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5k7v

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Revision as of 10:42, 27 September 2023

Computational Design of Self-Assembling Cyclic Protein Homooligomers

Structural highlights

5k7v is a 3 chain structure with sequence from Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.165Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Self-assembling cyclic protein homo-oligomers play important roles in biology, and the ability to generate custom homo-oligomeric structures could enable new approaches to probe biological function. Here we report a general approach to design cyclic homo-oligomers that employs a new residue-pair-transform method to assess the designability of a protein-protein interface. This method is sufficiently rapid to enable the systematic enumeration of cyclically docked arrangements of a monomer followed by sequence design of the newly formed interfaces. We use this method to design interfaces onto idealized repeat proteins that direct their assembly into complexes that possess cyclic symmetry. Of 96 designs that were characterized experimentally, 21 were found to form stable monodisperse homo-oligomers in solution, and 15 (four homodimers, six homotrimers, six homotetramers and one homopentamer) had solution small-angle X-ray scattering data consistent with the design models. X-ray crystal structures were obtained for five of the designs and each is very close to their corresponding computational model.

Computational design of self-assembling cyclic protein homo-oligomers.,Fallas JA, Ueda G, Sheffler W, Nguyen V, McNamara DE, Sankaran B, Pereira JH, Parmeggiani F, Brunette TJ, Cascio D, Yeates TR, Zwart P, Baker D Nat Chem. 2017 Apr;9(4):353-360. doi: 10.1038/nchem.2673. Epub 2016 Dec 5. PMID:28338692^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Fallas JA, Ueda G, Sheffler W, Nguyen V, McNamara DE, Sankaran B, Pereira JH, Parmeggiani F, Brunette TJ, Cascio D, Yeates TR, Zwart P, Baker D. Computational design of self-assembling cyclic protein homo-oligomers. Nat Chem. 2017 Apr;9(4):353-360. doi: 10.1038/nchem.2673. Epub 2016 Dec 5. PMID:28338692 doi:http://dx.doi.org/10.1038/nchem.2673

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5k7v"

@@ Line 3: / Line 3: @@
 <StructureSection load='5k7v' size='340' side='right'caption='[[5k7v]], [[Resolution|resolution]] 3.17&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5k7v]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K7V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K7V FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5k7v]] is a 3 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=5K7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K7V FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5k7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k7v OCA], [http://pdbe.org/5k7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k7v RCSB], [http://www.ebi.ac.uk/pdbsum/5k7v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k7v 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]] 3.165&#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=5k7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k7v OCA], [https://pdbe.org/5k7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k7v RCSB], [https://www.ebi.ac.uk/pdbsum/5k7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k7v ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 20: / Line 21: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Baker, D]]
+[[Category: Synthetic construct]]
-[[Category: Fallas, J A]]
+[[Category: Baker D]]
-[[Category: Pereira, J H]]
+[[Category: Fallas JA]]
-[[Category: Sankaran, B]]
+[[Category: Pereira JH]]
-[[Category: Ueda, G]]
+[[Category: Sankaran B]]
-[[Category: Zwart, P H]]
+[[Category: Ueda G]]
-[[Category: De novo design]]
+[[Category: Zwart PH]]
-[[Category: De novo protein]]
-[[Category: Rosetta]]

5k7v

From Proteopedia

Revision as of 10:42, 27 September 2023

Computational Design of Self-Assembling Cyclic Protein Homooligomers

Structural highlights

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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