2i7u - Revision history

OCA at 16:38, 13 December 2023

OCA — Wed, 13 Dec 2023 16:38:09 GMT

←Older revision		Revision as of 16:38, 13 December 2023
Line 1:		Line 1:

	==Structural and Dynamical Analysis of a Four-Alpha-Helix Bundle with Designed Anesthetic Binding Pockets==		==Structural and Dynamical Analysis of a Four-Alpha-Helix Bundle with Designed Anesthetic Binding Pockets==
-	<StructureSection load='2i7u' size='340' side='right'caption='[[2i7u~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>	+	<StructureSection load='2i7u' size='340' side='right'caption='[[2i7u]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2i7u]] is a 2 chain structure. The June 2015 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Receptor for Advanced Glycation End Products'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2015_6 10.2210/rcsb_pdb/mom_2015_6]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I7U FirstGlance]. <br>		<table><tr><td colspan='2'>[[2i7u]] is a 2 chain structure. The June 2015 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Receptor for Advanced Glycation End Products'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2015_6 10.2210/rcsb_pdb/mom_2015_6]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I7U FirstGlance]. <br>
-	</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=2i7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i7u OCA], [https://pdbe.org/2i7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i7u RCSB], [https://www.ebi.ac.uk/pdbsum/2i7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i7u ProSAT]</span></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2i7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i7u OCA], [https://pdbe.org/2i7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i7u RCSB], [https://www.ebi.ac.uk/pdbsum/2i7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i7u ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 23:
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Receptor for Advanced Glycation End Products]]		[[Category: Receptor for Advanced Glycation End Products]]
-	[[Category: Bondarenko, V]]	+	[[Category: Bondarenko V]]
-	[[Category: Brandon~~, N R~~]]	+	[[Category: Brandon NR]]
-	[[Category: Canlas, C]]	+	[[Category: Canlas C]]
-	[[Category: Cui, T]]	+	[[Category: Cui T]]
-	[[Category: Johansson~~, J S~~]]	+	[[Category: Johansson JS]]
-	[[Category: Ma, D]]	+	[[Category: Ma D]]
-	[[Category: Tang, P]]	+	[[Category: Tang P]]
-	[[Category: Xu, Y]]	+	[[Category: Xu Y]]
-	~~[[Category: Alpha helix]]~~	+
-	~~[[Category: Anesthetic binding]]~~	+
-	~~[[Category: De novo protein-ligand binding protein complex]]~~	+
-	~~[[Category: Four-alpha-helix bundle]]~~	+
-	~~[[Category: Homo dimer~~]]	+

OCA at 10:25, 12 January 2022

OCA — Wed, 12 Jan 2022 10:25:21 GMT

←Older revision		Revision as of 10:25, 12 January 2022
Line 3:		Line 3:
	<StructureSection load='2i7u' size='340' side='right'caption='[[2i7u]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2i7u' size='340' side='right'caption='[[2i7u]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2i7u]] is a 2 chain structure. The June 2015 RCSB PDB [~~http~~://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Receptor for Advanced Glycation End Products'' by David Goodsell is [~~http~~://dx.doi.org/10.2210/rcsb_pdb/mom_2015_6 10.2210/rcsb_pdb/mom_2015_6]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2I7U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2i7u]] is a 2 chain structure. The June 2015 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Receptor for Advanced Glycation End Products'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2015_6 10.2210/rcsb_pdb/mom_2015_6]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I7U FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2i7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i7u OCA], [~~http~~://pdbe.org/2i7u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2i7u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2i7u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2i7u ProSAT]</span></td></tr>	+	</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=2i7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i7u OCA], [https://pdbe.org/2i7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i7u RCSB], [https://www.ebi.ac.uk/pdbsum/2i7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i7u ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:42, 8 April 2020

OCA — Wed, 08 Apr 2020 07:42:54 GMT

←Older revision		Revision as of 07:42, 8 April 2020
Line 1:		Line 1:

	==Structural and Dynamical Analysis of a Four-Alpha-Helix Bundle with Designed Anesthetic Binding Pockets==		==Structural and Dynamical Analysis of a Four-Alpha-Helix Bundle with Designed Anesthetic Binding Pockets==
-	<StructureSection load='2i7u' size='340' side='right' caption='[[2i7u]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>	+	<StructureSection load='2i7u' size='340' side='right'caption='[[2i7u]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2i7u]] is a 2 chain structure. The June 2015 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Receptor for Advanced Glycation End Products'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2015_6 10.2210/rcsb_pdb/mom_2015_6]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2I7U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2i7u]] is a 2 chain structure. The June 2015 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Receptor for Advanced Glycation End Products'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2015_6 10.2210/rcsb_pdb/mom_2015_6]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2I7U FirstGlance]. <br>
-	</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=2i7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i7u OCA], [http://pdbe.org/2i7u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2i7u RCSB], [http://www.ebi.ac.uk/pdbsum/2i7u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2i7u ProSAT]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2i7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i7u OCA], [http://pdbe.org/2i7u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2i7u RCSB], [http://www.ebi.ac.uk/pdbsum/2i7u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2i7u ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Receptor for Advanced Glycation End Products]]		[[Category: Receptor for Advanced Glycation End Products]]

OCA at 08:03, 4 July 2018

OCA — Wed, 04 Jul 2018 08:03:15 GMT

←Older revision		Revision as of 08:03, 4 July 2018
Line 1:		Line 1:
		+
	==Structural and Dynamical Analysis of a Four-Alpha-Helix Bundle with Designed Anesthetic Binding Pockets==		==Structural and Dynamical Analysis of a Four-Alpha-Helix Bundle with Designed Anesthetic Binding Pockets==
	<StructureSection load='2i7u' size='340' side='right' caption='[[2i7u]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2i7u' size='340' side='right' caption='[[2i7u]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2i7u]] is a 2 chain structure. The June 2015 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Receptor for Advanced Glycation End Products'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2015_6 10.2210/rcsb_pdb/mom_2015_6]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I7U FirstGlance]. <br>		<table><tr><td colspan='2'>[[2i7u]] is a 2 chain structure. The June 2015 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Receptor for Advanced Glycation End Products'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2015_6 10.2210/rcsb_pdb/mom_2015_6]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I7U FirstGlance]. <br>
-	</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=2i7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i7u OCA], [http://pdbe.org/2i7u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2i7u RCSB], [http://www.ebi.ac.uk/pdbsum/2i7u PDBsum]</span></td></tr>	+	</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=2i7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i7u OCA], [http://pdbe.org/2i7u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2i7u RCSB], [http://www.ebi.ac.uk/pdbsum/2i7u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2i7u ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:55, 11 September 2015

OCA — Fri, 11 Sep 2015 00:55:50 GMT

←Older revision		Revision as of 00:55, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2i7u' size='340' side='right' caption='[[2i7u]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2i7u' size='340' side='right' caption='[[2i7u]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2i7u]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I7U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2i7u]] is a 2 chain structure. The June 2015 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Receptor for Advanced Glycation End Products'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2015_6 10.2210/rcsb_pdb/mom_2015_6]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I7U FirstGlance]. <br>
-	</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=2i7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i7u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2i7u RCSB], [http://www.ebi.ac.uk/pdbsum/2i7u PDBsum]</span></td></tr>	+	</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=2i7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i7u OCA], [http://pdbe.org/2i7u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2i7u RCSB], [http://www.ebi.ac.uk/pdbsum/2i7u PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 13:		Line 13:
	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 2i7u" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: RCSB PDB Molecule of the Month]]
		+	[[Category: Receptor for Advanced Glycation End Products]]
	[[Category: Bondarenko, V]]		[[Category: Bondarenko, V]]
	[[Category: Brandon, N R]]		[[Category: Brandon, N R]]

OCA at 08:58, 16 January 2015

OCA — Fri, 16 Jan 2015 08:58:01 GMT

←Older revision		Revision as of 08:58, 16 January 2015
Line 17:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bondarenko, V.]]	+	[[Category: Bondarenko, V]]
-	[[Category: Brandon, N R.]]	+	[[Category: Brandon, N R]]
-	[[Category: Canlas, C.]]	+	[[Category: Canlas, C]]
-	[[Category: Cui, T.]]	+	[[Category: Cui, T]]
-	[[Category: Johansson, J S.]]	+	[[Category: Johansson, J S]]
-	[[Category: Ma, D.]]	+	[[Category: Ma, D]]
-	[[Category: Tang, P.]]	+	[[Category: Tang, P]]
-	[[Category: Xu, Y.]]	+	[[Category: Xu, Y]]
	[[Category: Alpha helix]]		[[Category: Alpha helix]]
	[[Category: Anesthetic binding]]		[[Category: Anesthetic binding]]

OCA at 15:33, 12 October 2014

OCA — Sun, 12 Oct 2014 15:33:45 GMT

←Older revision		Revision as of 15:33, 12 October 2014
Line 1:		Line 1:
-	[[~~Image~~:2i7u.~~png\|left\|200px~~]]	+	==Structural and Dynamical Analysis of a Four-Alpha-Helix Bundle with Designed Anesthetic Binding Pockets==
		+	<StructureSection load='2i7u' size='340' side='right' caption='[[2i7u]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2i7u]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I7U FirstGlance]. <br>
		+	</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=2i7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i7u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2i7u RCSB], [http://www.ebi.ac.uk/pdbsum/2i7u PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The four-alpha-helix bundle mimics the transmembrane domain of the Cys-loop receptor family believed to be the protein target for general anesthetics. Using high resolution NMR, we solved the structure (PDB ID: 2I7U) of a prototypical dimeric four-alpha-helix bundle, (Aalpha2-L1M/L38M)2, with designed specific binding pockets for volatile anesthetics. Two monomers of the helix-turn-helix motif form an anti-parallel dimer as originally designed, but the high-resolution structure exhibits an asymmetric quaternary arrangement of the four helices. The two helices from the N-terminus to the linker (helices 1 and 1') are associated with each other in the dimer by the side-chain ring stacking of F12 and W15 along the long hydrophobic core and by a nearly perfect stretch of hydrophobic interactions between the complementary pairs of L4, L11, L18, and L25, all of which are located at the heptad e position along the helix-helix dimer interface. In comparison, the axes of the two helices from the linker to the C-terminus (helices 2 and 2') are wider apart from each other, creating a lateral access pathway around K47 from the aqueous phase to the center of the designed hydrophobic core. The site of the L38M mutation, which was previously shown to increase the halothane binding affinity by ~3.5 fold, is not part of the hydrophobic core presumably involved in the anesthetic binding but shows an elevated transverse relaxation (R2) rate. Qualitative analysis of the protein dynamics by reduced spectral density mapping revealed exchange contributions to the relaxation at many residues in the helices. This was confirmed by the quantitative analysis using the Model-Free approach and by the NMR relaxation dispersion measurements. The NMR structures and Autodock analysis suggest that the pocket with most favorable amphipathic property for anesthetic binding is located between the W15 side chains at the center of the dimeric hydrophobic core, with the possibility of two additional minor binding sites between the F12 and F52 ring stacks of each monomer. The high-resolution structure of the designed anesthetic-binding protein offers unprecedented atomistic details about possible sites for anesthetic-protein interactions that are essential to the understanding of molecular mechanisms of general anesthesia.

-	{~~{STRUCTURE_2i7u\| PDB=2i7u \| SCENE= }~~}	+	Four-{alpha}-Helix Bundle with Designed Anesthetic Binding Pockets I: Structural and Dynamical Analyses.,Ma D, Brandon NR, Cui T, Bondarenko V, Canlas C, Johansson JS, Tang P, Xu Y Biophys J. 2008 Feb 29;. PMID:18310240<ref>PMID:18310240</ref>

-	~~===Structural and Dynamical Analysis~~ of ~~a Four-Alpha-Helix Bundle with Designed Anesthetic Binding Pockets===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18310240}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[2i7u]] is a 2 chain structure. Full experimental information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA].~~	+	</StructureSection>
	[[Category: Bondarenko, V.]]		[[Category: Bondarenko, V.]]
	[[Category: Brandon, N R.]]		[[Category: Brandon, N R.]]

OCA: Protected "2i7u" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 12:20:15 GMT

Protected "2i7u" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:20, 7 January 2013

OCA at 12:20, 7 January 2013

OCA — Mon, 07 Jan 2013 12:20:12 GMT

←Older revision		Revision as of 12:20, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2i7u.png\|left\|200px]]		[[Image:2i7u.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2i7u", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
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	{{STRUCTURE_2i7u\| PDB=2i7u \| SCENE= }}		{{STRUCTURE_2i7u\| PDB=2i7u \| SCENE= }}

	===Structural and Dynamical Analysis of a Four-Alpha-Helix Bundle with Designed Anesthetic Binding Pockets===		===Structural and Dynamical Analysis of a Four-Alpha-Helix Bundle with Designed Anesthetic Binding Pockets===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18310240}}, adds the Publication Abstract to the page
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	{{ABSTRACT_PUBMED_18310240}}		{{ABSTRACT_PUBMED_18310240}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA].	+	[[2i7u]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA].
-		+
-	~~==Reference==~~	+
-	Four-{alpha}-Helix Bundle with Designed Anesthetic Binding Pockets I: Structural and Dynamical Analyses., Ma D, Brandon NR, Cui T, Bondarenko V, Canlas C, Johansson JS, Tang P, Xu Y, Biophys J. 2008 Feb 29;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18310240 18310240]	+
	[[Category: Bondarenko, V.]]		[[Category: Bondarenko, V.]]
	[[Category: Brandon, N R.]]		[[Category: Brandon, N R.]]
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	[[Category: Alpha helix]]		[[Category: Alpha helix]]
	[[Category: Anesthetic binding]]		[[Category: Anesthetic binding]]
-	[[Category: De novo protein/ligand binding protein complex]]	+	[[Category: De novo protein-ligand binding protein complex]]
	[[Category: Four-alpha-helix bundle]]		[[Category: Four-alpha-helix bundle]]
	[[Category: Homo dimer]]		[[Category: Homo dimer]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 16:03:23 2008''

OCA at 13:03, 28 July 2008

OCA — Mon, 28 Jul 2008 13:03:25 GMT

←Older revision		Revision as of 13:03, 28 July 2008
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-	[[Image:2i7u.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2i7u.png\|left\|200px]]

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	{{STRUCTURE_2i7u\| PDB=2i7u \| SCENE= }}		{{STRUCTURE_2i7u\| PDB=2i7u \| SCENE= }}

-	~~'''~~Structural and Dynamical Analysis of a Four-Alpha-Helix Bundle with Designed Anesthetic Binding Pockets~~'''~~	+	===Structural and Dynamical Analysis of a Four-Alpha-Helix Bundle with Designed Anesthetic Binding Pockets===


-	~~==Overview==~~	+	<!--
-	The ~~four-alpha-helix bundle mimics~~ the ~~transmembrane domain of the Cys-loop receptor family believed~~ to be the ~~protein target for general anesthetics. Using high resolution NMR, we solved the structure~~ (~~PDB ID~~: ~~2I7U) of a prototypical dimeric four-alpha-helix bundle, (Aalpha2-L1M~~/~~L38M)2, with designed specific binding pockets for volatile anesthetics~~. ~~Two monomers of the helix-turn-helix motif form an anti-parallel dimer as originally designed, but the high-resolution structure exhibits an asymmetric quaternary arrangement of the four helices~~. ~~The two helices from the N-terminus to the linker (helices 1 and 1'~~) are associated with each other in the dimer by the side-chain ring stacking of F12 and W15 along the long hydrophobic core and by a nearly perfect stretch of hydrophobic interactions between the complementary pairs of L4, L11, L18, and L25, all of which are located at the heptad e position along the helix-helix dimer interface. In comparison, the axes of the two helices from the linker to the C-terminus (helices 2 and 2') are wider apart from each other, creating a lateral access pathway around K47 from the aqueous phase to the center of the designed hydrophobic core. The site of the L38M mutation, which was previously shown to increase the halothane binding affinity by ~3.5 fold, is ~~not part of~~ the ~~hydrophobic core presumably involved in the anesthetic binding but shows an elevated transverse relaxation (R2) rate~~. Qualitative analysis of the protein dynamics by reduced spectral density mapping revealed exchange contributions to the relaxation at many residues in the helices. This was confirmed by the quantitative analysis using the Model-Free approach and by the NMR relaxation dispersion measurements. The NMR structures and Autodock analysis suggest that the pocket with most favorable amphipathic property for anesthetic binding is located between the W15 side chains at the center of the dimeric hydrophobic core, with the possibility of two additional minor binding sites between the F12 and F52 ring stacks of each monomer. The high-resolution structure of the designed anesthetic-binding protein offers unprecedented atomistic details about possible sites for anesthetic-protein interactions that are essential to the understanding of molecular mechanisms of general anesthesia.	+	The line below this paragraph, {{ABSTRACT_PUBMED_18310240}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18310240 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18310240}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I7U OCA].

	==Reference==		==Reference==
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	[[Category: Four-alpha-helix bundle]]		[[Category: Four-alpha-helix bundle]]
	[[Category: Homo dimer]]		[[Category: Homo dimer]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 07~~:11:20 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 16:03:23 2008''