Table 1.

Conditions for the atomistic MD simulation of the ClC exchanger from E. coli

Structure	Protonation state of E203	Protonation state of E148	Number of Cl− in primary pore	Formation of secondary pore
WT	X	X	2	X
			0	X
		O	2	X
			0	X
	O	X	2	X
			0	X
		O	2	X
			0	O
Y445F	O	X	0	X
		O	0	O
E203Q	E → Q	X	0	X
		O	0	X

The protonation states of two key glutamates (E203 and E148) are denoted by O (protonated) and X (deprotonated), respectively. The formation of the secondary pore during the 14 ns simulation is also denoted in the last column by O and X. The reference structure (E203 and E148 are deprotonated, and two chloride ions are in their binding sites) is shaded gray. Each configuration was equilibrated for 4 ns and an additional simulation was performed for 14 ns for each configuration to confirm whether the secondary pore had formed.