Subject: protein-water interactions and force fields

From: [email-masked] (Eldbjoerg S. Heimstad)
Date: Sat, 17 Aug 96 13:08:19 GMT

Non-bonded interactions between protein and water molecules:

I have wondered over a long time about the accuracy of estimating
the protein-water interactions of the different MM programs; parameters
for VDW radius etc. I am using CHARMM or CHARMm for my studies of protein
dynamics and protein stability.  I assume (from the studies of Privalov & co.,
Khechinashvili et al.) that hydration of especially polar group may be important
for the stability of the native protein structure.

I have been using the SBMD method where the protein is immersed in a 34 A or 40
A radius sphere of water. Does any of you have experience or thoughts about
how much the water should interact with the protein surface, how high may the
RMSD level be from X-ray structure (or starting structure) during simulation
(i.e. backbone atoms in a simulation of length 500 ps); is 2.5 -3.0 A a
reasonable value, or ?

What opininion do you have about sufficient amount of water; 10 A of water
molecules beyond the protein surface, or ? I am in this case thinking about a
sphere of water molecules in the connection with deformable boundaries.

All opinions and experience will be highly appreciated,

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# Eldbjoerg Sofie Heimstad                            #
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