mm:parameters:lipids:dplc_example_page
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mm:parameters:lipids:dplc_example_page [2013/07/30 18:44] joaocoimbra [DPPC] |
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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?70 }} | 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?70 }} | Name | //1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine// ||| | ||
| - | | ::: | 4-Letter code | POPC ||| | ||
| - | | ::: | sn<sub>1</sub>-sn<sub>2</sub> composition | 16:0/18:1(Δ<sup>9</sup>) ||| | ||
| - | | ::: | parameter files | {{ 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?70 }} | Name | //1-palmitoyl-2-linoleoyl-sn-glycero-phosphocholine// || | ||
| - | | ::: | 4-Letter code | PLPC || | ||
| - | | ::: | sn<sub>1</sub>-sn<sub>2</sub> composition | 16:0/18:2(Δ<sup>9,12</sup>) || | ||
| - | | ::: | parameter files | {{ 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.1375206261.txt.gz · Last modified: 2013/07/30 18:44 by joaocoimbra
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