9tnq: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 9tnq is ~~ON HOLD~~

==L41 G-quadruplex-forming aptamers targeting HMGB1 protein==

== Structural highlights ==

<table><tr><td colspan='2'>[[9tnq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9TNQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9TNQ FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 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=9tnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9tnq OCA], [https://pdbe.org/9tnq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9tnq RCSB], [https://www.ebi.ac.uk/pdbsum/9tnq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9tnq ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

High Mobility Group Box 1 (HMGB1) is a valuable therapeutic target in inflammatory, autoimmune diseases, and cancer. Recently, some of us identified a set of anti-HMGB1 aptamers, folding into G-quadruplex structures of different topology. Among them, L12 and L41 were the most effective aptamers as for affinity and activity towards the protein. Here, nuclear magnetic resonance (NMR) spectroscopy, corroborated by size exclusion high performance liquid chromatography (SE-HPLC) and circular dichroism (CD), allowed defining the structural features of L12 and L41. In-depth structural details were obtained for the monomeric forms of these aptamers in a K(+)-rich (100 mM K(+)) buffer, mimicking the intracellular environment. Under these conditions, both L12 and L41 folded in hybrid G-quadruplex structures. By cross-referencing the obtained data, we inferred that these structures were also the main monomeric folded species in the Na(+)-rich Phosphate Buffered Saline (PBS) buffer, mimicking the extracellular environment, suggesting that these aptamers share similar recognition patterns when interacting with the target protein. However, in PBS a higher amount of hybrid-2 G-quadruplex was observed for L12 than L41. Biolayer interferometry (BLI) analysis demonstrated a preference of HMGB1 for L12 over L41, in line with in vitro assays, showing higher ability to inhibit the HMGB1-induced cell migration for L12 than L41. These findings suggest that HMGB1 recognizes the hybrid-2 G-quadruplex folding of these aptamers, present in higher degree in L12 than L41. In summary, this work provides precious insights into the conformational preferences of L12 and L41, of crucial importance to design more effective HMGB1 inhibitors.

~~Authors~~:

Unraveling the NMR structures of G-quadruplex-forming aptamers acting as inhibitors of High Mobility Group Box 1 (HMGB1) pathological activity.,Trajkovski M, Platella C, Musumeci D, Napolitano E, Esposito CL, Catuogno S, Plavec J, Montesarchio D Int J Biol Macromol. 2026 Mar 24;357:151585. doi: 10.1016/j.ijbiomac.2026.151585. PMID:41881226<ref>PMID:41881226</ref>

~~Description~~:

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

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Homo sapiens]]

[[Category: Large Structures]]

[[Category: Catuogno S]]

[[Category: Esposito CL]]

[[Category: Montesarchio D]]

[[Category: Musumeci D]]

[[Category: Napolitano E]]

[[Category: Platella C]]

[[Category: Plavec J]]

[[Category: Trajkovski M]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9tnq is ON HOLD
+==L41 G-quadruplex-forming aptamers targeting HMGB1 protein==
+<StructureSection load='9tnq' size='340' side='right'caption='[[9tnq]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9tnq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9TNQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9TNQ FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR,  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=9tnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9tnq OCA], [https://pdbe.org/9tnq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9tnq RCSB], [https://www.ebi.ac.uk/pdbsum/9tnq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9tnq ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+High Mobility Group Box 1 (HMGB1) is a valuable therapeutic target in inflammatory, autoimmune diseases, and cancer. Recently, some of us identified a set of anti-HMGB1 aptamers, folding into G-quadruplex structures of different topology. Among them, L12 and L41 were the most effective aptamers as for affinity and activity towards the protein. Here, nuclear magnetic resonance (NMR) spectroscopy, corroborated by size exclusion high performance liquid chromatography (SE-HPLC) and circular dichroism (CD), allowed defining the structural features of L12 and L41. In-depth structural details were obtained for the monomeric forms of these aptamers in a K(+)-rich (100 mM K(+)) buffer, mimicking the intracellular environment. Under these conditions, both L12 and L41 folded in hybrid G-quadruplex structures. By cross-referencing the obtained data, we inferred that these structures were also the main monomeric folded species in the Na(+)-rich Phosphate Buffered Saline (PBS) buffer, mimicking the extracellular environment, suggesting that these aptamers share similar recognition patterns when interacting with the target protein. However, in PBS a higher amount of hybrid-2 G-quadruplex was observed for L12 than L41. Biolayer interferometry (BLI) analysis demonstrated a preference of HMGB1 for L12 over L41, in line with in vitro assays, showing higher ability to inhibit the HMGB1-induced cell migration for L12 than L41. These findings suggest that HMGB1 recognizes the hybrid-2 G-quadruplex folding of these aptamers, present in higher degree in L12 than L41. In summary, this work provides precious insights into the conformational preferences of L12 and L41, of crucial importance to design more effective HMGB1 inhibitors.
-Authors:
+Unraveling the NMR structures of G-quadruplex-forming aptamers acting as inhibitors of High Mobility Group Box 1 (HMGB1) pathological activity.,Trajkovski M, Platella C, Musumeci D, Napolitano E, Esposito CL, Catuogno S, Plavec J, Montesarchio D Int J Biol Macromol. 2026 Mar 24;357:151585. doi: 10.1016/j.ijbiomac.2026.151585. PMID:41881226<ref>PMID:41881226</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 9tnq" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Catuogno S]]
+[[Category: Esposito CL]]
+[[Category: Montesarchio D]]
+[[Category: Musumeci D]]
+[[Category: Napolitano E]]
+[[Category: Platella C]]
+[[Category: Plavec J]]
+[[Category: Trajkovski M]]