5yd3: Difference between revisions

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== Structural highlights ==

<table><tr><td colspan='2'>[[5yd3]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YD3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YD3 FirstGlance]. <br>

<table><tr><td colspan='2'>[[5yd3]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YD3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YD3 FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5yd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yd3 OCA], [http://pdbe.org/5yd3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yd3 RCSB], [http://www.ebi.ac.uk/pdbsum/5yd3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yd3 ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Molecular recognition is a fundamental event at the core of essentially every biological process. In particular, intermolecular H-bonds have been recognized as key stabilizing forces in antibody-antigen interactions resulting in exquisite specificity and high affinity. Although equally abundant, the role of intramolecular H-bonds is far less clear and not universally acknowledged. Herein, we have carried out a molecular-level study to dissect the contribution of intramolecular H-bonds in a flexible peptide for the recognition by an antibody. We show that intramolecular H-bonds may have a profound, multifaceted and favorable effect on the binding affinity by up to 2 kcal mol-1 of free energy. Collectively, our results suggest that antibodies are fine tuned to recognize transiently stabilized structures of flexible peptides in solution, for which intramolecular H-bonds play a key role.

Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody.,Miyanabe K, Akiba H, Kuroda D, Nakakido M, Kusano-Arai O, Iwanari H, Hamakubo T, Caaveiro JMM, Tsumoto K J Biochem. 2018 Jul 1;164(1):65-76. doi: 10.1093/jb/mvy032. PMID:29924367<ref>PMID:29924367</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Lk3 transgenic mice]]

[[Category: Caaveiro, J M.M]]

[[Category: Miyanabe, K]]

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@@ Line 3: / Line 3: @@
 <StructureSection load='5yd3' size='340' side='right' caption='[[5yd3]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5yd3]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YD3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YD3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5yd3]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YD3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YD3 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5yd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yd3 OCA], [http://pdbe.org/5yd3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yd3 RCSB], [http://www.ebi.ac.uk/pdbsum/5yd3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yd3 ProSAT]</span></td></tr>
 </table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Molecular recognition is a fundamental event at the core of essentially every biological process. In particular, intermolecular H-bonds have been recognized as key stabilizing forces in antibody-antigen interactions resulting in exquisite specificity and high affinity. Although equally abundant, the role of intramolecular H-bonds is far less clear and not universally acknowledged. Herein, we have carried out a molecular-level study to dissect the contribution of intramolecular H-bonds in a flexible peptide for the recognition by an antibody. We show that intramolecular H-bonds may have a profound, multifaceted and favorable effect on the binding affinity by up to 2 kcal mol-1 of free energy. Collectively, our results suggest that antibodies are fine tuned to recognize transiently stabilized structures of flexible peptides in solution, for which intramolecular H-bonds play a key role.
+Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody.,Miyanabe K, Akiba H, Kuroda D, Nakakido M, Kusano-Arai O, Iwanari H, Hamakubo T, Caaveiro JMM, Tsumoto K J Biochem. 2018 Jul 1;164(1):65-76. doi: 10.1093/jb/mvy032. PMID:29924367<ref>PMID:29924367</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 5yd3" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
+[[Category: Lk3 transgenic mice]]
 [[Category: Caaveiro, J M.M]]
 [[Category: Miyanabe, K]]