I am trying to model the active site of an enzyme with a catalytic triad. Any catalyst will bind the substrate transition state more tightly than the substrate itself, correct? I am using Autodoc Vina and Amber/MMPBSA to assess the binding values of various substrates to an active site of an enzyme that contains a catalytic triad. As I'm doing this, I'm wondering what the docking and dG energy values really mean- afterall, I'm performing these simulations with a subtrate/ intermediate in their stable states- Not their transition states. Thus, why would I have any reason to believe that my substrates will bind in the correct geometry with respect to the catalytic triad? Only the transition state would bind in such a way- correct?
Are we assuming that the substrate and the transition state are very close structurally? I think that would sometimes be the case but my knowledge is limited.
Is there any way to generate a proposed transition state with some available modeling program?
Is there a flaw in my thinking here? Thanks for any input
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Received on Sat Dec 15 2012 - 13:30:02 PST
