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. Author manuscript; available in PMC: 2017 Apr 20.
Published in final edited form as: J Phys Chem B. 2016 Oct 28;121(15):3352–3363. doi: 10.1021/acs.jpcb.6b08409

Figure 6.

Figure 6

The progress of twelve properties along the optimized string pathway were normalized, and then manually sorted for the purpose of showing a few key events in an ordered fashion. For each property, the extrema most closely resembling the inactive and active states were colored in blue and red, respectively, in order to visually display the evolution of the variable. The twelve properties are described in the following: SASA Y416 refers to the solvent accessible surface area of Y416, its value ranging from 244 (blue) to 266 Å2 (red); A-loop α-turn 1 refers to the average distance of the three i : i+4 hydrogen bonds in the short α-helix turn in the inactive A-loop between residues 413 to 419 (called d3 in Figure 2) used to reflect the opening of the A-loop, its value ranging from 2 (blue) to 10 Å (red); A-loop α-turn 2 refers to the i : i+4 hydrogen bond of the single turn α-helix in the inactive A-loop between residues 407 to 411, its value ranging from 2 (blue) to 10 Å (red); Arg419 to α-EF refers to the distance between R419 of the A-loop and the backbone of A434 from the α-EF helix, its value ranging from 2 (blue) to 10 Å (red).; the W260 side chain angles χ1 and χ2, its value ranging from −150° (blue) to −60° (red) and 0° (blue) to 110° (red), respectively; F424 to α-G refers to the distance between F424 of the A-loop and N468 of the αG helix, its value ranging from 10 (blue) to 2 Å (red); A-loop α-turn 3 refers to the i : i+4 hydrogen bond between R419 and K423 in the active A-loop, its value ranging from 10 (blue) to 2 Å (red); α-C to A-loop refers to the E310 to R409 salt-bridge distance (called d1 in Figure 2), its value ranging from 2 (blue) to 10 Å (red).; α-C to N-lobe refers to the E310 to K295 salt-bridge distance (called d2 in Figure 2), its value ranging from 10 (blue) to 2 Å (red).; R409 to Y416 refers to the distance between R409 and Y416, its value ranging from 10 (blue) to 2 Å (red); R-spine RMSD refers to the heavy atom RMSD of the regulatory spine residues (M314, L325, H384, F405, and D444) from the equilibrated re-assembled active structure, its value ranging from 1.8 (blue) to 0.6 Å (red).