Bilayer Deformation, Pores & Micellation Induced by Oxidized Lipids

Transcription

1 Supporting Information Bilayer Deformation, Pores & Micellation Induced by Oxidized Lipids Phansiri Boonnoy 1, Viwan Jarerattanachat 1,2, Mikko Karttunen 3*, and Jirasak Wongekkabut 1* 1 Department of Physics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand 2 Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom 3 Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, MetaForum, 5600 MB Eindhoven, the Netherlands * Corresponding Authors J.W.: jirasak.w@ku.ac.th, and M.K.: mkarttu@tue.nl Figures and Tables Figure S1. The structures of lipid molecules 2 Figure S2. Snapshots of a 12-al micelle (A) and a 9-al micelle (B) viewed along the y- direction 3 Figure S3. The time evolution of the position in along the z-direction for the oxidized functional groups from the center of bilayer of 50 % oxidized lipids mixture bilayer 4 Figure S4. Water molecules were pulled across the leaflet by the aldehyde groups in the oxidized lipid tails 5 Figure S5. Definitions of the angles and lengths. 6 Figure S6. Lipid geometries. 7 Table S1. Compositions of the lipid bilayers used in this study.. 8 Table S2. The average area per lipid, bilayer thickness and volume per lipid Table S3. The average angles Table S4. The fitting parameters of the θ A distribution by using Boltzmann distribution function Table S5. The lengths of lipid tails (l 1 and l 2 ) and the distances between the tail ends (l 3 ). 12 Table S6. Summary of packing analysis.. 13

2 Figure S1. The structures of lipid molecules; grey, blue, red, purple and white balls represent united carbon, nitrogen, oxygen, phosphorus and hydrogen atoms, respectively.

3 Figure S2. Snapshots of a 12-al micelle (A) and a 9-al micelle (B) viewed along the y-direction. Lipid chains are shown in cyan and green for 12-al and 9-al, respectively, choline groups in orange, phosphate groups in yellow and oxygens in the sn-2 chain in red. Water molecules are not show for clarity.

4 Figure S3. The time evolution of the position in along the z-direction for the oxidized functional groups from the center of bilayer of 50 % oxidized lipids mixture bilayer. The black line represents the average position of the phosphate group in each of the two leaflets (the bilayer is centered at z=0 nm). The blue, red, green and purple lines show the positions of the functional groups in the oxidized tails of 13-tc, 9-tc, 12-al and 9-al in one leaflet, respectively.

5 Figure S4. Water molecules were pulled across the leaflet by the aldehyde groups in the oxidized lipid tails. Green & yellow: 9-al lipids in the upper and lower leaflets, respectively. White: PLPC. Green, yellow and white spheres: Phosphorus atoms on the different lipids. Red spheres: Oxygens in 9-al sn-2 tails. Blue & gray: Oxygens and hydrogens of water molecules, respectively.

6 Figure S5. Definitions of the angles and lengths. The interior angles of the lipid tails are represented by θ A, θ B and θ C. The tilt angle (θ N ) between the sn-1 and the bilayer normal is used to determine lipid orientation. l 1 and l 2 represent the lengths of the sn-1 and sn-2 lipid tails, respectively and l 3 is the distance between the ends of lipid tails.

7 Figure S6. Lipid geometries: (A) PLPC- cylinder, (B) peroxide lipids (13-tc, 9-tc) - cylinder, (C) aldehyde lipids (12-al, 9-al) - truncated cone and (D) PDPC - cylinder.

8 Table S1. Compositions of the lipid bilayers used in this study. All simulations were run for 1 µs. System Description Concentration of PLPC:Oxidized oxidized lipid (%) lipid molecules Final structure 1 Pure PLPC 0 128:0 Bilayer 2 PLPC + 12-al 50 64:64 Bilayer with a pore 3 PLPC + 12-al 75 32:96 Bilayer with a pore 4 Pure 12-al 100 0:128 Micelle 5 PLPC + 9-al 50 64:64 Bilayer with a pore 6 PLPC + 9-al 75 32:96 Micelle 7 Pure 9-al 100 0:128 Micelle 8 PLPC + 13-tc 50 64:64 Bilayer 9 PLPC + 13-tc 75 32:96 Bilayer 10 Pure 13-tc 100 0:128 Bilayer 11 PLPC + 9-tc 50 64:64 Bilayer 12 PLPC + 9-tc 75 32:96 Bilayer 13 Pure 9-tc 100 0:128 Bilayer 14 PLPC + PDPC 50 64:64 Bilayer 15 PLPC + PDPC 75 32:96 Bilayer 16 Pure PDPC 100 0:128 Bilayer

9 Table S2. The average area per lipid, bilayer thickness and volume per lipid. The results of % oxidized lipids concentration were obtained from previous study. 1,2 Systems Area per lipid (nm 2 ) Bilayer thickness (nm) Volume per lipid (nm 3 ) Pure PLPC 0.66 ± ± ± % 13-tc 0.66 ± ± ± % 13-tc 0.67 ± ± ± % 13-tc 0.69 ± ± ± % 13-tc 0.74 ± ± ± % 13-tc 0.79 ± ± ± 0.01 Pure 13-tc 0.80 ± ± ± % 9-tc 0.66 ± ± ± % 9-tc 0.67 ± ± ± % 9-tc 0.68 ± ± ± % 9-tc 0.71 ± ± ± % 9-tc 0.74 ± ± ± 0.00 Pure 9-tc 0.78 ± ± ± % 12-al 0.66 ± ± ± % 12-al 0.67 ± ± ± % 12-al 0.69 ± ± ± % 12-al 0.72 ± ± ± % 12-al 0.74 ± ± ± 0.01 Pure12-al % 9-al 0.66 ± ± ± % 9-al 0.67 ± ± ± % 9-al 0.68 ± ± ± % 9-al 0.71 ± ± ± % 9-al Pure 9-al % PDPC 0.66 ± ± ± % PDPC 0.65 ± ± ± 0.00 Pure PDPC 0.65 ± ± ± 0.00

10 Table S3. The average angles. Systems θ A θ B θ C θ N PLPC OXPL PLPC OXPL PLPC OXPL PLPC OXPL Pure PLPC 48 ± ± 1-30 ± 1-50% 13-tc 48 ± 1 63 ± ± 1 66 ± 0 54 ± 1 32 ± 0 30 ± 0 75% 13-tc 50 ± 2 60 ± ± 2 66 ± 1 56 ± 1 34 ± 1 34 ± 1 Pure 13-tc - 63 ± ± 2-56 ± 1-36 ± 1 50% 9-tc 50 ± 1 55 ± ± 1 66 ± 1 60 ± 1 32 ± 0 31 ± 0 75% 9-tc 51 ± 1 57 ± ± 1 66 ± 1 60 ± 0 33 ± 1 32 ± 0 Pure 9-tc - 56 ± ± 1-60 ± 1-33 ± 1 50% 12-al 52 ± 1 71 ± ± 0 41 ± 1 34 ± 0 34 ± 0 75% 12-al 53 ± 2 66 ± ± 2 45 ± 1 36 ± 2 35 ± 1 Pure12-al - 67 ± ± % 9-al 54 ± 1 72 ± ± 0 37 ± 2 36 ± 0 35 ± 1 75% 9-al 47 ± 1 73 ± ± 0 37 ± Pure 9-al - 74 ± ± % PDPC 50 ± 0 48 ± ± 0 46 ± 1 32 ± 0 31 ± 0 75% PDPC 52 ± 1 49 ± ± 0 46 ± 1 32 ± 0 32 ± 0 Pure PDPC - 50 ± ± 0-32 ± 1

11 Table S4. The fitting parameters of the θ A distribution by using Boltzmann distribution function, y = a 2 θ A 2 exp( θ A 2 2b 2). Systems a Parameters b Mean (θ A ) PLPC OXPL PLPC OXPL PLPC OXPL PLPC OXPL Pure PLPC % 13-tc % 13-tc Pure 13-tc % 9-tc % 9-tc Pure 9-tc % 12-al % 12-al Pure 12-al % 9-al % 9-al Pure 9-al % PDPC % PDPC Pure PDPC σ

12 Table S5. The lengths of lipid tails (l 1 and l 2 ) and the distances between the tail ends (l 3 ). Systems l 1 (nm) l 2 (nm) l 3 (nm) l 1 : l 2 l 2 : l 3 Pure PLPC 1.95 ± ± ± Pure 13-tc 1.88 ± ± ± Pure 9-tc 1.89 ± ± ± Pure 12-al 1.91 ± ± ± Pure 9-al 1.86 ± ± ± Pure PDPC 1.91 ± ± ±

13 Table S6. Summary of packing analysis The packing parameter of the PLPC and oxidized lipid systems were calculated as followed. (1) Bilayers (PLPC, 13-tc, 9-tc and PDPC): For lipid bilayers composed N lipid molecules, the average chain volume is v c = V/N where V is the total bilayer volume. a is the usual average area per lipid, and l c is the haft-bilayer (=monolayer) thickness. (2) Cylindrical micelles (12-al, 9-al): For cylindrical micelles composed of N lipid molecules, the hydrocarbon chain volume can be defined as v c = V/N = Lπr 2 /N and the average surface area of the lipid head group as a = 2πrL/N, where V is the total volume of micelle, and L and r are the length and the radius of the cylindrical micelle, respectively. The radius of a cylindrical micelle can be estimated from the density of the phosphorus atoms. In case of 12-al micelle r = 1.99 ± 0.15 nm and r = 1.98 ± 0.27 nm for 9-al micelle. The snapshot of cylindrical micelle (Figure S2) shown that the oxygen atoms in sn-2 chain are pointing to the micelle surface at the lipid head group region and formed stable hydrogen bond with water, suggested that the oxygen atom has co-surface area with lipid head group. Thus, the critical hydrocarbon chain l c can be estimated from the average tail length of l 1 which represents the length of non-polar chain with pointing to the center of micelle. Thus, the l c of 12-al and 9-al lipids in micelle are 1.91 ± 0.01 and 1.86 ± 0.16 nm, respectively. Systems v c a l c Packing Parameter S = v c /al c Pure PLPC Pure 13-tc Pure 9-tc Pure 12-al Pure 9-al Pure PDPC

14 References (1) Wong-ekkabut, J.; Xu, Z.; Triampo, W.; Tang, I. M.; Peter Tieleman, D.; Monticelli, L. Effect of Lipid Peroxidation on the Properties of Lipid Bilayers: A Molecular Dynamics Study. Biophys. J. 2007, 93, (2) Jarerattanachat, V.; Karttunen, M.; Wong-ekkabut, J. Molecular Dynamics Study of Oxidized Lipid Bilayers in NaCl Solution. J. Phys. Chem. B 2013, 117,