Estimating the accuracy of the MARTINI model towards the investigation of Peripheral Protein-Membrane Interactions

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

C

D

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

Ubiquitin - fc 500; DOPC

Ubiquitin - fc 1000; DOPC

Ubiquitin - fc 500; 80% DOPC, 20% DOPS

Ubiquitin - fc 1000; 80% DOPC, 20% DOPS

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

HEW Lysozyme - fc 500; DOPC

HEW Lysozyme - fc 1000; DOPC

HEW Lysozyme - fc 500; 80% DOPC, 20% DOPS

HEW Lysozyme - fc 1000; 80% DOPC, 20% DOPS

A

B

E

F

G

H

Figure S1: Soluble proteins.

(A-D) Time trace of minimum distance values for each replica, between ubiquitin and bilayers of

different compositions at both values of fc.

(E-H) Time trace of minimum distance values for each replica, between HEW Lysozyme for and

bilayers of different compositions at both values of fc.

PDK1 PH Domain - fc 500; DOPC

PDK1 PH Domain - fc 1000; DOPC

PDK1 PH Domain - fc 500; 90% DOPC, 10% DOPS

PDK1 PH Domain - fc 1000; 90% DOPC, 10% DOPS

PDK1 PH Domain - fc 500; 80% DOPC, 20% DOPS

PDK1 PH Domain - fc 1000; 80% DOPC, 20% DOPS

PDK1 PH Domain - fc 500; 70% DOPC, 30% DOPS

PDK1 PH Domain - fc 1000; 70% DOPC, 30% DOPS

G

H

C

D

A

B

E

F

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Min. dist. btw protein and membrane (nm)

Figure S2: PDK1 PH Domain.

Time trace of minimum distance values between the PDK1 PH domain and bilayers of

different compositions at both values of fc.

C

D

Evectin-2 PH Domain - fc 500; DOPC

Evectin-2 PH Domain - fc 1000; DOPC

Evectin-2 PH Domain - fc 500; 80% DOPC, 20% DOPS

Evectin-2 PH Domain - fc 1000; 80% DOPC, 20% DOPS

Evectin-2 PH Domain - fc 500; 70% DOPC, 30% DOPS

Evectin-2 PH Domain - fc 1000; 70% DOPC, 30% DOPS

A

B

E

F

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

Figure S3: Evectin-2 PH Domain.

Time trace of minimum distance values between the Evectin-2 PH domain and bilayers of

different compositions at both values of fc.

C

D

Lactadherin C2 Domain - fc 500; DOPC

Lactadherin C2 Domain - fc 1000; DOPC

Lactadherin C2 Domain - fc 500; 90% DOPC, 10% DOPS

Lactadherin C2 Domain - fc 1000; 90% DOPC, 10% DOPS

Lactadherin C2 Domain - fc 500; 80% DOPC, 20% DOPS

Lactadherin C2 Domain - fc 1000; 80% DOPC, 20% DOPS

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane

(nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane

(nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

Figure S4: Lactadherin C2 Domain.

Time trace of minimum distance values between the Lactadherin C2 domain and bilayers of

different compositions at both values of fc.

A

B

C

D

FVa C2 Domain - fc 500; DOPC

FVa C2 Domain - fc 1000; DOPC

FVa C2 Domain - fc 500; 80% DOPC, 20% DOPS

FVa C2 Domain - fc 1000; 80% DOPC, 20% DOPS

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

Min. dist. btw protein and membrane (nm)

Figure S5: FVa C2 Domain.

Time trace of minimum distance values between the FVa C2 domain and bilayers of different

compositions at both values of fc.

C

D

PLA

2

- fc 500; DMPC

PLA

2

- fc 1000; DMPC

PLA

2

- fc 500; 80% DOPC, 20% DOPS

PLA

2

- fc 1000; 80% DOPC, 20% DOPS

E

F

PLA

2

- fc 500; DOPC

PLA2 - fc 1000; DOPC

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

G

H

Figure S6:

PLA

₂

.

(A
F) Time trace of minimum distance values between PLA

2

and bilayers of dierent compositions

at both values of fc. (G) Probability density distribution of protein
membrane minimum distances in DMPC

lipid bilayer at fc = 500 kJ/mol/nm

2

_{. (H) Percentage of binding of PLA}

2

at dierent membrane compositions.

C

D

Arf1 GDP - fc 500; DMPC

Arf1 GDP - fc 1000; DMPC

Arf1 GTP - fc 500; DOPC

Arf1 GTP - fc 1000; DOPC

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

Figure S7: Arf1 protein.

Time trace of minimum distance values between the Arf1 protein in the GDP-bound (A,B) or

GTP-bound conformer (C,D) and bilayers of different compositions at both values of fc.

C

D

Ricin - fc 500; DOPC

Ricin - fc 1000; DOPC

Ricin- fc 500; 70% DOPC, 30%DOPS

Ricin - fc 1000; 70% DOPC, 30%DOPS

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

2500

3000

3500

4000

Min. dist. btw protein and membrane (nm)

Figure S8: Ricin.

Time trace of minimum distance values between the ricin and bilayers of different compositions

at both values of fc.

C

D

Mastoparan - fc 500; DMPC

E

F

Mastoparan - fc 500; POPC

Mastoparan - fc 1000; POPC

Mastoparan - fc 500; DOPC

Mastoparan - fc 1000; DOPC

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

200

400

600

800

1000

Time (ns)

0 1 2 3 4

0

200

400

600

800

1000

Min. dist. btw protein and

membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

200

400

600

800

1000

Time (ns)

0 1 2 3 4

0

200

400

600

800

1000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

200

400

600

800

1000

Time (ns)

0 1 2 3 4

0

200

400

600

800

1000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

200

400

600

800

1000

Time (ns)

0 1 2 3 4

0

200

400

600

800

1000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

200

400

600

800

1000

Time (ns)

0 1 2 3 4

0

200

400

600

800

1000

Min. dist. btw protein and membrane (nm)

G

H

I

Figure S9: Mastoparan.

(A-F) Time trace of minimum distance values between Mastoparan and bilayers of

different compositions at both values of fc.

(G-I) Probability density distribution of protein-membrane minimum distances for different

lipid bilayers

A

Mastoparan - fc 1000; DMPC

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

200

400

600

800

1000

Time (ns)

0 1 2 3 4

0

200

400

600

800

1000

Min. dist. btw protein and membrane (nm)

C

D

Osh4 ALPS - fc 500; DMPC

Osh4 ALPS - fc 1000; DMPC

E

F

Osh4 ALPS - fc 500; POPC

Osh4 ALPS - fc 1000; POPC

Osh4 ALPS - fc 500; DOPC

Osh4 ALPS - fc 1000; DOPC

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

G

H

I

Figure S10: Osh4 ALPS peptide.

(A-F) Time trace of minimum distance values between the Osh4 ALPS peptide and bilayers of

different compositions at both values of fc.

(G-I) Probability density distribution of peptide-membrane minimum distances for different

lipid bilayers

C

D

ArfGAP1 ALPS - fc 500; DMPC

ArfGAP1 ALPS - fc 1000; DMPC

E

F

ArfGAP1 ALPS - fc 500; POPC

ArfGAP1 ALPS - fc 1000; POPC

ArfGAP1 ALPS - fc 500; DOPC

ArfGAP1 ALPS - fc 1000; DOPC

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

0

500

1000

1500

2000

Time (ns)

0 1 2 3 4

0

500

1000

1500

2000

Min. dist. btw protein and membrane (nm)

G

H

I

Figure S11: ArfGAP1 ALPS peptide.

(A-F) Time trace of minimum distance values between the ArfGAP1 ALPS peptide and bilayers of

different compositions at both values of fc.

(G-I) Probability density distribution of protein-membrane minimum distances for different

lipid bilayers