3ri0: Difference between revisions

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<StructureSection load='3ri0' size='340' side='right'caption='[[3ri0]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
<StructureSection load='3ri0' size='340' side='right'caption='[[3ri0]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ri0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RI0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RI0 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ri0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RI0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RI0 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.25&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3rfn|3rfn]], [[3rhu|3rhu]], [[3rij|3rij]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TTHA1699 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=3ri0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ri0 OCA], [https://pdbe.org/3ri0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ri0 RCSB], [https://www.ebi.ac.uk/pdbsum/3ri0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ri0 ProSAT]</span></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=3ri0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ri0 OCA], [https://pdbe.org/3ri0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ri0 RCSB], [https://www.ebi.ac.uk/pdbsum/3ri0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ri0 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/Q5SHN1_THET8 Q5SHN1_THET8]
Computational grafting of functional motifs onto scaffold proteins is a promising way to engineer novel proteins with pre-specified functionalities. Typically, protein grafting involves the transplantation of protein side chains from a functional motif onto structurally homologous regions of scaffold proteins. Using this approach, we previously transplanted the human immunodeficiency virus 2F5 and 4E10 epitopes onto heterologous proteins to design novel "epitope-scaffold" antigens. However, side-chain grafting is limited by the availability of scaffolds with compatible backbone for a given epitope structure and offers no route to modify backbone structure to improve mimicry or binding affinity. To address this, we report here a new and more aggressive computational method-backbone grafting of linear motifs-that transplants the backbone and side chains of linear functional motifs onto scaffold proteins. To test this method, we first used side-chain grafting to design new 2F5 epitope scaffolds with improved biophysical characteristics. We then independently transplanted the 2F5 epitope onto three of the same parent scaffolds using the newly developed backbone grafting procedure. Crystal structures of side-chain and backbone grafting designs showed close agreement with both the computational models and the desired epitope structure. In two cases, backbone grafting scaffolds bound antibody 2F5 with 30- and 9-fold higher affinity than corresponding side-chain grafting designs. These results demonstrate that flexible backbone methods for epitope grafting can significantly improve binding affinities over those achieved by fixed backbone methods alone. Backbone grafting of linear motifs is a general method to transplant functional motifs when backbone remodeling of the target scaffold is necessary.
 
Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope.,Azoitei ML, Ban YE, Julien JP, Bryson S, Schroeter A, Kalyuzhniy O, Porter JR, Adachi Y, Baker D, Pai EF, Schief WR J Mol Biol. 2011 Oct 31. PMID:22061265<ref>PMID:22061265</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ri0" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Thet8]]
[[Category: Thermus thermophilus HB8]]
[[Category: Adachi, Y]]
[[Category: Adachi Y]]
[[Category: Azoitei, M L]]
[[Category: Azoitei ML]]
[[Category: Baker, D]]
[[Category: Baker D]]
[[Category: Ban, Y A]]
[[Category: Ban YA]]
[[Category: Bryson, S]]
[[Category: Bryson S]]
[[Category: Julien, J P]]
[[Category: Julien JP]]
[[Category: Kalyuzhniy, O]]
[[Category: Kalyuzhniy O]]
[[Category: Pai, E F]]
[[Category: Pai EF]]
[[Category: Porter, J R]]
[[Category: Porter JR]]
[[Category: Schief, W R]]
[[Category: Schief WR]]
[[Category: Schroeter, A]]
[[Category: Schroeter A]]
[[Category: Szabo, E]]
[[Category: Szabo E]]
[[Category: De novo protein]]
[[Category: Epitope-scaffold]]
[[Category: Flexible backbone design]]
[[Category: Hiv]]
[[Category: Immunogen design]]
[[Category: Protein grafting]]

Latest revision as of 12:24, 14 March 2024

Epitope backbone grafting by computational design for improved presentation of linear epitopes on scaffold proteins

3ri0, resolution 2.25Å

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