1a8w: Difference between revisions

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-{{Seed}}
-[[Image:1a8w.png|left|200px]]
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+==A K+ CATION-INDUCED CONFORMATIONAL SWITCH WITHIN A LOOP SPANNING SEGMENT OF A DNA QUADRUPLEX CONTAINING G-G-G-C REPEATS, NMR, 8 STRUCTURES==
-The line below this paragraph, containing "STRUCTURE_1a8w", creates the "Structure Box" on the page.
+<StructureSection load='1a8w' size='340' side='right'caption='[[1a8w]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1a8w]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A8W FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1a8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a8w OCA], [https://pdbe.org/1a8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a8w RCSB], [https://www.ebi.ac.uk/pdbsum/1a8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a8w ProSAT]</span></td></tr>
-{{STRUCTURE_1a8w|  PDB=1a8w  |  SCENE=  }}
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We have identified a unique structural transition (in slow exchange on the NMR time scale) in the tertiary fold of the d(G-G-G-C-T4-G-G-G-C) quadruplex on proceeding from Na+ to K+ as counterion in aqueous solution. Both monovalent cation-dependent conformations exhibit certain common structural features, which include head-to-tail dimerization of two symmetry-related stem-hairpin loops, adjacent strands which are antiparallel to each other and adjacent stacked G(syn).G(anti). G(syn).G(anti) tetrads in the central core of the quadruplexes. The Na and K cation stabilized structures of the d(G-G-G-C-T4-G-G-G-C) quadruplexes differ in the conformations of the T-T-T-T loops, the relative alignment of G.C base-pairs positioned opposite each other through their major groove edges and potentially in the number of monovalent cation binding sites. We have identified potential K cation binding cavities within the symmetry-related T-T-T-G segments, suggesting the potential for two additional monovalent cation binding sites in the K cation-stabilized quadruplex relative to its Na cation-stabilized counterpart. Modeling studies suggest that the major groove edges of guanine residues in Watson-Crick G.C base-pairs could potentially be bridged by coordinated K cations in the d(G-G-G-C-T4-G-G-G-C) quadruplex in KCl solution in contrast to formation of G.C.G.C tetrads for the corresponding quadruplex in NaCl solution. Our results defining the molecular basis of a Na to K cation-dependent conformational switch in the loop spanning segment of the d(G-G-G-C-T4-G-G-G-C) quadruplex may have relevance to recent observations that specific K cation coordinated loop conformations within quadruplexes exhibit inhibitory activity against HIV integrase.
-===A K+ CATION-INDUCED CONFORMATIONAL SWITCH WITHIN A LOOP SPANNING SEGMENT OF A DNA QUADRUPLEX CONTAINING G-G-G-C REPEATS, NMR, 8 STRUCTURES===
+A K cation-induced conformational switch within a loop spanning segment of a DNA quadruplex containing G-G-G-C repeats.,Bouaziz S, Kettani A, Patel DJ J Mol Biol. 1998 Sep 25;282(3):637-52. PMID:9737927<ref>PMID:9737927</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_9737927}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1a8w" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 9737927 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9737927}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A8W OCA].
+[[Category: Bouaziz S]]
+[[Category: Kettani A]]
-==Reference==
+[[Category: Patel DJ]]
-A K cation-induced conformational switch within a loop spanning segment of a DNA quadruplex containing G-G-G-C repeats., Bouaziz S, Kettani A, Patel DJ, J Mol Biol. 1998 Sep 25;282(3):637-52. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9737927 9737927]
-[[Category: Bouaziz, S.]]
-[[Category: Kettani, A.]]
-[[Category: Patel, D J.]]
-[[Category: Cation dependent conformational transition]]
-[[Category: Deoxyribonucleic acid]]
-[[Category: Dna quadruplexes targeted to hiv integrase]]
-[[Category: G-g-g-c repeat-containing dna quadruplex]]
-[[Category: K+ cation coordination site]]
-[[Category: K+ cation encapsulation within a hairpin loop]]
-[[Category: Monovalent]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 16:23:59 2008''