VMD-L Mailing List

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Fri Sep 15 2006 - 12:07:51 CDT

Hi

 

As suggested by Dr. Ting, I am generating a POPC bilayer in VMD.

 

As I mentioned, my GPCR protein is 320 residues in size and following are
the XYZ dimensions

 

Z ~ 67 A

X ~ 54 A

Y ~ 50 A

 

1. In the VMD, we can only define the X and Y dimensions of the POPC
bilayer, so will it be fine if I go for something like X/Y = 60 or 65, so
that I can appropriately center my GPCR protein in the bilayer?

 

2. A reference for Dr. Harel Weinstein says "studies have shown the
appropriate distance between the solute protein and a simulation box
boundary to correspond to ~4 to 5 layers of lipid molecules" [Lipid Bilayer
used in the study was POPC bilayer] The AAPS Journal 2006; 7 (4) E871-E884.
Would that be taken care of by building a bilayer with X/Y dimensions of
5-10 A greater than the X/Y dimensions of protein?

 

3. I have realized that after embedding my GPCR in the POPC bilayer from
VMD, some parts of the EC and IC loops remain outside the water slab. So, is
there a way to increase the water slab of membrane a) either during membrane
building or b) can it be done independently after a membrane has been built?

 

I would appreciate any suggestions.

 

Thanks and Kind Regards

Akshay

 

  _____

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Ting Wang
Sent: Thursday, September 14, 2006 5:28 PM
To: akshay17_at_olemiss.edu; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: DPPC Bilayer Size

 

Hi Akshay,

 

VMD can not generate DPPC bilayer. Peter Tieleman's coordinates are fine but
you will probably later have problems of embedding your protein into the
membrane. A easier way is to generate POPC bilayer in VMD and use VMD
scripts to do later on jobs. I have 118 POPC lipids for my GPCR protein.

 

Ting

----- Original Message -----

From: Akshay Patny <mailto:akshay17_at_olemiss.edu>

To: vmd-l_at_ks.uiuc.edu

Sent: Thursday, September 14, 2006 11:49 AM

Subject: vmd-l: DPPC Bilayer Size

 

Hi All

 

I am trying to simulate a GPCR protein belonging to the rhodopsin family
with amino acid length of 320 residues. Also, I would be using the
pre-hydrated DPPC bilayer, can somebody suggest that for a GPCR protein of
roughly 320 aa, how big DPPC bilayer would be appropriate to use e.g. 128
DPPC bilayer is available from Peter Tieleman's website
http://moose.bio.ucalgary.ca/index.php?page=Main .

 

Also, can VMD 'membrane' van generate DPPC bilayer?

 

Thanks

Akshay Patny

Graduate Research Assistant
Faser Hall 417, Department of Medicinal Chemistry

Research Institute of Pharmaceutical Sciences
University of Mississippi
University, MS 38677
E-mail: akshay17_at_olemiss.edu
Tel: 662-915-1286 (office); Web: www.olemiss.edu