Table 1.

Summary of simulations

Label	System	tsim (ns)	Type	Start	Constraints	Size (#atoms)	Initial size (nm3)
S1a	WT	100	EQa	−	backbone	197,865	11.3 × 12.2 × 14.1
S1b		103	NpT	S1a	−		11.8 × 12.3 × 13.3
S2a	R366E	100	EQa	−	backbone	197,852	11.3 × 12.2 × 14.1
S2b		109	NpT	S2a	−		11.2 × 12.6 × 13.6
S2cb		100	EQa	S2a	backbone		11.2 × 12.6 × 13.6
S2d		82	NpT	S2c	−		11.3 × 12.8 × 13.4
S3a	R366E/F433S	100	EQa	−	backbone	197,843	11.3 × 12.2 × 14.1
S3b		104	NpT	S3a	−		12.4 × 11.5 × 13.4
S4a	R366N/Y517I	100	EQa	−	backbone	197,851	11.3 × 12.2 × 14.1
S4b		104	NpT	S4a	−		11.0 × 13.2 × 13.3
Total		1002

^aEQ indicates simulations that consisted of 1000 steps of minimization and 100 ns of dynamics with the protein backbone constrained (k = 1 kcal/mol/Ų) in the NpT ensemble (γ = 0.1 ps⁻¹).

^bA potassium ion found inside YidC was exchanged with a bulk water molecule before starting simulation S2c.