. 2019 Oct 28;4(20):18889–18899. doi: 10.1021/acsomega.9b02949

Table 2. Atomistic Simulations of Cinnamycin–Lipid Complexes in a Bilayer.

simulation name^a	simulation time (μs)	lipid bound	bilayer type	mutation	restrained residues^b
PE_HyASP	4 × 0.5	POPE	POPC
PE_HyASP_HyASP	2 × 0.5	POPE	POPC		HyAsp15
PE_HyASP_Ala(N)6Gly8HyAsp	2 × 0.5	POPE	POPC		Ala(N)6, Gly8, HyAsp15
PE_HyAsp_HyAsp	2 × 0.5	POPE	POPC		HyAsp15
PE_Asp	2 × 0.5	POPE	POPC	Asp15
PE_Asp_Asp	2 × 0.5	POPE	POPC	Asp15	Asp15⁺
PE_HyAsp_Ala(N)6	2 × 0.5	POPE	POPC		Ala(N)6
PE_HyAsp_Gly8	2 × 0.5	POPE	POPC		Gly8
mPE_HyAsp	6 × 0.5	POmPE	POPC

Simulations are named lipid_residue_setup, in which the lipid refers to the lipid in complex with cinnamycin, the residue denotes the amino acid at position 15 of cinnamycin, and the setup reflects either the restraints applied or changes in the bilayer.

Restraints applied in the simulations. Restraints specified with a + or – superscript denoting whether the side chain χ₁ angle is restrained in or away from the gauche(+) conformation, respectively, while the Ala(N)6 and Gly8 labels specify restraints put on the backbone to fix the backbone orientation of Phe7(HN) and Phe7(O) to fit the optimized structure (see details in the SI).