Table 1. Details of the LTPs tested in... | Rockefeller University Press

Table 1.

Details of the LTPs tested in this study

LTP	Structure source	Residues	Target Membrane	Proposed mechanism	Ligand in crystal structure	Lipids 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)	191–370^{^a}	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

LTP	Structure source	Residues	TargetMembrane	Proposed mechanism	Ligand in crystal structure	Lipids 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)	191–370^a	Plasma membrane, ER	Shuttle	DOG, detergent	DOPA, DOPC
Atg2	AF-P53855-F1	1–1,344	ER, preautophagosomal membrane	Bridge	-	DOPC
Csf1	AF	1–2,958Fragments:1–1,0001,001–2,0002,001–2,958	Plasma membrane, ER, mitochondrion	Bridge	-	DOPC
Vps13	AF	1–1,859Fragments:1–1,048948–1,859	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.

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

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