[gmx-users] transmembrane protein simulation

[Justin Lemkul]

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

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

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