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. Author manuscript; available in PMC: 2014 Aug 26.
Published in final edited form as: J Chem Inf Model. 2013 Aug 9;53(8):2047–2056. doi: 10.1021/ci400225w

Figure 4.

Figure 4

Representation of the effect of protonation of Asp-309 on the conformation of androstenedione binding and in the locking of the channel conformation. The trajectory with a deprotonated Asp-309 (tan) exhibits significant deviations around the androstenedione O3 oxygen atom, and the conformations of Asp-309 and Phe-221 are altered relative to the crystal structure. The simulated trajectory with a protonated Asp-309 (blue) demonstrates a conformation in this region more consistent with the crystal structure. The figures are rendered from the centroid frame of the most prevalent clusters from GROMOS++ clustering using the protocol described in the text.