6awm - Revision history

OCA at 07:29, 1 May 2024

OCA — Wed, 01 May 2024 07:29:38 GMT

←Older revision		Revision as of 07:29, 1 May 2024
Line 1:		Line 1:

	==PawL-Derived Peptide PLP-4==		==PawL-Derived Peptide PLP-4==
-	<StructureSection load='6awm' size='340' side='right'caption='[[6awm~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='6awm' size='340' side='right'caption='[[6awm]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6awm]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AWM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6AWM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6awm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Senecio_pinnatifolius Senecio pinnatifolius]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AWM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AWM FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6awm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6awm OCA], [~~http~~://pdbe.org/6awm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6awm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6awm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6awm ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6awm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6awm OCA], [https://pdbe.org/6awm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6awm RCSB], [https://www.ebi.ac.uk/pdbsum/6awm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6awm ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Orbitides are cyclic ribosomally-synthesized and post-translationally modified peptides (RiPPs) from plants; they consist of standard amino acids arranged in an unbroken chain of peptide bonds. These cyclic peptides are stable and range in size and topologies making them potential scaffolds for peptide drugs; some display valuable biological activities. Recently two orbitides whose sequences were buried in those of seed storage albumin precursors were said to represent the first observable step in the evolution of larger and hydrophilic bicyclic peptides. Here, guided by transcriptome data, we investigated peptide extracts of 40 species specifically for the more hydrophobic orbitides and confirmed 44 peptides by tandem mass spectrometry, as well as obtaining solution structures for four of them by NMR. Acquiring transcriptomes from the phylogenetically important Corymboideae family confirmed the precursor genes for the peptides (called PawS1-Like or PawL1) are confined to the Asteroideae, a subfamily of the huge plant family Asteraceae. To be confined to the Asteroideae indicates these peptides arose during the Eocene epoch around 45 Mya. Unlike other orbitides, all PawL-derived Peptides contain an Asp residue, needed for processing by asparaginyl endopeptidase. This study has revealed what is likely to be a very large new family of orbitides, uniquely buried alongside albumin and processed by asparaginyl endopeptidase.
-
-	A family of small, cyclic peptides buried in preproalbumin since the Eocene epoch.,Fisher MF, Zhang J, Taylor NL, Howard MJ, Berkowitz O, Debowski AW, Behsaz B, Whelan J, Pevzner PA, Mylne JS Plant Direct. 2018 Feb;2(2). doi: 10.1002/pld3.42. Epub 2018 Feb 28. PMID:30417166<ref>PMID:30417166</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6awm" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Fisher, M~~]]	+	[[Category: Senecio pinnatifolius]]
-	[[Category: ~~Howard,~~ M J]]	+	[[Category: Fisher M]]
-	[[Category: ~~Mylne, J S~~]]	+	[[Category: Howard MJ]]
-	[[Category: ~~Buried peptide]]~~	+	[[Category: Mylne JS]]
-	~~[[Category: Cyclic peptide]]~~	+
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Orbitide]]~~	+
-	~~[[Category: Plant peptide~~]]	+

OCA at 21:33, 28 October 2020

OCA — Wed, 28 Oct 2020 21:33:08 GMT

←Older revision		Revision as of 21:33, 28 October 2020
Line 1:		Line 1:

	==PawL-Derived Peptide PLP-4==		==PawL-Derived Peptide PLP-4==
-	<StructureSection load='6awm' size='340' side='right' caption='[[6awm]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='6awm' size='340' side='right'caption='[[6awm]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6awm]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AWM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6AWM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6awm]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AWM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6AWM FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6awm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6awm OCA], [http://pdbe.org/6awm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6awm RCSB], [http://www.ebi.ac.uk/pdbsum/6awm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6awm ProSAT]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6awm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6awm OCA], [http://pdbe.org/6awm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6awm RCSB], [http://www.ebi.ac.uk/pdbsum/6awm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6awm ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Fisher, M]]		[[Category: Fisher, M]]
	[[Category: Howard, M J]]		[[Category: Howard, M J]]

OCA at 20:53, 2 December 2018

OCA — Sun, 02 Dec 2018 20:53:28 GMT

←Older revision		Revision as of 20:53, 2 December 2018
Line 6:		Line 6:
	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6awm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6awm OCA], [http://pdbe.org/6awm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6awm RCSB], [http://www.ebi.ac.uk/pdbsum/6awm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6awm ProSAT]</span></td></tr>		</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6awm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6awm OCA], [http://pdbe.org/6awm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6awm RCSB], [http://www.ebi.ac.uk/pdbsum/6awm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6awm ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Orbitides are cyclic ribosomally-synthesized and post-translationally modified peptides (RiPPs) from plants; they consist of standard amino acids arranged in an unbroken chain of peptide bonds. These cyclic peptides are stable and range in size and topologies making them potential scaffolds for peptide drugs; some display valuable biological activities. Recently two orbitides whose sequences were buried in those of seed storage albumin precursors were said to represent the first observable step in the evolution of larger and hydrophilic bicyclic peptides. Here, guided by transcriptome data, we investigated peptide extracts of 40 species specifically for the more hydrophobic orbitides and confirmed 44 peptides by tandem mass spectrometry, as well as obtaining solution structures for four of them by NMR. Acquiring transcriptomes from the phylogenetically important Corymboideae family confirmed the precursor genes for the peptides (called PawS1-Like or PawL1) are confined to the Asteroideae, a subfamily of the huge plant family Asteraceae. To be confined to the Asteroideae indicates these peptides arose during the Eocene epoch around 45 Mya. Unlike other orbitides, all PawL-derived Peptides contain an Asp residue, needed for processing by asparaginyl endopeptidase. This study has revealed what is likely to be a very large new family of orbitides, uniquely buried alongside albumin and processed by asparaginyl endopeptidase.
		+
		+	A family of small, cyclic peptides buried in preproalbumin since the Eocene epoch.,Fisher MF, Zhang J, Taylor NL, Howard MJ, Berkowitz O, Debowski AW, Behsaz B, Whelan J, Pevzner PA, Mylne JS Plant Direct. 2018 Feb;2(2). doi: 10.1002/pld3.42. Epub 2018 Feb 28. PMID:30417166<ref>PMID:30417166</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6awm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:06, 8 March 2018

OCA — Thu, 08 Mar 2018 05:06:30 GMT

←Older revision		Revision as of 05:06, 8 March 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6awm ~~is ON HOLD until Paper Publication~~	+	==PawL-Derived Peptide PLP-4==
-		+	<StructureSection load='6awm' size='340' side='right' caption='[[6awm]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
-	~~Authors~~: ~~Fisher, M~~.~~, Mylne, J~~.S.~~, Howard, M~~.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6awm]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AWM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AWM FirstGlance]. <br>
-	~~Description~~: ~~PawL~~-~~Derived Peptide PLP~~-4	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6awm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6awm OCA], [http://pdbe.org/6awm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6awm RCSB], [http://www.ebi.ac.uk/pdbsum/6awm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6awm ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Fisher, M]]		[[Category: Fisher, M]]
-	[[Category: ~~Mylne~~, J.S]]	+	[[Category: Howard, M J]]
-	[[Category: ~~Howard~~, M.J]]	+	[[Category: Mylne, J S]]
		+	[[Category: Buried peptide]]
		+	[[Category: Cyclic peptide]]
		+	[[Category: De novo protein]]
		+	[[Category: Orbitide]]
		+	[[Category: Plant peptide]]

OCA: Protected "6awm" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:52:55 GMT

Protected "6awm" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:52, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 6awm is ON HOLD until Paper Publication Authors: Fisher, M., Mylne, J.S., Howard, M.J. Description: PawL-Derived Peptide PLP-4 [[Category: Unreleas...

OCA — Wed, 27 Sep 2017 16:52:54 GMT

New page: '''Unreleased structure''' The entry 6awm is ON HOLD until Paper Publication Authors: Fisher, M., Mylne, J.S., Howard, M.J. Description: PawL-Derived Peptide PLP-4 [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 6awm is ON HOLD until Paper Publication

Authors: Fisher, M., Mylne, J.S., Howard, M.J.

Description: PawL-Derived Peptide PLP-4
[[Category: Unreleased Structures]]
[[Category: Fisher, M]]
[[Category: Mylne, J.S]]
[[Category: Howard, M.J]]