. Author manuscript; available in PMC: 2022 Jun 3.

Published in final edited form as: J Phys Chem B. 2021 May 20;125(21):5572–5586. doi: 10.1021/acs.jpcb.1c01795

Table 1.

Description of simulations.

Simulations	Lipid composition ^a)	Time	Ensemble	Replicas	Initial struct.
Bilayer membrane (100 ns structure referred to as BI0)	176 POPC + 74 DOPE + 20 SAPI	100 ns	NPT	1	CHARMM-GUI
Bilayer membrane (100 ns structure referred to as BIe)	176 POPC + 74 DOPE + 20 SAPI	100 ns	NPγT	1	From above sim.
Lipid droplet (1 μs structure referred to as LD0)	176 POPC + 74 DOPE + 20 SAPI + 429 TRIO	2 μs	NPT	1	From previous simulation³⁸
Lipid droplet (300 ns structure referred to as LDe)	176 POPC + 74 DOPE + 20 SAPI + 429 TRIO	2.3 μs	NPγT	1	From above sim.
BI0 production run	Same as BI0 or BIe	400 ns	NVT	1	BI0
BIe production run	Same as BI0 or BIe	400 ns	NVT	1	BIe
LD0 production run	Same as LD0 or LDe	2 μs	NVT	1	LD0
LDe production run	Same as LD0 or LDe	2.3 μs	NVT	1	LDe
CCTα folding PMF	N/A	100 ns ^b)	NVT	10 ^c)	CHARMM-GUI
CCTα binding PMF	Same as LD0 or LDe	162 ns ^b)	NVT	36	LDe
BI0 + CCTα	Same as BI0 or BIe	1 μs ^b)	NVT	14	BI0
BIe + CCTα	Same as BI0 or BIe	1 μs ^b)	NVT	13	BIe
LD0 + CCTα	Same as LD0 or LDe	1 μs ^b)	NVT	14	LD0
LDe + CCTα	Same as LD0 or LDe	1 μs ^b)	NVT	13	LDe
LDe + W278V	Same as LD0 or LDe	1 μs ^b)	NVT	13	LDe

^a)

The total number of lipid molecules of each type in a system.

^b)

Simulation time length for each replica or window.

^c)

The number of windows in the replica-exchange umbrella sampling simulation.