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

[Thomas Piggot]

The abstract from the linked paper describes the method pretty well. By 
applying a high lateral pressure, the protein is forced into the membrane.

As for the other method that I had seen at a conference (which I meant 
to say in my previous message that I *couldn't* remember off the top of 
my head!), I believe it involved the use of the free energy code to 
slowly switch the protein on. As far as I am aware this method isn't 
published/freely available yet.

Cheers

Tom

On 06/03/2014 04:57 PM, Melsa Rose Ducut wrote:
> 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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-- 
Dr Thomas Piggot
University of Southampton, UK.