User:Susana Retamal/Sandbox1: Difference between revisions
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=Background Information= | =Background Information= | ||
Rsp1275 is a member of the Fnr-Crp family of transcriptional regulators. Homologues of the Fnr protein from ''E. coli'' have been identified in a variety of taxonomically diverse bacterial species. <ref>Spiro, S. 1994. The FNR family of transcriptional regulators. Antonie van Leeuwenhoek 66:23–36.</ref> | Rsp1275 is a member of the Fnr-Crp family of transcriptional regulators. Homologues of the Fnr protein from ''E. coli'' have been identified in a variety of taxonomically diverse bacterial species.<ref>Spiro, S. 1994. The FNR family of transcriptional regulators. Antonie van Leeuwenhoek 66:23–36.</ref><ref>PredictProtein: B Rost, G Yachdav and J Liu (2004). The PredictProtein Server. Nucleic Acids Research 32(Web Server issue):W321-W326.</ref>The bacterium ''Rhodobacter sphaeroides" 2.4.1 encodes 8 members of this family, however only 2 have known function. Models of 7 of them, including RSP1275, were successfully obtained using 3D-Jigsaw, all being very similar in structure to Crp (the only one with crystal structure solved). The DNA binding domain helix-turn-helix is located in the C-terminal, and the N-terminal part contains the allosteric effector domain. | ||
'' | '' | ||
= Structure of the Proposed rsp1275 modeling obtained using 3D-Jigsaw = | = Structure of the Proposed rsp1275 modeling obtained using 3D-Jigsaw = | ||
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<applet load='Rsp1275.pdb' size='300' frame='true' align='right' caption='Insert caption here' /> | <applet load='Rsp1275.pdb' size='300' frame='true' align='right' caption='Insert caption here' /> | ||
The highlighted <scene name='User:Susana_Retamal/Sandbox1/Rsp1275/10'> | The highlighted <scene name='User:Susana_Retamal/Sandbox1/Rsp1275/10'>alpha-helices</scene> of the protein. | ||
This is the <scene name='User:Susana_Retamal/Sandbox1/Rsp1275/12'>Amino to Carboxyl rainbow</scene> of the protein. | This is the <scene name='User:Susana_Retamal/Sandbox1/Rsp1275/12'>Amino to Carboxyl rainbow</scene> of the protein. | ||
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241 drprrrpli | 241 drprrrpli | ||
=Physico - Chemical parameters for Rsp1275= | =Physico - Chemical parameters for Rsp1275= | ||
From http://ca.expasy.org/tools/protparam.html | From http://ca.expasy.org/tools/protparam.html | ||
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*Ext. coefficient 29115 | *Ext. coefficient 29115 | ||
Abs 0.1% (=1 g/l) 1.039, assuming ALL Cys residues appear as half cystines | Abs 0.1% (=1 g/l) 1.039, assuming ALL Cys residues appear as half cystines | ||
*Ext. coefficient 28990 | *Ext. coefficient 28990 | ||
Abs 0.1% (=1 g/l) 1.035, assuming NO Cys residues appear as half cystines | Abs 0.1% (=1 g/l) 1.035, assuming NO Cys residues appear as half cystines | ||
'''Estimated half-life:''' | '''Estimated half-life:''' | ||
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* >20 hours (yeast, in vivo). | * >20 hours (yeast, in vivo). | ||
* >10 hours (Escherichia coli, in vivo). | * >10 hours (Escherichia coli, in vivo). | ||
'''Instability index:''' | '''Instability index:''' | ||
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The instability index (II) is computed to be 41.06 | The instability index (II) is computed to be 41.06 | ||
This classifies the protein as unstable. | This classifies the protein as unstable. | ||
'''Aliphatic index:''' 97.19 | '''Aliphatic index:''' 97.19 | ||
'''Grand average of hydropathicity (GRAVY):''' -0.097 | '''Grand average of hydropathicity (GRAVY):''' -0.097 | ||
'''Globe Predictio'''n: it appears as compact, as a globular domain. | '''Globe Predictio'''n: it appears as compact, as a globular domain. | ||
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'' | '' | ||