4d4e - Revision history

OCA at 07:19, 1 May 2024

2024-05-01T07:19:11Z

← Older revision		Revision as of 07:19, 1 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4d4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[4d4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D4E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=4d4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d4e OCA], [https://pdbe.org/4d4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d4e RCSB], [https://www.ebi.ac.uk/pdbsum/4d4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d4e ProSAT]</span></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=4d4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d4e OCA], [https://pdbe.org/4d4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d4e RCSB], [https://www.ebi.ac.uk/pdbsum/4d4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d4e ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Armadillo repeat proteins (ArmRP) recognize their target peptide in extended conformation and bind, in a first approximation, two residues per repeat. They may thus form the basis for building a modular system, in which each repeat is complementary to a piece of the target peptide. Accordingly, preselected repeats could be assembled into specific binding proteins on demand and thereby avoid the traditional generation of every new binding molecule by an independent selection from a library. Stacked armadillo repeats, each consisting of 42 amino acids arranged in three alpha-helices, build an elongated superhelical structure. Here, we analyzed curvature variations in natural ArmRPs, and identified a repeat pair from yeast importin-alpha as having the optimal curvature geometry to be complementary to a peptide over its whole length. We employed a symmetric in silico design to obtain a uniform sequence for a stackable repeat while maintaining the desired curvature geometry. Computationally designed armadillo repeat proteins (dArmRPs) had to be stabilized by mutations to remove regions of higher flexibility, which were identified by molecular dynamics (MD) simulations in explicit solvent. Using an N-capping repeat from the consensus-design approach, two different crystal structures of dArmRP were determined. Although the experimental structures of dArmRP deviated from the designed curvature, the insertion of the most conserved binding pockets of natural ArmRPs onto the surface of dArmRPs resulted in binders against the expected peptide with low nanomolar affinities, similar to the binders from the consensus-design series.

	Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition.,Reichen C, Hansen S, Forzani C, Honegger A, Fleishman SJ, Zhou T, Parmeggiani F, Ernst P, Madhurantakam C, Ewald C, Mittl PR, Zerbe O, Baker D, Caflisch A, Pluckthun A J Mol Biol. 2016 Sep 21. pii: S0022-2836(16)30376-X. doi:, 10.1016/j.jmb.2016.09.012. PMID:27664438<ref>PMID:27664438</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4d4e" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:46, 14 September 2022

2022-09-14T07:46:35Z

← Older revision		Revision as of 07:46, 14 September 2022
Line 3:		Line 3:
	<StructureSection load='4d4e' size='340' side='right'caption='[[4d4e]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4d4e' size='340' side='right'caption='[[4d4e]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4d4e]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D4E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4D4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[4d4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D4E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~</td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d49\|4d49]]~~</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=4d4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d4e OCA], [https://pdbe.org/4d4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d4e RCSB], [https://www.ebi.ac.uk/pdbsum/4d4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d4e ProSAT]</span></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=4d4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d4e OCA], [~~http~~://pdbe.org/4d4e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4d4e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4d4e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4d4e ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Synthetic construct ~~sequences~~]]		[[Category: Synthetic construct]]
	[[Category: Baker, D]]		[[Category: Baker D]]
	[[Category: Caflisch, A]]		[[Category: Caflisch A]]
	[[Category: Ewald, C]]		[[Category: Ewald C]]
	[[Category: Fleishman~~, S J~~]]		[[Category: Fleishman SJ]]
	[[Category: Forzani, C]]		[[Category: Forzani C]]
	[[Category: Honegger, A]]		[[Category: Honegger A]]
	[[Category: Madhurantakam, C]]		[[Category: Madhurantakam C]]
	[[Category: Mittl~~, P R.E~~]]		[[Category: Mittl PRE]]
	[[Category: Parmeggiani, F]]		[[Category: Parmeggiani F]]
	[[Category: Pluckthun, A]]		[[Category: Pluckthun A]]
	[[Category: Reichen, C]]		[[Category: Reichen C]]
	[[Category: Zerbe, O]]		[[Category: Zerbe O]]
	[[Category: Zhou, T]]		[[Category: Zhou T]]
	~~[[Category: Armadillo repeat protein]]~~
	~~[[Category: De novo protein~~]]

OCA at 09:31, 20 March 2019

2019-03-20T09:31:38Z

← Older revision		Revision as of 09:31, 20 March 2019
Line 1:		Line 1:

	==Crystal structure of computationally designed armadillo repeat proteins for modular peptide recognition.==		==Crystal structure of computationally designed armadillo repeat proteins for modular peptide recognition.==
	<StructureSection load='4d4e' size='340' side='right' caption='[[4d4e]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4d4e' size='340' side='right'caption='[[4d4e]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4d4e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[4d4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D4E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d49\|4d49]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d49\|4d49]]</td></tr>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
			[[Category: Synthetic construct sequences]]
	[[Category: Baker, D]]		[[Category: Baker, D]]
	[[Category: Caflisch, A]]		[[Category: Caflisch, A]]

OCA at 14:11, 5 October 2016

2016-10-05T14:11:52Z

← Older revision		Revision as of 14:11, 5 October 2016
Line 1:		Line 1:

	==Crystal structure of computationally designed armadillo repeat proteins for modular peptide recognition.==		==Crystal structure of computationally designed armadillo repeat proteins for modular peptide recognition.==
	<StructureSection load='4d4e' size='340' side='right' caption='[[4d4e]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4d4e' size='340' side='right' caption='[[4d4e]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d49\|4d49]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d49\|4d49]]</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=4d4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d4e OCA], [http://pdbe.org/4d4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d4e RCSB], [http://www.ebi.ac.uk/pdbsum/4d4e PDBsum]</span></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=4d4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d4e OCA], [http://pdbe.org/4d4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d4e RCSB], [http://www.ebi.ac.uk/pdbsum/4d4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d4e ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Armadillo repeat proteins (ArmRP) recognize their target peptide in extended conformation and bind, in a first approximation, two residues per repeat. They may thus form the basis for building a modular system, in which each repeat is complementary to a piece of the target peptide. Accordingly, preselected repeats could be assembled into specific binding proteins on demand and thereby avoid the traditional generation of every new binding molecule by an independent selection from a library. Stacked armadillo repeats, each consisting of 42 amino acids arranged in three alpha-helices, build an elongated superhelical structure. Here, we analyzed curvature variations in natural ArmRPs, and identified a repeat pair from yeast importin-alpha as having the optimal curvature geometry to be complementary to a peptide over its whole length. We employed a symmetric in silico design to obtain a uniform sequence for a stackable repeat while maintaining the desired curvature geometry. Computationally designed armadillo repeat proteins (dArmRPs) had to be stabilized by mutations to remove regions of higher flexibility, which were identified by molecular dynamics (MD) simulations in explicit solvent. Using an N-capping repeat from the consensus-design approach, two different crystal structures of dArmRP were determined. Although the experimental structures of dArmRP deviated from the designed curvature, the insertion of the most conserved binding pockets of natural ArmRPs onto the surface of dArmRPs resulted in binders against the expected peptide with low nanomolar affinities, similar to the binders from the consensus-design series.

			Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition.,Reichen C, Hansen S, Forzani C, Honegger A, Fleishman SJ, Zhou T, Parmeggiani F, Ernst P, Madhurantakam C, Ewald C, Mittl PR, Zerbe O, Baker D, Caflisch A, Pluckthun A J Mol Biol. 2016 Sep 21. pii: S0022-2836(16)30376-X. doi:, 10.1016/j.jmb.2016.09.012. PMID:27664438<ref>PMID:27664438</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 4d4e" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 20:18, 13 January 2016

2016-01-13T20:18:43Z

← Older revision		Revision as of 20:18, 13 January 2016
Line 1:		Line 1:
	'''~~Unreleased structure~~'''		==Crystal structure of computationally designed armadillo repeat proteins for modular peptide recognition.==
			<StructureSection load='4d4e' size='340' side='right' caption='[[4d4e]], [[Resolution\|resolution]] 2.00Å' scene=''>
	~~The entry~~ 4d4e is ~~ON HOLD until Paper Publication~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[4d4e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D4E FirstGlance]. <br>
	~~Authors~~: ~~Reichen, C~~.~~, Forzani, C~~.~~, Zhou, T~~., ~~Parmeggiani, F~~.~~, Fleishman, S~~.J., ~~Mittl~~, P.R.E., ~~Madhurantakam, C~~.~~, Honegger, A~~.~~, Ewald, C~~.~~, Zerbe, O.,~~ Baker, D., Caflisch, A~~., Pluckthun, A.~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d49\|4d49]]</td></tr>
	~~Description~~: ~~Crystal structure of computationally designed armadillo repeat proteins for modular peptide recognition.~~		<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=4d4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d4e OCA], [http://pdbe.org/4d4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d4e RCSB], [http://www.ebi.ac.uk/pdbsum/4d4e PDBsum]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
	[[Category: ~~Zerbe~~, O]]		__TOC__
			</StructureSection>
			[[Category: Baker, D]]
			[[Category: Caflisch, A]]
			[[Category: Ewald, C]]
			[[Category: Fleishman, S J]]
			[[Category: Forzani, C]]
	[[Category: Honegger, A]]		[[Category: Honegger, A]]
			[[Category: Madhurantakam, C]]
			[[Category: Mittl, P R.E]]
			[[Category: Parmeggiani, F]]
	[[Category: Pluckthun, A]]		[[Category: Pluckthun, A]]
	~~[[Category: Baker, D]]~~
	~~[[Category: Parmeggiani, F]]~~
	[[Category: Reichen, C]]		[[Category: Reichen, C]]
	[[Category: ~~Madhurantakam~~, ~~C]]~~		[[Category: Zerbe, O]]
	~~[[Category: Forzani, C]]~~
	~~[[Category: Mittl, P.R.E]]~~
	~~[[Category: Ewald, C]]~~
	~~[[Category: Caflisch, A]]~~
	~~[[Category: Fleishman, S.J~~]]
	[[Category: Zhou, T]]		[[Category: Zhou, T]]
			[[Category: Armadillo repeat protein]]
			[[Category: De novo protein]]

OCA at 13:46, 24 December 2014

2014-12-24T13:46:22Z

← Older revision		Revision as of 13:46, 24 December 2014
Line 6:		Line 6:

	Description: Crystal structure of computationally designed armadillo repeat proteins for modular peptide recognition.		Description: Crystal structure of computationally designed armadillo repeat proteins for modular peptide recognition.
			[[Category: Unreleased Structures]]
			[[Category: Zerbe, O]]
			[[Category: Honegger, A]]
			[[Category: Pluckthun, A]]
			[[Category: Baker, D]]
			[[Category: Parmeggiani, F]]
			[[Category: Reichen, C]]
			[[Category: Madhurantakam, C]]
			[[Category: Forzani, C]]
			[[Category: Mittl, P.R.E]]
			[[Category: Ewald, C]]
			[[Category: Caflisch, A]]
			[[Category: Fleishman, S.J]]
			[[Category: Zhou, T]]

OCA: Protected "4d4e" [edit=sysop:move=sysop]

2014-11-05T07:20:09Z

Protected "4d4e" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:20, 5 November 2014
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4d4e is ON HOLD until Paper Publication Authors: Reichen, C., Forzani, C., Zhou, T., Parmeggiani, F., Fleishman, S.J., Mittl, P.R.E., Madhurantakam,...

2014-11-05T07:20:07Z

New page: '''Unreleased structure''' The entry 4d4e is ON HOLD until Paper Publication Authors: Reichen, C., Forzani, C., Zhou, T., Parmeggiani, F., Fleishman, S.J., Mittl, P.R.E., Madhurantakam,...

New page

'''Unreleased structure'''

The entry 4d4e is ON HOLD until Paper Publication

Authors: Reichen, C., Forzani, C., Zhou, T., Parmeggiani, F., Fleishman, S.J., Mittl, P.R.E., Madhurantakam, C., Honegger, A., Ewald, C., Zerbe, O., Baker, D., Caflisch, A., Pluckthun, A.

Description: Crystal structure of computationally designed armadillo repeat proteins for modular peptide recognition.