supplementary - · pdf file620 67 314 24,000 48 16.0x15.8x16.3 4120.6 12 620 67 314 24,000 72...
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Supplementary 1
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Defining the membrane disruption mechanism of kalata B1 via coarse-grained molecular 3
dynamics simulations 4
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Wanapinun Nawae1, Supa Hannongbua2, and Marasri Ruengjitchatchawalya 3, 4, * 6
1Biological Engineering Program, King Mongkut’s University of Technology Thonburi, 126 Pracha 7
Uthit Rd., Bang Mod, Thung Khru, Bangkok, Thailand, 10140. E-mail: [email protected] 8
2Department of Chemistry, Kasetsart University, 50 Phaholyothin Rd., Ladyao Chatuchak, 9
Bangkok, Thailand, 10900. E-mail: [email protected] 10
3School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi 11
(Bang Khun Thian Campus), 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Rd., Tha Kham, 12
Bang Khun Thian, Bangkok , Thailand, 10150. 13
4Bioinformatics and Systems Biology program, King Mongkut’s University of Technology Thonburi 14
(Bang Khun Thian Campus), 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Rd., Tha Kham, 15
Bang Khun Thian, Bangkok , Thailand, 10150. E-mail: [email protected], Telephone: 16
+66-2470-7481, Fax: +66-2427-9623 17
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Supplementary figures 21
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Figure S1. Clustering behavior of kB1 molecules. The sizes of kB1 clusters are plotted for the 24
entire duration of the type 1 simulation. The number of the clusters in each cluster size is 25
represented by the color (see color scale bar). 26
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Figure S2. Distribution of the distance between all lipid head atoms to the COM of the 38
membrane. The center of the membrane is at 0 nm. The two highest peaks in each distribution 39
curve represent the upper and lower surfaces of the membrane. The distribution area and the 40
upper and lower bounds of the distribution curve represent the curved area and degree of 41
membrane curvature. For the type 1 simulation, the shape of the distribution curves were clearly 42
separated into two main areas of the upper and lower membrane layers, reflecting that the curve 43
spanned on small areas of the membrane. In contrast, when the number of kB1 was increased 44
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(type 2 and 3 simulations), the values were highly distributed, and the peaks of the distribution 45
curve were flattened, indicating that the membrane curvature increased and spanned on a large 46
area of the membrane (see Fig. 4). 47
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Figure S3. Analysis of hydrophobicity ratio of the membrane and kB1 cluster. The system was 65
divided into small slabs along the Z axis (area between red line pairs). The numbers of 66
hydrophobic and hydrophilic atoms in each slab were counted for the membrane and kB1 67
clusters. The hydrophobic ratio was the ratio of hydrophobic atoms and total atoms in each slab. 68
At 0 µs, only hydrophobic atoms in the slabs at the core of the membrane were observed; hence, 69
the hydrophobicity ratio was high in this area, whereas in the slabs at the membrane surface, 70
the atoms were mostly hydrophilic atoms (red and blue atoms represent NC3 and PO4 atoms, 71
respectively). Both hydrophobic and hydrophilic atoms were detected in most slabs of the curved 72
membrane (12 µs), especially at the curvature area (see dashed-line box in Fig. 5). The 73
calculation was also applied to the kB1 cluster (shown as the surface representation with green 74
hydrophilic amino acid residue and with white hydrophobic residues) located on the membrane 75
surface. Thus, as shown in Fig. 5, the position of the hydrophobicity ratio of the kB1 cluster was 76
higher than that of the membrane. 77
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Figure S4. Lipids were extracted from membrane. (a) The reference point can be any point 85
belonging to the lowest XY plane (grey plane) in the Z axis of the simulation box. Therefore, we 86
can compare the position of any molecules that locate at different positions in the simulation box 87
(arrow). The reference point was updated at every time step of the simulation trajectory 88
because the dimension of the simulation box might change when membrane was being curved 89
and the simulation algorithm attempts to control the pressure. (b) The distance of the COM of 90
each selected lipid, including lipid reside 496 (blue), 585 (green), 629 (brown), 748 (light green) 91
and 927 (violet) to the reference point are plotted as a function of time. Black and red lines show 92
the distance from the COM of the whole membrane and that of the membrane surface to the 93
reference point, respectively. 94
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Figure S5. Interaction energies of kB1 with the membrane, kB1 with water and total interaction 103
energy as a function of time. The interaction energy unit was an arbitrary unit in which only the 104
number of kB1 molecules was taken into account in the calculation using the g_energy program 105
(see –nmol option of this program in the GROMACS user manual, 106
http://manual.gromacs.org/current/online/g_energy.html). 107
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Figure S6. Insertion depth of kB1. (a) In this study, we chose the simulation system that 117
contained only one kB1 molecule for the distance measurement because the objective of this 118
measurement was to find the deepest distance that kB1 can insert into membrane and then 119
compare with that reported by (ref. 42 in the main manuscript). In addition, we only measured 120
the distance of Trp19 to the COM of the membrane because it is the largest residue of kB1 that 121
inserted into the membrane. Although the structure of single kB1 molecule is different from the 122
peptide used in the (ref. 42), the membrane curvature was observed for the first time when kB1 123
formed the wall-like clusters with overall configuration similar to the peptide used in the (ref. 124
42). (b) The distances of the COM of kB1 and that of Trp19 residue of kB1 to the COM of the 125
membrane were plotted as a function of time during 15-16 µs of the simulation of one kB1 126
molecule with the membrane. The distances of NC3, PO4, GL, C1, C2 (D2), C3 (D3), and C4 of 127
DPPC and DUPC to the COM of the membrane were also plotted as a function of time to 128
represent the level of each atom type in the upper leaflet of the membrane. The values are 129
obtained from the last 1 µs of the simulation of the kB1 monomer with the membrane. 130
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Figure S7. Membrane validation. Top view of (a) the constructed membrane at 4 µs of the 137
simulation of the pure membrane (see method) that used in this study, (b) the same membrane 138
as (a) after temperature of the system was increased to 400 K and (c) the same membrane as 139
(b) after temperature was cooled down to 310 K. DPPC, DUPC and CHOL are colored as lime, 140
cyan and yellow, respectively. Lipid molecules are represented as CPK models. Cluster of DPPC 141
and CHOL in (a) and (c) represents the lipid domain. To clarify the picture, water molecules are 142
not shown. Size of each grid space is 1x1 nm. 143
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Supplementary table 152
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Table S1. Detail of all simulation systems that were used to study kB1 oligomerization and the 154
progressive mechanism of membrane disruption. The initial Simulation box dimension and size 155
values were obtained at 200 ps of the production run of each system. 156
Simulation
type
Number
of DUPC
Number
of DPPC
Number
of CHOL
Number of
Water bead
Number
of kB1
Initial Simulation
box dimension
(nm)
Initial
box size
(nm3)
Time
(µs)
Type 1 620 67 314 24,000 24 16.6x16.4x14.8 4029.2 60
Type 2 620 67 314 24,000 +24(48) 16.4x16.2x15.6 4144.6 +12(24)
620 67 314 24,000 +24(72) 16.0x15.9x16.5 4197.6 +12(36)
620 67 314 24,000 +24(96) 16.4x16.3x16.1 4303.9 +12(48)
620 67 314 24,000 +24(12
0)
16.2x16.1x16.9 4407.9 +12(60)
Type 3
620 67 314 24,000 48 16.0x15.8x16.3 4120.6 12
620 67 314 24,000 72 16.1x15.9x16.5 4223.8 12
620 67 314 24,000 96 16.0x15.8x17.0 4297.6 12
620 67 314 24,000 120 16.1x16.0x17.1 4405.0 12
620 67 314 24,000 350 15.1x15.0x23.6 5345.4 12
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