. 2019 Dec 20;9:19479. doi: 10.1038/s41598-019-55722-6

Table 1.

List of the biased driven simulations performed for the OF ↔ IF transition, induced using different biasing protocols.

State	Protocol	Structural elements	Number of copies*	Runtime (ns)^†	Transition^‡	Total work (kcal/mol)
Na⁺-bound	RMSD	protein^¶	1	20	yes	511
Na⁺-bound	RMSD	TMs 1-10	1	20	yes	296
Na⁺-bound	RMSD	TMs 1-4,6-9	1	20	yes	188
Na⁺-bound	RMSD	TMs 1,3,6,8	1	20	yes	147
Na⁺-bound	RMSD	TMs 3,6	1	20	no	—
Na⁺-bound	RMSD	TMs 1,3	1	20	no	—
Na⁺-bound	RMSD	TMs 6,8	1	20	yes	106
Na⁺-bound	RMSD	TMs 1,8	3	5	yes	141 ± 18
Na⁺-bound	RMSD	TMs 1,8	2	20	yes	98 ± 0.45
apo	RMSD	TMs 1,8	3	5	yes	121 ± 6
apo	RMSD	TMs 1,8	2	20	yes	100 ± 5
Na⁺-bound	θ^§	TMs 1,8^#	1	20	no	—
Na⁺-bound	d^§	Na⁺ site^\|\|	2	20	no	—
Na⁺-bound	RMSD + θ	Na⁺ site + TMs 1,8	6	20	yes	78 ± 8
apo	RMSD + θ	Na⁺ site + TMs 1,8	6	20	yes	73 ± 4
Na⁺-bound	R_g + θ^§	Na⁺ site + TMs 1,8**	9	20	partial	—
apo	R_g + θ	Na⁺ site + TMs 1,8	2	20	partial	—
Na⁺-bound	d + θ	Na⁺ site + TMs 1,8	6	5	yes	93 ± 16
Na⁺-bound	d + θ	Na⁺ site + TMs 1,8	9	20	yes	78 ± 7
apo	d + θ	Na⁺ site + TMs 1,8	2	5	yes	91 ± 0.01
apo	d + θ	Na⁺ site + TMs 1,8	12	20	yes	69 ± 6

The work profiles associated with representative simulations are shown in Fig. 4.

^*Different force constants were tested and tuned when multiple copies were performed for the same collective variable.

^†Here runtime is just for the driven portion of the simulation, which is followed with restrained equilibrium and nonrestrained simulations for relaxation at the target state in most cases. The restrained equilibrium and nonrestrained simulations are always the same length or longer than the driven simulation runtime.

^‡The radius of gyrations of cytoplasmic and periplasmic gates were measured to evaluate the completion of the conformational transition of the transporter from OF to IF state. “partial” means that transition was achieved in a fraction of multiple copies.

^§θ: relative orientation; d: distance; R_g: radius of gyration.

^¶C_α atoms are selected for specific structural elements when RMSD is the collective variable.

^#Backbone heavy atoms are selected for specific structural elements when θ is the collective variable.

^||The distance of Na⁺-binding site is represented by two distances respectively between C_α atoms of A38 and A309, and those of I41 and T313.

**The radius of gyration of Na⁺-binding site is defined by C_α atoms of residues forming the site, i.e., A38, I41, A309, S312, and T313.