[gmx-users] transmembrane protein simulation

Justin Lemkul jalemkul at vt.edu
Thu Aug 10 03:39:32 CEST 2017

On 8/9/17 1:31 PM, abhisek Mondal wrote:
> Hi,
>      I have a predicted secondary structure of a transmembrane protein
> containing a really long alpha helix. If I place the secondary structure of
> the protein inside membrane (as done for KALP in tutorial) and following
> all the steps perform a production MD, is it possible to obtain a
> thermodynamically favorable tertiary structure of the same protein ? I mean
> generating the folds based on the membrane environment provided.

I'd be very skeptical.  Simulations can reasonably fold small motifs, but it 
requires a significant time scale and/or enhanced sampling approaches that may 
or may not be compatible with membranes.  Folding something large in such a 
medium (slowly diffusing lipids) will require extensive simulations as well as a 
very accurate force field.  I'm not sure if anyone has been able to make such an 
assessment in the literature yet.  What you're proposing is a very tall task, 
and potentially huge time investment for little or no useful data.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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