View source for 8qkd


==X-ray crystal structure of a de novo designed single-chain parallel coiled-coil alpha-helical barrel with 5 inner helices, sc-CC-5-24==
<StructureSection load='8qkd' size='340' side='right'caption='[[8qkd]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8qkd]] is a 1 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=8QKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8QKD FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=8qkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8qkd OCA], [https://pdbe.org/8qkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8qkd RCSB], [https://www.ebi.ac.uk/pdbsum/8qkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8qkd ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Computational protein design is advancing rapidly. Here we describe efficient routes starting from validated parallel and antiparallel peptide assemblies to design two families of alpha-helical barrel proteins with central channels that bind small molecules. Computational designs are seeded by the sequences and structures of defined de novo oligomeric barrel-forming peptides, and adjacent helices are connected by loop building. For targets with antiparallel helices, short loops are sufficient. However, targets with parallel helices require longer connectors; namely, an outer layer of helix-turn-helix-turn-helix motifs that are packed onto the barrels. Throughout these computational pipelines, residues that define open states of the barrels are maintained. This minimizes sequence sampling, accelerating the design process. For each of six targets, just two to six synthetic genes are made for expression in Escherichia coli. On average, 70% of these genes express to give soluble monomeric proteins that are fully characterized, including high-resolution structures for most targets that match the design models with high accuracy.

Rationally seeded computational protein design of a-helical barrels.,Albanese KI, Petrenas R, Pirro F, Naudin EA, Borucu U, Dawson WM, Scott DA, Leggett GJ, Weiner OD, Oliver TAA, Woolfson DN Nat Chem Biol. 2024 Jun 20. doi: 10.1038/s41589-024-01642-0. PMID:38902458<ref>PMID:38902458</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8qkd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Albanese KI]]
[[Category: Petrenas R]]
[[Category: Woolfson DN]]