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: [email protected] > To: [email protected] > 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
