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mm:parameters:lipids:pc
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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 | ||
 |
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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
mm/parameters/lipids/pc.1375721993.txt.gz · Last modified: 2013/08/05 17:59 by joaocoimbra
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