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==Elongated version of a de novo designed three helix bundle structure (GRa3D)==
==Elongated version of a de novo designed three helix bundle structure (GRa3D)==
<StructureSection load='6ds9' size='340' side='right' caption='[[6ds9]], [[Resolution|resolution]] 1.34&Aring;' scene=''>
<StructureSection load='6ds9' size='340' side='right'caption='[[6ds9]], [[Resolution|resolution]] 1.34&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6ds9]] is a 1 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=6DS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DS9 FirstGlance]. <br>
<table><tr><td colspan='2'>[[6ds9]] 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=6DS9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DS9 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.34&#8491;</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=6ds9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ds9 OCA], [http://pdbe.org/6ds9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ds9 RCSB], [http://www.ebi.ac.uk/pdbsum/6ds9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ds9 ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6ds9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ds9 OCA], [https://pdbe.org/6ds9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ds9 RCSB], [https://www.ebi.ac.uk/pdbsum/6ds9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ds9 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Cupredoxins are copper-dependent electron-transfer proteins that can be categorized as blue, purple, green, and red depending on the spectroscopic properties of the Cu(II) bound forms. Interestingly, despite significantly different first coordination spheres and nuclearity, all cupredoxins share a common Greek Key beta-sheet fold. We have previously reported the design of a red copper protein within a completely distinct three-helical bundle protein, alpha3DChC2. (1) While this design demonstrated that a beta-barrel fold was not requisite to recapitulate the properties of a native cupredoxin center, the parent peptide alpha3D was not sufficiently stable to allow further study through additional mutations. Here we present the design of an elongated protein GRANDalpha3D (GRalpha3D) with Delta Gu = -11.4 kcal/mol compared to the original design's -5.1 kcal/mol. Diffraction quality crystals were grown of GRalpha3D (a first for an alpha3D peptide) and solved to a resolution of 1.34 A. Examination of this structure suggested that Glu41 might interact with the Cu in our previously reported red copper protein. The previous bis(histidine)(cysteine) site (GRalpha3DChC2) was designed into this new scaffold and a series of variant constructs were made to explore this hypothesis. Mutation studies around Glu41 not only prove the proposed interaction, but also enabled tuning of the constructs' hyperfine coupling constant from 160 to 127 x 10(-4) cm(-1). X-ray absorption spectroscopy analysis is consistent with these hyperfine coupling differences being the result of variant 4p mixing related to coordination geometry changes. These studies not only prove that an Glu41-Cu interaction leads to the alpha3DChC2 construct's red copper protein like spectral properties, but also exemplify the exact control one can have in a de novo construct to tune the properties of an electron-transfer Cu site.
Clarifying the Copper Coordination Environment in a de Novo Designed Red Copper Protein.,Koebke KJ, Ruckthong L, Meagher JL, Mathieu E, Harland J, Deb A, Lehnert N, Policar C, Tard C, Penner-Hahn JE, Stuckey JA, Pecoraro VL Inorg Chem. 2018 Oct 1;57(19):12291-12302. doi: 10.1021/acs.inorgchem.8b01989., Epub 2018 Sep 18. PMID:30226758<ref>PMID:30226758</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6ds9" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Synthetic construct sequences]]
[[Category: Large Structures]]
[[Category: Koebke, K J]]
[[Category: Synthetic construct]]
[[Category: Meagher, J L]]
[[Category: Koebke KJ]]
[[Category: Pecoraro, V L]]
[[Category: Meagher JL]]
[[Category: Ruckthong, L R]]
[[Category: Pecoraro VL]]
[[Category: Stuckey, J A]]
[[Category: Ruckthong LR]]
[[Category: De novo protein]]
[[Category: Stuckey JA]]
[[Category: De novo scaffold]]
[[Category: Three helix bundle]]

Latest revision as of 14:36, 13 March 2024

Elongated version of a de novo designed three helix bundle structure (GRa3D)

6ds9, resolution 1.34Å

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