[gmx-users] Membrane protein tilt.

Xavier Periole x.periole at chem.rug.nl
Wed Jun 2 13:32:25 CEST 2004

John Simms wrote:

>I am asking for some advise, I work with a class of GPCRs (unrelated to the rhodopsin family inwhich a crystal structure exists and homology models can be build) and am in the middle of building a model de novo. My question is regarding transmembrane tilts with respect to the lipid bilayer. If I start with a helix normal to the membrane and let it run, will it adopt its equilibrium position (given enough time; within the constraints of computer power)? 
It will certainly adopt a conformation that you could call equilibrium 
position but will it be the
real one ??? That is difficult to say. Some simulations of helices in 
membrane environment
have been done lately (see Tieleman D.P., Sansom M. and other in pubmed).
The other point you have to consider is that the conformation you will 
have will probably
be different if the helix is alone or with the rest of the protein. It 
is unlikely that the helix alone
adopts the conformation in the protein !!

>The other question is there are alot of environments which this can be done in (methane, methanol, octane as well as a bilayer) anyone tried the environments for helical tilts and found best/worse?? Finally, has anyone done this using a monte carlo approach?
Octanol and real bilayers seem to be the best choices !



   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: md.chem.rug.nl/~periole

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