1k1i: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1k1i.gif|left|200px]]<br /><applet load="1k1i" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1k1i, resolution 2.20&Aring;" />
-'''BOVINE TRYPSIN-INHIBITOR COMPLEX'''<br />
-==Overview==
+==BOVINE TRYPSIN-INHIBITOR COMPLEX==
-The binding of a series of low molecular weight ligands towards trypsin, and thrombin has been studied by isothermal titration calorimetry and, protein crystallography. In a series of congeneric ligands, surprising, changes of protonation states occur and are overlaid on the binding, process. They result from induced pK(a) shifts depending on the local, environment experienced by the ligand and protein functional groups in the, complex (induced dielectric fit). They involve additional heat effects, that must be corrected before any conclusion on the binding enthalpy, (DeltaH) and entropy (DeltaS) can be drawn. After correction, trends in, both contributions can be interpreted in structural terms with respect to, the hydrogen bond inventory or residual ligand motions. For all inhibitors, studied, a strong negative heat capacity change (DeltaC(p)) is detected, thus binding becomes more exothermic and entropically less favourable with, increasing temperature. Due to a mutual compensation, Gibbs free energy, remains virtually unchanged. The strong negative DeltaC(p) value cannot, solely be explained by the removal of hydrophobic surface portions of the, protein or ligand from water exposure. Additional contributions must be, considered, presumably arising from modulations of the local water, structure, changes in vibrational modes or other ordering parameters. For, thrombin, smaller negative DeltaC(p) values are observed for ligand, binding in the presence of sodium ions compared to the other alkali ions, probably due to stabilising effects on the protein or changes in the bound, water structure.
+<StructureSection load='1k1i' size='340' side='right'caption='[[1k1i]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1k1i]] 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=1K1I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K1I FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#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=FD1:N-ALPHA-(2-NAPHTHYLSULFONYL)-N-(3-AMIDINO-L-PHENYLALANINYL)-D-PIPECOLINIC+ACID'>FD1</scene></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=1k1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1i OCA], [https://pdbe.org/1k1i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k1i RCSB], [https://www.ebi.ac.uk/pdbsum/1k1i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k1i ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]
+== 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/k1/1k1i_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=1k1i ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The binding of a series of low molecular weight ligands towards trypsin and thrombin has been studied by isothermal titration calorimetry and protein crystallography. In a series of congeneric ligands, surprising changes of protonation states occur and are overlaid on the binding process. They result from induced pK(a) shifts depending on the local environment experienced by the ligand and protein functional groups in the complex (induced dielectric fit). They involve additional heat effects that must be corrected before any conclusion on the binding enthalpy (DeltaH) and entropy (DeltaS) can be drawn. After correction, trends in both contributions can be interpreted in structural terms with respect to the hydrogen bond inventory or residual ligand motions. For all inhibitors studied, a strong negative heat capacity change (DeltaC(p)) is detected, thus binding becomes more exothermic and entropically less favourable with increasing temperature. Due to a mutual compensation, Gibbs free energy remains virtually unchanged. The strong negative DeltaC(p) value cannot solely be explained by the removal of hydrophobic surface portions of the protein or ligand from water exposure. Additional contributions must be considered, presumably arising from modulations of the local water structure, changes in vibrational modes or other ordering parameters. For thrombin, smaller negative DeltaC(p) values are observed for ligand binding in the presence of sodium ions compared to the other alkali ions, probably due to stabilising effects on the protein or changes in the bound water structure.
-==About this Structure==
+Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition.,Dullweber F, Stubbs MT, Musil D, Sturzebecher J, Klebe G J Mol Biol. 2001 Oct 26;313(3):593-614. PMID:11676542<ref>PMID:11676542</ref>
-K1I is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with CA and FD1 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1K1I OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition., Dullweber F, Stubbs MT, Musil D, Sturzebecher J, Klebe G, J Mol Biol. 2001 Oct 26;313(3):593-614. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11676542 11676542]
+</div>
+<div class="pdbe-citations 1k1i" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Trypsin 3D structures|Trypsin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bos taurus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Trypsin]]
+[[Category: Stubbs MT]]
-[[Category: Stubbs, M.T.]]
-[[Category: CA]]
-[[Category: FD1]]
-[[Category: hydrolase]]
-[[Category: serine protease]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:46:20 2007''