Table of Contents

Phosphatidylcholines (PC)

For each phospholipid, its name, 4-letter code, composition of aliphatic chains (sn1/sn2), and parameter files are presented. In addition, the values for volume per lipid (VL), area per lipid (AL), and bilayer thickness (DHH) in a bilayer setting are given, together with experimental data (when available). For the DOPC phospholipid, order parameters for the acyl chains are displayed and compared with experiment. These parameters were obtained under the General Amber Force Field (GAFF) terminology and general parameters.


DOPC

1,2-dioleoyl-sn-glycero-3-phosphocholine

Name 1,2-dioleoyl-sn-glycero-3-phosphocholine
4-Letter code DOPC
sn1-sn2 18:1(Δ9)/18:1(Δ9)
parameters frcmod prepc [Coimbra, 2013]
Validation
Value MD ± σ / Å Experimental / Å Reference
VL 1292 ± 2 1303 Nagle, 2000
Kučerka, 2005
Kučerka, 2008
AL 66 ± 1.2 72.5, 72.4, 67.4
DHH 39 ± 0.3 36.9, 36.7

DLPC

1,2-dilauroyl-sn-glycero-3-phosphocholine

Name 1,2-dilauroyl-sn-glycero-3-phosphocholine
4-Letter code DLPC
sn1-sn2 12:0/12:0
parameters frcmod prepc [Coimbra, 2013]
Validation
Value MD ± σ / Å Experimental / Å Reference
VL 927 ± 2 991 Kučerka, 2005
AL 45 ± 0.8 63.2, 60.8
DHH 39 ± 0.2 30.8

DMPC

1,2-dimyristoyl-sn-glycero-3-phosphocholine

Name 1,2-dimyristoyl-sn-glycero-3-phosphocholine
4-Letter code DMPC
sn1-sn2 14:0/14:0
parameters frcmod prepc [Coimbra, 2013]
Validation
Value MD ± σ / Å Experimental / Å Reference
VL 1023 ± 2 1101 Nagle, 2000
Kučerka, 2005
Kučerka, 2011
AL 53 ± 0.8 59.6, 59.9, 60.6
DHH 38 ± 0.2 36.0, 35.3

DPPC

1,2-dipalmitoyl-sn-glycero-3-phosphocholine

Name 1,2-dipalmitoyl-sn-glycero-3-phosphocholine
4-Letter code DPPC
sn1-sn2 16:0/16:0
parameters frcmod prepc [Coimbra, 2013]
Validation
Value MD ± σ / Å Experimental / Å Reference
VL 1123 ± 2 1232, 1229, 1144 Nagle, 2000
Kučerka, 2008
AL 51 ± 0.7 64.0, 63.1, 47.9
DHH 44 ± 0.2 38.0, 38.3, 44.2

POPC

1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine

Name 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine
4-Letter code POPC
sn1-sn2 16:0/18:1(Δ9)
parameters frcmod prepc [Coimbra, 2013]
Validation
Value MD ± σ / Å Experimental / Å Reference
VL 1224 ± 2 1256 Kučerka, 2005
AL 52 ± 1.0 68.3, 64.3
DHH 46 ± 0.3 37.0

PLPC

1-palmitoyl-2-linoleoyl-sn-glycero-phosphocholine

Name 1-palmitoyl-2-linoleoyl-sn-glycero-phosphocholine
4-Letter code PLPC
sn1-sn2 16:0/18:2(Δ9,12)
parameters frcmod prepc [Coimbra, 2013]
Validation
Value MD ± σ / Å
VL 1226 ± 3
AL 55 ± 1.2
DHH 44 ± 0.4

References

Coimbra, J.T.S.; Sousa, S.F.; Fernandes, P.A.; Rangel, M.; Ramos, M.J.. Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless ensemble . J. Biomol. Struct. Dyn., 2013