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
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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