User:Susana Retamal/Sandbox1: Difference between revisions

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*[[User:~~Susana Retamal~~/Sandbox1]]

=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><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 =

''

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=

1 mfvpapdati tncrncplrr kplflpfsds elsfmeqfkv gelvvapgvt lleegqgsah

61 lftvlsglgi rstmlengrr qvinflfpgd figlqaglag emrhsvestt tmvlcvfnra

121 dlwdlfreep eraydltwia aveehflget iaslgqrdat erlawallri herlsaigla

181 ergrvpmpwr qqdladalgl slvhtnktir rlretghalw eggtlfvdre rlatlaladp

241 drprrrpli

=Physico - Chemical parameters for Rsp1275=

From http://ca.expasy.org/tools/protparam.html

'''Number of amino acids: 249'''

'''Molecular weight: 28014.2'''

'''Theoretical pI: 6.10'''

'''Atomic composition:'''

Carbon C 1249

Hydrogen H 1986

Nitrogen N 360

Oxygen O 355

Sulfur S 9

Formula: C1249H1986N360O355S9

Total number of atoms: 3959

'''Extinction coefficients:'''

Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.

*Ext. coefficient 29115

Abs 0.1% (=1 g/l) 1.039, assuming ALL Cys residues appear as half cystines

*Ext. coefficient 28990

Abs 0.1% (=1 g/l) 1.035, assuming NO Cys residues appear as half cystines

~~=Background Information=~~

'''Estimated half-life:'''

~~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~~ (1) diverse bacterial species. The bacterium ''Rhodobacter spheroides 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.

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

~~=Evidence of Fnr~~-~~Crp protein Involvement~~ in ~~Transcriptional Response to NaCl=~~

'''The estimated half-life is''':

*30 hours (mammalian reticulocytes, in vitro).

* >20 hours (yeast, in vivo).

* >10 hours (Escherichia coli, in vivo).

~~=Physico - Chemical parameters for Rsp1275=~~

'''Instability index:'''

The instability index (II) is computed to be 41.06

This classifies the protein as unstable.

~~Number of amino acids~~: ~~249~~

'''Aliphatic index:''' 97.19

~~Molecular weight~~: ~~28014~~.2

'''Grand average of hydropathicity (GRAVY):''' -0.097

~~Theoretical pI~~: 6.10

'''Globe Predictio'''n: it appears as compact, as a globular domain.

'''Secondary Structure:'''

Helix 34.94%

Extended (sheet) 17.67%

Loop 47.39%

{| border="1"

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Line 157:

- POS: The position of the AA in the SEQRES derived sequence.

- 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.

- SCORE: The normalized conservation scores.

- 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 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.

- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.

Line 123:

Line 196:

19 L LEU65: 0.975 2* 0.108, 1.367 5,1 18/19 A,I,L,M,R,S,V

20 S SER66: -0.045 5 -0.697, 0.404 7,4 18/19 E,H,R,S,T

21 G GLY67: -1.418 9 -1.755,-1.277 9,9 18/19 G

22 L LEU68: 0.334 4 -0.344, 0.790 6,3 18/19 A,I,K,L,T,V

23 G GLY69: 0.572 3* -0.136, 1.367 5,1 18/19 A,G,I,L,M,V

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Line 359:

== Phylogenetic Tree of rsp1275 ==

http://consurf.tau.ac.il/results/1240240806/treeView.html

''

== Reference ==

''

''

== 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.

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

~~''Structure of the Proposed rsp1275'''<applet load='rsp1275~~.~~pdb' size='300' color='black' frame='true' align='right' caption='3D Image of proposed rsp1275 protein'/>~~

Acknownledment: Jill Zeilstra Ryalls, Adam Meade and Yana Fedotova.

@@ Line 1: / Line 1: @@
-*[[User:Susana Retamal/Sandbox1]]
+=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><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 =
+''
+<applet load='Rsp1275.pdb' size='300' frame='true' align='right' caption='Insert caption here' />
+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=
+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
+=Physico - Chemical parameters for Rsp1275=
+From http://ca.expasy.org/tools/protparam.html
+'''Number of amino acids: 249'''
+'''Molecular weight: 28014.2'''
+'''Theoretical pI: 6.10'''
+'''Atomic composition:'''
+Carbon      C	      1249
+Hydrogen    H	      1986
+Nitrogen    N	       360
+Oxygen      O	       355
+Sulfur      S	         9
+Formula: C1249H1986N360O355S9
+Total number of atoms: 3959
+'''Extinction coefficients:'''
+Extinction coefficients are in units of  M-1 cm-1, at 280 nm measured in water.
+*Ext. coefficient    29115
+Abs 0.1% (=1 g/l)   1.039, assuming ALL Cys residues appear as half cystines
+*Ext. coefficient    28990
+Abs 0.1% (=1 g/l)   1.035, assuming NO Cys residues appear as half cystines
-=Background Information=
+'''Estimated half-life:'''
-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 (1) diverse bacterial species. The bacterium ''Rhodobacter spheroides 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.
+The N-terminal of the sequence considered is M (Met).
-=Evidence of Fnr-Crp protein Involvement in Transcriptional Response to NaCl=
+'''The estimated half-life is''':
+*30 hours (mammalian reticulocytes, in vitro).
+* >20 hours (yeast, in vivo).
+* >10 hours (Escherichia coli, in vivo).
-=Physico - Chemical parameters for Rsp1275=
+'''Instability index:'''
+The instability index (II) is computed to be 41.06
+This classifies the protein as unstable.
-Number of amino acids: 249
+'''Aliphatic index:''' 97.19
-Molecular weight: 28014.2
+'''Grand average of hydropathicity (GRAVY):''' -0.097
-Theoretical pI: 6.10
+'''Globe Predictio'''n: it appears as compact, as a globular domain.
+'''Secondary Structure:'''
+Helix 34.94%
+Extended (sheet) 17.67%
+Loop 47.39%
 {| border="1"
@@ Line 92: / Line 157: @@
 - POS: The position of the AA in the SEQRES derived sequence.
 - 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.
 - SCORE: The normalized conservation scores.
 - 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 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.
 - RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.
@@ Line 123: / Line 196: @@
 	   L	    LEU65:	 0.975		  2*	 0.108, 1.367			    5,1			   18/19	A,I,L,M,R,S,V
 	   S	    SER66:	-0.045		  5	-0.697, 0.404			    7,4			   18/19	E,H,R,S,T
 	   G	    GLY67:	-1.418		  9	-1.755,-1.277			    9,9			   18/19	G
 	   L	    LEU68:	 0.334		  4	-0.344, 0.790			    6,3			   18/19	A,I,K,L,T,V
 	   G	    GLY69:	 0.572		  3*	-0.136, 1.367			    5,1			   18/19	A,G,I,L,M,V
@@ Line 286: / Line 359: @@
+== Phylogenetic Tree of rsp1275 ==
+http://consurf.tau.ac.il/results/1240240806/treeView.html
+''
+== Reference ==
+''
+<references/>
+''
+== Animated Image Construction ==
+''
+. Go to the POLYVIEW 3D homepage, http://polyview.cchmc.org/polyview3d.html
+. 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.
+. On the "chain color and rendering section" select 'cartoon' and 'secondary structure'.
+. On "advanced structural annotation" section select 'docking models in Capri format'.
+. 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 ==
+''
+. First retrieve your protein sequence from http://www.ncbi.nlm.nih.gov/.
+. 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.
+. 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.
+. You can edit your protein by using the scene authoring tools after loading the applet.
+Page Created by Susana Retamal, email:susana.retamal@gmail.com
-''Structure of the Proposed rsp1275'''<applet load='rsp1275.pdb' size='300' color='black' frame='true' align='right' caption='3D Image of proposed rsp1275 protein'/>
+Acknownledment: Jill Zeilstra Ryalls, Adam Meade and Yana Fedotova.