2mm3 - Revision history

OCA at 06:07, 15 May 2024

OCA — Wed, 15 May 2024 06:07:22 GMT

←Older revision		Revision as of 06:07, 15 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2mm3]] 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=2MM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MM3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2mm3]] 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=2MM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MM3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CHO:GLYCOCHENODEOXYCHOLIC+ACID'>CHO</scene>, <scene name='pdbligand=GCH:GLYCOCHOLIC+ACID'>GCH</scene></td></tr>	+	</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CHO:GLYCOCHENODEOXYCHOLIC+ACID'>CHO</scene>, <scene name='pdbligand=GCH:GLYCOCHOLIC+ACID'>GCH</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=2mm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mm3 OCA], [https://pdbe.org/2mm3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mm3 RCSB], [https://www.ebi.ac.uk/pdbsum/2mm3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mm3 ProSAT]</span></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=2mm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mm3 OCA], [https://pdbe.org/2mm3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mm3 RCSB], [https://www.ebi.ac.uk/pdbsum/2mm3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mm3 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:01, 8 March 2023

OCA — Wed, 08 Mar 2023 08:01:15 GMT

←Older revision		Revision as of 08:01, 8 March 2023
Line 1:		Line 1:

	==Solution NMR structure of the ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate==		==Solution NMR structure of the ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate==
-	<StructureSection load='2mm3' size='340' side='right'caption='[[2mm3~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>	+	<StructureSection load='2mm3' size='340' side='right'caption='[[2mm3]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2mm3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MM3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2mm3]] 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=2MM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MM3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CHO:GLYCOCHENODEOXYCHOLIC+ACID'>CHO</scene>, <scene name='pdbligand=GCH:GLYCOCHOLIC+ACID'>GCH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CHO:GLYCOCHENODEOXYCHOLIC+ACID'>CHO</scene>, <scene name='pdbligand=GCH:GLYCOCHOLIC+ACID'>GCH</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FABP6 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=2mm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mm3 OCA], [https://pdbe.org/2mm3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mm3 RCSB], [https://www.ebi.ac.uk/pdbsum/2mm3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mm3 ProSAT]</span></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=2mm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mm3 OCA], [https://pdbe.org/2mm3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mm3 RCSB], [https://www.ebi.ac.uk/pdbsum/2mm3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mm3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/FABP6_HUMAN FABP6_HUMAN]] Ileal protein which stimulates gastric acid and pepsinogen secretion. Seems to be able to bind to bile salts and bilirubins. Isoform 2 is essential for the survival of colon cancer cells to bile acid-induced apoptosis.<ref>PMID:17909007</ref>	+	[https://www.uniprot.org/uniprot/FABP6_HUMAN FABP6_HUMAN] Ileal protein which stimulates gastric acid and pepsinogen secretion. Seems to be able to bind to bile salts and bilirubins. Isoform 2 is essential for the survival of colon cancer cells to bile acid-induced apoptosis.<ref>PMID:17909007</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bencsura, A]]	+	[[Category: Bencsura A]]
-	[[Category: Cistola~~, D P~~]]	+	[[Category: Cistola DP]]
-	[[Category: Covey~~, D F~~]]	+	[[Category: Covey DF]]
-	[[Category: DeKoster~~, G T~~]]	+	[[Category: DeKoster GT]]
-	[[Category: Egyed, O]]	+	[[Category: Egyed O]]
-	[[Category: Horvath, G]]	+	[[Category: Horvath G]]
-	[[Category: Simon, A]]	+	[[Category: Simon A]]
-	[[Category: Tochtrop~~, G P~~]]	+	[[Category: Tochtrop GP]]
-	[[Category: Toke, O]]	+	[[Category: Toke O]]
-	~~[[Category: Enterohepatic circulation]]~~	+
-	~~[[Category: Lipid binding protein]]~~	+
-	~~[[Category: Lipid-binding protein]]~~	+
-	~~[[Category: Orthogonal beta sheet]]~~	+
-	~~[[Category: Positive binding cooperativity]]~~	+
-	~~[[Category: Site-selectivity~~]]	+

OCA at 15:17, 2 June 2021

OCA — Wed, 02 Jun 2021 15:17:14 GMT

←Older revision		Revision as of 15:17, 2 June 2021
Line 1:		Line 1:

	==Solution NMR structure of the ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate==		==Solution NMR structure of the ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate==
-	<StructureSection load='2mm3' size='340' side='right' caption='[[2mm3]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>	+	<StructureSection load='2mm3' size='340' side='right'caption='[[2mm3]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2mm3]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MM3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2MM3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2mm3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MM3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CHO:GLYCOCHENODEOXYCHOLIC+ACID'>CHO</scene>, <scene name='pdbligand=GCH:GLYCOCHOLIC+ACID'>GCH</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CHO:GLYCOCHENODEOXYCHOLIC+ACID'>CHO</scene>, <scene name='pdbligand=GCH:GLYCOCHOLIC+ACID'>GCH</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FABP6 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FABP6 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2mm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mm3 OCA], [~~http~~://pdbe.org/2mm3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2mm3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2mm3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2mm3 ProSAT]</span></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=2mm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mm3 OCA], [https://pdbe.org/2mm3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mm3 RCSB], [https://www.ebi.ac.uk/pdbsum/2mm3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mm3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/FABP6_HUMAN FABP6_HUMAN]] Ileal protein which stimulates gastric acid and pepsinogen secretion. Seems to be able to bind to bile salts and bilirubins. Isoform 2 is essential for the survival of colon cancer cells to bile acid-induced apoptosis.<ref>PMID:17909007</ref>	+	[[https://www.uniprot.org/uniprot/FABP6_HUMAN FABP6_HUMAN]] Ileal protein which stimulates gastric acid and pepsinogen secretion. Seems to be able to bind to bile salts and bilirubins. Isoform 2 is essential for the survival of colon cancer cells to bile acid-induced apoptosis.<ref>PMID:17909007</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[Fatty acid-binding protein\|Fatty acid-binding protein]]	+	*[[Fatty acid-binding protein 3D structures\|Fatty acid-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Bencsura, A]]		[[Category: Bencsura, A]]
	[[Category: Cistola, D P]]		[[Category: Cistola, D P]]

OCA at 23:14, 9 August 2018

OCA — Thu, 09 Aug 2018 23:14:35 GMT

←Older revision		Revision as of 23:14, 9 August 2018
Line 1:		Line 1:
		+
	==Solution NMR structure of the ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate==		==Solution NMR structure of the ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate==
	<StructureSection load='2mm3' size='340' side='right' caption='[[2mm3]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2mm3' size='340' side='right' caption='[[2mm3]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2mm3]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MM3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2MM3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2mm3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MM3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2MM3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CHO:GLYCOCHENODEOXYCHOLIC+ACID'>CHO</scene>, <scene name='pdbligand=GCH:GLYCOCHOLIC+ACID'>GCH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CHO:GLYCOCHENODEOXYCHOLIC+ACID'>CHO</scene>, <scene name='pdbligand=GCH:GLYCOCHOLIC+ACID'>GCH</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2mm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mm3 OCA], [http://pdbe.org/2mm3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2mm3 RCSB], [http://www.ebi.ac.uk/pdbsum/2mm3 PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FABP6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2mm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mm3 OCA], [http://pdbe.org/2mm3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2mm3 RCSB], [http://www.ebi.ac.uk/pdbsum/2mm3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2mm3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 2mm3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2mm3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Fatty acid-binding protein\|Fatty acid-binding protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Bencsura, A]]		[[Category: Bencsura, A]]
	[[Category: Cistola, D P]]		[[Category: Cistola, D P]]

OCA at 11:36, 30 December 2015

OCA — Wed, 30 Dec 2015 11:36:38 GMT

←Older revision		Revision as of 11:36, 30 December 2015
Line 10:		Line 10:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	Human ileal bile acid binding protein (I-BABP)~~, a member~~ of the ~~family~~ of ~~intracellular lipid binding proteins, is thought to play~~ a role in the enterohepatic circulation of bile salts. ~~Previously, we have shown by stopped-flow fluorescence analysis that positive~~ binding cooperativity ~~exhibited by I~~-~~BABP in its interactions with~~ glycocholate (GCA) and glycochenodeoxycholate (GCDA), the two ~~primary~~ bile salts in ~~humans~~, ~~is related to~~ a ~~slow conformational change in~~ the ~~protein. In this study, we used backbone~~ (15)~~N relaxation nuclear magnetic resonance (~~NMR~~) techniques to obtain residue-specific information about~~ the ~~internal dynamics~~ of ~~apo~~ I-BABP and the ~~doubly ligated I-BABP:GCA:GCDA complex on various time scales~~. ~~According to our NMR data,~~ bile salt binding ~~is accompanied by a slight rigidification of~~ the ~~(15)N-(1)H bond vectors on~~ the ~~picosecond to nanosecond time scale~~, ~~with most pronounced changes occurring in~~ the ~~C-D region~~. ~~In contrast to the minor effects~~ of ~~ligation on fast motions, relaxation dispersion NMR experiments indicate~~ a ~~marked difference between the two protein states on the microsecond to~~ millisecond time scale~~. In~~ the apo ~~form~~, ~~an extensive network of conformational fluctuations is detected throughout segments~~ of the ~~EFGHIJ beta~~-~~strands and~~ the ~~C-D loop, which cease upon complexation. Our NMR data are in agreement with~~ a ~~conformational~~ selection ~~model we proposed earlier for~~ I-BABP and ~~support the hypothesis of an allosteric mechanism~~ of ligand binding. ~~According to the NMR measurements, the helical cap region may have a less crucial role in mediating ligand entry and release than what has been indicated for fatty acid binding proteins~~.	+	Besides aiding digestion, bile salts are important signal molecules exhibiting a regulatory role in metabolic processes. Human ileal bile acid-binding protein (hI-BABP) is an intracellular carrier of bile salts in the epithelial cells of the distal small intestine and has a key role in the enterohepatic circulation of bile salts. Positive binding cooperativity combined with site-selectivity of glycocholate (GCA) and glycochenodeoxycholate (GCDA), the two most abundant bile salts in the human body, makes hI-BABP a unique member of the family of intracellular lipid binding proteins (iLBP). Solution NMR structure of the ternary complex of human I-BABP with GCA and GCDA reveals an extensive network of hydrogen bonds and hydrophobic interactions stabilizing the bound bile salts. Conformational changes accompanying bile salt binding affects four major regions in the protein including the C/D, E/F, and G/H loops as well as the helical segment. Most of these protein regions coincide with a previously described network of millisecond time scale fluctuations in the apo protein, a motion absent in the bound state. Comparison of the heterotypic doubly-ligated complex with the unligated form provides further evidence of a conformation selection mechanism of ligand entry. Structural and dynamic aspects of human I-BABP-bile salt interaction is discussed and compared with characteristics of ligand binding in other members of the iLBP family. This article is protected by copyright. All rights reserved.

-	~~Internal motions and exchange processes~~ in human ileal bile acid binding protein ~~as studied by backbone (15)N nuclear magnetic resonance spectroscopy~~.,Horvath G, ~~Kiraly P~~, ~~Tarkanyi G~~, Toke O ~~Biochemistry~~. ~~2012 Mar 6;51(9):1848-61~~. doi: 10.~~1021~~/~~bi201588q~~. ~~Epub 2012 Feb 27~~. PMID:~~22329738~~<ref>PMID:~~22329738~~</ref>	+	Structural determinants of ligand binding in the ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate obtained from solution NMR.,Horvath G, Bencsura A, Simon A, Tochtrop GP, DeKoster GT, Covey DF, Cistola DP, Toke O FEBS J. 2015 Nov 27. doi: 10.1111/febs.13610. PMID:26613247<ref>PMID:26613247</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

OCA at 02:09, 10 September 2015

OCA — Thu, 10 Sep 2015 02:09:47 GMT

←Older revision		Revision as of 02:09, 10 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[2mm3]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MM3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2MM3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2mm3]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MM3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2MM3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CHO:GLYCOCHENODEOXYCHOLIC+ACID'>CHO</scene>, <scene name='pdbligand=GCH:GLYCOCHOLIC+ACID'>GCH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CHO:GLYCOCHENODEOXYCHOLIC+ACID'>CHO</scene>, <scene name='pdbligand=GCH:GLYCOCHOLIC+ACID'>GCH</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2mm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mm3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2mm3 RCSB], [http://www.ebi.ac.uk/pdbsum/2mm3 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2mm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mm3 OCA], [http://pdbe.org/2mm3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2mm3 RCSB], [http://www.ebi.ac.uk/pdbsum/2mm3 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 10:		Line 10:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	Human ileal bile acid binding protein (I-BABP) is a member of the family of intracellular lipid-binding proteins ~~and~~ is thought to play a role in the enterohepatic circulation of bile salts. ~~Our group has previously~~ shown ~~that human I~~-~~BABP binds two molecules of glycocholate (GCA) with low intrinsic affinity but an extraordinary high degree of~~ positive cooperativity~~. Besides the strong positive cooperativity, human~~ I-BABP ~~exhibits a high degree of site selectivity~~ in its interactions with GCA and glycochenodeoxycholate (GCDA), the two ~~major~~ bile salts in humans. In this study, ~~on the basis of our first generation~~ nuclear magnetic resonance (NMR) ~~structure of~~ the ~~ternary complex~~ of ~~human~~ I-BABP ~~with GCA~~ and GCDA, ~~we introduced single~~-~~residue mutations at certain key positions~~ in the ~~binding pocket that might disrupt a hydrogen~~-~~bonding network~~, a ~~likely way of energetic communication~~ between the two ~~sites~~. ~~Macroscopic binding parameters were determined using isothermal titration calorimetry~~, ~~and site selectivity was monitored by NMR spectroscopy~~ of ~~isotopically enriched bile salts. According to our results, cooperativity~~ and ~~site selectivity~~ are ~~not linked~~ in ~~human~~ I-BABP~~. While cooperativity is governed by a subtle interplay of entropic~~ and ~~enthalpic contributions, site selectivity appears to be determined by more localized enthalpic effects~~. ~~Possible communication pathways between~~ the ~~two~~ binding ~~sites are discussed~~.	+	Human ileal bile acid binding protein (I-BABP), a member of the family of intracellular lipid binding proteins, is thought to play a role in the enterohepatic circulation of bile salts. Previously, we have shown by stopped-flow fluorescence analysis that positive binding cooperativity exhibited by I-BABP in its interactions with glycocholate (GCA) and glycochenodeoxycholate (GCDA), the two primary bile salts in humans, is related to a slow conformational change in the protein. In this study, we used backbone (15)N relaxation nuclear magnetic resonance (NMR) techniques to obtain residue-specific information about the internal dynamics of apo I-BABP and the doubly ligated I-BABP:GCA:GCDA complex on various time scales. According to our NMR data, bile salt binding is accompanied by a slight rigidification of the (15)N-(1)H bond vectors on the picosecond to nanosecond time scale, with most pronounced changes occurring in the C-D region. In contrast to the minor effects of ligation on fast motions, relaxation dispersion NMR experiments indicate a marked difference between the two protein states on the microsecond to millisecond time scale. In the apo form, an extensive network of conformational fluctuations is detected throughout segments of the EFGHIJ beta-strands and the C-D loop, which cease upon complexation. Our NMR data are in agreement with a conformational selection model we proposed earlier for I-BABP and support the hypothesis of an allosteric mechanism of ligand binding. According to the NMR measurements, the helical cap region may have a less crucial role in mediating ligand entry and release than what has been indicated for fatty acid binding proteins.

-	~~Determinants of cooperativity~~ and ~~site selectivity~~ in human ileal bile acid binding protein.,~~Toke O~~, ~~Monsey JD~~, ~~DeKoster GT~~, ~~Tochtrop GP, Tang C, Cistola DP~~ Biochemistry. ~~2006 Jan 24~~;45(3):~~727~~-37. PMID:~~16411748~~<ref>PMID:~~16411748~~</ref>	+	Internal motions and exchange processes in human ileal bile acid binding protein as studied by backbone (15)N nuclear magnetic resonance spectroscopy.,Horvath G, Kiraly P, Tarkanyi G, Toke O Biochemistry. 2012 Mar 6;51(9):1848-61. doi: 10.1021/bi201588q. Epub 2012 Feb 27. PMID:22329738<ref>PMID:22329738</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2mm3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:42, 24 December 2014

OCA — Wed, 24 Dec 2014 15:42:50 GMT

←Older revision		Revision as of 15:42, 24 December 2014
Line 2:		Line 2:
	<StructureSection load='2mm3' size='340' side='right' caption='[[2mm3]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2mm3' size='340' side='right' caption='[[2mm3]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2mm3]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MM3 OCA]. <br>	+	<table><tr><td colspan='2'>[[2mm3]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MM3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2MM3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CHO:GLYCOCHENODEOXYCHOLIC+ACID'>CHO</scene>, <scene name='pdbligand=GCH:GLYCOCHOLIC+ACID'>GCH</scene~~><br>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CHO:GLYCOCHENODEOXYCHOLIC+ACID'>CHO</scene>, <scene name='pdbligand=GCH:GLYCOCHOLIC+ACID'>GCH</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2mm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mm3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2mm3 RCSB], [http://www.ebi.ac.uk/pdbsum/2mm3 PDBsum]</span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2mm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mm3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2mm3 RCSB], [http://www.ebi.ac.uk/pdbsum/2mm3 PDBsum]</span></td></tr>	+	</table>
-	<table>	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FABP6_HUMAN FABP6_HUMAN]] Ileal protein which stimulates gastric acid and pepsinogen secretion. Seems to be able to bind to bile salts and bilirubins. Isoform 2 is essential for the survival of colon cancer cells to bile acid-induced apoptosis.<ref>PMID:17909007</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 13:		Line 14:
	Determinants of cooperativity and site selectivity in human ileal bile acid binding protein.,Toke O, Monsey JD, DeKoster GT, Tochtrop GP, Tang C, Cistola DP Biochemistry. 2006 Jan 24;45(3):727-37. PMID:16411748<ref>PMID:16411748</ref>		Determinants of cooperativity and site selectivity in human ileal bile acid binding protein.,Toke O, Monsey JD, DeKoster GT, Tochtrop GP, Tang C, Cistola DP Biochemistry. 2006 Jan 24;45(3):727-37. PMID:16411748<ref>PMID:16411748</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 19:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bencsura, A.]]	+	[[Category: Bencsura, A]]
-	[[Category: Cistola, D P.]]	+	[[Category: Cistola, D P]]
-	[[Category: Covey, D F.]]	+	[[Category: Covey, D F]]
-	[[Category: DeKoster, G T.]]	+	[[Category: DeKoster, G T]]
-	[[Category: Egyed, O.]]	+	[[Category: Egyed, O]]
-	[[Category: Horvath, G.]]	+	[[Category: Horvath, G]]
-	[[Category: Simon, A.]]	+	[[Category: Simon, A]]
-	[[Category: Tochtrop, G P.]]	+	[[Category: Tochtrop, G P]]
-	[[Category: Toke, O.]]	+	[[Category: Toke, O]]
	[[Category: Enterohepatic circulation]]		[[Category: Enterohepatic circulation]]
	[[Category: Lipid binding protein]]		[[Category: Lipid binding protein]]

OCA at 08:12, 7 May 2014

OCA — Wed, 07 May 2014 08:12:43 GMT

←Older revision		Revision as of 08:12, 7 May 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Solution NMR structure of the ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate==
		+	<StructureSection load='2mm3' size='340' side='right' caption='[[2mm3]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2mm3]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MM3 OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CHO:GLYCOCHENODEOXYCHOLIC+ACID'>CHO</scene>, <scene name='pdbligand=GCH:GLYCOCHOLIC+ACID'>GCH</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2mm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mm3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2mm3 RCSB], [http://www.ebi.ac.uk/pdbsum/2mm3 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human ileal bile acid binding protein (I-BABP) is a member of the family of intracellular lipid-binding proteins and is thought to play a role in the enterohepatic circulation of bile salts. Our group has previously shown that human I-BABP binds two molecules of glycocholate (GCA) with low intrinsic affinity but an extraordinary high degree of positive cooperativity. Besides the strong positive cooperativity, human I-BABP exhibits a high degree of site selectivity in its interactions with GCA and glycochenodeoxycholate (GCDA), the two major bile salts in humans. In this study, on the basis of our first generation nuclear magnetic resonance (NMR) structure of the ternary complex of human I-BABP with GCA and GCDA, we introduced single-residue mutations at certain key positions in the binding pocket that might disrupt a hydrogen-bonding network, a likely way of energetic communication between the two sites. Macroscopic binding parameters were determined using isothermal titration calorimetry, and site selectivity was monitored by NMR spectroscopy of isotopically enriched bile salts. According to our results, cooperativity and site selectivity are not linked in human I-BABP. While cooperativity is governed by a subtle interplay of entropic and enthalpic contributions, site selectivity appears to be determined by more localized enthalpic effects. Possible communication pathways between the two binding sites are discussed.

-	~~The entry 2mm3 is ON HOLD until May 02 2015~~	+	Determinants of cooperativity and site selectivity in human ileal bile acid binding protein.,Toke O, Monsey JD, DeKoster GT, Tochtrop GP, Tang C, Cistola DP Biochemistry. 2006 Jan 24;45(3):727-37. PMID:16411748<ref>PMID:16411748</ref>

-	~~Authors: Horvath~~, G.~~, Egyed, O~~., Bencsura, A., ~~Simon, A., Tochtrop, G.~~P., DeKoster, G.T., ~~Covey~~, ~~D.F~~., ~~Cistola, D~~.P., Toke, O.	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Solution NMR structure of the ternary complex of human ileal bile acid~~-binding protein ~~with glycocholate and glycochenodeoxycholate~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bencsura, A.]]
		+	[[Category: Cistola, D P.]]
		+	[[Category: Covey, D F.]]
		+	[[Category: DeKoster, G T.]]
		+	[[Category: Egyed, O.]]
		+	[[Category: Horvath, G.]]
		+	[[Category: Simon, A.]]
		+	[[Category: Tochtrop, G P.]]
		+	[[Category: Toke, O.]]
		+	[[Category: Enterohepatic circulation]]
		+	[[Category: Lipid binding protein]]
		+	[[Category: Lipid-binding protein]]
		+	[[Category: Orthogonal beta sheet]]
		+	[[Category: Positive binding cooperativity]]
		+	[[Category: Site-selectivity]]

OCA at 08:05, 2 April 2014

OCA — Wed, 02 Apr 2014 08:05:35 GMT

←Older revision		Revision as of 08:05, 2 April 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 2mm3 is ON HOLD	+	The entry 2mm3 is ON HOLD until May 02 2015

	Authors: Horvath, G., Egyed, O., Bencsura, A., Simon, A., Tochtrop, G.P., DeKoster, G.T., Covey, D.F., Cistola, D.P., Toke, O.		Authors: Horvath, G., Egyed, O., Bencsura, A., Simon, A., Tochtrop, G.P., DeKoster, G.T., Covey, D.F., Cistola, D.P., Toke, O.

	Description: Solution NMR structure of the ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate		Description: Solution NMR structure of the ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate

OCA: Protected "2mm3" [edit=sysop:move=sysop]

OCA — Wed, 19 Mar 2014 06:36:09 GMT

Protected "2mm3" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:36, 19 March 2014