User:Kristen Huber/Sandbox 1 - Revision history

Kristen Huber at 19:08, 4 May 2010

Kristen Huber — Tue, 04 May 2010 19:08:16 GMT

←Older revision		Revision as of 19:08, 4 May 2010
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	<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_dimer/1'>Caspase-9 Molecular Playground</scene>		<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_dimer/1'>Caspase-9 Molecular Playground</scene>

-
-	Molecular Playground banner: Cleaved Caspase-9, the active dimer.

	Caspase-9 in the active, “prepared to cut” state, exists as a dimer. The dimer can be described as two monomers of a large and small subunit related by two-fold symmetry. The dimer is formed through interactions of the amino acids on a β-strand from each monomer which forms a continuous central β –sheet [1]. In addition, a seven residue loop also makes interactions across the interface. A loop bundle exists in this molecule as well and when properly ordered, it is able to “bind and cut” its substrate.		Caspase-9 in the active, “prepared to cut” state, exists as a dimer. The dimer can be described as two monomers of a large and small subunit related by two-fold symmetry. The dimer is formed through interactions of the amino acids on a β-strand from each monomer which forms a continuous central β –sheet [1]. In addition, a seven residue loop also makes interactions across the interface. A loop bundle exists in this molecule as well and when properly ordered, it is able to “bind and cut” its substrate.
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	<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/1'>Caspase-9/XIAP BIR3 Molecular Playground</scene>		<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/1'>Caspase-9/XIAP BIR3 Molecular Playground</scene>

-
-	Molecular Playground banner: Caspase-9/XIAP BIR3 Complex, the inactive monomer.

	The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.		The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.

Kristen Huber at 19:06, 4 May 2010

Kristen Huber — Tue, 04 May 2010 19:06:31 GMT

←Older revision		Revision as of 19:06, 4 May 2010
Line 10:		Line 10:
	<applet load='1jxq' size='400' color='white' frame='true' align='right' caption='Caspase-9 Dimer'		<applet load='1jxq' size='400' color='white' frame='true' align='right' caption='Caspase-9 Dimer'

-	scene='User:Kristen_Huber/Sandbox_1/Caspase-9_dimer/1'>Caspase-9 Molecular Playground</~~scene~~>	+	scene='User:Kristen_Huber/Sandbox_1/Caspase-9_dimer/1'>Caspase-9 Molecular Playground</applet>

	<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_dimer/1'>Caspase-9 Molecular Playground</scene>		<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_dimer/1'>Caspase-9 Molecular Playground</scene>
Line 23:		Line 23:
	<applet load='1nw9' size='400' color='white' frame='true' align='right' caption='Caspase-9/XIAP-BIR3 Inhibitory Complex'		<applet load='1nw9' size='400' color='white' frame='true' align='right' caption='Caspase-9/XIAP-BIR3 Inhibitory Complex'

-	<scene='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/1'>Caspase-9/XIAP BIR3 Molecular Playground</~~scene~~>	+	scene='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/1'>Caspase-9/XIAP BIR3 Molecular Playground</applet>

	<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/1'>Caspase-9/XIAP BIR3 Molecular Playground</scene>		<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/1'>Caspase-9/XIAP BIR3 Molecular Playground</scene>
		+
		+
		+	Molecular Playground banner: Caspase-9/XIAP BIR3 Complex, the inactive monomer.

	The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.		The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.

Kristen Huber at 19:02, 4 May 2010

Kristen Huber — Tue, 04 May 2010 19:02:15 GMT

←Older revision		Revision as of 19:02, 4 May 2010
Line 10:		Line 10:
	<applet load='1jxq' size='400' color='white' frame='true' align='right' caption='Caspase-9 Dimer'		<applet load='1jxq' size='400' color='white' frame='true' align='right' caption='Caspase-9 Dimer'

-	<scene='User:Kristen_Huber/Sandbox_1/Caspase-9_dimer/1'>Caspase-9 Molecular Playground</scene>	+	scene='User:Kristen_Huber/Sandbox_1/Caspase-9_dimer/1'>Caspase-9 Molecular Playground</scene>

	<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_dimer/1'>Caspase-9 Molecular Playground</scene>		<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_dimer/1'>Caspase-9 Molecular Playground</scene>

Kristen Huber at 19:01, 4 May 2010

Kristen Huber — Tue, 04 May 2010 19:01:37 GMT

←Older revision		Revision as of 19:01, 4 May 2010
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	==Structure==		==Structure==
		+
		+	<applet load='1jxq' size='400' color='white' frame='true' align='right' caption='Caspase-9 Dimer'
		+
		+	<scene='User:Kristen_Huber/Sandbox_1/Caspase-9_dimer/1'>Caspase-9 Molecular Playground</scene>
		+
		+	<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_dimer/1'>Caspase-9 Molecular Playground</scene>


Line 17:		Line 23:
	<applet load='1nw9' size='400' color='white' frame='true' align='right' caption='Caspase-9/XIAP-BIR3 Inhibitory Complex'		<applet load='1nw9' size='400' color='white' frame='true' align='right' caption='Caspase-9/XIAP-BIR3 Inhibitory Complex'

-	scene='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/1'>Caspase-9/XIAP BIR3 Molecular Playground</scene>	+	<scene='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/1'>Caspase-9/XIAP BIR3 Molecular Playground</scene>

	<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/1'>Caspase-9/XIAP BIR3 Molecular Playground</scene>		<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/1'>Caspase-9/XIAP BIR3 Molecular Playground</scene>

Kristen Huber at 18:37, 4 May 2010

Kristen Huber — Tue, 04 May 2010 18:37:44 GMT

←Older revision		Revision as of 18:37, 4 May 2010
Line 15:		Line 15:
	==Caspase-9/XIAP-BIR3 Interaction==		==Caspase-9/XIAP-BIR3 Interaction==

-	<applet load='1nw9' size='~~300~~' frame='true' align='right' caption='~~Caspase-9 Dimer'scene='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/1'>Molecular Playground banner:~~ Caspase-9/XIAP ~~BIR~~-3 Inhibitory Complex~~, the inactive monomer.</scene>/>~~	+	<applet load='1nw9' size='400' color='white' frame='true' align='right' caption='Caspase-9/XIAP-BIR3 Inhibitory Complex'

		+	scene='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/1'>Caspase-9/XIAP BIR3 Molecular Playground</scene>
		+
		+	<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/1'>Caspase-9/XIAP BIR3 Molecular Playground</scene>

	The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.		The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.

Kristen Huber at 18:33, 4 May 2010

Kristen Huber — Tue, 04 May 2010 18:33:03 GMT

←Older revision		Revision as of 18:33, 4 May 2010
Line 15:		Line 15:
	==Caspase-9/XIAP-BIR3 Interaction==		==Caspase-9/XIAP-BIR3 Interaction==

		+	<applet load='1nw9' size='300' frame='true' align='right' caption='Caspase-9 Dimer'scene='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/1'>Molecular Playground banner: Caspase-9/XIAP BIR-3 Inhibitory Complex, the inactive monomer.</scene>/>

-	Molecular Playground banner: Caspase-9/XIAP BIR-3 Inhibitory Complex, the inactive monomer.

	The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.		The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.

Kristen Huber at 18:12, 4 May 2010

Kristen Huber — Tue, 04 May 2010 18:12:26 GMT

←Older revision		Revision as of 18:12, 4 May 2010
Line 20:		Line 20:
	The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.		The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.

-	<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/2'>TextToBeDisplayed</scene>

	==See Also==		==See Also==

Kristen Huber at 18:11, 4 May 2010

Kristen Huber — Tue, 04 May 2010 18:11:47 GMT

←Older revision		Revision as of 18:11, 4 May 2010
Line 1:		Line 1:
	One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].		One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].
-
-
-	<applet load='1nw9' size='400' color='white' frame='true' align='right' caption='Caspase-9/XIAP BIR3(Inactive Monomer)'
-
-	Molecular Playground banner: Caspase-9/XIAP BIR-3 Inhibitory Complex, the inactive monomer.

	Caspase-9 belongs to a family of "molecular scissors" called cysteine aspartate proteases. These proteases are the facilitators of apoptosis, the highly process of programmed cell death which is an important cellular process critical for normal development and stability of an organism.		Caspase-9 belongs to a family of "molecular scissors" called cysteine aspartate proteases. These proteases are the facilitators of apoptosis, the highly process of programmed cell death which is an important cellular process critical for normal development and stability of an organism.
Line 12:		Line 7:

	==Structure==		==Structure==
		+
		+
		+	Molecular Playground banner: Cleaved Caspase-9, the active dimer.

	Caspase-9 in the active, “prepared to cut” state, exists as a dimer. The dimer can be described as two monomers of a large and small subunit related by two-fold symmetry. The dimer is formed through interactions of the amino acids on a β-strand from each monomer which forms a continuous central β –sheet [1]. In addition, a seven residue loop also makes interactions across the interface. A loop bundle exists in this molecule as well and when properly ordered, it is able to “bind and cut” its substrate.		Caspase-9 in the active, “prepared to cut” state, exists as a dimer. The dimer can be described as two monomers of a large and small subunit related by two-fold symmetry. The dimer is formed through interactions of the amino acids on a β-strand from each monomer which forms a continuous central β –sheet [1]. In addition, a seven residue loop also makes interactions across the interface. A loop bundle exists in this molecule as well and when properly ordered, it is able to “bind and cut” its substrate.

	==Caspase-9/XIAP-BIR3 Interaction==		==Caspase-9/XIAP-BIR3 Interaction==
		+
		+
		+	Molecular Playground banner: Caspase-9/XIAP BIR-3 Inhibitory Complex, the inactive monomer.

	The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.		The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.

Kristen Huber: /* Caspase-9/XIAP-BIR3 Interaction */

Kristen Huber — Tue, 04 May 2010 18:06:58 GMT

Caspase-9/XIAP-BIR3 Interaction

←Older revision		Revision as of 18:06, 4 May 2010
Line 18:		Line 18:

	The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.		The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.
		+
		+	<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/2'>TextToBeDisplayed</scene>

	==See Also==		==See Also==

Kristen Huber at 18:06, 4 May 2010

Kristen Huber — Tue, 04 May 2010 18:06:16 GMT

←Older revision		Revision as of 18:06, 4 May 2010
Line 5:		Line 5:

	Molecular Playground banner: Caspase-9/XIAP BIR-3 Inhibitory Complex, the inactive monomer.		Molecular Playground banner: Caspase-9/XIAP BIR-3 Inhibitory Complex, the inactive monomer.
-

	Caspase-9 belongs to a family of "molecular scissors" called cysteine aspartate proteases. These proteases are the facilitators of apoptosis, the highly process of programmed cell death which is an important cellular process critical for normal development and stability of an organism.		Caspase-9 belongs to a family of "molecular scissors" called cysteine aspartate proteases. These proteases are the facilitators of apoptosis, the highly process of programmed cell death which is an important cellular process critical for normal development and stability of an organism.
Line 17:		Line 16:

	==Caspase-9/XIAP-BIR3 Interaction==		==Caspase-9/XIAP-BIR3 Interaction==
-
-	<scene name='User:Kristen_Huber/Sandbox_1/Caspase-9_xiap_bir3_complex/1'>TextToBeDisplayed</scene>

	The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.		The protein-protein interface of the Caspase-9/XIAP BIR3 complex is dominated by a high level of shape complimentarily, a large collection of van der Walls contacts, and 11 intermolecular hydrogen bonds scattered throughout the entire 2200 Å2 interface of the complex [2]. This interaction prevents caspase-9 from dimerizing as well as prevents the organization of the loop bundle thus making the molecule inactive.