[gmx-users] Problem in preparation of the enzyme/substrate complex

Mark Abraham Mark.Abraham at anu.edu.au
Thu Feb 19 14:04:08 CET 2009

Tsjerk Wassenaar wrote:
> Hi,
> Even worse, this looks like a transition-state product. The hydrogen
> originating from the serine will not just have wandered off. It is
> unlikely that it happened to go sit on the other oxygen. Rather, the
> other oxygen, which would originally be double-bonded would probably
> form a strong hydrogen bond with some other residue (histidine?),
> rendering the carbon exposed enough for a nucleophilic attack by
> serine, followed by a series of events likely resulting in HO-R' being
> cut off. You won't be able to properly describe the transition state
> using classical means only.

Yep. Enzyme mechanisms are extremely difficult to model well, and very 
expensive if/when you get the QM-MM model right.


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