[gmx-users] Help: protein-membrane docking

[Justin Lemkul]

On 9/16/14 1:04 PM, LIPSCOMB, THOMAS wrote:
> ?Dear Gromacs mailing list,
>
>
> I need to know if your program can simulate protein-membrane interactions as this website claims:
>
> http://www3.mpibpc.mpg.de/groups/de_groot/compbio1/p5/index.html#contents
>
>
> If it can then please help me use Gromacs to do small protein vs membrane interaction because I have never used Gromacs before, only UCSF DOCK6, Patchdock, and Firedock.  Is there a step-by-step tutorial?
>
>
> I am a college undergraduate doing a senior project in figuring out how a certain antimicrobial peptide works, to prepare to find a way to engineer decreasing its toxicity until it is an acceptable treatment for antibiotic-resistant bacteria.
>
>
> Vesicle studies in vitro show that the antimicrobial peptide (it's a very small protein) disrupts the cell membrane by interacting with the membrane itself (and bursting the vesicles that way) and not by interacting with the cellular proteins (the vesicles do not have those), but the studies do not explain the details of that interaction with the membrane.  Maybe the peptide pokes holes or forms pore complexes or maybe forms some kind of disruptive sheets that adhere to the membrane.
>
> ?
>
> My project is to simulate the antimicrobial peptide on the computer to find out how it disrupts the cell membrane.
>

Gromacs does not do docking, but what you want to do is easily achievable with 
normal MD simulations or biased steered MD.  There are numerous published 
studies of antimicrobial peptides interacting with membranes using MD.  I would 
suggest you model your approach after one of those.  Gromacs is well suited for 
doing such work.

-Justin

-- 
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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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