1yyj: Difference between revisions

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-{{Seed}}
-[[Image:1yyj.png|left|200px]]
-<!--
+==The NMR solution structure of a redesigned apocytochrome b562:Rd-apocyt b562==
-The line below this paragraph, containing "STRUCTURE_1yyj", creates the "Structure Box" on the page.
+<StructureSection load='1yyj' size='340' side='right'caption='[[1yyj]]' 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'>[[1yyj]] 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=1YYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YYJ 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=1yyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yyj OCA], [https://pdbe.org/1yyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yyj RCSB], [https://www.ebi.ac.uk/pdbsum/1yyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yyj ProSAT]</span></td></tr>
-{{STRUCTURE_1yyj|  PDB=1yyj  |  SCENE=  }}
+</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/yy/1yyj_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=1yyj ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Structures of intermediates and transition states in protein folding are usually characterized by amide hydrogen exchange and protein engineering methods and interpreted on the basis of the assumption that they have native-like conformations. We were able to stabilize and determine the high-resolution structure of a partially unfolded intermediate that exists after the rate-limiting step of a four-helix bundle protein, Rd-apocyt b(562), by multidimensional NMR methods. The intermediate has partial native-like secondary structure and backbone topology, consistent with our earlier native state hydrogen exchange results. However, non-native hydrophobic interactions exist throughout the structure. These and other results in the literature suggest that non-native hydrophobic interactions may occur generally in partially folded states. This can alter the interpretation of mutational protein engineering results in terms of native-like side chain interactions. In addition, since the intermediate exists after the rate-limiting step and Rd-apocyt b(562) folds very rapidly (k(f) approximately 10(4) s(-1)), these results suggest that non-native hydrophobic interactions, in the absence of topological misfolding, are repaired too rapidly to slow folding and cause the accumulation of folding intermediates. More generally, these results illustrate an approach for determining the high-resolution structure of folding intermediates.
-===The NMR solution structure of a redesigned apocytochrome b562:Rd-apocyt b562===
+Specific non-native hydrophobic interactions in a hidden folding intermediate: implications for protein folding.,Feng H, Takei J, Lipsitz R, Tjandra N, Bai Y Biochemistry. 2003 Nov 4;42(43):12461-5. PMID:14580191<ref>PMID:14580191</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_14580191}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1yyj" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 14580191 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14580191}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Homo sapiens]]
-YYJ is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YYJ OCA].
+[[Category: Large Structures]]
+[[Category: Bai Y]]
-==Reference==
+[[Category: Feng H]]
-<ref group="xtra">PMID:14580191</ref><references group="xtra"/>
+[[Category: Lipsitz R]]
-[[Category: BSGC, Berkeley Structural Genomics Center.]]
+[[Category: Takei J]]
-[[Category: Bai, Y.]]
+[[Category: Tjandra N]]
-[[Category: Feng, H.]]
-[[Category: Lipsitz, R.]]
-[[Category: Takei, J.]]
-[[Category: Tjandra, N.]]
-[[Category: Berkeley structural genomics center]]
-[[Category: Bsgc]]
-[[Category: Four helix protein]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 22:09:06 2009''