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| | ==Protein A binding by an engineered Affibody molecule== | | ==Protein A binding by an engineered Affibody molecule== |
| - | <StructureSection load='2m5a' size='340' side='right' caption='[[2m5a]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='2m5a' size='340' side='right'caption='[[2m5a]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2m5a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus] and [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M5A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2M5A FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2m5a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M5A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M5A FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1h0t|1h0t]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">spa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</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=2m5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m5a OCA], [https://pdbe.org/2m5a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m5a RCSB], [https://www.ebi.ac.uk/pdbsum/2m5a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m5a 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=2m5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m5a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2m5a RCSB], [http://www.ebi.ac.uk/pdbsum/2m5a PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/SPA_STAAU SPA_STAAU] |
| - | Affibody molecules are engineered binding proteins, in which the three-helix bundle motif of the Z domain derived from protein A is used as a scaffold for sequence variation. We used phage display to select Affibody binders to staphylococcal protein A itself. The best binder, called ZpA963, binds with similar affinity and kinetics to the five homologous E, D, A, B and C domains of protein A, and to a five-domain protein A construct with an average dissociation constant, KD, of approximately 20 nM. The structure of ZpA963 in complex with the Z domain shows that it interacts with a surface on Z that is identical in the five protein A domains, which explains the multi-domain affinity. This property allows for high-affinity binding by dimeric Affibody molecules that simultaneously engage two protein A domains in a complex. We studied two ZpA963 dimers in which the subunits were linked by a C-terminal disulfide in a symmetric dimer or head-to-tail in a fusion protein, respectively. The dimers both bind protein A with high affinity, very slow off-rates and with saturation-dependent kinetics that can be understood in terms of dimer binding to multiple sites. The head-to-tail (ZpA963)2htt dimer binds with an off-rate of koff </= 5 x 10-6 s-1 and an estimated KD </= 16 pM. The results illustrate how dimers of selected monomer binding proteins can provide an efficient route for engineering of high-affinity binders to targets that contain multiple homologous domains or repeated structural units.
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| - | High-affinity binding to staphylococcal protein A by an engineered dimeric Affibody molecule.,Lindborg M, Dubnovitsky A, Olesen K, Bjorkman T, Abrahmsen L, Feldwisch J, Hard T Protein Eng Des Sel. 2013 Aug 7. PMID:23924760<ref>PMID:23924760</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Staphylococcus aureus]] | | [[Category: Staphylococcus aureus]] |
| | [[Category: Synthetic construct]] | | [[Category: Synthetic construct]] |
| - | [[Category: Hard, T]] | + | [[Category: Hard T]] |
| - | [[Category: Affibody molecule]]
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| - | [[Category: Binding protein]]
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| - | [[Category: Protein some]]
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| - | [[Category: Protein binding]]
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| - | [[Category: Protein engineering]]
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| - | [[Category: Z domain]]
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