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<StructureSection load='6d0t' size='340' side='right'caption='[[6d0t]], [[Resolution|resolution]] 1.63&Aring;' scene=''>
<StructureSection load='6d0t' size='340' side='right'caption='[[6d0t]], [[Resolution|resolution]] 1.63&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6d0t]] 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=6D0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D0T FirstGlance]. <br>
<table><tr><td colspan='2'>[[6d0t]] 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=6D0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D0T 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=6d0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d0t OCA], [http://pdbe.org/6d0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d0t RCSB], [http://www.ebi.ac.uk/pdbsum/6d0t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d0t ProSAT]</span></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]] 1.63&#8491;</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=6d0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d0t OCA], [https://pdbe.org/6d0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d0t RCSB], [https://www.ebi.ac.uk/pdbsum/6d0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d0t ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The regular arrangements of beta-strands around a central axis in beta-barrels and of alpha-helices in coiled coils contrast with the irregular tertiary structures of most globular proteins, and have fascinated structural biologists since they were first discovered. Simple parametric models have been used to design a wide range of alpha-helical coiled-coil structures, but to date there has been no success with beta-barrels. Here we show that accurate de novo design of beta-barrels requires considerable symmetry-breaking to achieve continuous hydrogen-bond connectivity and eliminate backbone strain. We then build ensembles of beta-barrel backbone models with cavity shapes that match the fluorogenic compound DFHBI, and use a hierarchical grid-based search method to simultaneously optimize the rigid-body placement of DFHBI in these cavities and the identities of the surrounding amino acids to achieve high shape and chemical complementarity. The designs have high structural accuracy and bind and fluorescently activate DFHBI in vitro and in Escherichia coli, yeast and mammalian cells. This de novo design of small-molecule binding activity, using backbones custom-built to bind the ligand, should enable the design of increasingly sophisticated ligand-binding proteins, sensors and catalysts that are not limited by the backbone geometries available in known protein structures.
De novo design of a fluorescence-activating beta-barrel.,Dou J, Vorobieva AA, Sheffler W, Doyle LA, Park H, Bick MJ, Mao B, Foight GW, Lee MY, Gagnon LA, Carter L, Sankaran B, Ovchinnikov S, Marcos E, Huang PS, Vaughan JC, Stoddard BL, Baker D Nature. 2018 Sep 12. pii: 10.1038/s41586-018-0509-0. doi:, 10.1038/s41586-018-0509-0. PMID:30209393<ref>PMID:30209393</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6d0t" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Synthetic construct sequences]]
[[Category: Synthetic construct]]
[[Category: Baker, D]]
[[Category: Baker D]]
[[Category: Bick, M J]]
[[Category: Bick MJ]]
[[Category: Carter, L]]
[[Category: Carter L]]
[[Category: Dou, J]]
[[Category: Dou J]]
[[Category: Doyle, L A]]
[[Category: Doyle LA]]
[[Category: Foight, G W]]
[[Category: Foight GW]]
[[Category: Huang, P]]
[[Category: Huang P]]
[[Category: Lee, M]]
[[Category: Lee M]]
[[Category: Mao, B]]
[[Category: Mao B]]
[[Category: Marcos, E]]
[[Category: Marcos E]]
[[Category: Ovchinnikov, S]]
[[Category: Ovchinnikov S]]
[[Category: Park, H]]
[[Category: Park H]]
[[Category: Sankaran, B]]
[[Category: Sankaran B]]
[[Category: Sheffler, W]]
[[Category: Sheffler W]]
[[Category: Stoddard, B L]]
[[Category: Stoddard BL]]
[[Category: Vaughan, J C]]
[[Category: Vaughan JC]]
[[Category: Vorobieva, A A]]
[[Category: Vorobieva AA]]
[[Category: Beta-barrel]]
[[Category: De novo protein]]
[[Category: Design]]

Latest revision as of 14:31, 13 March 2024

De novo design of a fluorescence-activating beta barrel - BB1

6d0t, resolution 1.63Å

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