Hello all,
I would like to generate a potential of mean force (PMF) for the
insertion of a small molecule (amino acid, organic molecule, etc) into a
lipid membrane. The "reaction coordinate" in this case would be the
"depth" of the molecule relative to the center plane of the membrane.
This seems a little tricky to define using the available restraint
setups. The simplest would be to use an nmr restraint to constrain the
distance between the center of mass of the membrane and molecule (or
some representative subset of atoms such as the C1 atoms of the PC
residues of each DOPC molecule), but this could potentially allow the
molecule to "rotate" its way along the depth axis without changing the
distance from its center of mass to the membrane center of mass.
Does anybody know of a better way to do this? For example, is it
possible to make the restraint force only be applied along the z-axis,
which could serve as a proxy for depth. Although ideally the third
principal axis of the membrane would be used as the restraint force
direction.
-Wesley Botello-Smith
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Received on Thu Dec 11 2014 - 15:00:02 PST
