[gmx-users] Binding energy of membrane protein to the membrane lipids
sojovictor at gmail.com
Sun Feb 23 17:54:57 CET 2014
Thanks, Justin! That's really helpful indeed.
You are correct, I want to know what's the energy change in replacing one
lipid with the other, hypothesising that going to the "wrong" lipid will
imply an energetic cost.
Via umbrella sampling, I would thus:
1) Set up a full system with protein, lipids, solvent, and ions.
2) Pull the protein perpendicularly out of the membrane and into the solvent
(which means I'd need a lot of solvent in the direction of the pull, such
that there's always enough space to fit the protein and still avoid boundary
interactions, as you explain in you tutorial, thanks!).
3) Do the exact same thing with the other system, independently.
4) See just by eye what the difference is and hope it matches my prediction.
Now, my question about using umbrella sampling for this purpose: is it
reasonable to use the whole membrane (say, the group of lipids) as my
immobile reference? In your tutorial you use a chain, in which all members
are covalently bound to each other, so I didn't know whether you could use a
group of independent molecules instead. I assume it will be fine, then.
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