3ojd: Difference between revisions
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< | ==Anti-Indolicidin monoclonal antibody V2D2 (Fab fragment)== | ||
<StructureSection load='3ojd' size='340' side='right'caption='[[3ojd]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
You may | == Structural highlights == | ||
or the | <table><tr><td colspan='2'>[[3ojd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OJD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OJD 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]] 2Å</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=3ojd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ojd OCA], [https://pdbe.org/3ojd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ojd RCSB], [https://www.ebi.ac.uk/pdbsum/3ojd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ojd ProSAT]</span></td></tr> | ||
</table> | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oj/3ojd_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ojd ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Drug discovery initiatives often depend critically on knowledge of ligand-receptor interactions. However, the identity or structure of the target receptor may not be known in every instance. The concept of receptor surrogate, a molecular environment mimic of natural receptor, may prove beneficial under such circumstances. Here, we demonstrate the potential of monoclonal antibodies (mAbs) to act as surrogate receptors for a class of innate immune peptide antibiotics, a strategy that can help comprehend their action mechanism and identify chemical entities crucial for activity. A panel of antibody surrogates was raised against indolicidin, a tryptophan-rich cationic broad spectrum antimicrobial peptide of innate immune origin. Employing an elegant combination of thermodynamics, crystallography, and molecular modeling, interactions of the peptide with a high affinity anti-indolicidin monoclonal antibody were analyzed and were used to identify a motif that contained almost the entire antibiotic activity of native indolicidin. The analysis clarified the interaction of the peptide with previously proposed targets such as bacterial cell membrane and DNA and could further be correlated with antimicrobial compounds whose actions involve varied other mechanisms. These features suggest a multipronged assault pathway for indolicidin. Remarkably, the anti-indolicidin mAb surrogate was able to isolate additional independent bactericidal sequences from a random peptide library, providing compelling evidence as to the physiological relevance of surrogate receptor concept and suggesting applications in receptor-based pharmacophore research. | |||
An antibody as surrogate receptor reveals determinants of activity of an innate immune Peptide antibiotic.,Lomash S, Nagpal S, Salunke DM J Biol Chem. 2010 Nov 12;285(46):35750-8. Epub 2010 Sep 13. PMID:20837490<ref>PMID:20837490</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3ojd" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Mus musculus]] | [[Category: Mus musculus]] | ||
[[Category: Lomash | [[Category: Lomash S]] | ||
[[Category: Salunke | [[Category: Salunke DM]] | ||
Latest revision as of 19:55, 1 November 2023
Anti-Indolicidin monoclonal antibody V2D2 (Fab fragment)Anti-Indolicidin monoclonal antibody V2D2 (Fab fragment)
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedDrug discovery initiatives often depend critically on knowledge of ligand-receptor interactions. However, the identity or structure of the target receptor may not be known in every instance. The concept of receptor surrogate, a molecular environment mimic of natural receptor, may prove beneficial under such circumstances. Here, we demonstrate the potential of monoclonal antibodies (mAbs) to act as surrogate receptors for a class of innate immune peptide antibiotics, a strategy that can help comprehend their action mechanism and identify chemical entities crucial for activity. A panel of antibody surrogates was raised against indolicidin, a tryptophan-rich cationic broad spectrum antimicrobial peptide of innate immune origin. Employing an elegant combination of thermodynamics, crystallography, and molecular modeling, interactions of the peptide with a high affinity anti-indolicidin monoclonal antibody were analyzed and were used to identify a motif that contained almost the entire antibiotic activity of native indolicidin. The analysis clarified the interaction of the peptide with previously proposed targets such as bacterial cell membrane and DNA and could further be correlated with antimicrobial compounds whose actions involve varied other mechanisms. These features suggest a multipronged assault pathway for indolicidin. Remarkably, the anti-indolicidin mAb surrogate was able to isolate additional independent bactericidal sequences from a random peptide library, providing compelling evidence as to the physiological relevance of surrogate receptor concept and suggesting applications in receptor-based pharmacophore research. An antibody as surrogate receptor reveals determinants of activity of an innate immune Peptide antibiotic.,Lomash S, Nagpal S, Salunke DM J Biol Chem. 2010 Nov 12;285(46):35750-8. Epub 2010 Sep 13. PMID:20837490[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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