1uto: Difference between revisions

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-{{Seed}}
-[[Image:1uto.png|left|200px]]
-<!--
+==Trypsin specificity as elucidated by LIE calculations, X-ray structures and association constant measurements==
-The line below this paragraph, containing "STRUCTURE_1uto", creates the "Structure Box" on the page.
+<StructureSection load='1uto' size='340' side='right'caption='[[1uto]], [[Resolution|resolution]] 1.15&Aring;' 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'>[[1uto]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UTO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UTO 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">X-ray diffraction, [[Resolution|Resolution]] 1.15&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEA:2-PHENYLETHYLAMINE'>PEA</scene></td></tr>
-{{STRUCTURE_1uto|  PDB=1uto  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1uto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uto OCA], [https://pdbe.org/1uto PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uto RCSB], [https://www.ebi.ac.uk/pdbsum/1uto PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uto ProSAT]</span></td></tr>
+</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/ut/1uto_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1uto ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The variation in inhibitor specificity for five different amine inhibitors bound to CST, BT, and the cold-adapted AST has been studied by use of association constant measurements, structural analysis of high-resolution crystal structures, and the LIE method. Experimental data show that AST binds the 1BZA and 2BEA inhibitors 0.8 and 0.5 kcal/mole more strongly than BT. However, structural interactions and orientations of the inhibitors within the S1 site have been found to be virtually identical in the three enzymes studied. For example, the four water molecules in the inhibitor-free structures of AST and BT are channeled into similar positions in the S1 site, and the nitrogen atom(s) of the inhibitors are found in two cationic binding sites denoted Position1 and Position2. The hydrophobic binding contributions for all five inhibitors, estimated by the LIE calculations, are also in the same order (-2.1 +/- 0.2 kcal/mole) for all three enzymes. Our hypothesis is therefore that the observed variation in inhibitor binding arises from different electrostatic interactions originating from residues outside the S1 site. This is well illustrated by AST, in which Asp 150 and Glu 221B, despite some distance from the S1 binding site, lower the electrostatic potential of the S1 site and thus enhance substrate binding. Because the trends in the experimentally determined binding energies were reproduced by the LIE calculations after adding the contribution from long-range interactions, we find this method very suitable for rational studies of protein-substrate interactions.
-===TRYPSIN SPECIFICITY AS ELUCIDATED BY LIE CALCULATIONS, X-RAY STRUCTURES AND ASSOCIATION CONSTANT MEASUREMENTS===
+Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements.,Leiros HK, Brandsdal BO, Andersen OA, Os V, Leiros I, Helland R, Otlewski J, Willassen NP, Smalas AO Protein Sci. 2004 Apr;13(4):1056-70. PMID:15044735<ref>PMID:15044735</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1uto" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15044735}}, adds the Publication Abstract to the page
+*[[Trypsin 3D structures|Trypsin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15044735 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15044735}}
+__TOC__
+</StructureSection>
-==About this Structure==
-UTO is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UTO OCA].
-==Reference==
-<ref group="xtra">PMID:15044735</ref><references group="xtra"/>
 [[Category: Bos taurus]]
-[[Category: Trypsin]]
+[[Category: Large Structures]]
-[[Category: Andersen, O A.]]
+[[Category: Andersen OA]]
-[[Category: Brandsdal, B O.]]
+[[Category: Brandsdal BO]]
-[[Category: Helland, R.]]
+[[Category: Helland R]]
-[[Category: Leiros, H K.S.]]
+[[Category: Leiros H-KS]]
-[[Category: Leiros, I.]]
+[[Category: Leiros I]]
-[[Category: Os, V.]]
+[[Category: Os V]]
-[[Category: Otlewski, J.]]
+[[Category: Otlewski J]]
-[[Category: Smalas, A O.]]
+[[Category: Smalas AO]]
-[[Category: Willassen, N P.]]
+[[Category: Willassen NP]]
-[[Category: Binding free energy]]
-[[Category: Cold-adaptation]]
-[[Category: Electrostatic interaction]]
-[[Category: Inhibitor specificity]]
-[[Category: Molecular dynamic]]
-[[Category: Trypsin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 02:39:53 2009''