Comparative Molecular Dynamics Simulation Studies of Protegrin-1 Monomer and Dimer in Two Different Lipid Bilayers Huan Rui, Jinhyuk Lee, Wonpil Im

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Comparative Molecular Dynamics Simulation Studies of Protegrin-1 Monomer and Dimer in Two Different Lipid Bilayers Huan Rui, Jinhyuk Lee, Wonpil Im Biophysical Journal Volume 97, Issue 3, Pages 787-795 (August 2009) DOI: 10.1016/j.bpj.2009.05.029 Copyright © 2009 Biophysical Society Terms and Conditions

Figure 1 Tilt angle (τ) and rotation angle (ρ) distributions in (Top) DLPC and (Bottom) POPC bilayers. Structures with chemical shift root-mean-square deviations (δσ) <4 ppm are highlighted (black circles) in the DLPC bilayer distributions. Systems M1 (blue), M2 (green), and M3 (red) are shown in different colors for clarity. Biophysical Journal 2009 97, 787-795DOI: (10.1016/j.bpj.2009.05.029) Copyright © 2009 Biophysical Society Terms and Conditions

Figure 2 (A) Molecular structure of PG-1 Tyr7 and Phe12 rotamers with χ1= −160° (green), χ1= −60° (cyan), and χ1= 60° (magenta). The PG-1 peptide (green) is shown in cartoon representation. (B) The population of the Tyr7χ1 angle in the DLPC (upper) and POPC (lower) bilayers. (C) The population of Phe12χ1 angle in the DLPC (upper) and POPC (lower) bilayers. Systems M1 (blue), M2 (green), and M3 (red) are shown in different colors for clarity. The molecular structure of PG-1 is produced with PyMOL (41). Biophysical Journal 2009 97, 787-795DOI: (10.1016/j.bpj.2009.05.029) Copyright © 2009 Biophysical Society Terms and Conditions

Figure 3 Schematic illustrations of the H-bonding pattern of PG-1 monomer and dimer in DLPC (A and B) and POPC (C and D) bilayers. The residues that form H-bonds with the lipid headgroups are shown in orange and those that do not are in green. Dotted lines represent inter- and intramolecular H-bonds and solid lines represent disulfide bonds. The putative lipid headgroup regions are illustrated by light orange boxes. Biophysical Journal 2009 97, 787-795DOI: (10.1016/j.bpj.2009.05.029) Copyright © 2009 Biophysical Society Terms and Conditions

Figure 4 Average contact numbers of guanidinium-water (cyan), guanidinium-lipid headgroups (orange), and guanidinium-lipid tails (green) in (A) DLPC and (B) POPC bilayers. Heavy atoms within 4.5 Å are counted as interacting pairs. The results for systems M1 (left), M2 (middle), and M3 (right) are shown for each arginine residue. Biophysical Journal 2009 97, 787-795DOI: (10.1016/j.bpj.2009.05.029) Copyright © 2009 Biophysical Society Terms and Conditions

Figure 5 Fractions of intermolecular H-bonds of PG-1 dimer in (A) DLPC and (B) POPC bilayers. Systems D1 (blue), D2 (green), and D3 (red) are presented in different colors for clarity. Biophysical Journal 2009 97, 787-795DOI: (10.1016/j.bpj.2009.05.029) Copyright © 2009 Biophysical Society Terms and Conditions