mm:parameters:lipids:dplc_example_page
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mm:parameters:lipids:dplc_example_page [2013/07/30 18:46] joaocoimbra [PLPC] |
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| - | ====== Phospholipids ====== | ||
| - | The following charge parameters for 12 distinct phospholipids were determined, following an AMBER compatible approach. These parameters were validated by building a bilayer system for each phospholipid type and by comparing structural and dynamical values with experimental data available. When considering the DOPC phospholipid a good correlation with experimental available data was obtained. For each phospholipid, its name, 4-letter code, composition of aliphatic chains (sn<sub>1</sub>/sn<sub>2</sub>), and parameter files are presented. In addition, the values for volume per lipid (V<sub>L</sub>), area per lipid (A<sub>L</sub>), and bilayer thickness (D<sub>HH</sub>) 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. | ||
| - | |||
| - | {{ mm:parameters:lipids:docmem.png?200 }} | ||
| - | |||
| - | ---- | ||
| - | |||
| - | |||
| - | ===== Phosphatidylcholines (PC) ===== | ||
| - | |||
| - | |||
| - | ==== DOPC ==== | ||
| - | //1,2-dioleoyl-sn-glycero-3-phosphocholine// | ||
| - | |||
| - | | {{ mm:parameters:lipids:dopc.png?60 }} | Name | //1,2-dioleoyl-sn-glycero-3-phosphocholine// ||| | ||
| - | | ::: | 4-Letter code | DOPC ||| | ||
| - | | ::: | sn<sub>1</sub>-sn<sub>2</sub> | 18:1(Δ<sup>9</sup>)/18:1(Δ<sup>9</sup>) ||| | ||
| - | | ::: | parameters | {{ mm:parameters:lipids:doc_frcmod.zip | frcmod }} {{ mm:parameters:lipids:doc_prepc.zip | prepc }} || [[#references | [Coimbra, 2013]]] | | ||
| - | | ::: | **Validation** |||| | ||
| - | | ::: | //Value// | //MD ± σ / Å// | //Experimental / Å// | //Reference (Exp.)// | | ||
| - | | ::: | //V<sub>L</sub>// | 1292 ± 2 | 1303 | [[http://www.ncbi.nlm.nih.gov/pubmed/11063882|Nagle, 2000]] [[http://www.ncbi.nlm.nih.gov/pubmed/16604469|Kučerka, 2005]] [[http://www.cell.com/biophysj/abstract/S0006-3495(08)78383-8|, 2008]] | | ||
| - | | ::: | //A<sub>L</sub>// | 66 ± 1.2 | 72.5, 72.4, 67.4 | ::: | | ||
| - | | ::: | //D<sub>HH</sub>// | 39 ± 0.3 | 36.9, 36.7 | ::: | | ||
| - | | {{ mm:parameters:lipids:scd_doc.png?450 }} ||||| | ||
| - | |||
| - | ==== DLPC ==== | ||
| - | //1,2-dilauroyl-sn-glycero-3-phosphocholine// | ||
| - | |||
| - | | {{ mm:parameters:lipids:dlpc.png?70 }} | Name | //1,2-dilauroyl-sn-glycero-3-phosphocholine// ||| | ||
| - | | ::: | 4-Letter code | DLPC ||| | ||
| - | | ::: | sn<sub>1</sub>-sn<sub>2</sub> | 12:0/12:0 ||| | ||
| - | | ::: | parameters | {{ mm:parameters:lipids:dlc_frcmod.zip | frcmod }} {{ mm:parameters:lipids:dlc_prepc.zip | prepc }} || [[#references | [Coimbra, 2013]]] | | ||
| - | | ::: | **Validation** |||| | ||
| - | | ::: | //Value// | //MD ± σ / Å// | //Experimental / Å// | //Reference (Exp.)// | | ||
| - | | ::: | //V<sub>L</sub>// | 927 ± 2 | 991 | [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305359/|Kučerka, 2005]] | | ||
| - | | ::: | //A<sub>L</sub>// | 45 ± 0.8 | 63.2, 60.8 | ::: | | ||
| - | | ::: | //D<sub>HH</sub>// | 39 ± 0.2 | 30.8 | ::: | | ||
| - | |||
| - | |||
| - | ==== DMPC ==== | ||
| - | //1,2-dimyristoyl-sn-glycero-3-phosphocholine// | ||
| - | |||
| - | | {{ mm:parameters:lipids:dmpc.png?70 }} | Name | //1,2-dimyristoyl-sn-glycero-3-phosphocholine// ||| | ||
| - | | ::: | 4-Letter code | DMPC ||| | ||
| - | | ::: | sn<sub>1</sub>-sn<sub>2</sub> | 14:0/14:0 ||| | ||
| - | | ::: | parameters | {{ mm:parameters:lipids:dmc_frcmod.zip | frcmod }} {{ mm:parameters:lipids:dmc_prepc.zip | prepc }} || [[#references | [Coimbra, 2013]]] | | ||
| - | | ::: | **Validation** |||| | ||
| - | | ::: | //Value// | //MD ± σ / Å// | //Experimental / Å// | //Reference (Exp.)// | | ||
| - | | ::: | //V<sub>L</sub>// | 1023 ± 2 | 1101 | [[http://www.ncbi.nlm.nih.gov/pubmed/11063882|Nagle, 2000]] [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305359/|Kučerka, 2005]] [[http://www.ncbi.nlm.nih.gov/pubmed/21819968|, 2011]] | | ||
| - | | ::: | //A<sub>L</sub>// | 53 ± 0.8 | 59.6, 59.9, 60.6 | ::: | | ||
| - | | ::: | //D<sub>HH</sub>// | 38 ± 0.2 | 36.0, 35.3 | ::: | | ||
| - | |||
| - | |||
| - | ==== DPPC ==== | ||
| - | //1,2-dipalmitoyl-sn-glycero-3-phosphocholine// | ||
| - | |||
| - | | {{ mm:parameters:lipids:dppc.png?65 }} | Name | //1,2-dipalmitoyl-sn-glycero-3-phosphocholine// ||| | ||
| - | | ::: | 4-Letter code | DPPC ||| | ||
| - | | ::: | sn<sub>1</sub>-sn<sub>2</sub> | 16:0/16:0 ||| | ||
| - | | ::: | parameters | {{ mm:parameters:lipids:dpc_frcmod.zip | frcmod }} {{ mm:parameters:lipids:dpc_prepc.zip | prepc }} || [[#references | [Coimbra, 2013]]] | | ||
| - | | ::: | **Validation** |||| | ||
| - | | ::: | //Value// | //MD ± σ / Å// | //Experimental / Å// | //Reference (Exp.)// | | ||
| - | | ::: | //V<sub>L</sub>// | 1123 ± 2 | 1232, 1229, 1144 | [[http://www.ncbi.nlm.nih.gov/pubmed/11063882|Nagle, 2000]] [[http://www.cell.com/biophysj/abstract/S0006-3495(08)78383-8|Kučerka, 2008]] | | ||
| - | | ::: | //A<sub>L</sub>// | 51 ± 0.7 | 64.0, 63.1, 47.9 | ::: | | ||
| - | | ::: | //D<sub>HH</sub>// | 44 ± 0.2 | 38.0, 38.3, 44.2 | ::: | | ||
| - | |||
| - | |||
| - | ==== POPC ==== | ||
| - | //1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine// | ||
| - | |||
| - | | {{ mm:parameters:lipids:popc.png?60 }} | Name | //1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine// ||| | ||
| - | | ::: | 4-Letter code | POPC ||| | ||
| - | | ::: | sn<sub>1</sub>-sn<sub>2</sub> | 16:0/18:1(Δ<sup>9</sup>) ||| | ||
| - | | ::: | parameters | {{ mm:parameters:lipids:poc_frcmod.zip | frcmod }} {{ mm:parameters:lipids:poc_prepc.zip | prepc }} || [[#references | [Coimbra, 2013]]] | | ||
| - | | ::: | **Validation** |||| | ||
| - | | ::: | //Value// | //MD ± σ / Å// | //Experimental / Å// | //Reference (Exp.)// | | ||
| - | | ::: | //V<sub>L</sub>// | 1224 ± 2 | 1256 | [[http://www.ncbi.nlm.nih.gov/pubmed/16604469|Kučerka, 2005]] | | ||
| - | | ::: | //A<sub>L</sub>// | 52 ± 1.0 | 68.3, 64.3 | ::: | | ||
| - | | ::: | //D<sub>HH</sub>// | 46 ± 0.3 | 37.0 | ::: | | ||
| - | |||
| - | |||
| - | ==== PLPC ==== | ||
| - | //1-palmitoyl-2-linoleoyl-sn-glycero-phosphocholine// | ||
| - | |||
| - | | {{ mm:parameters:lipids:plpc.png?60 }} | Name | //1-palmitoyl-2-linoleoyl-sn-glycero-phosphocholine// || | ||
| - | | ::: | 4-Letter code | PLPC || | ||
| - | | ::: | sn<sub>1</sub>-sn<sub>2</sub> | 16:0/18:2(Δ<sup>9,12</sup>) || | ||
| - | | ::: | parameters | {{ mm:parameters:lipids:plc_frcmod.zip | frcmod }} {{ mm:parameters:lipids:plc_prepc.zip | prepc }} | [[#references | [Coimbra, 2013]]] | | ||
| - | | ::: | **Validation** ||| | ||
| - | | ::: | //Value// | //MD ± σ / Å// || | ||
| - | | ::: | //V<sub>L</sub>// | 1226 ± 3 || | ||
| - | | ::: | //A<sub>L</sub>// | 55 ± 1.2 || | ||
| - | | ::: | //D<sub>HH</sub>// | 44 ± 0.4 || | ||
| - | |||
| - | |||
| - | ===== Phosphatidylethanolamines (PE) ===== | ||
| - | |||
| - | |||
| - | ==== DLPE ==== | ||
| - | //1,2-dilauroyl-sn-glycero-3-phosphoethanolamine// | ||
| - | |||
| - | | {{ mm:parameters:lipids:dlpe.png?70 }} | Name | //1,2-dilauroyl-sn-glycero-3-phosphoethanolamine// ||| | ||
| - | | ::: | 4-Letter code | DLPE ||| | ||
| - | | ::: | sn<sub>1</sub>-sn<sub>2</sub> composition | 12:0/12:0 ||| | ||
| - | | ::: | parameter files | {{ mm:parameters:lipids:dle_frcmod.zip | frcmod }} {{ mm:parameters:lipids:dle_prepc.zip | prepc }} || [[#references | [Coimbra, 2013]]] | | ||
| - | | ::: | **Validation** |||| | ||
| - | | ::: | Value | MD ± σ / Å | Experimental / Å | Reference (Exp.) | | ||
| - | | ::: | V<sub>L</sub> | 854 ± 2 | 907, 863 | [[http://www.ncbi.nlm.nih.gov/pubmed/11063882|Nagle 2000]] [[http://www.ncbi.nlm.nih.gov/pubmed/3768325|McIntosh 1986]] | | ||
| - | | ::: | A<sub>L</sub> | 40 ± 0.4 | 51.2, 41.0 | ::: | | ||
| - | | ::: | D<sub>HH</sub> | 40 ± 0.1 | 35.6, 33.0, 39.8 | ::: | | ||
| - | |||
| - | |||
| - | ==== DMPE ==== | ||
| - | //1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine// | ||
| - | |||
| - | | {{ mm:parameters:lipids:dmpe.png?70 }} | Name | //1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine// ||| | ||
| - | | ::: | 4-Letter code | DMPE ||| | ||
| - | | ::: | sn<sub>1</sub>-sn<sub>2</sub> composition | 14:0/14:0 ||| | ||
| - | | ::: | parameter files | {{ mm:parameters:lipids:dme_frcmod.zip | frcmod }} {{ mm:parameters:lipids:dme_prepc.zip | prepc }} || [[#references | [Coimbra, 2013]]] | | ||
| - | | ::: | **Validation** |||| | ||
| - | | ::: | Value | MD ± σ / Å ||| | ||
| - | | ::: | V<sub>L</sub> | 961 ± 2 ||| | ||
| - | | ::: | A<sub>L</sub> | 44 ± 0.7 ||| | ||
| - | | ::: | D<sub>HH</sub> | 42 ± 0.1 ||| | ||
| - | |||
| - | |||
| - | ==== DPPE ==== | ||
| - | //1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine// | ||
| - | |||
| - | | {{ mm:parameters:lipids:dppe.png?70 }} | Name | //1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine// ||| | ||
| - | | ::: | 4-Letter code | DPPE ||| | ||
| - | | ::: | sn<sub>1</sub>-sn<sub>2</sub> composition | 16:0/16:0 ||| | ||
| - | | ::: | parameter files | {{ mm:parameters:lipids:dpe_frcmod.zip | frcmod }} {{ mm:parameters:lipids:dpe_prepc.zip | prepc }} || [[#references | [Coimbra, 2013]]] | | ||
| - | | ::: | **Validation** |||| | ||
| - | | ::: | Value | MD ± σ / Å ||| | ||
| - | | ::: | V<sub>L</sub> | 1066 ± 3 ||| | ||
| - | | ::: | A<sub>L</sub> | 44 ± 0.5 ||| | ||
| - | | ::: | D<sub>HH</sub> | 47 ± 0.3 ||| | ||
| - | |||
| - | |||
| - | ==== DSPE ==== | ||
| - | //1,2-distearoyl-sn-glycero-3-phosphoethanolamine// | ||
| - | |||
| - | | {{ mm:parameters:lipids:dspe.png?70 }} | Name | //1,2-distearoyl-sn-glycero-3-phosphoethanolamine// ||| | ||
| - | | ::: | 4-Letter code | DSPE ||| | ||
| - | | ::: | sn<sub>1</sub>-sn<sub>2</sub> composition | 18:0/18:0 ||| | ||
| - | | ::: | parameter files | {{ mm:parameters:lipids:dse_frcmod.zip | frcmod }} {{ mm:parameters:lipids:dse_prepc.zip | prepc }} || [[#references | [Coimbra, 2013]]] | | ||
| - | | ::: | **Validation** |||| | ||
| - | | ::: | Value | MD ± σ / Å ||| | ||
| - | | ::: | V<sub>L</sub> | 1162 ± 3 ||| | ||
| - | | ::: | A<sub>L</sub> | 43 ± 0.3 ||| | ||
| - | | ::: | D<sub>HH</sub> | 52 ± 0.2 ||| | ||
| - | |||
| - | |||
| - | ==== POPE ==== | ||
| - | //1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine// | ||
| - | |||
| - | | {{ mm:parameters:lipids:pope.png?70 }} | Name | //1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine// ||| | ||
| - | | ::: | 4-Letter code | POPE ||| | ||
| - | | ::: | sn<sub>1</sub>-sn<sub>2</sub> composition | 16:0/18:1(Δ<sup>9</sup>) ||| | ||
| - | | ::: | parameter files | {{ mm:parameters:lipids:poe_frcmod.zip | frcmod }} {{ mm:parameters:lipids:poe_prepc.zip | prepc }} || [[#references | [Coimbra, 2013]]] | | ||
| - | | ::: | **Validation** |||| | ||
| - | | ::: | Value | MD ± σ / Å | Experimental / Å | Reference (Exp.) | | ||
| - | | ::: | V<sub>L</sub> | 1149 ± 3 | 1185 | [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1302872/|Rappolt 2003]] | | ||
| - | | ::: | A<sub>L</sub> | 46 ± 0.6 | 61.0 | ::: | | ||
| - | | ::: | D<sub>HH</sub> | 48 ± 0.3 | 39.0 | ::: | | ||
| - | |||
| - | |||
| - | ==== PLPE ==== | ||
| - | //1-palmitoyl-2-linoleoyl-sn-glycero-phosphoethanolamine// | ||
| - | |||
| - | | {{ mm:parameters:lipids:plpe.png?70 }} | Name | //1-palmitoyl-2-linoleoyl-sn-glycero-phosphoethanolamine// || | ||
| - | | ::: | 4-Letter code | PLPE || | ||
| - | | ::: | sn<sub>1</sub>-sn<sub>2</sub> composition | 16:0/18:2(Δ<sup>9,12</sup>) || | ||
| - | | ::: | parameter files | {{ mm:parameters:lipids:ple_frcmod.zip | frcmod }} {{ mm:parameters:lipids:ple_prepc.zip | prepc }} | [[#references | [Coimbra, 2013]]] | | ||
| - | | ::: | **Validation** ||| | ||
| - | | ::: | Value | MD ± σ / Å || | ||
| - | | ::: | V<sub>L</sub> | 1152 ± 2 || | ||
| - | | ::: | A<sub>L</sub> | 48 ± 0.5 || | ||
| - | | ::: | D<sub>HH</sub> | 46 ± 0.3 || | ||
| - | |||
| - | |||
| - | ===== References ===== | ||
| - | Coimbra, J.T.S.; Sousa, S.F.; Fernandes, P.A.; Rangel, M.; Ramos, M.J.. [[http://www.tandfonline.com/doi/abs/10.1080/07391102.2012.750250?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed#.UfAXYY1wrt4 | Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless | ||
| - | ensemble]] . //J. Biomol. Struct. Dyn.//, **2013** | ||
mm/parameters/lipids/dplc_example_page.1375206391.txt.gz · Last modified: 2013/07/30 18:46 by joaocoimbra
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