protein stability in a membrane and SMD

From: Martin, Erik W (Erik.Martin_at_STJUDE.ORG)
Date: Fri Feb 17 2017 - 17:14:31 CST

Iím wondering if anyone has run a simulation to assess the stability of a protein that sits in the membrane? Iím not talking about a transmembrane protein, but rather one that floats at a certain depth. My plan was to perturb the equilibrium position in the starting structure by rotating it, say, 45 degrees and seeing if it relaxed back to the correct conformation. Iím wondering if I could get more interesting information by doing simulated pulling. It seems like it would be straight forward to try and pull the protein into or out of the membrane, but would there be a way to put in a rotational force?

Thanks a lot,
Erik

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