The detailed methods are described in the Supporting Information . In summary, we embedded 10 membrane proteins in
a previously characterized model of the plasma membrane.20 (link) The starting structures of the 10 membrane proteins
simulated in this study were taken from the Protein Data Bank or obtained
from the corresponding publication: aquaporin-1 (AQP1, PDB ID 1J4N);98 (link) prostaglandin H2 synthase (COX1, PDB ID 1Q4G);99 (link) the dopamine transporter (DAT, PDB ID 4M48);44 (link) the epidermal growth factor receptor (EGFR);77 (link) AMPA-sensitive glutamate receptor 2 (GluA2,
PDB ID 3KG2);100 (link) glucose transporter 1 (GluT1, PDB ID 4PYP);101 (link) voltage-dependent Shaker potassium channel 1.2 (Kv1.2,
PDB ID 3LUT,102 (link) residues 32 to 4421 for each monomer); sodium,
potassium pump (Na,K-ATPase, PDB ID 4HYT);103 (link) δ-opioid
receptor (δ-OPR, PDB ID 4N6H);104 (link) and P-glycoprotein
(P-gp, PDB ID 4M1M).105 (link) In each system, four copies of each
protein were included and positioned at a distance of ca. 20 nm from
each other. Proteins were simulated using standard Martini protocols
with minor variations between systems to accommodate system-specific
issues (Supporting Information ). The following
lipid classes were included: cholesterol (CHOL), in both leaflets;
charged lipids phosphatidylserine (PS), phosphatidic acid (PA), phosphatidylinositol
(PI), and the PI-phosphate, PI-bisphosphate, and PI-trisphosphate
(PIPs) placed in the inner leaflet; and ganglioside (GM) in the outer
leaflet. The zwitterionic phosphatidylcholine (PC), phosphatidylethanolamine
(PE), and sphingomyelin (SM) lipids were placed in both leaflets,
with PC and SM primarily in the outer leaflet and PE in the inner
leaflet. Ceramide (CER), diacylglycerol (DAG), and lysophosphatidylcholine
(LPC) lipids were also included, with all the LPC in the inner leaflet,
and CER and DAG primarily in the outer leaflet. The details of the
Martini lipids used in this study can be found on the Martini Lipidome
webpage (http://www.cgmartini.nl/index.php/force-field-parameters/lipids ) and are described by Ingolfsson et al., and Wassenaar et al.20 (link),106 (link) The exact lipid composition of each system is given in the Supporting Information . The systems are ca. 42
× 42 nm in the membrane plane (x and y), including 4 proteins and ca. 6000 lipids.
Production
runs were performed in the presence of weak position
restraints applied to the protein backbone beads, with a force constant
of 1 kJ mol–1 nm–2, preventing
proteins from associating with each other. Each of the systems has
been simulated for 30 μs, which turned out to be adequate to
obtain convergence of major lipid components in the lipid shells around
the individual copies of the proteins (Supporting Information ). Additional control simulations were performed
in the AQP1 system, in order to test the effects of simulation length,
position restraints on the proteins, lipid composition, and water
model on the results of lipid composition near the proteins (Supporting Information ).
Simulations were
performed using the GROMACS simulation package
version 4.6.3,107 (link) with the Martini v2.2
force field parameters,62 (link),63 (link) and standard simulation
settings.108 (link) Additional details are provided
inSupporting Information . All the analyses
were performed on the last 5 μs of each simulation system.
a previously characterized model of the plasma membrane.20 (link) The starting structures of the 10 membrane proteins
simulated in this study were taken from the Protein Data Bank or obtained
from the corresponding publication: aquaporin-1 (AQP1, PDB ID 1J4N);98 (link) prostaglandin H2 synthase (COX1, PDB ID 1Q4G);99 (link) the dopamine transporter (DAT, PDB ID 4M48);44 (link) the epidermal growth factor receptor (EGFR);77 (link) AMPA-sensitive glutamate receptor 2 (GluA2,
PDB ID 3KG2);100 (link) glucose transporter 1 (GluT1, PDB ID 4PYP);101 (link) voltage-dependent Shaker potassium channel 1.2 (Kv1.2,
PDB ID 3LUT,102 (link) residues 32 to 4421 for each monomer); sodium,
potassium pump (Na,K-ATPase, PDB ID 4HYT);103 (link) δ-opioid
receptor (δ-OPR, PDB ID 4N6H);104 (link) and P-glycoprotein
(P-gp, PDB ID 4M1M).105 (link) In each system, four copies of each
protein were included and positioned at a distance of ca. 20 nm from
each other. Proteins were simulated using standard Martini protocols
with minor variations between systems to accommodate system-specific
issues (
lipid classes were included: cholesterol (CHOL), in both leaflets;
charged lipids phosphatidylserine (PS), phosphatidic acid (PA), phosphatidylinositol
(PI), and the PI-phosphate, PI-bisphosphate, and PI-trisphosphate
(PIPs) placed in the inner leaflet; and ganglioside (GM) in the outer
leaflet. The zwitterionic phosphatidylcholine (PC), phosphatidylethanolamine
(PE), and sphingomyelin (SM) lipids were placed in both leaflets,
with PC and SM primarily in the outer leaflet and PE in the inner
leaflet. Ceramide (CER), diacylglycerol (DAG), and lysophosphatidylcholine
(LPC) lipids were also included, with all the LPC in the inner leaflet,
and CER and DAG primarily in the outer leaflet. The details of the
Martini lipids used in this study can be found on the Martini Lipidome
webpage (
× 42 nm in the membrane plane (x and y), including 4 proteins and ca. 6000 lipids.
Production
runs were performed in the presence of weak position
restraints applied to the protein backbone beads, with a force constant
of 1 kJ mol–1 nm–2, preventing
proteins from associating with each other. Each of the systems has
been simulated for 30 μs, which turned out to be adequate to
obtain convergence of major lipid components in the lipid shells around
the individual copies of the proteins (
in the AQP1 system, in order to test the effects of simulation length,
position restraints on the proteins, lipid composition, and water
model on the results of lipid composition near the proteins (
Simulations were
performed using the GROMACS simulation package
version 4.6.3,107 (link) with the Martini v2.2
force field parameters,62 (link),63 (link) and standard simulation
settings.108 (link) Additional details are provided
in
were performed on the last 5 μs of each simulation system.