I have a system with two proteins and a membrane as following
protein-1, protein-2, and membrane bilayer.
I would like to know whether the protein-2 binds first to protein-1 or the membrane to protein-1 using molecular dynamics simulation. Could some please suggest any way to find which one has preference to bind first? It would be great if someone can suggest a way to confirm that experimentally as well.
Can we confirm that with the binding affinity calculations?
It depends on the type of simulations you're doing. One long equilibrium simulation will likely not be sufficient. If you really want to computationally measure differences in binding affinity between protein-1protein-2, protein-1membrane, and protein-2membrane, you will need lots of sampling from many separate runs. If you're interested in this, I'd highly recommend Dan Zuckerman's Statistical biophysics blog where he talks about trajectory ensembles.
http://statisticalbiophysicsblog.org/?p=92
As for how you could measure it computationally, you might look average contacts between each group or key residues/lipid types, average membrane insertion times, buried surface area between each group. Still , I can't emphasize enough that any information gathered that lacks a large enough trajectory ensemble will be anecdotal at best.
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