James D Watson/Proteins Intro - Revision history

Eran Hodis: Redirecting to User:James D Watson/Proteins Intro

Eran Hodis — Sat, 14 Mar 2009 23:14:54 GMT

Redirecting to User:James D Watson/Proteins Intro

←Older revision		Revision as of 23:14, 14 March 2009
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-	#REDIRECT [[~~http://proteopedia.org/wiki/index.php/~~User:James D Watson/Proteins Intro]]	+	#REDIRECT [[User:James D Watson/Proteins Intro]]

James D Watson: Redirecting to Http://proteopedia.org/wiki/index.php/User:James D Watson/Proteins Intro

James D Watson — Thu, 26 Jun 2008 07:32:53 GMT

Redirecting to Http://proteopedia.org/wiki/index.php/User:James D Watson/Proteins Intro

←Older revision		Revision as of 07:32, 26 June 2008
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-	~~==Introduction to proteins==~~	+	#REDIRECT [[http://proteopedia.org/wiki/index.php/User:James D Watson/Proteins Intro]]
-	This is an example private page that could be used in teaching. I will copy some of the info from the 5p21 page and use it here to expand details and bring in other aspects like structural superpositions.	+
-		+
-	~~==5p21 Overview==~~	+
-		+
-	~~{{STRUCTURE_5p21 \| PDB=5p21 \| SCENE= }}~~	+
-		+
-	The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp has been determined at 1.35 A resolution. 211 water molecules have been built into the electron density. The structure has been refined to a final R-factor of 19.8% for all data between 6 A and 1.35 A. The binding sites of the nucleotide and the magnesium ion are revealed in high detail and consists of a characteristic <scene name='5p21/Ligand_binding_site/1'>Walker motif</scene> (GXXXXGK[T/S]). For the stretch of amino acid residues 61-65, the temperature factors of backbone atoms are four times the average value of 16.1 A2 due to the multiple conformations. In one of these conformations, the side chain of Gln61 makes contact with a water molecule, which is perfectly placed to be the nucleophile attacking the gamma-phosphate of GTP. Based on this observation, we propose a mechanism for GTP hydrolysis involving mainly Gln61 and Glu63 as activating species for in-line attack of water. Nucleophilic displacement is facilitated by hydrogen bonds from residues Thr35, Gly60 and Lys16. A mechanism for rate enhancement by GAP is also proposed.	+
-		+
-		+
-	~~==About this Structure==~~	+
-	~~5P21 is a [[Single protein]] structure of sequence from~~ [http://~~en.wikipedia~~.org/wiki/~~Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=5P21 OCA].~~	+
-		+
-	~~==Reference==~~	+
-	Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis., Pai EF, Krengel U, Petsko GA, Goody RS, Kabsch W, Wittinghofer A, EMBO J. 1990 Aug;9(8):2351-9. PMID:[http:/~~/www.ncbi.nlm.nih.gov/pubmed/2196171 2196171~~]	+
-		+
-		+
-	~~{{Clear}}~~	+
-		+
-		+
-	~~==Structural superposition==~~	+
-		+
-	The viewer below left shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21 <nowiki>-</nowiki> coloured orange) with Gdp-bound human rab21 gtpase (PDB entry 1z0i <nowiki>-</nowiki> coloured blue), the structural superposition was made using the MSDfold(SSM)[http://www.ebi.ac.uk/msd-srv/ssm/ 1] server at the EBI[http://www.ebi.ac.uk 2]. Note that the global fold of these two proteins is almost identical yet their sequence identity is only 29.6% (as determined using FASTA). The viewer below right shows the p-loops of both structures superposed. The ligands bound superpose particularly well and comparison of the two p-loops loops show significant structural similarity but also highlights the sequence differences between the two proteins.	+
-	~~<applet load='5p21' size='350' frame='true' align='left' script='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1' />~~	+
-	~~<applet load='5p21' size='350' frame='true' align='right' script='James_D_Watson/Proteins_Intro/Superposition_ras_ploops/2' />~~	+
-		+
-		+
-	~~{{Clear}}~~	+

James D Watson at 10:42, 5 June 2008

James D Watson — Thu, 05 Jun 2008 10:42:29 GMT

←Older revision		Revision as of 10:42, 5 June 2008
Line 1:		Line 1:
	==Introduction to proteins==		==Introduction to proteins==
-	This ~~will be the start of~~ an ~~attempt to create a topic based~~ page that could be used in teaching. I will ~~spend more time editing~~ it ~~asap~~.	+	This is an example private page that could be used in teaching. I will copy some of the info from the 5p21 page and use it here to expand details and bring in other aspects like structural superpositions.
-	~~<scene name~~=~~'James_D_Watson/Proteins_Intro/Ligand_binding_site_ras/1'>Click to see walker motif</scene>~~	+
		+	==5p21 Overview==

	{{STRUCTURE_5p21 \| PDB=5p21 \| SCENE= }}		{{STRUCTURE_5p21 \| PDB=5p21 \| SCENE= }}
		+
		+	The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp has been determined at 1.35 A resolution. 211 water molecules have been built into the electron density. The structure has been refined to a final R-factor of 19.8% for all data between 6 A and 1.35 A. The binding sites of the nucleotide and the magnesium ion are revealed in high detail and consists of a characteristic <scene name='5p21/Ligand_binding_site/1'>Walker motif</scene> (GXXXXGK[T/S]). For the stretch of amino acid residues 61-65, the temperature factors of backbone atoms are four times the average value of 16.1 A2 due to the multiple conformations. In one of these conformations, the side chain of Gln61 makes contact with a water molecule, which is perfectly placed to be the nucleophile attacking the gamma-phosphate of GTP. Based on this observation, we propose a mechanism for GTP hydrolysis involving mainly Gln61 and Glu63 as activating species for in-line attack of water. Nucleophilic displacement is facilitated by hydrogen bonds from residues Thr35, Gly60 and Lys16. A mechanism for rate enhancement by GAP is also proposed.
		+
		+
		+	==About this Structure==
		+	5P21 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5P21 OCA].
		+
		+	==Reference==
		+	Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis., Pai EF, Krengel U, Petsko GA, Goody RS, Kabsch W, Wittinghofer A, EMBO J. 1990 Aug;9(8):2351-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2196171 2196171]
		+

	{{Clear}}		{{Clear}}

James D Watson: /* Structural superposition */

James D Watson — Thu, 05 Jun 2008 10:37:51 GMT

Structural superposition

←Older revision		Revision as of 10:37, 5 June 2008
Line 10:		Line 10:
	==Structural superposition==		==Structural superposition==

-	The viewer below left shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21 <nowiki>-</nowiki> coloured ~~red~~) with Gdp-bound human rab21 gtpase (PDB entry 1z0i <nowiki>-</nowiki> coloured blue), the structural superposition was made using the MSDfold(SSM)[http://www.ebi.ac.uk/msd-srv/ssm/ 1] server at the EBI[http://www.ebi.ac.uk 2]. Note that the global fold of these two proteins is almost identical yet their sequence identity is only 29.6% (as determined using FASTA). The viewer below right shows the p-loops of both structures superposed. The ligands bound superpose particularly well and comparison of the two p-loops loops show significant structural similarity but also highlights the sequence differences between the two proteins.	+	The viewer below left shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21 <nowiki>-</nowiki> coloured orange) with Gdp-bound human rab21 gtpase (PDB entry 1z0i <nowiki>-</nowiki> coloured blue), the structural superposition was made using the MSDfold(SSM)[http://www.ebi.ac.uk/msd-srv/ssm/ 1] server at the EBI[http://www.ebi.ac.uk 2]. Note that the global fold of these two proteins is almost identical yet their sequence identity is only 29.6% (as determined using FASTA). The viewer below right shows the p-loops of both structures superposed. The ligands bound superpose particularly well and comparison of the two p-loops loops show significant structural similarity but also highlights the sequence differences between the two proteins.
	<applet load='5p21' size='350' frame='true' align='left' script='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1' />		<applet load='5p21' size='350' frame='true' align='left' script='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1' />
	<applet load='5p21' size='350' frame='true' align='right' script='James_D_Watson/Proteins_Intro/Superposition_ras_ploops/2' />		<applet load='5p21' size='350' frame='true' align='right' script='James_D_Watson/Proteins_Intro/Superposition_ras_ploops/2' />

James D Watson: /* Structural superposition */

James D Watson — Thu, 05 Jun 2008 10:37:16 GMT

Structural superposition

←Older revision		Revision as of 10:37, 5 June 2008
Line 10:		Line 10:
	==Structural superposition==		==Structural superposition==

-	The viewer below left shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21 coloured red) with Gdp-bound human rab21 gtpase (PDB entry 1z0i - coloured blue), the structural superposition was made using the MSDfold(SSM)[http://www.ebi.ac.uk/msd-srv/ssm/ 1] server at the EBI[http://www.ebi.ac.uk 2]. Note that the global fold of these two proteins is almost identical yet their sequence identity is only 29.6% (as determined using FASTA). The viewer below right shows the p-loops of both structures superposed. The ligands bound superpose particularly well and comparison of the two p-loops loops show significant structural similarity but also highlights the sequence differences between the two proteins.	+	The viewer below left shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21 <nowiki>-</nowiki> coloured red) with Gdp-bound human rab21 gtpase (PDB entry 1z0i <nowiki>-</nowiki> coloured blue), the structural superposition was made using the MSDfold(SSM)[http://www.ebi.ac.uk/msd-srv/ssm/ 1] server at the EBI[http://www.ebi.ac.uk 2]. Note that the global fold of these two proteins is almost identical yet their sequence identity is only 29.6% (as determined using FASTA). The viewer below right shows the p-loops of both structures superposed. The ligands bound superpose particularly well and comparison of the two p-loops loops show significant structural similarity but also highlights the sequence differences between the two proteins.
	<applet load='5p21' size='350' frame='true' align='left' script='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1' />		<applet load='5p21' size='350' frame='true' align='left' script='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1' />
	<applet load='5p21' size='350' frame='true' align='right' script='James_D_Watson/Proteins_Intro/Superposition_ras_ploops/2' />		<applet load='5p21' size='350' frame='true' align='right' script='James_D_Watson/Proteins_Intro/Superposition_ras_ploops/2' />

James D Watson at 10:34, 5 June 2008

James D Watson — Thu, 05 Jun 2008 10:34:27 GMT

←Older revision		Revision as of 10:34, 5 June 2008
Line 10:		Line 10:
	==Structural superposition==		==Structural superposition==

-	The viewer below shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21 coloured red) with Gdp-bound human rab21 gtpase (PDB entry 1z0i - coloured blue), the structural superposition was made using the MSDfold(SSM)[http://www.ebi.ac.uk/msd-srv/ssm/ 1] server at the EBI[http://www.ebi.ac.uk 2]. Note that the global fold of these two proteins is almost identical yet their sequence identity is only 29.6% (as determined using FASTA). The ligands bound superpose well and comparison of the ~~ligand binding~~ loops show significant structural similarity.	+	The viewer below left shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21 coloured red) with Gdp-bound human rab21 gtpase (PDB entry 1z0i - coloured blue), the structural superposition was made using the MSDfold(SSM)[http://www.ebi.ac.uk/msd-srv/ssm/ 1] server at the EBI[http://www.ebi.ac.uk 2]. Note that the global fold of these two proteins is almost identical yet their sequence identity is only 29.6% (as determined using FASTA). The viewer below right shows the p-loops of both structures superposed. The ligands bound superpose particularly well and comparison of the two p-loops loops show significant structural similarity but also highlights the sequence differences between the two proteins.
-	<applet load='5p21' size='~~400~~' frame='true' align='left' script='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1' />	+	<applet load='5p21' size='350' frame='true' align='left' script='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1' />
		+	<applet load='5p21' size='350' frame='true' align='right' script='James_D_Watson/Proteins_Intro/Superposition_ras_ploops/2' />
		+

	{{Clear}}		{{Clear}}

James D Watson: /* Structural superposition */

James D Watson — Thu, 05 Jun 2008 10:07:41 GMT

Structural superposition

←Older revision		Revision as of 10:07, 5 June 2008
Line 10:		Line 10:
	==Structural superposition==		==Structural superposition==

-	The viewer below shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21) with Gdp-bound human rab21 gtpase (PDB entry 1z0i), the structural superposition was made using the MSDfold(SSM)[http://www.ebi.ac.uk/msd-srv/ssm/ 1] server at the EBI[http://www.ebi.ac.uk 2]. Note that the global fold of these two proteins is almost identical yet their sequence identity is only 29.6% (as determined using FASTA). The ligands bound superpose well and comparison of the ligand binding loops show significant structural similarity.	+	The viewer below shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21 coloured red) with Gdp-bound human rab21 gtpase (PDB entry 1z0i - coloured blue), the structural superposition was made using the MSDfold(SSM)[http://www.ebi.ac.uk/msd-srv/ssm/ 1] server at the EBI[http://www.ebi.ac.uk 2]. Note that the global fold of these two proteins is almost identical yet their sequence identity is only 29.6% (as determined using FASTA). The ligands bound superpose well and comparison of the ligand binding loops show significant structural similarity.
-		+	<applet load='5p21' size='400' frame='true' align='left' script='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1' />
-	<~~scene name~~='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1'~~>Ras superposition<~~/~~scene~~>	+

	{{Clear}}		{{Clear}}

James D Watson at 09:13, 5 June 2008

James D Watson — Thu, 05 Jun 2008 09:13:09 GMT

←Older revision		Revision as of 09:13, 5 June 2008
Line 12:		Line 12:
	The viewer below shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21) with Gdp-bound human rab21 gtpase (PDB entry 1z0i), the structural superposition was made using the MSDfold(SSM)[http://www.ebi.ac.uk/msd-srv/ssm/ 1] server at the EBI[http://www.ebi.ac.uk 2]. Note that the global fold of these two proteins is almost identical yet their sequence identity is only 29.6% (as determined using FASTA). The ligands bound superpose well and comparison of the ligand binding loops show significant structural similarity.		The viewer below shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21) with Gdp-bound human rab21 gtpase (PDB entry 1z0i), the structural superposition was made using the MSDfold(SSM)[http://www.ebi.ac.uk/msd-srv/ssm/ 1] server at the EBI[http://www.ebi.ac.uk 2]. Note that the global fold of these two proteins is almost identical yet their sequence identity is only 29.6% (as determined using FASTA). The ligands bound superpose well and comparison of the ligand binding loops show significant structural similarity.

-	<~~applet load~~='~~Image:Ras_superposed.pdb' size='400' frame='true' align='left~~' />	+	<scene name='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1'>Ras superposition</scene>

	{{Clear}}		{{Clear}}

James D Watson at 08:52, 5 June 2008

James D Watson — Thu, 05 Jun 2008 08:52:11 GMT

←Older revision		Revision as of 08:52, 5 June 2008
Line 13:		Line 13:

	<applet load='Image:Ras_superposed.pdb' size='400' frame='true' align='left' />		<applet load='Image:Ras_superposed.pdb' size='400' frame='true' align='left' />
		+
		+	{{Clear}}

James D Watson at 08:51, 5 June 2008

James D Watson — Thu, 05 Jun 2008 08:51:39 GMT

←Older revision		Revision as of 08:51, 5 June 2008
Line 11:		Line 11:

	The viewer below shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21) with Gdp-bound human rab21 gtpase (PDB entry 1z0i), the structural superposition was made using the MSDfold(SSM)[http://www.ebi.ac.uk/msd-srv/ssm/ 1] server at the EBI[http://www.ebi.ac.uk 2]. Note that the global fold of these two proteins is almost identical yet their sequence identity is only 29.6% (as determined using FASTA). The ligands bound superpose well and comparison of the ligand binding loops show significant structural similarity.		The viewer below shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21) with Gdp-bound human rab21 gtpase (PDB entry 1z0i), the structural superposition was made using the MSDfold(SSM)[http://www.ebi.ac.uk/msd-srv/ssm/ 1] server at the EBI[http://www.ebi.ac.uk 2]. Note that the global fold of these two proteins is almost identical yet their sequence identity is only 29.6% (as determined using FASTA). The ligands bound superpose well and comparison of the ligand binding loops show significant structural similarity.
		+
		+	<applet load='Image:Ras_superposed.pdb' size='400' frame='true' align='left' />