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. The bacterium ''Rhodobacter sphaeroides 2.4.1'' encodes 8 members of this family, however only 2 have known function. The modeling of 7 of them 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. Rsp1275 has been linked with salt-tolerance in ''Rhodobacter spheroides''. Different genes coding for the Fnr-Crp proteins of unknown function have been cloned and a multicopy test was performed to evaluate these as potential regulators of NaCl-responsive genes.
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'''
<applet load='Rsp1275.pdb' size='300' frame='true' align='right' caption='Insert caption here' />
 
<scene name='User:Susana_Retamal/Sandbox1/Rsp1275/8'>TextToBeDisplayed</scene>
<scene name='User:Susana_Retamal/Sandbox1/Rsp1275/8'>3D-Jigsaw image of rsp1275</scene>
 
{{Template:ColorKey_Amino2CarboxyRainbow}}


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.


=Protein Sequence=
=Protein Sequence=


mfvpapdati tncrncplrr kplflpfsds elsfmeqfkv gelvvapgvt lleegqgsah lftvlsglgi rstmlengrr qvinflfpgd figlqaglag emrhsvestt tmvlcvfnra  dlwdlfreep eraydltwia aveehflget iaslgqrdat erlawallri herlsaigla  ergrvpmpwr qqdladalgl slvhtnktir rlretghalw eggtlfvdre rlatlaladp  drprrrpli
1 mfvpapdati tncrncplrr kplflpfsds elsfmeqfkv gelvvapgvt lleegqgsah


61 lftvlsglgi rstmlengrr qvinflfpgd figlqaglag emrhsvestt tmvlcvfnra


=Evidence of Fnr-Crp protein Involvement in Transcriptional Response to NaCl=
121 dlwdlfreep eraydltwia aveehflget iaslgqrdat erlawallri herlsaigla


181 ergrvpmpwr qqdladalgl slvhtnktir rlretghalw eggtlfvdre rlatlaladp


241 drprrrpli


It has been proposed that Fnr-Crp protein encoded by rsp1275 is a transcription factor responsible for salt-responsive changes in the transcriptome. In addition, it's likely that rsp1275 interacts with a small ligand (potentially Na or Cl).


=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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The N-terminal of the sequence considered is M (Met).
The N-terminal of the sequence considered is M (Met).


The estimated half-life is:
'''The estimated half-life is''':
   
   
*30 hours (mammalian reticulocytes, in vitro).
*30 hours (mammalian reticulocytes, in vitro).
* >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.  
Line 166: Line 157:


- POS: The position of the AA in the SEQRES derived sequence.
- POS: The position of the AA in the SEQRES derived sequence.
- SEQ: The SEQRES derived sequence in one letter code.
- SEQ: The SEQRES derived sequence in one letter code.
- 3LATOM: The ATOM derived sequence in three letter code, including the AA's positions as they appear in the PDB file and the chain identifier.
- 3LATOM: The ATOM derived sequence in three letter code, including the AA's positions as they appear in the PDB file and the chain identifier.
- SCORE: The normalized conservation scores.
- SCORE: The normalized conservation scores.
- COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable).
- COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable).
- CONFIDENCE INTERVAL: When using the bayesian method for calculating rates, a confidence interval is assigned to each of the inferred evolutionary conservation scores.
- CONFIDENCE INTERVAL: When using the bayesian method for calculating rates, a confidence interval is assigned to each of the inferred evolutionary conservation scores.
- CONFIDENCE INTERVAL COLORS: When using the bayesian method for calculating rates. The color scale representing the lower and upper bounds of the confidence interval.
- CONFIDENCE INTERVAL COLORS: When using the bayesian method for calculating rates. The color scale representing the lower and upper bounds of the confidence interval.
- MSA DATA: The number of aligned sequences having an amino acid (non-gapped) from the overall number of sequences at each position.
- MSA DATA: The number of aligned sequences having an amino acid (non-gapped) from the overall number of sequences at each position.
- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.
- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.


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=References=
''
== Reference ==
''
<references/>
 
''
== Animated Image Construction ==
''
 
1. Go to the POLYVIEW 3D homepage, http://polyview.cchmc.org/polyview3d.html
 
2. On the submission form, first select 'animation' in the "type of request" section, select the size of the animation to be generated in pixels(here the size is 600), then upload the PDB format protein structure file in the "source of structural data" section.
 
3. On the "chain color and rendering section" select 'cartoon' and 'secondary structure'.
 
4. On "advanced structural annotation" section select 'docking models in Capri format'.
 
5. Any other forms for the animation may be selected by referring to the "Samples" according to the protein structure to be animated.
 
''
== JMol Image Construction ==
''
 
1. First retrieve your protein sequence from http://www.ncbi.nlm.nih.gov/.
 
2. Go to 3D-JIGSAW page http://bmm.cancerresearchuk.org/~3djigsaw/ and paste the sequence on the submission page. A .pdb format image of your protein will be sent to you on your email which can be opened by RASMOL.
 
3. Upload this file on Proteopedia and then load the JMol applet for the protein following instructions on the Help:Editing page http://www.proteopedia.org/wiki/index.php/Help:Editing.
 
4. You can edit your protein by using the scene authoring tools after loading the applet.
 


*Spiro, S. 1994. The FNR family of transcriptional regulators. Antonie van Leeuwenhoek 66:23–36.
*PredictProtein: B Rost, G Yachdav and J Liu (2004). The PredictProtein Server. Nucleic Acids Research 32(Web Server issue):W321-W326.


Page Created by Susana Retamal, email:susana.retamal@gmail.com
Page Created by Susana Retamal, email:susana.retamal@gmail.com


Acknownledment: Jill Zeilstra Ryalls, Adam Meade and Yana Fedotova.
Acknownledment: Jill Zeilstra Ryalls, Adam Meade and Yana Fedotova.
Retrieved from "https://proteopedia.openfox.io/w/User:Susana_Retamal/Sandbox1"