I'm working with an enzyme where some of the loops are playing important roles in catalysis. How could I study the relation of loop flexibility with the re-activity (computationally)?
MD simualtion approach will be useful.You can observe the flexibility of loop over time .
Perform the MD simulation of Enzyme-substrate complex to check the flexibilty of loop.
Thanks for your replies. I had already performed MD simulation of the enzyme at 300/350/400/450 & 500 K. I have done the analysis of loop flexibility by using RMSD, RMSF and Essential Dynamics. My question is how I could relate those finding with the reactivity.
You can't directly correlate the loop flexibility with the enzyme catalysis, up to my knowledge. I suppose, the flexible loop does play key role in subtrate insertion and/or product release. So, in general this type of event is reflected in the total kcat of the enzyme. You perform any free energy simulation to get the DG and tereby the rate of the loop openning, using TST and thus interpret this event with the catalysis. Hope, it'll help u.
Thanks Tarak and sorry for replying late. Your answer really helps me. I would actually going through kind of same direction as you suggested. Could you please explain what is TST and what would be the recommended method according to you for free energy simulation? (I'm trying with MMPBSA/GBSA in AMBER.
Sorry for replying late, was bit busy with schedule.
Metadynamics would be a fair choice for ur purpose.
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