Table 1.

AFM simulation analysis of the EC and C domains of Pgp X-ray crystal structures (PDB IDs: 4M1M^a, 6C0V^b).

			Protein Positioning method
PDB ID	Domain	Protrusion Measurement	TMDETd	O’Marae	OPMf	Avg. ± S.D.
4M1Ma	EC	Height (Å)	26.7	13.4	24.1	21.4 ± 7.0
		Volume-106 (Å3)	0.117	0.023	0.095	0.078 ± 0.049
	Mc	Width (Å)	39.8	58.3	40.8 ± 1.2	46.3 ± 10.4
	C	Height (Å)	67.5	72.1	77.3	72.3 ± 4.9
		Volume 106 (Å3)	1.062	1.147	1.232	1.147 ± 0.085
6C0Vb	EC	Height (Å)	19.2	15.5	17.8	17.5 ± 1.9
		Volume 106 (Å3)	0.080	0.053	0.075	0.069 ± 0.014
	Mc	Width (Å)	43.3	58.3	42.2 ± 1.2	47.9 ± 9.0
	C	Height (Å)	78.4	73.9	74.8	75.7 ± 2.4
		Volume 106 (Å3)	1.256	1.159	1.185	1.200 ± 0.050
4M1Ma and 6C0Vb	EC	Height (Å)				19.5 ± 5.1
		Volume 106 (Å3)				0.074 ± 0.033
	Mc	Width (Å)				47.1 ± 8.7
	C	Height (Å)				74.0 ± 3.9
		Volume 106 (Å3)				1.174 ± 0.069

^aThe AFM image was simulated using the “open” mouse Pgp X-ray crystal structure (PDB ID: 4M1M, [14,15]).

^bThe AFM image was simulated using the “closed” human Pgp X-ray crystal structure (PDB ID: 6C0V, [17]).

^cThe membrane width. With the TMDET and OPM approaches, the membrane width was calculated by taking the sum of the hydrophobic thickness and 9.6 Å to account for the two phosphate head groups. With the O’Mara et al. protocol, the membrane dimensions were estimated using a PyMOL script as described in the Materials and Methods with the membrane-bound Pgp models in [35].

^dPgp was positioned in the membrane using the TMDET method [33]

^ePgp was positioned in the membrane according to O’Mara et al. [35].

^fPgp was positioned in the membrane according to the OPM method [34].