On 8/9/17 1:31 PM, abhisek Mondal wrote:

     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

jalem...@vt.edu | (540) 231-3129

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