Table 1.

Details of the LTPs tested in this study

LTPStructure sourceResiduesTarget
Membrane		Proposed mechanismLigand in crystal structureLipids tested in MD simulations
CPTP 4K8N (Simanshu et al., 2013) 8–214 Golgi, plasma membrane, endosome, nucleus Shuttle Ceramide-1-phosphate DOPA, DOPC, DPPA, DPSM, Chol, TO 
MlaC 5UWA (Ekiert et al., 2017) 24–208 Bacterial outer membrane, bacterial inner membrane Shuttle DOG DOPE, DOPS, DPPE, DPSM, Chol, TO 
PCTP 1lN1 (Roderick et al., 2002) 8–210 - Shuttle DLPC DOPC, DOPS, DPPC, DPSM, Chol, TO 
NF1 2E2X (Welti et al., 2007) 1,567–1,816 Plasma membrane,
nucleus, nucleolus 		Shuttle POPE DOPE, DOPC, DPPE, DPSM, Chol, TO 
PITP 1T27 (Yoder et al., 2001) 2–270 Nucleus Shuttle DOPC DOPC, DOPS, DPPC, DPSM, Chol, TO 
Sfh1 3B74 (Schaaf et al., 2008) 101–274 Nucleus Shuttle DOPE DOPE, DOPS, DPPE, DPSM, Chol, TO 
FABP1 1O8V (Jakobsson et al., 2003) 1–133  Shuttle Palmitic acid DOPE, OLAC 
Osh4 1ZHY (Im et al., 2005) 2–354 Golgi, ER Shuttle Chol Chol 
NPC2 5KWY (Li et al., 2016) 20–151 ER, lysosome Shuttle Chol sulfate DOPC, DPPC, DPSM, Chol, TO 
ApoM 2YG2 (Christoffersen et al., 2011) 38–188 - Shuttle S1P OLAC, DOPC, DPPC, DPSM, Chol, TO 
Miga2 8EDV (Hong et al., 2022) 307–567 Mitochondria Shuttle DPPE DOPE, OLAC, DPPE, DPSM, Chol, TO 
StARD11 2E3R (Kudo et al., 2008) 364–598 Golgi, ER Shuttle C18-Ceramide DOPA, DOPC, DPPC, DPSM, Chol, TO 
Osh6 4B2Z (Maeda et al., 2013) 1–434 Plasma membrane, ER Shuttle DSPS DOPC, DOPS 
FABP1 Δ6 1O8V 7–133 - - Palmitic acid DOPE, OLAC, DPPE, DPSM, Chol, TO 
Osh6-Δ69 4B2Z 69–434 - - DSPS DOPC, DOPS, DPPS, DPSM, Chol, TO 
Osh4-Δ29 1ZHY 30–354 - - Chol DOPC, DPPC, DPSM, Chol, TO 
JHBP 2RQF (Suzuki et al., 2011) 1–225 - - Juvenile hormone III DOPC, DOPS 
Takeout 3E8T (Hamiaux et al., 2009) 5–220 - - Ubiquinone-8 DOPC, DOPS 
Svf1 AF-Q05515-F1 1–481 Golgi, ER, nucleus ? - DOPC 
SNX25 AF-Q9H3E2-F1 1–840 Endosome ? - DOPC 
AsmA AF-P28249-F1 27–577 Plasma membrane ? - DOPC 
Mdm31 AF-P38880-F1 141–579 Mitochondrion ? - DOPC 
Lec1 AF-Q06839-F1 1–1,073 Mitochondrion ? - DOPC 
Nvj3 AF-Q03983-F1 71–463 Nucleus, vacuole, ER ? - DOPC 
Atg2 6A9J (Osawa et al., 2019) 2–379 ER, preautophagosomal membrane Bridge DOPE DOPE, DOPS 
Vps13 6CBC (Kumar et al., 2018) 1–329 Nucleus, vacuole, mitochondrion, endosome, peroxisome, prospore membrane Bridge - DOPC, DOPE 
E-Syt2 4P42 (Schauder et al., 2014) 191–370a Plasma membrane, ER Shuttle DOG, detergent DOPA, DOPC 
Atg2 AF-P53855-F1 1–1,344 ER, preautophagosomal membrane Bridge - DOPC 
Csf1 AF 1–2,958
Fragments:
1–1,000
1,001–2,000
2,001–2,958 		Plasma membrane, ER, mitochondrion Bridge - DOPC 
Vps13 AF 1–1,859
Fragments:
1–1,048
948–1,859 		Endosome, mitochondrion, prospore membrane, vacuole, nucleus, peroxisome, Golgi Bridge - DOPC 
LTPStructure sourceResiduesTarget
Membrane		Proposed mechanismLigand in crystal structureLipids tested in MD simulations
CPTP 4K8N (Simanshu et al., 2013) 8–214 Golgi, plasma membrane, endosome, nucleus Shuttle Ceramide-1-phosphate DOPA, DOPC, DPPA, DPSM, Chol, TO 
MlaC 5UWA (Ekiert et al., 2017) 24–208 Bacterial outer membrane, bacterial inner membrane Shuttle DOG DOPE, DOPS, DPPE, DPSM, Chol, TO 
PCTP 1lN1 (Roderick et al., 2002) 8–210 - Shuttle DLPC DOPC, DOPS, DPPC, DPSM, Chol, TO 
NF1 2E2X (Welti et al., 2007) 1,567–1,816 Plasma membrane,
nucleus, nucleolus 		Shuttle POPE DOPE, DOPC, DPPE, DPSM, Chol, TO 
PITP 1T27 (Yoder et al., 2001) 2–270 Nucleus Shuttle DOPC DOPC, DOPS, DPPC, DPSM, Chol, TO 
Sfh1 3B74 (Schaaf et al., 2008) 101–274 Nucleus Shuttle DOPE DOPE, DOPS, DPPE, DPSM, Chol, TO 
FABP1 1O8V (Jakobsson et al., 2003) 1–133  Shuttle Palmitic acid DOPE, OLAC 
Osh4 1ZHY (Im et al., 2005) 2–354 Golgi, ER Shuttle Chol Chol 
NPC2 5KWY (Li et al., 2016) 20–151 ER, lysosome Shuttle Chol sulfate DOPC, DPPC, DPSM, Chol, TO 
ApoM 2YG2 (Christoffersen et al., 2011) 38–188 - Shuttle S1P OLAC, DOPC, DPPC, DPSM, Chol, TO 
Miga2 8EDV (Hong et al., 2022) 307–567 Mitochondria Shuttle DPPE DOPE, OLAC, DPPE, DPSM, Chol, TO 
StARD11 2E3R (Kudo et al., 2008) 364–598 Golgi, ER Shuttle C18-Ceramide DOPA, DOPC, DPPC, DPSM, Chol, TO 
Osh6 4B2Z (Maeda et al., 2013) 1–434 Plasma membrane, ER Shuttle DSPS DOPC, DOPS 
FABP1 Δ6 1O8V 7–133 - - Palmitic acid DOPE, OLAC, DPPE, DPSM, Chol, TO 
Osh6-Δ69 4B2Z 69–434 - - DSPS DOPC, DOPS, DPPS, DPSM, Chol, TO 
Osh4-Δ29 1ZHY 30–354 - - Chol DOPC, DPPC, DPSM, Chol, TO 
JHBP 2RQF (Suzuki et al., 2011) 1–225 - - Juvenile hormone III DOPC, DOPS 
Takeout 3E8T (Hamiaux et al., 2009) 5–220 - - Ubiquinone-8 DOPC, DOPS 
Svf1 AF-Q05515-F1 1–481 Golgi, ER, nucleus ? - DOPC 
SNX25 AF-Q9H3E2-F1 1–840 Endosome ? - DOPC 
AsmA AF-P28249-F1 27–577 Plasma membrane ? - DOPC 
Mdm31 AF-P38880-F1 141–579 Mitochondrion ? - DOPC 
Lec1 AF-Q06839-F1 1–1,073 Mitochondrion ? - DOPC 
Nvj3 AF-Q03983-F1 71–463 Nucleus, vacuole, ER ? - DOPC 
Atg2 6A9J (Osawa et al., 2019) 2–379 ER, preautophagosomal membrane Bridge DOPE DOPE, DOPS 
Vps13 6CBC (Kumar et al., 2018) 1–329 Nucleus, vacuole, mitochondrion, endosome, peroxisome, prospore membrane Bridge - DOPC, DOPE 
E-Syt2 4P42 (Schauder et al., 2014) 191–370a Plasma membrane, ER Shuttle DOG, detergent DOPA, DOPC 
Atg2 AF-P53855-F1 1–1,344 ER, preautophagosomal membrane Bridge - DOPC 
Csf1 AF 1–2,958
Fragments:
1–1,000
1,001–2,000
2,001–2,958 		Plasma membrane, ER, mitochondrion Bridge - DOPC 
Vps13 AF 1–1,859
Fragments:
1–1,048
948–1,859 		Endosome, mitochondrion, prospore membrane, vacuole, nucleus, peroxisome, Golgi Bridge - DOPC 

Abbreviations: Chol, cholesterol; OLAC, oleic acid; DOG, dioleyl-glycerol; DLPC, dilauroyl-phosphatidylcholine; POPE, 1-Palmitoyl-2-oleoyl-phosphatidylethanolamine; DSPS, distearoyl-phosphatidylserine; S1P, sphingosine 1-phosphate. The four-letter structure IDs are from the RCSB PDB while the ones starting with "AF" are from AlphaFold.

a

Both chains A and B of the LTP were considered for the simulation.

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