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.... 9 Table S3. The average angles... 10 Table S4. The fitting parameters of the θ A distribution by using Boltzmann distribution function...... 11 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
Figure S1. The structures of lipid molecules; grey, blue, red, purple and white balls represent united carbon, nitrogen, oxygen, phosphorus and hydrogen atoms, respectively.
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.
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.
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.
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.
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.
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
Table S2. The average area per lipid, bilayer thickness and volume per lipid. The results of 6.25-25% 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 ± 0.00 3.76 ± 0.00 1.23 ± 0.00 6.25% 13-tc 0.66 ± 0.00 3.70 ± 0.01 1.23 ± 0.00 12.5% 13-tc 0.67 ± 0.00 3.66 ± 0.00 1.24 ± 0.00 25% 13-tc 0.69 ± 0.00 3.56 ± 0.01 1.24 ± 0.00 50% 13-tc 0.74 ± 0.00 3.35 ± 0.01 1.23 ± 0.00 75% 13-tc 0.79 ± 0.01 3.13 ± 0.01 1.23 ± 0.01 Pure 13-tc 0.80 ± 0.00 3.02 ± 0.05 1.20 ± 0.02 6.25% 9-tc 0.66 ± 0.00 3.72 ± 0.00 1.24 ± 0.00 12.5% 9-tc 0.67 ± 0.01 3.67 ± 0.02 1.23 ± 0.00 25% 9-tc 0.68 ± 0.01 3.60 ± 0.01 1.23 ± 0.00 50% 9-tc 0.71 ± 0.01 3.46 ± 0.03 1.23 ± 0.00 75% 9-tc 0.74 ± 0.00 3.29 ± 0.01 1.22 ± 0.00 Pure 9-tc 0.78 ± 0.00 3.13 ± 0.01 1.22 ± 0.00 6.25% 12-al 0.66 ± 0.00 3.67 ± 0.00 1.23 ± 0.00 12.5% 12-al 0.67 ± 0.00 3.62 ± 0.00 1.22 ± 0.00 25% 12-al 0.69 ± 0.00 3.47 ± 0.01 1.20 ± 0.00 50% 12-al 0.72 ± 0.00 3.20 ± 0.02 1.16 ± 0.00 75% 12-al 0.74 ± 0.01 3.03 ± 0.03 1.12 ± 0.01 Pure12-al - - - 6.25% 9-al 0.66 ± 0.00 3.67 ± 0.01 1.22 ± 0.00 12.5% 9-al 0.67 ± 0.00 3.59 ± 0.02 1.21 ± 0.00 25% 9-al 0.68 ± 0.00 3.44 ± 0.01 1.18 ± 0.00 50% 9-al 0.71 ± 0.01 3.15 ± 0.01 1.12 ± 0.00 75% 9-al - - - Pure 9-al - - - 50% PDPC 0.66 ± 0.00 3.46 ± 0.00 1.13 ± 0.00 75% PDPC 0.65 ± 0.00 3.30 ± 0.01 1.08 ± 0.00 Pure PDPC 0.65 ± 0.00 3.15 ± 0.00 1.02 ± 0.00
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 - - - 66 ± 1-30 ± 1-50% 13-tc 48 ± 1 63 ± 2-125 ± 1 66 ± 0 54 ± 1 32 ± 0 30 ± 0 75% 13-tc 50 ± 2 60 ± 1-118 ± 2 66 ± 1 56 ± 1 34 ± 1 34 ± 1 Pure 13-tc - 63 ± 1-115 ± 2-56 ± 1-36 ± 1 50% 9-tc 50 ± 1 55 ± 1-113 ± 1 66 ± 1 60 ± 1 32 ± 0 31 ± 0 75% 9-tc 51 ± 1 57 ± 1-110 ± 1 66 ± 1 60 ± 0 33 ± 1 32 ± 0 Pure 9-tc - 56 ± 2-111 ± 1-60 ± 1-33 ± 1 50% 12-al 52 ± 1 71 ± 1 - - 64 ± 0 41 ± 1 34 ± 0 34 ± 0 75% 12-al 53 ± 2 66 ± 1 - - 64 ± 2 45 ± 1 36 ± 2 35 ± 1 Pure12-al - 67 ± 2 - - - 44 ± 1 - - 50% 9-al 54 ± 1 72 ± 1 - - 64 ± 0 37 ± 2 36 ± 0 35 ± 1 75% 9-al 47 ± 1 73 ± 1 - - 67 ± 0 37 ± 1 - - Pure 9-al - 74 ± 2 - - - 37 ± 1 - - 50% PDPC 50 ± 0 48 ± 0 - - 65 ± 0 46 ± 1 32 ± 0 31 ± 0 75% PDPC 52 ± 1 49 ± 0 - - 64 ± 0 46 ± 1 32 ± 0 32 ± 0 Pure PDPC - 50 ± 1 - - - 46 ± 0-32 ± 1
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 0.0051-31 - 49-21 - 50% 13-tc 0.0052 0.0034 30 41 48 65 20 28 75% 13-tc -0.0049-0.0037 32 39 51 62 22 26 Pure 13-tc - 0.0034-40 - 64-27 50% 9-tc -0.0049-0.0041 32 36 51 57 22 24 75% 9-tc -0.0047-0.0040 32 37 51 59 22 25 Pure 9-tc - 0.0041-36 - 57-24 50% 12-al 0.0046 0.0028 33 46 53 73 22 31 75% 12-al 0.0043 0.0027 34 48 54 77 23 32 Pure 12-al - 0.0032-43 - 69-29 50% 9-al 0.0043 0.0027 34 48 54 77 23 32 75% 9-al 0.0053 0.0027 29 48 56 77 20 32 Pure 9-al - 0.0027-47 - 75-32 50% PDPC -0.0048 0.0050 32 31 51 49 22 21 75% PDPC 0.0045 0.0049 33 32 53 51 22 22 Pure PDPC - 0.0049-32 - 51-22 σ
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 ± 0.01 1.96 ± 0.01 1.62 ± 0.03 0.99 1.21 Pure 13-tc 1.88 ± 0.02 1.84 ± 0.02 1.94 ± 0.03 1.02 0.95 Pure 9-tc 1.89 ± 0.01 1.83 ± 0.01 1.75 ± 0.06 1.03 1.04 Pure 12-al 1.91 ± 0.01 1.46 ± 0.02 1.86 ± 0.03 1.31 0.78 Pure 9-al 1.86 ± 0.16 1.26 ± 0.01 1.93 ± 0.04 1.48 0.65 Pure PDPC 1.91 ± 0.01 1.43 ± 0.00 1.49 ± 0.03 1.34 0.96
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 1.21 0.65 1.87 0.99 Pure 13-tc 1.20 0.80 1.51 0.99 Pure 9-tc 1.22 0.78 1.51 1.00 Pure 12-al 1.04 1.05 1.91 0.52 Pure 9-al 0.93 0.94 1.86 0.53 Pure PDPC 1.02 0.65 1.57 0.99
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