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. 2003 Apr;84(4):2345–2356. doi: 10.1016/S0006-3495(03)75040-1

TABLE 1.

Simulations performed

Simulation Model Waters Duration (ns) Core Cα RMSD(nm) P + F region Cα RMSD (nm)
WT0 Wild-type 0 2* 0.18 0.16
WT1 Wild-type 1 2 0.16 0.13
WT3 Wild-type 3 2 0.16 0.15
VT0 V127T 0 2 0.24 0.17
VT1 V127T 1 2 0.17 0.18
VT3 V127T 3 2 0.28 0.24
GF0 G135F 0 2 0.21 0.17
GF1 G135F 1 2 0.24 0.15
GF3 G135F 3 2 0.24 0.15
MC0 M137C 0 2 0.19 0.13
MC1 M137C 1 2 0.18 0.15
MC3 M137C 3 2 0.24 0.18
*

The WT0 simulation was extended to 5 ns to check for any further significant structural drift after 2 ns. We therefore report RMSDs for the last 0.5 ns of the 2-ns and of the 5-ns simulation period.

Summary of simulations performed, defining the nomenclature used in the text. The number of waters per subunit positioned behind the selectivity filter in the initial setup of the systems was: 0 = no waters behind filter; 1 = a single water per subunit behind filter, as in the high [K+] structure of KcsA (PDB code 1K4C); and 3 = three waters per subunit behind the filter, as in the low [K+] structure of KcsA (PDB code 1K4D). RMSD values are calculated over the final 500 ps of each simulation for the Cα atoms of the core TM region (i.e., M1 and M2 helices plus P + F region (the latter defined as residues T116 to G135).