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. Author manuscript; available in PMC: 2013 Mar 20.
Published in final edited form as: Biochemistry. 2012 Mar 7;51(11):2199–2212. doi: 10.1021/bi201888a

Figure 3. Pore cross-sections (8 ns MD frame) at different axial positions.

Figure 3

Sections are ordered from extracellular (right-most) to intracellular (left-most). TMs are numbered in white. Individual amino acids from TMs 3, 6, 9 & 12 are labeled. See Figure 5 for the exact bilayer position of each section. Colors: transmembrane domain 1 (green), transmembrane domain 2 (blue), TMs 3 & 9 (yellow), TMs 6 & 12 (red), labeled residues (white). The gray area is the cross section of a space-filling model of the pore (casting) defined in more detail in Figures 4 and 5. Scale bar is 10 Å. Labeled amino acids occupy sites where engineered cysteines were found to be reactive toward externally applied, thiol-directed reagents as detailed in the text.