vdW
> term ?
The hydrophobic effect is an indirect effect arising from solvation. There
is no specific term in the force field that represents it (for explict
solvent); rather, it arises "naturally" from the nature of the interactions.
>
> - Starting from a wild type fold, I mutated a residue. Using the GBSA
> strategy, I get a dE(effective) value of 8 kcal/mol and a dG value of 13
> kcal/mol between the mutant and the wild type protein (1 nanosec productive
> MD with GB). Can I conclude that the mutation present a stabilisation or a
> de-stabilisation effect ? To my opinion, such a dG is too small...
>
Are you using a real thermodynamic cycle: perform the mutation in the protein,
then again in small model system (e.g. a single amino acid), then compute
delta-delta-G by difference of the above two numbers. A single mutation
delta-G value has no meaning, just differences. And, as others have said,
13 kcal is actually pretty big.
...good luck..dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Fri May 09 2003 - 17:53:01 PDT
