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. Author manuscript; available in PMC: 2011 Nov 24.
Published in final edited form as: J Am Chem Soc. 2010 Oct 27;132(46):16442–16449. doi: 10.1021/ja105001a

Figure 2.

Figure 2

A) Important pore lining residues in the MD-equilibrated GLIC. Acidic, basic, hydrophilic and hydrophobic residues are shown in red, blue, green, and white VDW format, respectively. The permeation pore is highlighted in yellow; and B) comparison of MD-calculated single ion PMFs for transporting Na+ (blue line) and Cl− (red line) ions along the channel centerline of System A. Grey line shows another set of PMF calculations for Na+ using different initial configurations and slightly different MD protocols. The standard deviation for the Na+ PMF near the intracellular entrance (−55 Å < z < −45 Å) was high.