User:Tsung-Yi Lin/Sandbox - Revision history

Tsung-Yi Lin at 18:44, 9 November 2010

Tsung-Yi Lin — Tue, 09 Nov 2010 18:44:58 GMT

←Older revision		Revision as of 18:44, 9 November 2010
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	== Reference ==		== Reference ==
-	*Twenty years of therapy for HIV-1 infection~~, Roger J Pomerantz & David L Horn~~, Nature Medicine 9, 867-873, ~~2003~~	+	*<ref name= "{history}"> Roger J Pomerantz & David L Horn, Twenty years of therapy for HIV-1 infection, Nature Medicine, 2003, 9, 867-873, </ref>
		+	<references/>

	*Retroviral proteases, Ben M Dunn, Maureen M Goodenow, Alla Gustchina, and Alexander Wlodawer, Genome Biol. 2002; 3(4): reviews3006.1–reviews3006.7.		*Retroviral proteases, Ben M Dunn, Maureen M Goodenow, Alla Gustchina, and Alexander Wlodawer, Genome Biol. 2002; 3(4): reviews3006.1–reviews3006.7.

Tsung-Yi Lin: /* HIV genome and protease */

Tsung-Yi Lin — Thu, 11 Dec 2008 08:03:36 GMT

HIV genome and protease

←Older revision		Revision as of 08:03, 11 December 2008
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	[[Image:Infection_process.jpg\|350px]]		[[Image:Infection_process.jpg\|350px]]

-	== HIV genome and protease ==	+	== HIV genome and HIV-1 protease ==

	HIV genome contains three main genes: gag, pol, and env.		HIV genome contains three main genes: gag, pol, and env.

Tsung-Yi Lin: /* HIV-1 protease */

Tsung-Yi Lin — Thu, 11 Dec 2008 08:02:55 GMT

HIV-1 protease

←Older revision		Revision as of 08:02, 11 December 2008
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	'''HIV-1 Protease''' is a viral aspartic protease that responsible for maturation of [http://en.wikipedia.org/wiki/HIV human immunodeficiency virus (HIV)].		'''HIV-1 Protease''' is a viral aspartic protease that responsible for maturation of [http://en.wikipedia.org/wiki/HIV human immunodeficiency virus (HIV)].

-	HIV-1 protease cleaves an [http://en.wikipedia.org/wiki/HIV human immunodeficiency virus (HIV)] precursor proteins, such as cleaving the [http://en.wikipedia.org/wiki/HIV#Replication_cycle env protein],[http://en.wikipedia.org/wiki/Gp160 glycoprotein (GP) 160], into [http://en.wikipedia.org/wiki/Gp160#gp41 gp41]	+	HIV-1 protease cleaves an [http://en.wikipedia.org/wiki/HIV human immunodeficiency virus (HIV)] precursor proteins, such as cleaving the [http://en.wikipedia.org/wiki/HIV#Replication_cycle env protein], [http://en.wikipedia.org/wiki/Gp160 glycoprotein (GP) 160], into [http://en.wikipedia.org/wiki/Gp160#gp41 gp41]
	and [http://en.wikipedia.org/wiki/Gp160#gp120 gp120]. [http://en.wikipedia.org/wiki/Gp160#gp120 Gp120] protrudes from the surface of HIV and binds to CD4+ T cells and [http://en.wikipedia.org/wiki/Gp160#gp41 gp41]		and [http://en.wikipedia.org/wiki/Gp160#gp120 gp120]. [http://en.wikipedia.org/wiki/Gp160#gp120 Gp120] protrudes from the surface of HIV and binds to CD4+ T cells and [http://en.wikipedia.org/wiki/Gp160#gp41 gp41]
	embedded in the outer envelope help [http://en.wikipedia.org/wiki/Gp160#gp120 gp120] bind CD4+ T cells, and they both play a role in HIV's infection of [http://en.wikipedia.org/wiki/CD4_cell CD4+ T cells]. Therefore, HIV-1 protease make the virus have the ability to infect new cells by the cleave process. In other words, HIV-1 protease is responsible for maturation of the [http://en.wikipedia.org/wiki/Virion virion] by cleaving proteins into their mature form.		embedded in the outer envelope help [http://en.wikipedia.org/wiki/Gp160#gp120 gp120] bind CD4+ T cells, and they both play a role in HIV's infection of [http://en.wikipedia.org/wiki/CD4_cell CD4+ T cells]. Therefore, HIV-1 protease make the virus have the ability to infect new cells by the cleave process. In other words, HIV-1 protease is responsible for maturation of the [http://en.wikipedia.org/wiki/Virion virion] by cleaving proteins into their mature form.

Tsung-Yi Lin: /* HIV-1 protease structure */

Tsung-Yi Lin — Thu, 11 Dec 2008 08:02:00 GMT

HIV-1 protease structure

←Older revision		Revision as of 08:02, 11 December 2008
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	[[Image:Binding and catalytic site.jpg\|550px]]		[[Image:Binding and catalytic site.jpg\|550px]]
		+
		+	== Structure analysis ==
		+
		+	The concavity analysis shown below can be used to determine possible binding spots. The most likely spot shown red determined with [http://hotpatch.mbi.ucla.edu/ HotPatch]
		+
		+	[[Image:Concavity.png\|460px]]
		+
		+	Conserved residues for this protein was analyzed with [http://consurf.tau.ac.il/index.html ConSurf]
		+
		+	[[Image:ConSurf outptus.jpg\|460px]]

	== Reference ==		== Reference ==

Tsung-Yi Lin: /* HIV-1 protease structure */

Tsung-Yi Lin — Thu, 11 Dec 2008 07:54:13 GMT

HIV-1 protease structure

←Older revision		Revision as of 07:54, 11 December 2008
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	*This domain is quite useful in dimer stabilization, as well as the catalytic site stability.		*This domain is quite useful in dimer stabilization, as well as the catalytic site stability.
	*The interface between the core and terminal domains is composed primarily of small hydrophobic residues. The helix of the terminal domain packs against several beta-strands of the core domain.		*The interface between the core and terminal domains is composed primarily of small hydrophobic residues. The helix of the terminal domain packs against several beta-strands of the core domain.
		+
		+	[[Image:Domains.png\|550px]]

	''The flap domains''		''The flap domains''
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	*Flexible flaps enclose the active site and provide important ligand binding interactions.		*Flexible flaps enclose the active site and provide important ligand binding interactions.

-	[[Image:~~Domains~~.~~png~~\|550px]]	+	[[Image:Binding and catalytic site.jpg\|550px]]

	== Reference ==		== Reference ==

Tsung-Yi Lin: /* HIV-1 protease structure */

Tsung-Yi Lin — Thu, 11 Dec 2008 07:50:40 GMT

HIV-1 protease structure

←Older revision		Revision as of 07:50, 11 December 2008
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	*It consists 99 amino acids, which forming 10 β-strand and 1 α-helix.		*It consists 99 amino acids, which forming 10 β-strand and 1 α-helix.
-	[[Image:Mechanism.jpg\|~~350px~~]]	+	[[Image:Mechanism.jpg\|650px]]


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	*Flexible flaps enclose the active site and provide important ligand binding interactions.		*Flexible flaps enclose the active site and provide important ligand binding interactions.

-	[[Image:Domains.png\|~~350px~~]]	+	[[Image:Domains.png\|550px]]

	== Reference ==		== Reference ==

Tsung-Yi Lin: /* HIV-1 protease structure */

Tsung-Yi Lin — Thu, 11 Dec 2008 07:50:05 GMT

HIV-1 protease structure

←Older revision		Revision as of 07:50, 11 December 2008
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	*It consists 99 amino acids, which forming 10 β-strand and 1 α-helix.		*It consists 99 amino acids, which forming 10 β-strand and 1 α-helix.
-	[[Image:~~Example~~.jpg]]	+	[[Image:Mechanism.jpg\|350px]]


	'''Domains in HIV-1 protease'''		'''Domains in HIV-1 protease'''
		+
	''Terminal domain or dimerization domain''		''Terminal domain or dimerization domain''
	*Consists of the termini four-stranded beta-sheet; (residues 1-4, and 95-99 of each monomer), the turn encompassing residues 4-9, and the helix (residues 86-94 of each monomer). This domain is quite crucial in dimer formation and stabilization of an active PR.		*Consists of the termini four-stranded beta-sheet; (residues 1-4, and 95-99 of each monomer), the turn encompassing residues 4-9, and the helix (residues 86-94 of each monomer). This domain is quite crucial in dimer formation and stabilization of an active PR.
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	*These are two; one from each monomer.		*These are two; one from each monomer.
	*Composed of primarily four beta-strand structures; and is quite compact.		*Composed of primarily four beta-strand structures; and is quite compact.
-	Residues 10-32 and 63-85 from each monomer make up the domain sequence	+	*Residues 10-32 and 63-85 from each monomer make up the domain sequence
	*The conserved Asp25-Thr26-Gly27 catalytic triad, is situated at the interface of the core domains from the two monomers.		*The conserved Asp25-Thr26-Gly27 catalytic triad, is situated at the interface of the core domains from the two monomers.
	*This domain is quite useful in dimer stabilization, as well as the catalytic site stability.		*This domain is quite useful in dimer stabilization, as well as the catalytic site stability.
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	*Flexible flaps enclose the active site and provide important ligand binding interactions.		*Flexible flaps enclose the active site and provide important ligand binding interactions.

-	[[Image:~~Example~~.~~jpg~~]]	+	[[Image:Domains.png\|350px]]

	== Reference ==		== Reference ==

Tsung-Yi Lin: /* HIV-1 protease structure */

Tsung-Yi Lin — Thu, 11 Dec 2008 07:47:30 GMT

HIV-1 protease structure

←Older revision		Revision as of 07:47, 11 December 2008
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	'''Domains in HIV-1 protease'''		'''Domains in HIV-1 protease'''
-	*Terminal domain or dimerization domain	+	''Terminal domain or dimerization domain''
-	Consists of the termini four-stranded beta-sheet; (residues 1-4, and 95-99 of each monomer), the turn encompassing residues 4-9, and the helix (residues 86-94 of each monomer). This domain is quite crucial in dimer formation and stabilization of an active PR.	+	*Consists of the termini four-stranded beta-sheet; (residues 1-4, and 95-99 of each monomer), the turn encompassing residues 4-9, and the helix (residues 86-94 of each monomer). This domain is quite crucial in dimer formation and stabilization of an active PR.

-	*The core domains	+	''The core domains''
-	These are two; one from each monomer.	+	*These are two; one from each monomer.
-	Composed of primarily four beta-strand structures; and is quite compact.	+	*Composed of primarily four beta-strand structures; and is quite compact.
	Residues 10-32 and 63-85 from each monomer make up the domain sequence		Residues 10-32 and 63-85 from each monomer make up the domain sequence
-	The conserved Asp25-Thr26-Gly27 catalytic triad, is situated at the interface of the core domains from the two monomers.	+	*The conserved Asp25-Thr26-Gly27 catalytic triad, is situated at the interface of the core domains from the two monomers.
-	This domain is quite useful in dimer stabilization, as well as the catalytic site stability.	+	*This domain is quite useful in dimer stabilization, as well as the catalytic site stability.
-	The interface between the core and terminal domains is composed primarily of small hydrophobic residues. The helix of the terminal domain packs against several beta-strands of the core domain.	+	*The interface between the core and terminal domains is composed primarily of small hydrophobic residues. The helix of the terminal domain packs against several beta-strands of the core domain.

-	*The flap domains	+	''The flap domains''
-	This domain includes a mostly solvent exposed loop (residue 33-43) preceding the beta hairpin containing the flaps (residue 44-63).	+	*This domain includes a mostly solvent exposed loop (residue 33-43) preceding the beta hairpin containing the flaps (residue 44-63).
-	Flexible flaps enclose the active site and provide important ligand binding interactions	+	*Flexible flaps enclose the active site and provide important ligand binding interactions.
		+
		+	[[Image:Example.jpg]]

	== Reference ==		== Reference ==

Tsung-Yi Lin: /* HIV-1 protease structure */

Tsung-Yi Lin — Thu, 11 Dec 2008 07:44:45 GMT

HIV-1 protease structure

←Older revision		Revision as of 07:44, 11 December 2008
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	== HIV-1 protease structure ==		== HIV-1 protease structure ==
		+	'''Family and Biological unit'''

		+	*HIV-1 protease belongs to aspartic family, which also includes digestive enzyme pepsin, the lysosomal cathepsin, share common catalytic mechanism

		+	*It functions as a homodimer (two identical polypeptide chains) with only one active site.
		+
		+	*It consists 99 amino acids, which forming 10 β-strand and 1 α-helix.
		+	[[Image:Example.jpg]]
		+
		+
		+	'''Domains in HIV-1 protease'''
		+	*Terminal domain or dimerization domain
		+	Consists of the termini four-stranded beta-sheet; (residues 1-4, and 95-99 of each monomer), the turn encompassing residues 4-9, and the helix (residues 86-94 of each monomer). This domain is quite crucial in dimer formation and stabilization of an active PR.
		+
		+	*The core domains
		+	These are two; one from each monomer.
		+	Composed of primarily four beta-strand structures; and is quite compact.
		+	Residues 10-32 and 63-85 from each monomer make up the domain sequence
		+	The conserved Asp25-Thr26-Gly27 catalytic triad, is situated at the interface of the core domains from the two monomers.
		+	This domain is quite useful in dimer stabilization, as well as the catalytic site stability.
		+	The interface between the core and terminal domains is composed primarily of small hydrophobic residues. The helix of the terminal domain packs against several beta-strands of the core domain.
		+
		+	*The flap domains
		+	This domain includes a mostly solvent exposed loop (residue 33-43) preceding the beta hairpin containing the flaps (residue 44-63).
		+	Flexible flaps enclose the active site and provide important ligand binding interactions

	== Reference ==		== Reference ==

Tsung-Yi Lin: /* family and biological unit */

Tsung-Yi Lin — Thu, 11 Dec 2008 07:33:56 GMT

family and biological unit

←Older revision		Revision as of 07:33, 11 December 2008
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	== HIV-1 protease structure ==		== HIV-1 protease structure ==

-	~~== family and biological unit ==~~	+

	== Reference ==		== Reference ==