[gmx-users] Inserting aquaporin-1 in a bilayer with multiple lipids

[Melsa Rose Ducut]

Thank for you replies Tom and Justin. I really appreciate it.

Tom, May I know the method they used to insert the protein? I can't see the full paper of the publication you shared. 

Justin, I still wasn't able to use the script you sent me. I'm still trying though. Thank you for that. This is the command I'm using

perl inflategro.pl system.gro 4 DPPC DOPC DLPC DSPC system_inflated.gro 5 area.dat

and then this is the result

Reading..... 
Scaling lipids....
There are 0 lipids...
Illegal division by zero at inflategro.pl line 298.

(I changed the file name to inflategro.pl)


-Melsa 


On Tuesday, June 3, 2014 9:45 PM, Piggot T. <T.Piggot at soton.ac.uk> wrote:
 


It is worth noting that not all insertion methods involve the deletion of lipids, for example:

http://pubs.acs.org/doi/abs/10.1021/ct500046e

There was another similar method I saw recently on a poster at a conference, which did not require the deletion of lipids either. I can remember the full details off hand, but could dig out the information if anyone is particularly interested.

Additionally, if you shrink your protein a huge amount using g_membed (to say, something like 10% of it's original size), you can also dramatically reduce the numbers of lipids you delete upon insertion. Obviously, this will have a greater influence on the membrane surrounding the protein though (once the protein is 'grown' back to full size) and so you may require longer periods to re-equilibrate the membrane.

That all said, Justin is right that having 128 lipids in your membrane will most likely not be enough (especially with a rectangular/square membrane) to give you sufficient distance between your periodic images even without deleting lipids during insertion.

Cheers

Tom
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: 03 June 2014 13:33
To: gmx-users at gromacs.org; Melsa Rose Ducut
Subject: Re: [gmx-users] Inserting aquaporin-1 in a bilayer with multiple lipids

On 6/3/14, 6:10 AM, Melsa Rose Ducut wrote:
> Dear gromacs user,
>
> I have an all-atom bilayer with 32 DSPC, 32 DPPC, 32 DOPC, 32 DLPC and 6000 water molecules. I used GROMOS53a6 as my force field. I want to make another system with the same lipids, 32 DSPC, 32 DPPC, 32 DOPC, 32 DLPC and 6000 water molecules but with aquaporin-1 at the center. How do you think can I do this? Thank you.
>

Did the script I gave you not work?

The most common approach is to embed the protein in the existing membrane patch.
  Whether or not your patch is large enough to accommodate an aquaporin remains
to be seen, though my gut instinct is you'll probably need a bigger membrane.
Insertion will, by necessity, delete lipids, so you almost certainly won't be
able to keep the "exact" same membrane, but you can certainly create a larger
patch that has the same lipid ratio, which is all that really matters in the end.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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