. 2018 Sep 13;115(8):1445–1456. doi: 10.1016/j.bpj.2018.09.002

Table 1.

Summary of All Molecular Dynamics Simulations Reported in This Work

System	Notes	Length of Each Simulation	Temperature and Number of Repeats
CG_LpxR	Coarse-grained system	2 μs	310 K (×2)
CG_LpxR	Coarse-grained system	2 μs	323 K (×1)
Apo Model	X-ray structure with water and Ca²⁺ as reported by Rutten et al. (5)	300 ns (×2)	310 K
Apo Model		1 μs (×1)	323 K
Apo Model^a	As above but with positional restraints for the first 100 ns	300 ns (×2)	310 K
Apo Model^a		1 μs (×1)	323 K
Apo Unbiased	X-ray structure with key water and Ca²⁺ removed from the starting structure	300 ns (×2)	310 K
Apo Unbiased		1 μs (×1)	323 K
Ligand-Bound Model	X-ray structure with water and Ca²⁺ and modeled in substrate as reported by Rutten et al. (5)	300 ns (×2)	310 K
Ligand-Bound Model		1 μs (×1)	323 K
Ligand-Bound Model^a	As above but with positional restraints for the first 100 ns	300 ns (×2)	310 K
Ligand-Bound Model^a		1 μs (×1)	323 K
Ligand-Bound Unbiased	X-ray structure with modeled in substrate but without water and Ca²⁺	300 ns (×2)	310 K
Ligand-Bound Unbiased		1 μs (×1)	323 K
H122_p^b	H122 is Nε protonated	300 ns (×2)	310 K
H122_p^b	H122 is Nε protonated	1 μs (×1)	323 K
D10A	Single point mutation in protein	300 ns (×2)	310 K
D10A	Single point mutation in protein	1 μs (×1)	323 K
D11A	Single point mutation in protein	300 ns (×2)	310 K
D11A	Single point mutation in protein	1 μs (×1)	323 K
T34A	Single point mutation in protein	300 ns (×2)	310 K
T34A	Single point mutation in protein	1 μs (×1)	323 K
H122A	Single point mutation in protein	300 ns (×2)	310 K
H122A	Single point mutation in protein	1 μs (×1)	323 K
Bond Break Model	Scissile bond removed in substrate	500 ns	310 K (×2)
Bond Break Model	Scissile bond removed in substrate	500 ns	323 K (×1)
Bond Break Unbiased	As above but with key water and Ca²⁺ removed from the starting structure	500 ns	310 K (×2)
Bond Break Unbiased		500 ns	323 K (×1)
Micelle	Protein in self-assembled DPC micelle	500 ns	323 K (×3)
Apo_DPPC	X-ray structure inserted into simple DPPC membrane	500 ns	310 K (×2)
Apo_DPPC	X-ray structure inserted into simple DPPC membrane	500 ns	323 K (×1)

The total simulation time was 29.6 μs.

In these systems, the protein, Ca²⁺ ion, and modeled water molecule were subjected to positional restraints for the first 100 ns of simulation; see Methods for more details.

H122 is Nε protonated in this simulation, whereas it is Nδ protonated in all other simulations.