Armando J. de Jesus, Ormacinda R. White, Aaron D. Flynn, Hang Yin

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Determinants of Curvature-Sensing Behavior for MARCKS-Fragment Peptides Armando J. de Jesus, Ormacinda R. White, Aaron D. Flynn, Hang Yin Biophysical Journal Volume 110, Issue 9, Pages 1980-1992 (May 2016) DOI: 10.1016/j.bpj.2016.04.007 Copyright © 2016 Biophysical Society Terms and Conditions

Figure 1 Flowchart summary of the rationale employed in the choice of peptide sequences used. For the full-length MARCKS-ED, two patterns can be observed: 1) charged residues at the termini of the full-length MARCKS-ED; and 2) FSF sequences that are adjacent to charged residues on either one side or both sides. (a) MARCKS-ED was divided into two “halves” (MRX1 and MRX2), each containing an FSF group and terminating in charged residues. (b) MRX3 and MRX4 explored the effect of reducing the number of Lys at one terminus. (c) MRX5 explored the effect of replacing R with K. (d) MRX6 explored the effect of a terminal F. (e) MRX 7 provided a comparison of MRX5 and MRX6. To see this figure in color, go online. Biophysical Journal 2016 110, 1980-1992DOI: (10.1016/j.bpj.2016.04.007) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 2 Fluorescence enhancement of NBD-labeled peptides MARCKS-ED, MRX1, MRX2, MRX3, MRX4, MRX5, MRX6, and MRX7 with 30-, 100-, and 400-nm lipid vesicles containing 60% POPC, 15% POPE, 15% cholesterol, and 10% POPS ([peptide] = 500 nM, [lipid] = 500 μM). ∗p < 0.01. To see this figure in color, go online. Biophysical Journal 2016 110, 1980-1992DOI: (10.1016/j.bpj.2016.04.007) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 3 Fluorescence enhancement of NBD-labeled peptides MARCKS-ED, MRX1, MRX2, MRX3, MRX4, MRX5, MRX6, and MRX7 with 30-, 100- and 400-nm lipid vesicles containing 70% POPC, 15% POPE, and 15% cholesterol ([peptide] = 500 nM, [lipid] = 500 μM). To see this figure in color, go online. Biophysical Journal 2016 110, 1980-1992DOI: (10.1016/j.bpj.2016.04.007) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 4 Fluorescence enhancement of annexin V with PC only or PC/PS (3:1) 30-, 100-, or 400-nm lipid vesicles ([annexin] = 0.32 μM, [lipid] = 100 μM). To see this figure in color, go online. Biophysical Journal 2016 110, 1980-1992DOI: (10.1016/j.bpj.2016.04.007) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 5 Atomistic model of (a) MARCKS-ED, (b) MRX2, and (c) MRX6 interacting with membrane bilayers after ∼75 ns of simulation. Lipid tails, water molecules, and some atoms in the foreground were removed for clarity. Lys residues are represented as cyan spheres and Phe residues as purple spheres. The lipid headgroups are shown as choline nitrogen (light violet), phosphate phosphorus (light yellow), and one of the sn-2 carbonyl oxygen (pink). To see this figure in color, go online. Biophysical Journal 2016 110, 1980-1992DOI: (10.1016/j.bpj.2016.04.007) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 6 Time series of the average side-chain depths of Lys, Phe, and Ser residues for (a) MARCKS-ED, (b) MRX2, and (c) MRX6. The horizontal lines represent the average depth of the headgroup components, choline N (top horizontal line), phosphate P (middle horizontal line), and glycerol carbonyl carbons (bottom horizontal line). To see this figure in color, go online. Biophysical Journal 2016 110, 1980-1992DOI: (10.1016/j.bpj.2016.04.007) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 7 Histograms of side-chain depths calculated from the simulation trajectory showing the distribution of the z-coordinates of the centers of mass of the side chains of Lys, Phe, and Ser residues for (a) MARCKS-ED, (b) MRX2, and (c) MRX6. To see this figure in color, go online. Biophysical Journal 2016 110, 1980-1992DOI: (10.1016/j.bpj.2016.04.007) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 8 Radial distribution of headgroup oxygen atoms from POPS and POPC lipids around the Lys side chains of (a) MARCKS-ED, (b) MRX2, and (c) MRX6. To see this figure in color, go online. Biophysical Journal 2016 110, 1980-1992DOI: (10.1016/j.bpj.2016.04.007) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 9 Time series of the number of lipid headgroup oxygen atoms (phosphate oxygens of POPC and POPS lipids, and carboxyl oxygens in the choline region of POPS lipids) solvating the hydrogens in the amine moieties terminating the Lys (a and b) and Arg (c) side chains. Fig. 9 b shows the solvation of Lys residues on a per-residue basis. To see this figure in color, go online. Biophysical Journal 2016 110, 1980-1992DOI: (10.1016/j.bpj.2016.04.007) Copyright © 2016 Biophysical Society Terms and Conditions