User:Ona Ambrozaite/Sandbox 1 - Revision history

Ona Ambrozaite at 18:24, 25 April 2020

Ona Ambrozaite — Sat, 25 Apr 2020 18:24:12 GMT

←Older revision		Revision as of 18:24, 25 April 2020
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	[https://www.ncbi.nlm.nih.gov/pubmed/?term=Differential+expression+of+milk+protein+genes+during+lactation+in+the+common+brushtail+possum]		[https://www.ncbi.nlm.nih.gov/pubmed/?term=Differential+expression+of+milk+protein+genes+during+lactation+in+the+common+brushtail+possum]
		+
		+	[https://www.ebi.ac.uk/pdbe/entry/pdb/2r73/protein/1]
		+
		+	[https://www.mrc-lmb.cam.ac.uk/rajini/views/matrix.html?allchains=2R73_B-C-A-D-&variant=no&cutoff=0.5&tab=chord&type=0&displayMode=pairSticks&chains=B,B&pdb=2R73_B&mychain=B&colorless=1&color1=cyan&color2=magenta&center=22&ring=ringone&highlightedsplom=&click=no&view=chord&colorbyproperty=0&resetview=0&highlighted=22,23,24,25,56&colors=0X428bca,0XC1BFBF,0XC1BFBF,0XC1BFBF,0XC1BFBF&group1=2&group2=2]

Ona Ambrozaite at 18:01, 25 April 2020

Ona Ambrozaite — Sat, 25 Apr 2020 18:01:44 GMT

←Older revision		Revision as of 18:01, 25 April 2020
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	<Structure 2R73 scene='83/837887/Trichosurin1_/5' align='right' caption='Surface Area of the Possum Milk Whey Lipocalin Trichosurin at pH 8.2 (PDB code 2r73)' />		<Structure 2R73 scene='83/837887/Trichosurin1_/5' align='right' caption='Surface Area of the Possum Milk Whey Lipocalin Trichosurin at pH 8.2 (PDB code 2r73)' />

-	As expected for an extracellular protein, trichosurin displays a large amount of [[hydrophilic]] <scene name='83/837887/Trichosurin1_/5'>surface area</scene>, with the more [[hydrophobic]] areas between the helix, the outside of the barrel, and the dimer interface where ligands such as 2-naphthol can bind. The binding site is found in the centre of the β-barrel and can be occupied by water and isopropanol molecules from the corresponding crystallization medium. In fact, researchers were able to crystallize trichosurin with 2-naphthol and 4-ethylphenol, the presence of which provides clues to the function of trichosurin.	+	As expected for an extracellular protein, trichosurin displays a large amount of [[hydrophilic]] <scene name='83/837887/Trichosurin1_/5'>surface area</scene>, with the more [[hydrophobic]] areas within the barrels themselves and between the helix, the outside of the barrel, and the dimer interface where ligands such as 2-naphthol can bind. The binding site is found in the centre of the β-barrel and can be occupied by water and isopropanol molecules from the corresponding crystallization medium. In fact, researchers were able to crystallize trichosurin with 2-naphthol and 4-ethylphenol, the presence of which provides clues to the function of trichosurin.

	Overall, trichosurin follows the general lipocalin superfamily fold pattern by having a β-barrel, several extended loop regions between β strands that close the ends of the barrel, and a helix near the C-terminus which is common to all lipocalins. There's also a major conserved feature of the lipocalin fold, a '''disulfide bond''', formed by <scene name='83/837887/Disulfide_bond/1'>two cysteines (Cys73 and Cys166)</scene> in each chain that ties the C-terminus to the corresponding β-strand. There are also '''N-linked glycosylations''' on Asp67 and Asp148 that could help keep trichosurin in solution, which is important since it is a secreted protein that needs to remain soluble and not aggregate. It could also facilitate the folding process and exert quality control to monitor trichosurin's folding.		Overall, trichosurin follows the general lipocalin superfamily fold pattern by having a β-barrel, several extended loop regions between β strands that close the ends of the barrel, and a helix near the C-terminus which is common to all lipocalins. There's also a major conserved feature of the lipocalin fold, a '''disulfide bond''', formed by <scene name='83/837887/Disulfide_bond/1'>two cysteines (Cys73 and Cys166)</scene> in each chain that ties the C-terminus to the corresponding β-strand. There are also '''N-linked glycosylations''' on Asp67 and Asp148 that could help keep trichosurin in solution, which is important since it is a secreted protein that needs to remain soluble and not aggregate. It could also facilitate the folding process and exert quality control to monitor trichosurin's folding.

Ona Ambrozaite at 19:00, 23 April 2020

Ona Ambrozaite — Thu, 23 Apr 2020 19:00:28 GMT

←Older revision		Revision as of 19:00, 23 April 2020
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	== Evolutionarily Related Proteins ==		== Evolutionarily Related Proteins ==

-	[[Image:Trichosurin Structural Features.png\|300px\|left\|thumb\| Evolutionarily Conserved and Variable Regions of Possum Milk Whey Lipocalin Trichosurin at pH 8.2]]	+	[[Image:Trichosurin Structural Features.png\|300px\|left\|thumb\| Evolutionarily Conserved and Variable Regions of Possum Milk Whey Lipocalin Trichosurin Chain A at pH 8.2]]

	[[Image:Trichosurin Conserved Residues of Chain A Sequence.png\|300px\|left\|thumb\| Conserved and Variable Amino Acid Residues of Possum Milk Whey Lipocalin Trichosurin Chain A]]		[[Image:Trichosurin Conserved Residues of Chain A Sequence.png\|300px\|left\|thumb\| Conserved and Variable Amino Acid Residues of Possum Milk Whey Lipocalin Trichosurin Chain A]]

Ona Ambrozaite at 18:55, 23 April 2020

Ona Ambrozaite — Thu, 23 Apr 2020 18:55:42 GMT

←Older revision		Revision as of 18:55, 23 April 2020
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	It is known that '''phenolic compounds''' are found in plants and used to deter herbivores, including possums, who then have to metabolize these compounds. It has also been shown that female possums concentrate phenolic compounds in their milk, which could act as a '''priming source for the young's liver to produce detoxifying enzymes''' that they can then use to survive while eating toxic plant sources.		It is known that '''phenolic compounds''' are found in plants and used to deter herbivores, including possums, who then have to metabolize these compounds. It has also been shown that female possums concentrate phenolic compounds in their milk, which could act as a '''priming source for the young's liver to produce detoxifying enzymes''' that they can then use to survive while eating toxic plant sources.

-	When other plant phenolics such as cinneol and gallic acid were tested in binding trichosurin, they displayed size and hydrogen-bonding groups ~~that~~ makes them appropriate ligands for trichosurin. Researchers also note that the hypothesis of phenolic compounds '''priming detoxification pathways''' would explain the high level of sequence conservation of trichosurin among metatherians.	+	When other plant phenolics such as cinneol and gallic acid were tested in binding trichosurin, they displayed size and hydrogen-bonding groups, which makes them appropriate ligands for trichosurin. Researchers also note that the hypothesis of phenolic compounds '''priming detoxification pathways''' would explain the high level of sequence conservation of trichosurin among metatherians.

	== Available 3D Structures ==		== Available 3D Structures ==

Ona Ambrozaite at 18:52, 23 April 2020

Ona Ambrozaite — Thu, 23 Apr 2020 18:52:55 GMT

←Older revision		Revision as of 18:52, 23 April 2020
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	== Relevance ==		== Relevance ==

-	Trichosurin, an important marsupial milk protein, is '''highly conserved''' across metatherians. The opossum, a metatherian, shared a common ancestor with humans around 130 million years ago and is of particular importance to study the differences between the development of metatherians and other mammals. In opossums, lactation is divided into three stages ~~that~~ each ~~have~~ a very unique milk composition, and trichosurin is one of three predominant lipocalins found in the milk of T. vulpecula <ref>PMID: 2636424</ref>, <ref>PMID: 9493361</ref>.	+	Trichosurin, an important marsupial milk protein, is '''highly conserved''' across metatherians. The opossum, a metatherian, shared a common ancestor with humans around 130 million years ago and is of particular importance to study the differences between the development of metatherians and other mammals. In opossums, lactation is divided into three stages, each has a very unique milk composition, and trichosurin is one of three predominant lipocalins found in the milk of ''T. vulpecula'' <ref>PMID: 2636424</ref>, <ref>PMID: 9493361</ref>.

	It is known that '''phenolic compounds''' are found in plants and used to deter herbivores, including possums, who then have to metabolize these compounds. It has also been shown that female possums concentrate phenolic compounds in their milk, which could act as a '''priming source for the young's liver to produce detoxifying enzymes''' that they can then use to survive while eating toxic plant sources.		It is known that '''phenolic compounds''' are found in plants and used to deter herbivores, including possums, who then have to metabolize these compounds. It has also been shown that female possums concentrate phenolic compounds in their milk, which could act as a '''priming source for the young's liver to produce detoxifying enzymes''' that they can then use to survive while eating toxic plant sources.

Ona Ambrozaite at 18:50, 23 April 2020

Ona Ambrozaite — Thu, 23 Apr 2020 18:50:13 GMT

←Older revision		Revision as of 18:50, 23 April 2020
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	== Relevance ==		== Relevance ==

-	Trichosurin, an important marsupial milk protein, is '''highly conserved''' across metatherians. The opossum, a metatherian, ~~shares~~ a common ancestor with humans around 130 million years ago, is of particular importance to study the differences between the development of metatherians and other mammals. In opossums, lactation is divided into three stages that each have a very unique milk composition, and trichosurin is one of three predominant lipocalins found in the milk of T. vulpecula <ref>PMID: 2636424</ref>, <ref>PMID: 9493361</ref>.	+	Trichosurin, an important marsupial milk protein, is '''highly conserved''' across metatherians. The opossum, a metatherian, shared a common ancestor with humans around 130 million years ago and is of particular importance to study the differences between the development of metatherians and other mammals. In opossums, lactation is divided into three stages that each have a very unique milk composition, and trichosurin is one of three predominant lipocalins found in the milk of T. vulpecula <ref>PMID: 2636424</ref>, <ref>PMID: 9493361</ref>.

	It is known that '''phenolic compounds''' are found in plants and used to deter herbivores, including possums, who then have to metabolize these compounds. It has also been shown that female possums concentrate phenolic compounds in their milk, which could act as a '''priming source for the young's liver to produce detoxifying enzymes''' that they can then use to survive while eating toxic plant sources.		It is known that '''phenolic compounds''' are found in plants and used to deter herbivores, including possums, who then have to metabolize these compounds. It has also been shown that female possums concentrate phenolic compounds in their milk, which could act as a '''priming source for the young's liver to produce detoxifying enzymes''' that they can then use to survive while eating toxic plant sources.

Ona Ambrozaite at 18:38, 23 April 2020

Ona Ambrozaite — Thu, 23 Apr 2020 18:38:27 GMT

←Older revision		Revision as of 18:38, 23 April 2020
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	Overall, trichosurin follows the general lipocalin superfamily fold pattern by having a β-barrel, several extended loop regions between β strands that close the ends of the barrel, and a helix near the C-terminus which is common to all lipocalins. There's also a major conserved feature of the lipocalin fold, a '''disulfide bond''', formed by <scene name='83/837887/Disulfide_bond/1'>two cysteines (Cys73 and Cys166)</scene> in each chain that ties the C-terminus to the corresponding β-strand. There are also '''N-linked glycosylations''' on Asp67 and Asp148 that could help keep trichosurin in solution, which is important since it is a secreted protein that needs to remain soluble and not aggregate. It could also facilitate the folding process and exert quality control to monitor trichosurin's folding.		Overall, trichosurin follows the general lipocalin superfamily fold pattern by having a β-barrel, several extended loop regions between β strands that close the ends of the barrel, and a helix near the C-terminus which is common to all lipocalins. There's also a major conserved feature of the lipocalin fold, a '''disulfide bond''', formed by <scene name='83/837887/Disulfide_bond/1'>two cysteines (Cys73 and Cys166)</scene> in each chain that ties the C-terminus to the corresponding β-strand. There are also '''N-linked glycosylations''' on Asp67 and Asp148 that could help keep trichosurin in solution, which is important since it is a secreted protein that needs to remain soluble and not aggregate. It could also facilitate the folding process and exert quality control to monitor trichosurin's folding.

-	The binding preference for small phenolic compounds such as 2-naphthol and 4-ethylphenol with high Kd values signifies that very similar compounds can have higher affinities and act as natural ligands ~~for~~ trichosurin as well.	+	The binding preference for small phenolic compounds such as 2-naphthol and 4-ethylphenol with high Kd values signifies that very similar compounds can have higher affinities and act as natural ligands of trichosurin as well.

	== Evolutionarily Related Proteins ==		== Evolutionarily Related Proteins ==

Ona Ambrozaite at 18:36, 23 April 2020

Ona Ambrozaite — Thu, 23 Apr 2020 18:36:52 GMT

←Older revision		Revision as of 18:36, 23 April 2020
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	As expected for an extracellular protein, trichosurin displays a large amount of [[hydrophilic]] <scene name='83/837887/Trichosurin1_/5'>surface area</scene>, with the more [[hydrophobic]] areas between the helix, the outside of the barrel, and the dimer interface where ligands such as 2-naphthol can bind. The binding site is found in the centre of the β-barrel and can be occupied by water and isopropanol molecules from the corresponding crystallization medium. In fact, researchers were able to crystallize trichosurin with 2-naphthol and 4-ethylphenol, the presence of which provides clues to the function of trichosurin.		As expected for an extracellular protein, trichosurin displays a large amount of [[hydrophilic]] <scene name='83/837887/Trichosurin1_/5'>surface area</scene>, with the more [[hydrophobic]] areas between the helix, the outside of the barrel, and the dimer interface where ligands such as 2-naphthol can bind. The binding site is found in the centre of the β-barrel and can be occupied by water and isopropanol molecules from the corresponding crystallization medium. In fact, researchers were able to crystallize trichosurin with 2-naphthol and 4-ethylphenol, the presence of which provides clues to the function of trichosurin.

-	Overall, trichosurin follows the general lipocalin superfamily fold pattern by having a β-barrel, several extended loop regions between β strands that close the ends of the barrel, and a helix near the C-terminus which is common to all lipocalins. There's also a major conserved feature of the lipocalin fold, a '''disulfide bond''', formed by <scene name='83/837887/Disulfide_bond/1'>two cysteines (Cys73 and Cys166)</scene> in each chain that ties the C-terminus to the corresponding β-strand. There are also '''N-linked glycosylations''' on Asp67 and Asp148 that could help keep trichosurin in solution, which is important since ~~it’s~~ a secreted protein that needs to remain soluble and not aggregate. It could also facilitate the folding process and exert quality control to monitor trichosurin's folding.	+	Overall, trichosurin follows the general lipocalin superfamily fold pattern by having a β-barrel, several extended loop regions between β strands that close the ends of the barrel, and a helix near the C-terminus which is common to all lipocalins. There's also a major conserved feature of the lipocalin fold, a '''disulfide bond''', formed by <scene name='83/837887/Disulfide_bond/1'>two cysteines (Cys73 and Cys166)</scene> in each chain that ties the C-terminus to the corresponding β-strand. There are also '''N-linked glycosylations''' on Asp67 and Asp148 that could help keep trichosurin in solution, which is important since it is a secreted protein that needs to remain soluble and not aggregate. It could also facilitate the folding process and exert quality control to monitor trichosurin's folding.

	The binding preference for small phenolic compounds such as 2-naphthol and 4-ethylphenol with high Kd values signifies that very similar compounds can have higher affinities and act as natural ligands for trichosurin as well.		The binding preference for small phenolic compounds such as 2-naphthol and 4-ethylphenol with high Kd values signifies that very similar compounds can have higher affinities and act as natural ligands for trichosurin as well.

Ona Ambrozaite at 18:35, 23 April 2020

Ona Ambrozaite — Thu, 23 Apr 2020 18:35:25 GMT

←Older revision		Revision as of 18:35, 23 April 2020
Line 22:		Line 22:
	As expected for an extracellular protein, trichosurin displays a large amount of [[hydrophilic]] <scene name='83/837887/Trichosurin1_/5'>surface area</scene>, with the more [[hydrophobic]] areas between the helix, the outside of the barrel, and the dimer interface where ligands such as 2-naphthol can bind. The binding site is found in the centre of the β-barrel and can be occupied by water and isopropanol molecules from the corresponding crystallization medium. In fact, researchers were able to crystallize trichosurin with 2-naphthol and 4-ethylphenol, the presence of which provides clues to the function of trichosurin.		As expected for an extracellular protein, trichosurin displays a large amount of [[hydrophilic]] <scene name='83/837887/Trichosurin1_/5'>surface area</scene>, with the more [[hydrophobic]] areas between the helix, the outside of the barrel, and the dimer interface where ligands such as 2-naphthol can bind. The binding site is found in the centre of the β-barrel and can be occupied by water and isopropanol molecules from the corresponding crystallization medium. In fact, researchers were able to crystallize trichosurin with 2-naphthol and 4-ethylphenol, the presence of which provides clues to the function of trichosurin.

-	Overall, trichosurin follows the general lipocalin superfamily fold pattern by having a β-barrel, several extended loop regions between β strands that close the ends of the barrel, a helix near the C-terminus which is common to all lipocalins~~, and~~ a major conserved feature of the lipocalin fold, a '''disulfide bond''', formed by <scene name='83/837887/Disulfide_bond/1'>two cysteines (Cys73 and Cys166)</scene> in each chain that ties the C-terminus to the corresponding β-strand. There are also '''N-linked glycosylations''' on Asp67 and Asp148 that could help keep trichosurin in solution, which is important since it’s a secreted protein that needs to remain soluble and not aggregate. It could also facilitate the folding process and exert quality control to monitor trichosurin's folding.	+	Overall, trichosurin follows the general lipocalin superfamily fold pattern by having a β-barrel, several extended loop regions between β strands that close the ends of the barrel, and a helix near the C-terminus which is common to all lipocalins. There's also a major conserved feature of the lipocalin fold, a '''disulfide bond''', formed by <scene name='83/837887/Disulfide_bond/1'>two cysteines (Cys73 and Cys166)</scene> in each chain that ties the C-terminus to the corresponding β-strand. There are also '''N-linked glycosylations''' on Asp67 and Asp148 that could help keep trichosurin in solution, which is important since it’s a secreted protein that needs to remain soluble and not aggregate. It could also facilitate the folding process and exert quality control to monitor trichosurin's folding.

	The binding preference for small phenolic compounds such as 2-naphthol and 4-ethylphenol with high Kd values signifies that very similar compounds can have higher affinities and act as natural ligands for trichosurin as well.		The binding preference for small phenolic compounds such as 2-naphthol and 4-ethylphenol with high Kd values signifies that very similar compounds can have higher affinities and act as natural ligands for trichosurin as well.

Ona Ambrozaite at 18:07, 23 April 2020

Ona Ambrozaite — Thu, 23 Apr 2020 18:07:58 GMT

←Older revision		Revision as of 18:07, 23 April 2020
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	The fully functional trichosurin consists of two monomers joining to form a <scene name='83/837887/Dimer/1'>dimer</scene> of identical '''eight-stranded, anti-parallel β-barrels''' <ref>PMID: 11058743</ref>. The study of lipocalin dimerization modes has shown six variations in orientation, with trichosurin adding a seventh one to the list. Overall, there are '''four main chains''' (A, B, C, and D) in the dimer, with each chain a length of 166 amino acids. There is also a signal sequence at the N-terminus of the chain that is cleaved before a fully functional molecule is formed. Currently, there are two crystal structures of trichosurin that can be found at RCSB, one determined at pH 8.2 and another at a lower pH of 4.6.		The fully functional trichosurin consists of two monomers joining to form a <scene name='83/837887/Dimer/1'>dimer</scene> of identical '''eight-stranded, anti-parallel β-barrels''' <ref>PMID: 11058743</ref>. The study of lipocalin dimerization modes has shown six variations in orientation, with trichosurin adding a seventh one to the list. Overall, there are '''four main chains''' (A, B, C, and D) in the dimer, with each chain a length of 166 amino acids. There is also a signal sequence at the N-terminus of the chain that is cleaved before a fully functional molecule is formed. Currently, there are two crystal structures of trichosurin that can be found at RCSB, one determined at pH 8.2 and another at a lower pH of 4.6.
-	With regards to the binding cavity, there are the three asparagine residues, Asn49, Asn97 and Asn127, which lie in the pocket and offer hydrogen-bonding sites for a potential ligand, especially Asn49. The shape and charge distribution within the pocket suggest that small hydrophobic molecules can be accommodated within, with such sites providing the necessary hydrogen bonding opportunities.	+	With regards to the binding cavity, there are the <scene name='83/837887/Binding_cavity/1'>three asparagine residues, Asn49, Asn97 and Asn127</scene>, which lie in the pocket and offer hydrogen-bonding sites for a potential ligand, especially Asn49. The shape and charge distribution within the pocket suggest that small hydrophobic molecules can be accommodated within, with such sites providing the necessary hydrogen bonding opportunities.

	The SCOP website classifies trichosurin as a '''fatty acid retinoid binding protein''', just like the nematode fatty acid retinoid binding protein from ''Necator americanus'' species. Trichosurin belongs to the '''calycin beta-barrel core domain superfamily''', as indicated by the search results on the CATH website, which emphasizes the presence of the β-barrels throughout the structure.		The SCOP website classifies trichosurin as a '''fatty acid retinoid binding protein''', just like the nematode fatty acid retinoid binding protein from ''Necator americanus'' species. Trichosurin belongs to the '''calycin beta-barrel core domain superfamily''', as indicated by the search results on the CATH website, which emphasizes the presence of the β-barrels throughout the structure.