[gmx-users] Which membrane result is more reliable?

[Justin A. Lemkul]

Kirill Bessonov wrote:
> Hello Justin,
> 
> You helped me before, and I am grateful for that. So basically my summer 
> research had ended up with the following results:
> 
> I have included my *.ipt files this message is long.
> 
> *My question: 1)why once simulation is giving  me stable aplha-helix and 
> other is not if membranes are similar and conditions kept constant.
> 
> *                     2) Which result to use, most probale. Does lipid 
> density might of affected the stability?
> 
> 
> 
> ->200ns  Simulation of the same peptide in the DMPC only box and in 
> DMPC/DMPE box [1:1 ratio] but results are different and I want to ask 
> why as this data will go as part of the paper.

There is nothing that suggests to me you should expect similar results under 
these different conditions.  Many proteins will behave wildly differently in the 
presence of different headgroup charges and chemical functional groups.

As for DMPC, the quaternary amine group is capable of electrostatic 
interactions, while DMPE can participate in hydrogen bonding as well as 
electrostatic interactions, within the lipids and also with the protein.  I can 
think of one example immediately where PE and PC headgroups induce structural 
changes in proteins, I'm sure there are more.

> 
> *System:* peptide that is placed on TOP of the membrane, interacting 
> with lipids (no inserted into the membrane, but floating on top) and 
> above there are water molecules
> _*
> DMPC membrane simulation - STABLE Peptide Helix, no uncoiling:*_
> 
> -> 248 DMPC molecules
> ->Box 9.03 x 9.03 x 10.15 as found at the bottom of gro file (I think 
> this dimensions are nm units?)

Yes, per Chapter 2 in the GROMACS manual, the standard unit of length is nm.

> -> Threfore I calculated that Area per Lipid is only: 2facesx90.3^2 
> A^2/248DMPC = 65.75 A^2/lipid which is low
> 

Can you guarantee that no part of your protein occupies this lateral space?  If 
the protein is interacting with the lipids, I would think that this calculation 
is inappropriate.

> -> When I was using InflatGro(which I modified to be much more friendly 
> and accepts 2 lipids) to check the lipid density the values were:

The InflateGRO code (by its own admission) also overestimates area per lipid.  I 
would not use these data at face value.  Might I put in a plug for a program 
developed in our own lab, designed for these exact situations:

http://www.bevanlab.biochem.vt.edu/GridMAT-MD/

<snip>

> I used the same *.mdp file
> *I used following dmpe.ipt  and dmpc files * attached that to my 1st 
> impression are identical
> 

There are no attachments.  I don't know what you mean by claiming they are 
identical.  PE and PC lipids behave differently.

-Justin

> 
> 
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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