4a4t: Difference between revisions

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-[[Image:4a4t.jpg|left|200px]]
-<!--
+==UNAC Tetraloops: To What Extent Can They Mimic GNRA Tetraloops==
-The line below this paragraph, containing "STRUCTURE_4a4t", creates the "Structure Box" on the page.
+<StructureSection load='4a4t' size='340' side='right'caption='[[4a4t]], [[NMR_Ensembles_of_Models | 5 NMR models]]' 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'>[[4a4t]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4A4T FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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=4a4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a4t OCA], [https://pdbe.org/4a4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4a4t RCSB], [https://www.ebi.ac.uk/pdbsum/4a4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4a4t ProSAT]</span></td></tr>
--->
+</table>
-{{STRUCTURE_4a4t|  PDB=4a4t  |  SCENE=  }}
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structures of four small RNAs each containing a different version of the UNAC loop were determined in solution using NMR spectroscopy and restrained molecular dynamics. The UMAC tetraloops (where M is A or C) exhibited a typical GNRA fold including at least one hydrogen bond between the first U and fourth C. In contrast, UGAC and UUAC tetraloops have a different orientation of the first and fourth residues, such that they do not closely mimic the GNRA fold. Although the UMAC tetraloops are excellent structural mimics of the GNRA tetraloop backbone, sequence comparisons typically do not reveal co-variation between the two loop types. The limited covariation is attributed to differences in the location of potential hydrogen bond donors and acceptors as a result of the replacement of the terminal A of GNRA with C in the UMAC version. Thus, UMAC loops do not readily form the common GNRA tetraloop-receptor interaction. The loop at positions 863-866 in E. coli 16S ribosomal RNA appears to be a major exception. However, in this case the GNRA loop does not in fact engage in the usual base to backbone tertiary interactions. In summary, UMAC loops are not just an alternative sequence version of the GNRA loop family, but instead they expand the types of interactions, or lack thereof, that are possible. From a synthetic biology perspective their inclusion in an artificial RNA may allow the establishment of a stable loop structure while minimizing unwanted long range interactions or permitting alternative long-range interactions. (c) 2012 Wiley Periodicals, Inc. Biopolymers 97: 617-628, 2012.
-===UNAC Tetraloops: To What Extent Can They Mimic GNRA Tetraloops===
+UNAC tetraloops: to what extent do they mimic GNRA tetraloops?,Zhao Q, Huang HC, Nagaswamy U, Xia Y, Gao X, Fox GE Biopolymers. 2012 Aug;97(8):617-28. doi: 10.1002/bip.22049. PMID:22605553<ref>PMID:22605553</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_22605553}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 4a4t" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 22605553 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_22605553}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[4a4t]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A4T OCA].
+[[Category: Fox, G]]
+[[Category: Gao, X]]
-==Reference==
+[[Category: Huang, H]]
-<ref group="xtra">PMID:022605553</ref><references group="xtra"/>
+[[Category: Nagaswamy, U]]
-[[Category: Fox, G.]]
+[[Category: Xia, Y]]
-[[Category: Gao, X.]]
+[[Category: Zhao, Q]]
-[[Category: Huang, H.]]
-[[Category: Nagaswamy, U.]]
-[[Category: Xia, Y.]]
-[[Category: Zhao, Q.]]
 [[Category: Evolution]]
 [[Category: Rna]]
 [[Category: Umac tetraloop]]