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HUPO Proteomics Standards Initiative Molecular Interaction
Source
Name:ebi: European Bioinformatics Institute

ExperimentList
Experiment #2
Name:zahnd-2007-1
Description:A designed ankyrin repeat protein evolved to picomolar affinity to Her2.
pubmed17466328 [primary reference]
psi-parPAR:1317 [exp scope]
Host Organism: in vitro (taxid: -1)
Interaction detection method:
Name:ribosome display
pubmed11551470 [primary-reference]
pubmed12167034 [see-also]
psi-parPAR:0098 [identity]
Participant identification method:
Name:nucleotide sequence: nucleotide sequence identification (go synonym: sequence cloning)
pubmed14755292 [primary-reference]
psi-parPAR:0078 [identity]
author-listZahnd C., Wyler E., Schwenk JM., Steiner D., Lawrence MC., McKern NM., Pecorari F., Ward CW., Joos TO., Pluckthun A.
journalJ. Mol. Biol. (0022-2836)
publication year2007
screening rounds3
Experiment #10
Name:zahnd-2007-3
Description:A designed ankyrin repeat protein evolved to picomolar affinity to Her2.
pubmed17466328 [primary reference]
psi-parPAR:1317 [exp scope]
Host Organism: in vitro (taxid: -1)
Interaction detection method:
Name:affinity chrom: affinity chromatography technology (go synonym: Affinity purification)
pubmed7708014 [primary-reference]
psi-parPAR:0004 [identity]
Participant identification method:
Name:weight by comassie: molecular weight estimation by coomasie staining
pubmed14755292 [primary-reference]
psi-parPAR:0818 [identity]
author-listZahnd C., Wyler E., Schwenk JM., Steiner D., Lawrence MC., McKern NM., Pecorari F., Ward CW., Joos TO., Pluckthun A.
journalJ. Mol. Biol. (0022-2836)
publication year2007
Experiment #13
Name:zahnd-2007-4
Description:A designed ankyrin repeat protein evolved to picomolar affinity to Her2.
pubmed17466328 [primary reference]
psi-parPAR:1134 [exp scope]
Host Organism: in vitro (taxid: -1)
Interaction detection method:
Name:spr: surface plasmon resonance (go synonym: BIAcore(r)) (go synonym: Optical biosensor) (go synonym: BIAcore(r)) (go synonym: Optical biosensor)
pubmed12120258 [method reference]
pubmed16338355 [method reference]
pubmed11896282 [primary-reference]
psi-parPAR:0107 [identity]
Participant identification method:
Name:predetermined: predetermined participant
pubmed14755292 [primary-reference]
psi-parPAR:0396 [identity]
author-listZahnd C., Wyler E., Schwenk JM., Steiner D., Lawrence MC., McKern NM., Pecorari F., Ward CW., Joos TO., Pluckthun A.
journalJ. Mol. Biol. (0022-2836)
publication year2007
exp-modificationConstruction of point mutants: The mutations were introduced by a PCR-based approach. Two fragments were amplified overlapping in the region of the desired mutation. In a second PCR reaction with outer primers only, the fragments were joined to yield the mutated sequence. Clone G3-D was constructed with a single PCR reaction using a long reverse primer, as the mutation was near to the C terminus. DNA of all clones was isolated from agarose gels and cloned via BamHI and HindIII into pQE-30 (Qiagen). Plasmids were prepared, sequenced and the mass of the expressed and purified clones was verified with mass spectrometry (MALDI-TOF).
equipmentBiacore 3000 (Biacore)
Experiment #19
Name:zahnd-2007-2
Description:A designed ankyrin repeat protein evolved to picomolar affinity to Her2.
pubmed17466328 [primary reference]
psi-parPAR:1317 [exp scope]
Host Organism: ecolx: Escherichia coli
Interaction detection method:
Name:cDNA expression
pubmed123456789 [primary-reference]
psi-parPAR:1056 [identity]
Participant identification method:
Name:predetermined: predetermined participant
pubmed14755292 [primary-reference]
psi-parPAR:0396 [identity]
author-listZahnd C., Wyler E., Schwenk JM., Steiner D., Lawrence MC., McKern NM., Pecorari F., Ward CW., Joos TO., Pluckthun A.
journalJ. Mol. Biol. (0022-2836)
publication year2007
expression vectorVector pAT224, Genbank accession number AY327139
Experiment #22
Name:zahnd-2007-5
Description:A designed ankyrin repeat protein evolved to picomolar affinity to Her2.
pubmed17466328 [primary reference]
psi-parPAR:1054 [exp scope]
Host Organism: in vitro (taxid: -1)
Interaction detection method:
Name:sandwich immunoassay
pubmed12454649 [primary-reference]
psi-parPAR:0695 [identity]
Participant identification method:
Name:antibody detection: identification by antibody
pubmed14755292 [primary-reference]
psi-parPAR:0421 [identity]
author-listZahnd C., Wyler E., Schwenk JM., Steiner D., Lawrence MC., McKern NM., Pecorari F., Ward CW., Joos TO., Pluckthun A.
journalJ. Mol. Biol. (0022-2836)
publication year2007
protocolEach sample was immobilized on Luminex beads of distinguishable color-code according to the manufacturer's protocol (Luminex-Corp., Austin, Tx, USA).

InteractorList
Interactor #4
Name:h10-2-g3_2jab: Designed Ankyrin Repeat Protein (DARPin) binding human epidermal growth factor receptor (Her2)
wwpdb2jab [identity]
Interactor Type:
Name:darpin: ankyrin repeat (go synonym: ankyrin scaffold)
pubmed14755292 [primary-reference]
psi-parPAR:1099 [identity]
Organism: in vitro (taxid: -1)
Sequence:MRGSHHHHHH GSDLGKKLLE AARAGQDDEV RILMANGADV NAKDEYGLTP LYLATAHGHL EIVEVLLKNG ADVNAVDAIG FTPLHLAAFI GHLEIAEVLL KHGADVNAQD KFGKTAFDIS IGNGNEDLAE ILQKLN
Interactor #6
Name:erbb2_human: Receptor tyrosine-protein kinase erbB-2 precursor (gene name: ERBB2) (gene name synonym: HER2) (gene name synonym: NEU) (gene name synonym: NGL)
uniprotkbP04626 [identity]
uniprotkbQ14256 [secondary-ac]
uniprotkbQ9UMK4 [secondary-ac]
uniprotkbQ6LDV1 [secondary-ac]
rcsb pdb1OVC
rcsb pdb1N8Z
rcsb pdb2A91
rcsb pdb1QR1
rcsb pdb1S78
interproIPR001245
interproIPR000719
interproIPR004019
interproIPR008266
interproIPR006211
interproIPR006212
interproIPR000494
goGO:0045765
goGO:0050679
goGO:0007507
goGO:0046982
goGO:0030879
goGO:0043125
goGO:0006468
goGO:0048015
goGO:0005006
goGO:0007399
goGO:0043406
goGO:0005886
goGO:0042802
goGO:0004716
goGO:0007169
goGO:0016021
ensemblENSG00000141736
Interactor Type:
Name:protein
soSO:0000358 [identity]
pubmed14755292 [primary-reference]
psi-parPAR:0326 [identity]
Organism: human: Homo sapiens
Sequence:MELAALCRWG LLLALLPPGA ASTQVCTGTD MKLRLPASPE THLDMLRHLY QGCQVVQGNL ELTYLPTNAS LSFLQDIQEV QGYVLIAHNQ VRQVPLQRLR IVRGTQLFED NYALAVLDNG DPLNNTTPVT GASPGGLREL QLRSLTEILK GGVLIQRNPQ LCYQDTILWK DIFHKNNQLA LTLIDTNRSR ACHPCSPMCK GSRCWGESSE DCQSLTRTVC AGGCARCKGP LPTDCCHEQC AAGCTGPKHS DCLACLHFNH SGICELHCPA LVTYNTDTFE SMPNPEGRYT FGASCVTACP YNYLSTDVGS CTLVCPLHNQ EVTAEDGTQR CEKCSKPCAR VCYGLGMEHL REVRAVTSAN IQEFAGCKKI FGSLAFLPES FDGDPASNTA PLQPEQLQVF ETLEEITGYL YISAWPDSLP DLSVFQNLQV IRGRILHNGA YSLTLQGLGI SWLGLRSLRE LGSGLALIHH NTHLCFVHTV PWDQLFRNPH QALLHTANRP EDECVGEGLA CHQLCARGHC WGPGPTQCVN CSQFLRGQEC VEECRVLQGL PREYVNARHC LPCHPECQPQ NGSVTCFGPE ADQCVACAHY KDPPFCVARC PSGVKPDLSY MPIWKFPDEE GACQPCPINC THSCVDLDDK GCPAEQRASP LTSIISAVVG ILLVVVLGVV FGILIKRRQQ KIRKYTMRRL LQETELVEPL TPSGAMPNQA QMRILKETEL RKVKVLGSGA FGTVYKGIWI PDGENVKIPV AIKVLRENTS PKANKEILDE AYVMAGVGSP YVSRLLGICL TSTVQLVTQL MPYGCLLDHV RENRGRLGSQ DLLNWCMQIA KGMSYLEDVR LVHRDLAARN VLVKSPNHVK ITDFGLARLL DIDETEYHAD GGKVPIKWMA LESILRRRFT HQSDVWSYGV TVWELMTFGA KPYDGIPARE IPDLLEKGER LPQPPICTID VYMIMVKCWM IDSECRPRFR ELVSEFSRMA RDPQRFVVIQ NEDLGPASPL DSTFYRSLLE DDDMGDLVDA EEYLVPQQGF FCPDPAPGAG GMVHHRHRSS STRSGGGDLT LGLEPSEEEA PRSPLAPSEG AGSDVFDGDL GMGAAKGLQS LPTHDPSPLQ RYSEDPTVPL PSETDGYVAP LTCSPQPEYV NQPDVRPQPP SPREGPLPAA RPAGATLERP KTLSPGKNGV VKDVFAFGGA VENPEYLTPQ GGAAPQPHPP PAFSPAFDNL YYWDQDPPER GAPPSTFKGT PTAENPEYLG LDVPV
Interactor #24
Name:sp185_ab: sp185 antibody from BenderMed Systems
Interactor Type:
Name:mab: monoclonal antibody
pubmed14755292 [primary-reference]
psi-parPAR:1051 [identity]
Organism: mouse: Mus musculus
supplierBenderMed Systems

InteractionList
Interaction #1
Name:lib_screen: Library screening experiment producing h10-2-g3 / 2jab a designed ankyrin repeat (DARPin) binding human epidermal growth factor receptor 2 (Her2)
pubmed16963452 [see-also]
Experiments: zahnd-2007-1
Participant #3
h10-2-g3_2jab
Biological Role:
Name:affinity reagent: protein affinity reagent (go synonym: par)
pubmed14755292 [primary-reference]
psi-parPAR:1117 [identity]
Experimental Role:
Name:generation product
pubmed14755292 [primary-reference]
psi-parPAR:1154 [identity]
Name:prey
pubmed14755292 [primary-reference]
psi-parPAR:0498 [identity]
Host Organism: ecolx: Escherichia coli
Participant #5
erbb2_human
Biological Role:
Name:par target: protein affinity reagent target
pubmed14755292 [primary-reference]
psi-parPAR:1120 [identity]
Experimental Role:
Name:bait
pubmed14755292 [primary-reference]
psi-parPAR:0496 [identity]
Feature #7biotin tag (biotin tag) [ 0 .. 0 ]
Feature #8extracellular domain (ecd) [ 0 .. 0 ]
Host Organism: unknown: Unknown (taxid: -3)
Interaction Type:
Name:physical interaction (go synonym: aggregation)
pubmed14755292 [primary-reference]
psi-parPAR:0218 [identity]
Modelledfalse
Intra molecularfalse
Negativefalse
Interaction #9
Name:h10-2-g3_2jab_purif: Purification of expressed h10-2-g3 / 2jab DARPin binding Her2
intactEBI-36125 (1) [preceding interaction]
Experiments: zahnd-2007-3
Participant #11
h10-2-g3_2jab
Biological Role:
Name:par target: protein affinity reagent target
pubmed14755292 [primary-reference]
psi-parPAR:1120 [identity]
Experimental Role:
Name:generation product
pubmed14755292 [primary-reference]
psi-parPAR:1154 [identity]
Host Organism: ecolx: Escherichia coli
Interaction Type:
Name:physical interaction (go synonym: aggregation)
pubmed14755292 [primary-reference]
psi-parPAR:0218 [identity]
Modelledfalse
Intra molecularfalse
Negativefalse
Interaction #12
Name:darpin_affinity: Affinity determination of DARPins including h10-2-g3_2jab
Experiments: zahnd-2007-4
Participant #14
erbb2_human
Biological Role:
Name:par target: protein affinity reagent target
pubmed14755292 [primary-reference]
psi-parPAR:1120 [identity]
Experimental Role:
Name:bait
pubmed14755292 [primary-reference]
psi-parPAR:0496 [identity]
Feature #15biotin tag (biotin tag) [ 0 .. 0 ]
Feature #16extracellular domain (ecd) [ 0 .. 0 ]
Host Organism: unknown: Unknown (taxid: -3)
Participant #17
h10-2-g3_2jab
Biological Role:
Name:affinity reagent: protein affinity reagent (go synonym: par)
pubmed14755292 [primary-reference]
psi-parPAR:1117 [identity]
Experimental Role:
Name:prey
pubmed14755292 [primary-reference]
psi-parPAR:0498 [identity]
Host Organism: ecolx: Escherichia coli
Interaction Type:
Name:direct interaction
pubmed14755292 [primary-reference]
psi-parPAR:0407 [identity]
Modelledfalse
Intra molecularfalse
Negativefalse
Parameters
Kd:0.091 x 10 0
ka:112.3 x 10 0
kd:0.102 x 10 0
figure legendTable 1, Figure 2
Interaction #18
Name:h10-2-g3_2jab_expr-1: Expression of H10-2-G3 / 2jab, a high affinity binder for Her2
Experiments: zahnd-2007-2
Participant #20
h10-2-g3_2jab
Biological Role:
Name:unspecified role
pubmed14755292 [primary-reference]
psi-parPAR:0499 [identity]
Experimental Role:
Name:intermediate product
pubmed14755292 [primary-reference]
psi-parPAR:1126 [identity]
Host Organism: in vitro (taxid: -1)
Interaction Type:
Name:physical interaction (go synonym: aggregation)
pubmed14755292 [primary-reference]
psi-parPAR:0218 [identity]
Modelledfalse
Intra molecularfalse
Negativefalse
Interaction #21
Name:h10-2-g3_sensitivity: Sensitivity determination of DARPins including h10-2-g3_2jab
Experiments: zahnd-2007-5
Participant #23
sp185_ab
Biological Role:
Name:unspecified role
pubmed14755292 [primary-reference]
psi-parPAR:0499 [identity]
Experimental Role:
Name:secondary par: secondary protein affinity reagent (go synonym: detection antibody)
pubmed14755292 [primary-reference]
psi-parPAR:1186 [identity]
Participant #25
h10-2-g3_2jab
Biological Role:
Name:affinity reagent: protein affinity reagent (go synonym: par)
pubmed14755292 [primary-reference]
psi-parPAR:1117 [identity]
Experimental Role:
Name:bait
pubmed14755292 [primary-reference]
psi-parPAR:0496 [identity]
Feature #26biotin tag (n-terminal region) [ 0 .. 0 ]
Feature #27fusion protein (n-terminal region) [ 0 .. 0 ]
Host Organism: ecolx: Escherichia coli
Participant #28
erbb2_human
Biological Role:
Name:par target: protein affinity reagent target
pubmed14755292 [primary-reference]
psi-parPAR:1120 [identity]
Experimental Role:
Name:prey
pubmed14755292 [primary-reference]
psi-parPAR:0498 [identity]
Feature #29extracellular domain (ecd) [ 0 .. 0 ]
Host Organism: unknown: Unknown (taxid: -3)
Interaction Type:
Name:direct interaction
pubmed14755292 [primary-reference]
psi-parPAR:0407 [identity]
Modelledfalse
Intra molecularfalse
Negativefalse
figure legendFigure 6a
results commentConcentration H10-2-G3 (pg/,ml) : Signal/Noise ratio; 2:2, 9:3, 40:9, 200:60, 1000:200, 5000:800, 20000:3000

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