Hi Sébastian,
I think the "magic word" in this issue would be surface tension and the
proper ensemble for the simulation NPgammaT. This is very well discussed
in the paper I advised to you a couple of days ago. The issue is by no
means trivial, although I'm not an expert to judge it. You can find an
imho very well-founded theoretical discussion in, e.g., Lindahl, E. and
Edholm, O. Spatial and energetic-entropic decomposition of surface
tension in lipid bilayers from molecular dynamics simulations. J. Chem.
Phys.(2000)113, 3882.
Good luck!
Felipe
On 08/15/2012 08:23 PM, Sebastien Cote wrote:
Thanks for the advices Chris.
My peptide is known to be more favorably to PE than PC membrane that is why I
am using POPE.
Experimentally, the liquid phase transition is at 298K for POPE (if I am not
mistaken). Is your 323K refer to some simulations?
At first I wanted to use the new CHARMM36 lipids parameters because they are
supposed to solve the previous CHARMM27 issue with the area per lipid. However,
I am consistently obtained smaller APL then experiment and I am not able to
reproduce the published APL obtained for POPE, even if I am starting from their
equilibrated 80-POPE membrane and use same simulation conditions. That was the
reason for starting this thread on the mailing list.
Unfortunately, my peptide conformational space in solution is only
well-represented by CHARMM27 (equivalently in CHARMM36), so I can not use
Berger's lipid parameters with OPLS or GROMOS even if it would be preferable as
they do not have APL inconsistency and are united-atom.
I will made some tests in the NPAT ensemble. Perhaps the NPAT effects can be
made neglegible by using bigger membrane compared to my peptide's size (?).
Sebastien
----------------------------------------
From: chris.ne...@mail.utoronto.ca
To: gmx-users@gromacs.org
Date: Wed, 15 Aug 2012 17:29:29 +0000
Subject: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
The area per lipid (APL) will certainly affect the free energy of
peptide/protein binding to a lipid bilayer.
I have not used charmm lipids extensively, but from what I understand they
older charmm lipids required
NPAT to get the correct APL. The newer charmm lipids were supposed to solve
that problem, but I have heard
it said that, though the problem has been alleviated to some extend, it still
remains.
If I were you, I'd use POPC in place of POPE. POPE is notorious for giving
too-small APL's in simulations and I think
it even requires temperatures of 323 K to enter the liquid phase.
That said, I don't have a specific answer to your question of whether there are
other affects of NPAT vs. NPT.
It is plausible that NPAT-based fluctuations could affect the pathway or the
kinetics.
PS: I was not referring to lipid rafts, but the separate diffusion of the upper
and lower leaflets. Once the peptide is
fully inserted, if it spans both leaflets, this will tend to reduce this
leaflet-specific diffusion and would represent an
entropic penalty for binding (not sure how large).
Chris.
Dear Peter,
I also used h-bonds and I also switch LJ interaction from 0.8 nm to 1.2 nm (as
in Klauda's paper). I will retry with a more solvated membrane.
Would you have any thought on how the NPAT ensemble might affect
peptide-membrane interactions like I am studying i.e. peptide is totally
solvated, then adsorb, and finally may insert? The paper on peptide-membrane
interaction like this usually use united-atom lipid in the NPT ensemble. Most
of the work I have seen on Charmm membrane in the NPAT ensemble were for
embedded membrane protein.
Sorry, but I only have experience with large pre-embedded membrane proteins,
and those are governed both by signal sequences and post-translational
modification.
Chris's last email on the subject might lead to the hypothesis that lipid
raft translation as the leaflets "slide" past one another could be a
contributing factor to adsorbption of your species.
Thanks,
Sebastien
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