Michael Purol Sandbox 1 - Revision history

David Canner at 10:39, 1 October 2010

David Canner — Fri, 01 Oct 2010 10:39:56 GMT

←Older revision		Revision as of 10:39, 1 October 2010
Line 33:		Line 33:
	==About this Structure==		==About this Structure==
	1BD8 is a 1 chain 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=1BD8 OCA].		1BD8 is a 1 chain 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=1BD8 OCA].
		+
		+	==Additional Resources==
		+	For additional information, see: [[Cancer]]
		+	<br />

	==References==		==References==

Michael Purol at 16:15, 3 November 2009

Michael Purol — Tue, 03 Nov 2009 16:15:50 GMT

←Older revision		Revision as of 16:15, 3 November 2009
Line 22:		Line 22:
	==Cancer Prevention==		==Cancer Prevention==

-	In a 2005 study by Ceruti et al., researchers determined that, in addition to, and perhaps even independent of its role as a cell cycle inhibitor, p19INK4d is involved in the maintenence of DNA integrity and, therefore, would contribute to cancer prevention. [3] This study shows that p19INK4d is the only INK4 protein whose expression is induced by UV light in neuroblastoma cells, and that this expression clearly reduces UV-induced (DNA-damage-induced) apoptosis by enhancing cellular ability to repair damaged DNA. [3]	+	In a 2005 study by Ceruti et al., researchers determined that in addition to and perhaps even independent of its role as a cell cycle inhibitor, p19INK4d is involved in the maintenence of DNA integrity and, therefore, would contribute to cancer prevention. [3] This study shows that p19INK4d is the only INK4 protein whose expression is induced by UV light in neuroblastoma cells, and that this expression clearly reduces UV-induced (DNA-damage-induced) apoptosis by enhancing cellular ability to repair damaged DNA. [3]

	==Low et al. (2009) Study==		==Low et al. (2009) Study==

Michael Purol at 16:15, 3 November 2009

Michael Purol — Tue, 03 Nov 2009 16:15:04 GMT

←Older revision		Revision as of 16:15, 3 November 2009
Line 22:		Line 22:
	==Cancer Prevention==		==Cancer Prevention==

-	In a 2005 study by Ceruti et al., researchers determined that, in addition to its role as a cell cycle inhibitor, p19INK4d is involved in the maintenence of DNA integrity and, therefore, would contribute to cancer prevention. [3] This study shows that p19INK4d is the only INK4 protein whose expression is induced by UV light in neuroblastoma cells, and that this expression clearly reduces UV-induced (DNA-damage-induced) apoptosis by enhancing cellular ability to repair damaged DNA. [3]	+	In a 2005 study by Ceruti et al., researchers determined that, in addition to, and perhaps even independent of its role as a cell cycle inhibitor, p19INK4d is involved in the maintenence of DNA integrity and, therefore, would contribute to cancer prevention. [3] This study shows that p19INK4d is the only INK4 protein whose expression is induced by UV light in neuroblastoma cells, and that this expression clearly reduces UV-induced (DNA-damage-induced) apoptosis by enhancing cellular ability to repair damaged DNA. [3]

	==Low et al. (2009) Study==		==Low et al. (2009) Study==
Line 28:		Line 28:
	This study took an in-depth look at the structural consequences of phosphorylation at different sites of p19INK4d. Low et al. replaced Phe 86 with a trytophan residue which acted as a fluorescence-sensitive probe within a pseudo-wild type (in stability and function) mutant that displayed a hyperfluorescent intermediate which could be detected in unfolding and folding kinetics, but not at equilibrium conditions.		This study took an in-depth look at the structural consequences of phosphorylation at different sites of p19INK4d. Low et al. replaced Phe 86 with a trytophan residue which acted as a fluorescence-sensitive probe within a pseudo-wild type (in stability and function) mutant that displayed a hyperfluorescent intermediate which could be detected in unfolding and folding kinetics, but not at equilibrium conditions.

-	Researchers then mimicked known phosphorylation sites with glutamate substitutions at <scene name='Michael_Purol_Sandbox_1/Ser_66/1'>Ser 66</scene> and <scene name='Michael_Purol_Sandbox_1/Ser_76/1'>Ser 76</scene> within ''E. coli'' to test the impact of introduced negative charges at these positions on the structural stability of P19INK4d. Results indicated that ~~both~~ mutants with the glutamate substitutions at Ser 76 ~~only and doubly-substituted~~ mutants with glutamate substitutions at Ser 66 and 76 were significantly destabilized in comparison to the wild-type protein, while mutants with only a Ser 66 glutamate substitution showed no significant destabilization. In particular, the results supported earlier findings that a negative charge at Ser 76 severely decreases protein stability in AR1 and AR2 by affecting the hydrogen bonding pattern of the adjacent residues, leading to a partial unfolding reaction and a higher flexibility of the loop. These findings suggest that phosphorylation or mimetic mutation at Ser 76 position allows ubiquitin ligase to access <scene name='Michael_Purol_Sandbox_1/Lys_62/1'>Lys 62</scene> ~~more easily~~ and thus tag p19INK4d for degradation at the proteasome. [4]	+	Researchers then mimicked known phosphorylation sites with glutamate substitutions at <scene name='Michael_Purol_Sandbox_1/Ser_66/1'>Ser 66</scene> and <scene name='Michael_Purol_Sandbox_1/Ser_76/1'>Ser 76</scene> within ''E. coli'' to test the impact of introduced negative charges at these positions on the structural stability of P19INK4d. Results indicated that mutants with the glutamate substitutions at Ser 76, as well as mutants with glutamate substitutions at both Ser 66 and 76, were significantly destabilized in comparison to the wild-type protein, while mutants with only a Ser 66 glutamate substitution showed no significant destabilization. In particular, the results supported earlier findings that a negative charge at Ser 76 severely decreases protein stability in AR1 and AR2 by affecting the hydrogen bonding pattern of the adjacent residues, leading to a partial unfolding reaction and higher flexibility in the loop. These findings suggest that phosphorylation or mimetic mutation at Ser 76 position allows ubiquitin ligase to more readily access <scene name='Michael_Purol_Sandbox_1/Lys_62/1'>Lys 62</scene> and thus tag p19INK4d for degradation at the proteasome. [4]

Michael Purol at 16:01, 3 November 2009

Michael Purol — Tue, 03 Nov 2009 16:01:25 GMT

←Older revision		Revision as of 16:01, 3 November 2009
Line 22:		Line 22:
	==Cancer Prevention==		==Cancer Prevention==

-	In a 2005 study by Ceruti et al., researchers determined that, in addition to ~~and independent of~~ its role as a cell cycle inhibitor, p19INK4d is involved in the maintenence of DNA integrity and, therefore, would contribute to cancer prevention. [3] This study shows that p19INK4d is the only INK4 protein whose expression is induced by UV light in neuroblastoma cells, and that this expression clearly reduces UV-induced (DNA-damage-induced) apoptosis by enhancing cellular ability to repair damaged DNA. [3]	+	In a 2005 study by Ceruti et al., researchers determined that, in addition to its role as a cell cycle inhibitor, p19INK4d is involved in the maintenence of DNA integrity and, therefore, would contribute to cancer prevention. [3] This study shows that p19INK4d is the only INK4 protein whose expression is induced by UV light in neuroblastoma cells, and that this expression clearly reduces UV-induced (DNA-damage-induced) apoptosis by enhancing cellular ability to repair damaged DNA. [3]

	==Low et al. (2009) Study==		==Low et al. (2009) Study==

Michael Purol at 15:49, 3 November 2009

Michael Purol — Tue, 03 Nov 2009 15:49:47 GMT

←Older revision		Revision as of 15:49, 3 November 2009
Line 18:		Line 18:
	==Cancer==		==Cancer==

-	Loss of INK4 gene product function, particularly that of p16(INK4a), is found in 10-60% of human tumors, suggesting that broadly applicable anticancer therapies might be based on restoration of p16INK4a CDK inhibitory function. Although much less frequent, defects of p19INK4d have also been associated with human cancer (osteosarcomas). [1] In human osteosarcomas, p19INK4d function has been found to be altered ~~or inhibited~~ by phosphorylation at ~~both~~ Ser 66 and Ser 76, and ~~also ubiquitinated~~ at Lys 62. [5]	+	Loss of INK4 gene product function, particularly that of p16(INK4a), is found in 10-60% of human tumors, suggesting that broadly applicable anticancer therapies might be based on restoration of p16INK4a CDK inhibitory function. Although much less frequent, defects of p19INK4d have also been associated with human cancer (osteosarcomas). [1] In human osteosarcomas, p19INK4d function has been found to be altered by phosphorylation at Ser 66 and Ser 76 and ubiquitination at Lys 62. [5]
		+
		+	==Cancer Prevention==
		+
		+	In a 2005 study by Ceruti et al., researchers determined that, in addition to and independent of its role as a cell cycle inhibitor, p19INK4d is involved in the maintenence of DNA integrity and, therefore, would contribute to cancer prevention. [3] This study shows that p19INK4d is the only INK4 protein whose expression is induced by UV light in neuroblastoma cells, and that this expression clearly reduces UV-induced (DNA-damage-induced) apoptosis by enhancing cellular ability to repair damaged DNA. [3]

	==Low et al. (2009) Study==		==Low et al. (2009) Study==
Line 26:		Line 30:
	Researchers then mimicked known phosphorylation sites with glutamate substitutions at <scene name='Michael_Purol_Sandbox_1/Ser_66/1'>Ser 66</scene> and <scene name='Michael_Purol_Sandbox_1/Ser_76/1'>Ser 76</scene> within ''E. coli'' to test the impact of introduced negative charges at these positions on the structural stability of P19INK4d. Results indicated that both mutants with the glutamate substitutions at Ser 76 only and doubly-substituted mutants with glutamate substitutions at Ser 66 and 76 were significantly destabilized in comparison to the wild-type protein, while mutants with only a Ser 66 glutamate substitution showed no significant destabilization. In particular, the results supported earlier findings that a negative charge at Ser 76 severely decreases protein stability in AR1 and AR2 by affecting the hydrogen bonding pattern of the adjacent residues, leading to a partial unfolding reaction and a higher flexibility of the loop. These findings suggest that phosphorylation or mimetic mutation at Ser 76 position allows ubiquitin ligase to access <scene name='Michael_Purol_Sandbox_1/Lys_62/1'>Lys 62</scene> more easily and thus tag p19INK4d for degradation at the proteasome. [4]		Researchers then mimicked known phosphorylation sites with glutamate substitutions at <scene name='Michael_Purol_Sandbox_1/Ser_66/1'>Ser 66</scene> and <scene name='Michael_Purol_Sandbox_1/Ser_76/1'>Ser 76</scene> within ''E. coli'' to test the impact of introduced negative charges at these positions on the structural stability of P19INK4d. Results indicated that both mutants with the glutamate substitutions at Ser 76 only and doubly-substituted mutants with glutamate substitutions at Ser 66 and 76 were significantly destabilized in comparison to the wild-type protein, while mutants with only a Ser 66 glutamate substitution showed no significant destabilization. In particular, the results supported earlier findings that a negative charge at Ser 76 severely decreases protein stability in AR1 and AR2 by affecting the hydrogen bonding pattern of the adjacent residues, leading to a partial unfolding reaction and a higher flexibility of the loop. These findings suggest that phosphorylation or mimetic mutation at Ser 76 position allows ubiquitin ligase to access <scene name='Michael_Purol_Sandbox_1/Lys_62/1'>Lys 62</scene> more easily and thus tag p19INK4d for degradation at the proteasome. [4]

-	==Ceruti et al. (2005) Study==

	==About this Structure==		==About this Structure==

Michael Purol at 15:34, 3 November 2009

Michael Purol — Tue, 03 Nov 2009 15:34:20 GMT

←Older revision		Revision as of 15:34, 3 November 2009
Line 27:		Line 27:

	==Ceruti et al. (2005) Study==		==Ceruti et al. (2005) Study==
		+
		+	==About this Structure==
		+	1BD8 is a 1 chain 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=1BD8 OCA].

	==References==		==References==

Michael Purol at 15:31, 3 November 2009

Michael Purol — Tue, 03 Nov 2009 15:31:01 GMT

←Older revision		Revision as of 15:31, 3 November 2009
Line 18:		Line 18:
	==Cancer==		==Cancer==

-	In human osteosarcomas, p19INK4d function has been found to be altered or inhibited by phosphorylation at both Ser 66 and Ser 76, and also ubiquitinated at Lys 62. [5]	+	Loss of INK4 gene product function, particularly that of p16(INK4a), is found in 10-60% of human tumors, suggesting that broadly applicable anticancer therapies might be based on restoration of p16INK4a CDK inhibitory function. Although much less frequent, defects of p19INK4d have also been associated with human cancer (osteosarcomas). [1] In human osteosarcomas, p19INK4d function has been found to be altered or inhibited by phosphorylation at both Ser 66 and Ser 76, and also ubiquitinated at Lys 62. [5]

	==Low et al. (2009) Study==		==Low et al. (2009) Study==
Line 29:		Line 29:

	==References==		==References==
-	[1] ~~Barrick D~~. (~~2009~~). ~~Biological Regulation via Ankyrin Repeat Folding~~. ~~Acs Chemical Biology 4~~,19-22.	+	[1] Baumgartner R, Fernandez-Catalan C, Winoto A, Huber R, Engh RA, Holak TA. (1998). Structure of human cyclin-dependent kinase inhibitor p19(INK4d): comparison to known ankyrin-repeat-containing structures and implications for the dysfunction of tumor suppressor p16(INK4a). Structure with Folding & Design 6,1279-1290.

	[2] Brotherton DH, Dhanaraj V, Wick S, Brizuela L, Domaille PJ, Volyanik E, Xu X, Parisini E, Smith BO, Archer SJ and others. (1998). Crystal structure of the complex of the cyclin D dependent kinase Cdk6 bound to the cell-cycle inhibitor p19(INK4d). Nature 395,244-250.		[2] Brotherton DH, Dhanaraj V, Wick S, Brizuela L, Domaille PJ, Volyanik E, Xu X, Parisini E, Smith BO, Archer SJ and others. (1998). Crystal structure of the complex of the cyclin D dependent kinase Cdk6 bound to the cell-cycle inhibitor p19(INK4d). Nature 395,244-250.

Michael Purol at 14:59, 3 November 2009

Michael Purol — Tue, 03 Nov 2009 14:59:38 GMT

←Older revision		Revision as of 14:59, 3 November 2009
Line 13:		Line 13:
	==p19INK4d Structure==		==p19INK4d Structure==

-	The four INK4 proteins share a similar sturcture consisting of either four (p15 & p16) or five (p18 and '''p19''') ankyrin repeats (AR). The binding interactions between p19INK4d and CDK4/6 occur primarily at AR 1 and AR2. Phosphorylation sites of p19INK4d have been identified at Ser 66 and Ser 76, and Ubiquitination ligase has been found to attack the Lys 62 position.	+	The four INK4 proteins share a similar sturcture consisting of either four (p15 & p16) or five (p18 and '''p19''') ankyrin repeats (AR). The binding interactions between p19INK4d and CDK4/6 occur primarily at AR 1 and AR2. Phosphorylation sites of p19INK4d have been identified at <scene name='Michael_Purol_Sandbox_1/Ser_66/1'>Ser 66</scene> and <scene name='Michael_Purol_Sandbox_1/Ser_76/1'>Ser 76</scene>, and Ubiquitination ligase has been found to attack the <scene name='Michael_Purol_Sandbox_1/Lys_62/1'>Lys 62</scene> position. [4]

-	<scene name='Michael_Purol_Sandbox_1/Lys_62/1'>Lys 62</scene>
-
-	<scene name='Michael_Purol_Sandbox_1/Ser_66/1'>Ser 66</scene>
-
-	<scene name='Michael_Purol_Sandbox_1/Ser_76/1'>Ser 76</scene>

	==Cancer==		==Cancer==

Michael Purol at 14:57, 3 November 2009

Michael Purol — Tue, 03 Nov 2009 14:57:25 GMT

←Older revision		Revision as of 14:57, 3 November 2009
Line 13:		Line 13:
	==p19INK4d Structure==		==p19INK4d Structure==

-	The four INK4 proteins share a similar sturcture consisting of either four (p15 & p16) or five (p18 and '''p19''') ankyrin repeats (AR).	+	The four INK4 proteins share a similar sturcture consisting of either four (p15 & p16) or five (p18 and '''p19''') ankyrin repeats (AR). The binding interactions between p19INK4d and CDK4/6 occur primarily at AR 1 and AR2. Phosphorylation sites of p19INK4d have been identified at Ser 66 and Ser 76, and Ubiquitination ligase has been found to attack the Lys 62 position.

	<scene name='Michael_Purol_Sandbox_1/Lys_62/1'>Lys 62</scene>		<scene name='Michael_Purol_Sandbox_1/Lys_62/1'>Lys 62</scene>
Line 29:		Line 29:
	This study took an in-depth look at the structural consequences of phosphorylation at different sites of p19INK4d. Low et al. replaced Phe 86 with a trytophan residue which acted as a fluorescence-sensitive probe within a pseudo-wild type (in stability and function) mutant that displayed a hyperfluorescent intermediate which could be detected in unfolding and folding kinetics, but not at equilibrium conditions.		This study took an in-depth look at the structural consequences of phosphorylation at different sites of p19INK4d. Low et al. replaced Phe 86 with a trytophan residue which acted as a fluorescence-sensitive probe within a pseudo-wild type (in stability and function) mutant that displayed a hyperfluorescent intermediate which could be detected in unfolding and folding kinetics, but not at equilibrium conditions.

-	Researchers then mimicked known phosphorylation sites with glutamate substitutions at <scene name='Michael_Purol_Sandbox_1/Ser_66/1'>Ser 66</scene> and <scene name='Michael_Purol_Sandbox_1/Ser_76/1'>Ser 76</scene> within ''E. coli'' to test the impact of introduced negative charges at these positions on the structural stability of P19INK4d. Results indicated that mutants with the glutamate substitutions at Ser 76 ~~by itself,~~ and mutants with glutamate substitutions at ~~both~~ Ser 66 and 76 were significantly destabilized in comparison to the wild-type protein, while mutants with only a Ser 66 glutamate substitution showed no significant destabilization. In particular, the results supported earlier findings that a negative charge at Ser 76 severely decreases protein stability in AR1 and AR2 by affecting the hydrogen bonding pattern of the adjacent residues, leading to higher flexibility of the loop. These findings suggest that phosphorylation or mimetic mutation at Ser 76 position allows ubiquitin ligase to access Lys 62 more easily and thus tag ~~p19~~ for degradation at the proteasome. [4]	+	Researchers then mimicked known phosphorylation sites with glutamate substitutions at <scene name='Michael_Purol_Sandbox_1/Ser_66/1'>Ser 66</scene> and <scene name='Michael_Purol_Sandbox_1/Ser_76/1'>Ser 76</scene> within ''E. coli'' to test the impact of introduced negative charges at these positions on the structural stability of P19INK4d. Results indicated that both mutants with the glutamate substitutions at Ser 76 only and doubly-substituted mutants with glutamate substitutions at Ser 66 and 76 were significantly destabilized in comparison to the wild-type protein, while mutants with only a Ser 66 glutamate substitution showed no significant destabilization. In particular, the results supported earlier findings that a negative charge at Ser 76 severely decreases protein stability in AR1 and AR2 by affecting the hydrogen bonding pattern of the adjacent residues, leading to a partial unfolding reaction and a higher flexibility of the loop. These findings suggest that phosphorylation or mimetic mutation at Ser 76 position allows ubiquitin ligase to access <scene name='Michael_Purol_Sandbox_1/Lys_62/1'>Lys 62</scene> more easily and thus tag p19INK4d for degradation at the proteasome. [4]

	==Ceruti et al. (2005) Study==		==Ceruti et al. (2005) Study==

Michael Purol at 14:37, 3 November 2009

Michael Purol — Tue, 03 Nov 2009 14:37:17 GMT

←Older revision		Revision as of 14:37, 3 November 2009
Line 23:		Line 23:
	==Cancer==		==Cancer==

-	In human osteosarcomas, p19INK4d has been found to ~~phosphorylated~~ at both Ser 66 and Ser 76, and also ubiquitinated at Lys 62.	+	In human osteosarcomas, p19INK4d function has been found to be altered or inhibited by phosphorylation at both Ser 66 and Ser 76, and also ubiquitinated at Lys 62. [5]

	==Low et al. (2009) Study==		==Low et al. (2009) Study==
Line 29:		Line 29:
	This study took an in-depth look at the structural consequences of phosphorylation at different sites of p19INK4d. Low et al. replaced Phe 86 with a trytophan residue which acted as a fluorescence-sensitive probe within a pseudo-wild type (in stability and function) mutant that displayed a hyperfluorescent intermediate which could be detected in unfolding and folding kinetics, but not at equilibrium conditions.		This study took an in-depth look at the structural consequences of phosphorylation at different sites of p19INK4d. Low et al. replaced Phe 86 with a trytophan residue which acted as a fluorescence-sensitive probe within a pseudo-wild type (in stability and function) mutant that displayed a hyperfluorescent intermediate which could be detected in unfolding and folding kinetics, but not at equilibrium conditions.

-	Researchers then mimicked known phosphorylation sites with glutamate substitutions at <scene name='Michael_Purol_Sandbox_1/Ser_66/1'>Ser 66</scene> and <scene name='Michael_Purol_Sandbox_1/Ser_76/1'>Ser 76</scene> within ''E. coli'' to test the impact of introduced negative charges at these positions on the structural stability of P19INK4d.	+	Researchers then mimicked known phosphorylation sites with glutamate substitutions at <scene name='Michael_Purol_Sandbox_1/Ser_66/1'>Ser 66</scene> and <scene name='Michael_Purol_Sandbox_1/Ser_76/1'>Ser 76</scene> within ''E. coli'' to test the impact of introduced negative charges at these positions on the structural stability of P19INK4d. Results indicated that mutants with the glutamate substitutions at Ser 76 by itself, and mutants with glutamate substitutions at both Ser 66 and 76 were significantly destabilized in comparison to the wild-type protein, while mutants with only a Ser 66 glutamate substitution showed no significant destabilization. In particular, the results supported earlier findings that a negative charge at Ser 76 severely decreases protein stability in AR1 and AR2 by affecting the hydrogen bonding pattern of the adjacent residues, leading to higher flexibility of the loop. These findings suggest that phosphorylation or mimetic mutation at Ser 76 position allows ubiquitin ligase to access Lys 62 more easily and thus tag p19 for degradation at the proteasome. [4]

	==Ceruti et al. (2005) Study==		==Ceruti et al. (2005) Study==