mm:parameters:lipids:example_page
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mm:parameters:lipids:example_page [2013/07/24 18:55] ruineves created |
mm:parameters:lipids:example_page [2013/07/25 19:24] (current) joaocoimbra |
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| - | ====== 1,2-Dilauroyl-//sn//-glycero-3-phosphocholine - **DLPC **====== | + | ====== Phospholipids ====== |
| - | The avian viral S integrase shows preference by manganese(II) over magnesium. In both cases the metal atom is bonded to two aspartates and four water molecules. | + | 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. Some validation results are displayed at the end of the page, and for the DOPC phospholipid a good correlation with experimental available data was obtained. |
| - | | **Coordination Sphere** | **Oxidation state:** Mn(II) \\ **Spin multiplicity:** 6 | | ||
| - | | {{ :mm:parameters:manganese:non-parameterized_ddwwww_.png?200 |}} | {{ :mm:parameters:manganese:octahedral_highspin_d5.png?400|}} ((The schemes represent geometrical dispositions for crystal lattices. These should be roughly similar to the corresponding distorted geometries in enzymatic coordination spheres.)) | | ||
| + | ==== DLPC ==== | ||
| + | //1,2-dilauroyl-sn-glycero-3-phosphocholine// | ||
| - | ---- | + | | {{ LINK PARA A IMAGEM }} | 1,2-dilauroyl-sn-glycero-3-phosphocholine | |
| + | | ::: | 12:0/12:0 | | ||
| + | | ::: | frcmod, prepc | | ||
| + | | ::: | Reference | | ||
| - | ===== Structure chosen to parameterize ===== | ||
| - | | **TEST PROTEIN** || | + | ==== DMPC ==== |
| - | | //Protein// | Integrase | | + | //1,2-dimyristoyl-sn-glycero-3-phosphocholine// |
| - | | //PDB Code// | 1A5V | | + | |
| - | | //Crystallographic Resolution// | 1.90 | | + | |
| - | | //Organism// | Rous Sarcoma Virus | | + | |
| - | | [[http://www.pnas.org/content/95/9/4831.long | [Lubkowski, 1998]]] || | + | |
| + | | {{ LINK PARA A IMAGEM }} | 1,2-dimyristoyl-sn-glycero-3-phosphocholine | | ||
| + | | ::: | 14:0/14:0 | | ||
| + | | ::: | frcmod, prepc | | ||
| + | | ::: | Reference | | ||
| - | ===== Parameters Determined ===== | ||
| - | ==== Atom Types ==== | + | ==== DPPC ==== |
| + | //1,2-dipalmitoyl-sn-glycero-3-phosphocholine// | ||
| - | | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | + | | {{ LINK PARA A IMAGEM }} | 1,2-dipalmitoyl-sn-glycero-3-phosphocholine | |
| - | | MN | M1 | 54.938 | {{ :mm:parameters:manganese:parameterized_ddwwww_.png?120 |}} | | + | | ::: | 16:0/16:0 | |
| - | | OD1 | D1 | 15.9994 | ::: | | + | | ::: | frcmod, prepc | |
| - | | OD2 | D2 | 15.9994 | ::: | | + | | ::: | Reference | |
| - | | OW | W1 | 15.9994 | ::: | | + | |
| - | | OW | W2 | 15.9994 | ::: | | + | |
| - | | OW | W3 | 15.9994 | ::: | | + | |
| - | | OW | W4 | 15.9994 | ::: | | + | |
| - | | HW | HM | 1.00794 | ::: | | + | |
| - | ==== Bond Parameters ==== | + | ====== 1,2-dioleoyl-sn-glycero-3-phosphocholine - DOPC ====== |
| - | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>** | **l / Å** | **REFERENCE** | | ||
| - | | M1-D1 | 86.69 | 2.0912 | [[#references | [Neves, 2013]]] | | ||
| - | | M1-D2 | 73.44 | 2.1278 | ::: | | ||
| - | | M1-W1 | 41.1 | 2.2458 | ::: | | ||
| - | | M1-W2 | 58.63 | 2.1786 | ::: | | ||
| - | | M1-W3 | 34.55 | 2.3171 | ::: | | ||
| - | | M1-W4 | 25.05 | 2.3835 | ::: | | ||
| - | | D1-C | 656 | 1.25 | | ||
| - | | D2-C | 656 | 1.25 | | ||
| - | | W1-HM | 553 | 0.9572 | | ||
| - | | W2-HM | 553 | 0.9572 | | ||
| - | | W3-HM | 553 | 0.9572 | | ||
| - | | W4-HM | 553 | 0.9572 | | ||
| + | | {{ LINK PARA A IMAGEM }} | DOPC | | ||
| + | | ::: | CONTEUDO2 | | ||
| + | | ::: | CONTEUDO3 | | ||
| - | ==== Angles Parameters ==== | + | ====== 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine - POPC ====== |
| - | | **ANGLE** | **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>** | **θ / deg** | **REFERENCE** | | ||
| - | | D1-M1-D2 | 38.782 | 108.3864 | [[#references | [Neves, 2013]]] | | ||
| - | | D1-M1-W1 | 52.48 | 86.0095 | ::: | | ||
| - | | D1-M1-W2 | 40.523 | 93.9632 | ::: | | ||
| - | | D1-M1-W3 | 14.18 | 90.4522 | ::: | | ||
| - | | D1-M1-W4 | 22.791 | 173.2496 | ::: | | ||
| - | | D2-M1-W1 | 26.46 | 97.5246 | ::: | | ||
| - | | D2-M1-W2 | 55.17 | 91.2115 | ::: | | ||
| - | | D2-M1-W3 | 14.57 | 157.0825 | ::: | | ||
| - | | D2-M1-W4 | 49.51 | 85.9497 | ::: | | ||
| - | | W1-M1-W2 | 22.81 | 165.2888 | ::: | | ||
| - | | W1-M1-W3 | 21.4 | 75.017 | ::: | | ||
| - | | W1-M1-W4 | 30.33 | 100.0581 | ::: | | ||
| - | | W2-M1-W3 | 16.61 | 92.3995 | ::: | | ||
| - | | W2-M1-W4 | 21.06 | 84.0447 | ::: | | ||
| - | | W3-M1-W4 | 16.8 | 84.2736 | ::: | | ||
| - | | M1-D1-C | 52.071 | 128.7239 | ::: | | ||
| - | | M1-D2-C | 46.53 | 125.6353 | ::: | | ||
| - | | M1-W1-HM | 24.91 | 107.2734 | ::: | | ||
| - | | M1-W2-HM | 24.17 | 105.0104 | ::: | | ||
| - | | M1-W3-HM | 7.36 | 101.1843 | ::: | | ||
| - | | M1-W4-HM | 7.764 | 101.9263 | ::: | | ||
| - | | HM-W1-HM | 100 | 104.52 | | ||
| - | | HM-W2-HM | 100 | 104.52 | | ||
| - | | HM-W3-HM | 100 | 104.52 | | ||
| - | | HM-W4-HM | 100 | 104.52 | | ||
| - | | D1-C-CT | 70 | 117 | | ||
| - | | D1-C-O2 | 80 | 126 | | ||
| - | | D2-C-CT | 70 | 117 | | ||
| - | | D2-C-O2 | 80 | 126 | | ||
| - | ==== Van der Waals Parameters ==== | + | | {{ LINK PARA A IMAGEM }} | POPC | |
| + | | ::: | CONTEUDO2 | | ||
| + | | ::: | CONTEUDO3 | | ||
| - | | **ATOM TYPE** | **R<sub>i</sub> / Å** | **ε<sub>i</sub> / kcal mol<sup>-1</sup>** | **REFERENCE** | | + | ====== 1-palmitoyl-2-linoleoyl-sn-glycero-phosphocholine ????? - PLPC ====== |
| - | | M1 | 1.4544 | 0.03 | [[http://pubs.acs.org/doi/abs/10.1021/jp054177x | [Babu, 2006]]] | | + | |
| - | | HM | 0.6 | 0.0157 | | | + | |
| - | ===== Validation of Parameters from MD Simulations ===== | + | | {{ LINK PARA A IMAGEM }} | PLPC | |
| + | | ::: | CONTEUDO2 | | ||
| + | | ::: | CONTEUDO3 | | ||
| - | ==== Bond Parameters ==== | ||
| - | | **BOND** | **l<sub>0 crystal</sub>** | **l<sub>0 opt</sub>** | **‹l›<sub>MD</sub> ± σ(l)** | **‹l›<sub>MD</sub> ± 2σ(l)** | | + | ====== 1,2-dilauroyl-sn-glycero-3-phosphoethanolamine - DLPE ====== |
| - | | M1-D1 | 2.22 | 2.09 | 2.25 ± 0.06 | [2.13; 2.37] | | + | |
| - | | M1-D2 | 2.23 | 2.13 | 2.18 ± 0.07 | [2.04; 2.31] | | + | |
| - | | M1-W1 | 2.10 | 2.25 | 2.23 ± 0.09 | [2.05; 2.40] | | + | |
| - | | M1-W2 | 2.18 | 2.18 | 2.16 ± 0.08 | [2.01; 2.31] | | + | |
| - | | M1-W3 | 2.17 | 2.32 | 2.3 ± 0.1 | [2.1; 2.5] | | + | |
| - | | M1-W4 | 2.51 | 2.38 | 2.4 ± 0.1 | [2.1; 2.6] | | + | |
| - | ==== Angle Parameters ==== | ||
| - | | **ANGLE** | **θ<sub>0 crystal</sub>** | **θ<sub>0 QM</sub>** | **‹θ›<sub>MD</sub> ± σ(θ)** | **‹θ›<sub>MD</sub> ± 2σ(θ)** | | + | | {{ LINK PARA A IMAGEM }} | DLPE | |
| - | | D1-M1-D2 | 90.6 | 108.4 | 105 ± 5 | [95; 116] | | + | | ::: | CONTEUDO2 | |
| - | | D1-M1-W1 | 87.3 | 86.0 | 85 ± 4 | [76; 94] | | + | | ::: | CONTEUDO3 | |
| - | | D1-M1-W2 | 94.2 | 94.0 | 104 ± 6 | [92; 117] | | + | |
| - | | D1-M1-W3 | 84.5 | 90.5 | 99 ± 7 | [85; 114] | | + | |
| - | | D1-M1-W4 | 171.9 | 173.2 | 171 ± 4 | [162; 179] | | + | ====== 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine - DMPE ====== |
| - | | D2-M1-W1 | 89.9 | 97.5 | 96 ± 7 | [83; 109] | | + | |
| - | | D2-M1-W2 | 90.2 | 91.2 | 88 ± 5 | [79; 98] | | + | |
| - | | D2-M1-W3 | 179.0 | 157.1 | 149 ± 7 | [136; 163] | | + | | {{ LINK PARA A IMAGEM }} | DMPE | |
| - | | D2-M1-W4 | 97.4 | 85.9 | 80 ± 5 | [71; 89] | | + | | ::: | CONTEUDO2 | |
| - | | W1-M1-W2 | 178.6 | 165.3 | 164 ± 5 | [153; 175] | | + | | ::: | CONTEUDO3 | |
| - | | W1-M1-W3 | 90.9 | 75.0 | 70 ± 7 | [56; 84] | | + | |
| - | | W1-M1-W4 | 94.2 | 100.1 | 94 ± 6 | [83; 106] | | + | ====== 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine - DPPE ====== |
| - | | W2-M1-W3 | 89.1 | 92.4 | 101 ± 10 | [82; 120] | | + | |
| - | | W2-M1-W4 | 84.4 | 84.0 | 75 ± 9 | [57; 93] | | + | |
| - | | W3-M1-W4 | 87.5 | 84.3 | 76 ± 7 | [62; 89] | | + | | {{ LINK PARA A IMAGEM }} | DPPE | |
| + | | ::: | CONTEUDO2 | | ||
| + | | ::: | CONTEUDO3 | | ||
| + | |||
| + | ====== 1,2-distearoyl-sn-glycero-3-phosphoethanolamine - DSPE ====== | ||
| + | |||
| + | |||
| + | | {{ LINK PARA A IMAGEM }} | DSPE | | ||
| + | | ::: | CONTEUDO2 | | ||
| + | | ::: | CONTEUDO3 | | ||
| + | |||
| + | ====== 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine - POPE ====== | ||
| + | |||
| + | |||
| + | | {{ LINK PARA A IMAGEM }} | POPE | | ||
| + | | ::: | CONTEUDO2 | | ||
| + | | ::: | CONTEUDO3 | | ||
| + | |||
| + | ====== 1-palmitoyl-2-linoleoyl-sn-glycero-phosphoethanolamine ????? - PLPE ====== | ||
| + | |||
| + | |||
| + | | {{ LINK PARA A IMAGEM }} | PLPE | | ||
| + | | ::: | CONTEUDO2 | | ||
| + | | ::: | CONTEUDO3 | | ||
| - | ===== Downloads ===== | ||
| - | | //Parameter File// | {{:mm:parameters:manganese:frcmod.zip| .frcmod}} | | ||
| - | | //Coordination Sphere Charges// | {{:mm:parameters:manganese:ddwwww_mn-ii.zip| .off}} | | ||
| - | | //Integrase’s PDB File (1A5V.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:integrase.zip| .pdb, leaprc}} | | ||
| ===== References ===== | ===== References ===== | ||
| - | Neves, R.P.P.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. [[http://pubs.acs.org/doi/abs/10.1021/ct400055v | Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins]] . //J. Chem. Theory Comput.//, **2013**, 9 (6), 2718–2732 | + | 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/example_page.1374688558.txt.gz · Last modified: 2013/07/24 18:55 by ruineves
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