[gmx-users] How to incorporate WALP and KALP peptide in a Martini bilayer

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 12 22:02:21 CEST 2010

Sanku M wrote:
> Hi,
>   I am using MARTINI coarse-grained force-field to study interaction of 
> a transmembrane peptide WALP or KALP in a lipid-bilayer.  So,I  was 
> planning to insert a martini KALP or WALP peptide inside a martini DPPC 
> bilayer in a transmembrane manner. For that purpose, I was going through 
> the MARTINI JCTC paper( vol.4 , page-819 )  introducing the protein 
> force-field where a simulation study of KALP peptide in a bilayer has 
> been discussed ( in page 828 of that paper) .  But, I did not get any 
> details how the KALP or WALP peptide are inserted in a bilayer as 
> initial configuration.
> So, I was wondering if I can get some help on how to insert this WALP 
> peptide in to Martini DPPC bilayer . I guess, there may be some way of 
> pulling , that may do the trick, but I am not sure how to keep it 
> trans-membrane as well during pulling . So, Any suggestions will be 
> helpful. 

In principle, building a CG membrane protein system and an atomistic one don't 
really differ, so you can follow the membrane protein tutorial.  You might have 
to modify the inflategro.pl script to recognize the atom naming for MARTINI 
lipids, though.



> Sanku
> P.S:
> I tried MARTINI coarse-grained simulation if the WALP peptide can get 
> spontaneously inserted in a 128-lipid DPPC bilayer( after starting from 
> a bulk water phase)  in a transmembrane manner . But, looks like it does 
> not get inserted in bilayer in a transmembrane manner, after 500 ns 
> simualtion. At the most, they remain in the interface of water 
> and lipids. I ran multiple configurations but in some cases it goes 
> other side of membrane. in some cases, it remained parallel in 
> interface.but never got inserted in a trans-membrane manner.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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