7eh3: Difference between revisions
New page: '''Unreleased structure''' The entry 7eh3 is ON HOLD Authors: Percipalle, M., Hunashal, Y., Esposito, G., Fogolari, F. Description: Structure of Nanobody Nb23 in solution using NMR spe... |
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==Structure of Nanobody Nb23 in solution using NMR spectroscopy== | |||
<StructureSection load='7eh3' size='340' side='right'caption='[[7eh3]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EH3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EH3 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 10 models</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=7eh3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eh3 OCA], [https://pdbe.org/7eh3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eh3 RCSB], [https://www.ebi.ac.uk/pdbsum/7eh3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eh3 ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
BACKGROUND: Nanobodies, or VHHs, are derived from heavy chain-only antibodies (hcAbs) found in camelids. They overcome some of the inherent limitations of monoclonal antibodies (mAbs) and derivatives thereof, due to their smaller molecular size and higher stability, and thus present an alternative to mAbs for therapeutic use. Two nanobodies, Nb23 and Nb24, have been shown to similarly inhibit the self-aggregation of very amyloidogenic variants of beta2-microglobulin. Here, the structure of Nb23 was modeled with the Chemical-Shift (CS)-Rosetta server using chemical shift assignments from nuclear magnetic resonance (NMR) spectroscopy experiments, and used as prior knowledge in PONDEROSA restrained modeling based on experimentally assessed internuclear distances. Further validation was comparatively obtained with the results of molecular dynamics trajectories calculated from the resulting best energy-minimized Nb23 conformers. METHODS: 2D and 3D NMR spectroscopy experiments were carried out to determine the assignment of the backbone and side chain hydrogen, nitrogen and carbon resonances to extract chemical shifts and interproton separations for restrained modeling. RESULTS: The solution structure of isolated Nb23 nanobody was determined. CONCLUSIONS: The structural analysis indicated that isolated Nb23 has a dynamic CDR3 loop distributed over different orientations with respect to Nb24, which could determine differences in target antigen affinity or complex lability. | |||
Structure of Nanobody Nb23.,Percipalle M, Hunashal Y, Steyaert J, Fogolari F, Esposito G Molecules. 2021 Jun 11;26(12). pii: molecules26123567. doi:, 10.3390/molecules26123567. PMID:34207949<ref>PMID:34207949</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[ | </div> | ||
[[Category: | <div class="pdbe-citations 7eh3" style="background-color:#fffaf0;"></div> | ||
[[Category: Esposito | |||
[[Category: Fogolari | ==See Also== | ||
[[Category: Percipalle | *[[Antibody 3D structures|Antibody 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Esposito G]] | |||
[[Category: Fogolari F]] | |||
[[Category: Hunashal Y]] | |||
[[Category: Percipalle M]] | |||
Latest revision as of 09:15, 21 November 2024
Structure of Nanobody Nb23 in solution using NMR spectroscopyStructure of Nanobody Nb23 in solution using NMR spectroscopy
Structural highlights
Publication Abstract from PubMedBACKGROUND: Nanobodies, or VHHs, are derived from heavy chain-only antibodies (hcAbs) found in camelids. They overcome some of the inherent limitations of monoclonal antibodies (mAbs) and derivatives thereof, due to their smaller molecular size and higher stability, and thus present an alternative to mAbs for therapeutic use. Two nanobodies, Nb23 and Nb24, have been shown to similarly inhibit the self-aggregation of very amyloidogenic variants of beta2-microglobulin. Here, the structure of Nb23 was modeled with the Chemical-Shift (CS)-Rosetta server using chemical shift assignments from nuclear magnetic resonance (NMR) spectroscopy experiments, and used as prior knowledge in PONDEROSA restrained modeling based on experimentally assessed internuclear distances. Further validation was comparatively obtained with the results of molecular dynamics trajectories calculated from the resulting best energy-minimized Nb23 conformers. METHODS: 2D and 3D NMR spectroscopy experiments were carried out to determine the assignment of the backbone and side chain hydrogen, nitrogen and carbon resonances to extract chemical shifts and interproton separations for restrained modeling. RESULTS: The solution structure of isolated Nb23 nanobody was determined. CONCLUSIONS: The structural analysis indicated that isolated Nb23 has a dynamic CDR3 loop distributed over different orientations with respect to Nb24, which could determine differences in target antigen affinity or complex lability. Structure of Nanobody Nb23.,Percipalle M, Hunashal Y, Steyaert J, Fogolari F, Esposito G Molecules. 2021 Jun 11;26(12). pii: molecules26123567. doi:, 10.3390/molecules26123567. PMID:34207949[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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