Table 1. Peripheral Proteins Tested and CG Simulation Detailsf.
protein | PDB id | bilayer composition | test type | force field | starting configuration | simulation length (ns) | no. of simulations | total time (ns) |
---|---|---|---|---|---|---|---|---|
BtPI-PLC | 3EA1/2OR2 | DMPC | MBTa | 2.2P | MBOc | 500 | 5 | 2500 |
MDTb | 2.2P | MBSd | 500 | 5 | 2500 | |||
MBT | 2.3P | MBO | 500 | 5 | 2500 | |||
MBT | 2.3P | ROe | 1000 | 5 | 5000 | |||
PH domain (PLC-δ1) | 1MAI | POPC/POPS/PIP2/PIP3 (73:20:5:2) | MBT | 2.2P | RO | 1000 | 1 | 1000 |
MBT | 2.3P | RO | 1000 | 1 | 1000 | |||
PR3 | 1FUJ | POPC | MBT | 2.2P | MBO | 1000 | 1 | 1000 |
MBT | 2.3P | MBO | 1000 | 1 | 1000 | |||
Equinatoxin | 1IAZ | POPC | MBT | 2.2P | MBO | 500 | 1 | 500 |
MBT | 2.3P | MBO | 500 | 1 | 500 | |||
PLA2 | 1POA | DMPC | MBT | 2.2P | RO | 1000 | 1 | 1000 |
MBT | 2.3P | RO | 1000 | 1 | 1000 | |||
PC-specific SaPI-PLC | 4I8Y | POPC | MBT | 2.2P | RO | 1000 | 1 | 1000 |
MBT | 2.3P | RO | 1000 | 1 | 1000 | |||
WT SaPI-PLC | 4F2T | POPC | MBT | 2.3P | RO | 500 | 2 | 1000 |
GLTP | 1WBE | POPC | MBT | 2.2P | RO | 400 + 362 | 2 | 762 |
MBT | 2.3P | RO and MBO | 500 | 2 | 1000 |
MBT: membrane binding test.
MDT: membrane detachment test.
MBO: membrane-binding orientation.
MBS: membrane-bound structure.
RO: randomized orientation.
Tests with other interaction levels are reported in Table S1 and are not included here.