3qxw: Difference between revisions
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==Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody== | ==Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody== | ||
<StructureSection load='3qxw' size='340' side='right' caption='[[3qxw]], [[Resolution|resolution]] 1.85Å' scene=''> | <StructureSection load='3qxw' size='340' side='right' caption='[[3qxw]], [[Resolution|resolution]] 1.85Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3qxw]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3qxw]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_glama Camelus glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXW FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1i3u|1i3u]], [[2x6m|2x6m]], [[3qxt|3qxt]], [[3qxv|3qxv]], [[3qxu|3qxu]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1i3u|1i3u]], [[2x6m|2x6m]], [[3qxt|3qxt]], [[3qxv|3qxv]], [[3qxu|3qxu]]</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=3qxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxw RCSB], [http://www.ebi.ac.uk/pdbsum/3qxw PDBsum]</span></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=3qxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxw OCA], [http://pdbe.org/3qxw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qxw RCSB], [http://www.ebi.ac.uk/pdbsum/3qxw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxw ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3qxw" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Camelus glama]] | ||
[[Category: Fanning, S W]] | [[Category: Fanning, S W]] | ||
[[Category: Horn, J R]] | [[Category: Horn, J R]] | ||
Revision as of 15:49, 4 August 2016
Free structure of an anti-methotrexate CDR1-4 Graft VHH AntibodyFree structure of an anti-methotrexate CDR1-4 Graft VHH Antibody
Structural highlights
Publication Abstract from PubMedConventional anti-hapten antibodies typically bind low-molecular weight compounds (haptens) in the crevice between the variable heavy and light chains. Conversely, heavy chain-only camelid antibodies, which lack a light chain, must rely entirely on a single variable domain to recognize haptens. While several anti-hapten VHHs have been generated, little is known regarding the underlying structural and thermodynamic basis for hapten recognition. Here, an anti-methotrexate VHH (anti-MTX VHH) was generated using grafting methods whereby the three complementarity determining regions (CDRs) were inserted onto an existing VHH framework. Thermodynamic analysis of the anti-MTX VHH CDR1-3 Graft revealed a micromolar binding affinity, while the crystal structure of the complex revealed a somewhat surprising noncanonical binding site which involved MTX tunneling under the CDR1 loop. Due to the close proximity of MTX to CDR4, a nonhypervariable loop, the CDR4 loop sequence was subsequently introduced into the CDR1-3 graft, which resulted in a dramatic 1000-fold increase in the binding affinity. Crystal structure analysis of both the free and complex anti-MTX CDR1-4 graft revealed CDR4 plays a significant role in both intermolecular contacts and binding site conformation that appear to contribute toward high affinity binding. Additionally, the anti-MTX VHH possessed relatively high specificity for MTX over closely related compounds aminopterin and folate, demonstrating that VHH domains are capable of binding low-molecular weight ligands with high affinity and specificity, despite their reduced interface. An anti-hapten camelid antibody reveals a cryptic binding site with significant energetic contributions from a nonhypervariable loop.,Fanning SW, Horn JR Protein Sci. 2011 Jul;20(7):1196-207. doi: 10.1002/pro.648. Epub 2011 May, 23. PMID:21557375[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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