TABLE 2.

List of simulations

	Sequence	Angle formed by helix with interfacial plane (°)	Cα atom of peptide in plane with average position of lipid P8 atom	Total simulation time (ns)
PER1	FPIPLPYCWLCRALIKRIQAMIPKG	90	W-9	20
PER2	FPIPLPYCWLCRALIKRIQAMIPKG	90	C-11	10
PER3	FPIPLPYCWLCRALIKRIQAMIPKG	90	A-13	10
PAR1	FPIPLPYCWLCRALIKRIQAMIPKG	0	W-9*	10
PAR2	FPIPLPYCWLCRALIKRIQAMIPKG	0	W-9*	10
PAR3	FPIPLPYCWLCRALIKRIQAMIPKG	0	W-9*	10
PAR4	FPIPLPYCWLCRALIKRIQAMIPKG	0	C-11	10
PAR5	FPIPLPYCWLCRALIKRIQAMIPKG	0	A-13	10
MUT1	WLCRALIKRIQAMIPKG	90	W-9	10
MUT2	FPIPLPYCWLCAALIAAIQAMIPAG	90	W-9	10
MUT3	WLCAALIAAIQAMIPAG	90	W-9	10
MUT4	FPIPLPYCWLCAALIKRIQAMIPAG	90	W-9	10
MUT5	LPYCWLCRALIKRIQAMIPKG	90	W-9	10
WAT	FPIPLPYCWLCRALIKRIQAMPIKG	—	SP-B1–25 in water	20

All the PER simulations begin with the peptide perpendicular to the interface and the PAR simulations begin with the peptide parallel to the interface. MUT simulations were performed on peptides that were mutated from the original sequence, and they begin with the peptide perpendicular to the interface.

PAR1, PAR2, and PAR3 differ in the orientation of the hydrophobic sequence (residues 1–8) with respect to the interface. In PAR1, the sequence is embedded in the lipid tail region, in PAR2, the sequence is embedded in the water subphase, and in PAR3, the sequence is embedded in the interfacial region. These orientations were achieved by rotating the peptide by 90° at a time about its principal helical axis. PER2 is inserted deeper into the lipid tail region than is PER1, and PER3 is deeper than PER2.