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<StructureSection load='3q9n' size='340' side='right'caption='[[3q9n]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3q9n' size='340' side='right'caption='[[3q9n]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3q9n]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q9N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q9N FirstGlance]. <br>
<table><tr><td colspan='2'>[[3q9n]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q9N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q9N FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMS:CARBAMOYL+SARCOSINE'>CMS</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</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]] 2&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3q9u|3q9u]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMS:CARBAMOYL+SARCOSINE'>CMS</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</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=3q9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q9n OCA], [https://pdbe.org/3q9n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q9n RCSB], [https://www.ebi.ac.uk/pdbsum/3q9n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q9n 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=3q9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q9n OCA], [https://pdbe.org/3q9n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q9n RCSB], [https://www.ebi.ac.uk/pdbsum/3q9n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q9n ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The de novo design of protein-protein interfaces is a stringent test of our understanding of the principles underlying protein-protein interactions and would enable unique approaches to biological and medical challenges. Here we describe a motif-based method to computationally design protein-protein complexes with native-like interface composition and interaction density. Using this method we designed a pair of proteins, Prb and Pdar, that heterodimerize with a Kd of 130 nM, 1000-fold tighter than any previously designed de novo protein-protein complex. Directed evolution identified two point mutations that improve affinity to 180 pM. Crystal structures of an affinity-matured complex reveal binding is entirely through the designed interface residues. Surprisingly, in the in vitro evolved complex one of the partners is rotated 180 degrees relative to the original design model, yet still maintains the central computationally designed hotspot interaction and preserves the character of many peripheral interactions. This work demonstrates that high-affinity protein interfaces can be created by designing complementary interaction surfaces on two noninteracting partners and underscores remaining challenges.
A De Novo Protein Binding Pair By Computational Design and Directed Evolution.,Karanicolas J, Corn JE, Chen I, Joachimiak LA, Dym O, Peck SH, Albeck S, Unger T, Hu W, Liu G, Delbecq S, T Montelione G, P Spiegel C, Liu DR, Baker D Mol Cell. 2011 Apr 22;42(2):250-260. Epub 2011 Mar 31. PMID:21458342<ref>PMID:21458342</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3q9n" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ankyrin 3D structures|Ankyrin 3D structures]]
*[[Ankyrin 3D structures|Ankyrin 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Albeck, S]]
[[Category: Albeck S]]
[[Category: Baker, D]]
[[Category: Baker D]]
[[Category: Chen, I]]
[[Category: Chen I]]
[[Category: Chung, S]]
[[Category: Chung S]]
[[Category: Corn, J E]]
[[Category: Corn JE]]
[[Category: Delbecq, S]]
[[Category: Delbecq S]]
[[Category: Dym, O]]
[[Category: Dym O]]
[[Category: Hu, W]]
[[Category: Hu W]]
[[Category: ISPC, Israel Structural Proteomics Center]]
[[Category: Joachimiak LA]]
[[Category: Joachimiak, L A]]
[[Category: Karanicolas J]]
[[Category: Karanicolas, J]]
[[Category: Liu D]]
[[Category: Liu, D]]
[[Category: Liu G]]
[[Category: Liu, G]]
[[Category: Montelione GT]]
[[Category: Montelione, G T]]
[[Category: Spiegel C]]
[[Category: Spiegel, C]]
[[Category: Unger T]]
[[Category: Unger, T]]
[[Category: De novo protein]]
[[Category: Prb-binding designed ankyrin repeat]]
[[Category: Protein binding]]
[[Category: Structural genomic]]

Latest revision as of 11:38, 14 March 2024

In silico and in vitro co-evolution of a high affinity complementary protein-protein interface

3q9n, resolution 2.00Å

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