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.
http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations
-Justin
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
MILES-IGERT Trainee
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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