[gmx-users] GPCR/any protein modelling

David L. Bostick dbostick at physics.unc.edu
Fri Aug 9 19:28:50 CEST 2002


I have a very stable >10 ns trajectory of halorhodopsin in a DPPC bilayer.
It is quite stable!  I think the lipid environment is quite important for
the 7 helix barrel structure of such a protein.  Also.. if you are
simulating rhodopsin, you must also be sure you have a properly
parameterized retinal moiety... which I believe is unavailable as a
standard residue.


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
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Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

On Fri, 9 Aug 2002, Peter C. Lai wrote:

> On Fri, Aug 09, 2002 at 11:42:56AM +0100, Chris Shaw wrote:
> >
> > Hello All,
> >
> > I am attempting to model a GPCR based on the recently reported crystal structure of rhodopsin. I have done this and are now trying to do some MD on this model. This is where it goes wrong. I have tried to do some MD run on the model as with the "Getting started tutorial". Short runs in water i.e. 50 ps all is fine, however during longer runs i.e. 500 ps (again in water) the secondary structure of the model degrades greatly. Could anyone help me as to where I am going wrong. ANY HELP WOULD BE GREATLY APPRECIATED!!!!
> >
> 1. the solvent as water should work, as the helices are hydrophobic
> and should actually pack the helices more, if anything else.
> One would expect the protein to denature if run with an organic
> solvent (e.g. decane). Make sure your helices are oriented correctly
> (hydrophobic facing out, hydrophilic facing in).
> Of course, I haven't specifically used GROMACS to
> run MD on the helices (see below).
> 2. How are they falling apart?
> 3. When I use Discover to run MD on a GPCR, secondary structure falls
> apart also (helical elongation and helical destruction in terms of dihedryl violations).
> I did this in a vacuum (non-solvated).  THe solution is to add constraints
> and fix angles (and/or translation) of the helical alpha carbons.
> hope this helps any.
> > Cheers
> >
> > Chris
> >
> >
> >
> >
> > ---------------------------------
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> --
> Peter C. Lai
> University of Connecticut
> Dept. of Molecular and Cell Biology | Undergraduate Research Assistant
> Yale University School of Medicine
> Center for Medical Informatics | Research Assistant
> http://cowbert.2y.net/
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