[gmx-users] Adding a substrate into protein-lipid bilayer system

[MPI]

> >
> >>> I wonder when it is appropriate to add NH3 into the system and how to
> >>> setup the control of temperature coupling in thermostats.
> >>> For example,
> >>>
> >>> 1.  add NH3 first with the protein and  then embed protein-NH3  into the lipid
> >>> or
> >>> 2.  embed the protein into  lipid with an equilibration,  followed by
> >>> adding NH3 into the system
> >
> >
> >> If you want NH3 to pass through the channel, I'd say (2), more or less, but
> >> really you should add NH3 as a cosolvent as part of the equilibration.  Add the
> >> NH3 in the box, add water, and equilibrate.
> >
> >       If choosing (2), what is the concern ?
> > Why adding NH3 as part of water_and_ions after protein-lipid  is
> > equilibrated already ?
> > Choosing (2), I have to go through equilibration twice.
> >
> No you don't.  You add NH3 into the box, then solvate with water.  See
> http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
> I'm saying that (2) is in general more logical for your purpose (as I understand
> it) but you don't do two separate equilibrations.  Moreover, it is unlikely that
> you'll be able to find space in an equilibrated layer of water to insert NH3
> molecules.

Hi Justin,

  Thank you very much for the details.


> > Also,  if the substrate is a very small ligand, is the protocol the
> > same ?  Namely, adding a new substrate AFTER protein-lipid is
> > equilibrated.  Then perform another equilibration for the substrate +
> > protein-lipid.
> >
> This is context-dependent.  If you want to simulate a protein-ligand complex in
> a bilayer, you add the ligand first into the protein (crystal structure,
> docking, etc).  If you want to observe partitioning from bulk solvent of the
> ligand into the protein's binding site, then it's the same.  Put the required
> number of ligands into the box where the solvent will be, then add the solvent
> (water).

If I understand this correctly, you actually suggested adding a ligand
BEFORE adding the solvent and BEFORE the protein is embedded into
lipid bilayer. Is this correct ?

I am concerned about the sequential  order of adding a substrate and
embedding a protein into a bilayer.

Which one goes first ?



> >
> >
> >>> Also,  if the substrate has a charge, which order is preferred ?
> >
> >
> >> Charge shouldn't affect the protocol.
> >
> > Did you mean  when adding a new substrate, eg, NH4+ or Ca2+  into a
> > protein-lipid system,  one has to remove all ions  and water in the
> > equilibrated protein-lipid system,  put back ions and water again and
> > finally equilibrate the new system right after ?
> >
> Or just build it in sequence from scratch without having to remove water and
> ions.  That's what I'm suggesting above.  The cosolvent/ligand/whatever is
> always added before the water.  It's easier and faster in practical terms,

Before the water, it means "you add ligand at the very beginning
BEFORE protein is embedded into bilayer, correct ? "

If so, what about the temperature coupling ?


(1) tc-grps         = Protein DPPC  water_and_ions_and_LIG

or

(2) tc-grps         = Protein_LIG  DPPC  water_and_ions


It seems to me if LIG = NH3/NH4,  then (1) is preferred  but if LIG is
a small drug "MOVING" along the channel,  dose (2) make sense ?
or  (3) tc-grps         = Protein DPPC LIG  water_and_ions ?


> because if you have to remove solvent, then what was the point of the initial
> equilibration?

The initial equilibration is for inserting protein into the bilayer.
One can add any substrate afterwards without  worrying about the
process of inserting a protein into bilayer. Dose it make sense to you
?

Thanks,

Dewey