5dns: Difference between revisions
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The | ==t1428 loop variant in P3221== | ||
<StructureSection load='5dns' size='340' side='right'caption='[[5dns]], [[Resolution|resolution]] 3.56Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5dns]] 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=5DNS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DNS 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]] 3.561Å</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=5dns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dns OCA], [https://pdbe.org/5dns PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dns RCSB], [https://www.ebi.ac.uk/pdbsum/5dns PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dns ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The ability to design and construct structures with atomic level precision is one of the key goals of nanotechnology. Proteins offer an attractive target for atomic design because they can be synthesized chemically or biologically and can self-assemble. However, the generalized protein folding and design problem is unsolved. One approach to simplifying the problem is to use a repetitive protein as a scaffold. Repeat proteins are intrinsically modular, and their folding and structures are better understood than large globular domains. Here, we have developed a class of synthetic repeat proteins based on the pentapeptide repeat family of beta-solenoid proteins. We have constructed length variants of the basic scaffold and computationally designed de novo loops projecting from the scaffold core. The experimentally solved 3.56-A resolution crystal structure of one designed loop matches closely the designed hairpin structure, showing the computational design of a backbone extension onto a synthetic protein core without the use of backbone fragments from known structures. Two other loop designs were not clearly resolved in the crystal structures, and one loop appeared to be in an incorrect conformation. We have also shown that the repeat unit can accommodate whole-domain insertions by inserting a domain into one of the designed loops. | |||
Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension.,MacDonald JT, Kabasakal BV, Godding D, Kraatz S, Henderson L, Barber J, Freemont PS, Murray JW Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10346-51. doi:, 10.1073/pnas.1525308113. Epub 2016 Aug 29. PMID:27573845<ref>PMID:27573845</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5dns" style="background-color:#fffaf0;"></div> | ||
[[Category: Kabasakal | == References == | ||
[[Category: Murray | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Kabasakal BV]] | |||
[[Category: MacDonald JT]] | |||
[[Category: Murray JW]] | |||
Latest revision as of 00:51, 29 June 2023
t1428 loop variant in P3221t1428 loop variant in P3221
Structural highlights
Publication Abstract from PubMedThe ability to design and construct structures with atomic level precision is one of the key goals of nanotechnology. Proteins offer an attractive target for atomic design because they can be synthesized chemically or biologically and can self-assemble. However, the generalized protein folding and design problem is unsolved. One approach to simplifying the problem is to use a repetitive protein as a scaffold. Repeat proteins are intrinsically modular, and their folding and structures are better understood than large globular domains. Here, we have developed a class of synthetic repeat proteins based on the pentapeptide repeat family of beta-solenoid proteins. We have constructed length variants of the basic scaffold and computationally designed de novo loops projecting from the scaffold core. The experimentally solved 3.56-A resolution crystal structure of one designed loop matches closely the designed hairpin structure, showing the computational design of a backbone extension onto a synthetic protein core without the use of backbone fragments from known structures. Two other loop designs were not clearly resolved in the crystal structures, and one loop appeared to be in an incorrect conformation. We have also shown that the repeat unit can accommodate whole-domain insertions by inserting a domain into one of the designed loops. Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension.,MacDonald JT, Kabasakal BV, Godding D, Kraatz S, Henderson L, Barber J, Freemont PS, Murray JW Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10346-51. doi:, 10.1073/pnas.1525308113. Epub 2016 Aug 29. PMID:27573845[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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