8ame - Revision history

OCA at 18:12, 20 September 2023

OCA — Wed, 20 Sep 2023 18:12:27 GMT

←Older revision		Revision as of 18:12, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='8ame' size='340' side='right'caption='[[8ame]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='8ame' size='340' side='right'caption='[[8ame]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[8ame]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Blennius_americanus Blennius~~ americanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AME FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[8ame]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zoarces_americanus Zoarces americanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AME 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=8ame FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ame OCA], [https://pdbe.org/8ame PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ame RCSB], [https://www.ebi.ac.uk/pdbsum/8ame PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ame ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.9Å</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=8ame FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ame OCA], [https://pdbe.org/8ame PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ame RCSB], [https://www.ebi.ac.uk/pdbsum/8ame PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ame ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ANP12_ZOAAM ANP12_ZOAAM] Contributes to protect fish blood from freezing at subzero sea water temperatures. Lowers the blood freezing point. Binds to nascent ice crystals and prevents further growth.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Blennius americanus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Baardsnes, J]]	+	[[Category: Zoarces americanus]]
-	[[Category: Davies~~, P L~~]]	+	[[Category: Baardsnes J]]
-	[[Category: Deluca~~, C I~~]]	+	[[Category: Davies PL]]
-	[[Category: Graether~~, S P~~]]	+	[[Category: Deluca CI]]
-	[[Category: Hill~~, G A~~]]	+	[[Category: Graether SP]]
-	[[Category: Jia, Z]]	+	[[Category: Hill GA]]
-	~~[[Category: Antifreeze protein]]~~	+	[[Category: Jia Z]]
-	~~[[Category: Ice binding protein]]~~	+
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: Thermal hysteresis protein~~]]	+

OCA at 16:04, 3 November 2021

OCA — Wed, 03 Nov 2021 16:04:27 GMT

←Older revision		Revision as of 16:04, 3 November 2021
Line 1:		Line 1:

	==TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N14SA16H==		==TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N14SA16H==
-	<StructureSection load='8ame' size='340' side='right' caption='[[8ame]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='8ame' size='340' side='right'caption='[[8ame]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[8ame]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Blennius_americanus Blennius americanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AME OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=8AME FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[8ame]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Blennius_americanus Blennius americanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AME 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=8ame FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ame OCA], [~~http~~://pdbe.org/8ame PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=8ame RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/8ame PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=8ame 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=8ame FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ame OCA], [https://pdbe.org/8ame PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ame RCSB], [https://www.ebi.ac.uk/pdbsum/8ame PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ame ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 10:		Line 10:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/am/8ame_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/am/8ame_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 27:		Line 27:

	==See Also==		==See Also==
-	*[[Antifreeze protein\|Antifreeze protein]]	+	*[[Antifreeze protein 3D structures\|Antifreeze protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Blennius americanus]]		[[Category: Blennius americanus]]
		+	[[Category: Large Structures]]
	[[Category: Baardsnes, J]]		[[Category: Baardsnes, J]]
	[[Category: Davies, P L]]		[[Category: Davies, P L]]

OCA at 01:24, 5 August 2016

OCA — Fri, 05 Aug 2016 01:24:34 GMT

←Older revision		Revision as of 01:24, 5 August 2016
Line 1:		Line 1:
		+
	==TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N14SA16H==		==TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N14SA16H==
	<StructureSection load='8ame' size='340' side='right' caption='[[8ame]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='8ame' size='340' side='right' caption='[[8ame]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[8ame]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Zoarces_americanus Zoarces~~ americanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8AME FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[8ame]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Blennius_americanus Blennius americanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8AME 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=8ame FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ame OCA], [http://www.rcsb.org/pdb/explore.do?structureId=8ame RCSB], [http://www.ebi.ac.uk/pdbsum/8ame 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=8ame FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ame OCA], [http://pdbe.org/8ame PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=8ame RCSB], [http://www.ebi.ac.uk/pdbsum/8ame PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=8ame ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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=8ame ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 24:
	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 8ame" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 30:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Zoarces~~ americanus]]	+	[[Category: Blennius americanus]]
	[[Category: Baardsnes, J]]		[[Category: Baardsnes, J]]
	[[Category: Davies, P L]]		[[Category: Davies, P L]]

OCA at 16:52, 10 December 2014

OCA — Wed, 10 Dec 2014 16:52:06 GMT

←Older revision		Revision as of 16:52, 10 December 2014
Line 1:		Line 1:
-	[[~~Image~~:8ame.~~png\|left~~\|200px]]	+	==TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N14SA16H==
		+	<StructureSection load='8ame' size='340' side='right' caption='[[8ame]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8ame]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Zoarces_americanus Zoarces americanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8AME 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=8ame FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ame OCA], [http://www.rcsb.org/pdb/explore.do?structureId=8ame RCSB], [http://www.ebi.ac.uk/pdbsum/8ame PDBsum]</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/am/8ame_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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Some cold water marine fishes avoid cellular damage because of freezing by expressing antifreeze proteins (AFPs) that bind to ice and inhibit its growth; one such protein is the globular type III AFP from eel pout. Despite several studies, the mechanism of ice binding remains unclear because of the difficulty in modeling the AFP-ice interaction. To further explore the mechanism, we have determined the x-ray crystallographic structure of 10 type III AFP mutants and combined that information with 7 previously determined structures to mainly analyze specific AFP-ice interactions such as hydrogen bonds. Quantitative assessment of binding was performed using a neural network with properties of the structure as input and predicted antifreeze activity as output. Using the cross-validation method, a correlation coefficient of 0.60 was obtained between measured and predicted activity, indicating successful learning and good predictive power. A large loss in the predictive power of the neural network occurred after properties related to the hydrophobic surface were left out, suggesting that van der Waal's interactions make a significant contribution to ice binding. By combining the analysis of the neural network with antifreeze activity and x-ray crystallographic structures of the mutants, we extend the existing ice-binding model to a two-step process: 1) probing of the surface for the correct ice-binding plane by hydrogen-bonding side chains and 2) attractive van der Waal's interactions between the other residues of the ice-binding surface and the ice, which increases the strength of the protein-ice interaction.

-	~~{{STRUCTURE_8ame\| PDB=8ame \| SCENE= }}~~	+	Quantitative and qualitative analysis of type III antifreeze protein structure and function.,Graether SP, DeLuca CI, Baardsnes J, Hill GA, Davies PL, Jia Z J Biol Chem. 1999 Apr 23;274(17):11842-7. PMID:10207002<ref>PMID:10207002</ref>

-	~~===TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N14SA16H===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10207002}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[8ame]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Zoarces_americanus Zoarces americanus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=8AME OCA].~~	+

	==See Also==		==See Also==
	*[[Antifreeze protein\|Antifreeze protein]]		*[[Antifreeze protein\|Antifreeze protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010207002<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Zoarces americanus]]		[[Category: Zoarces americanus]]
-	[[Category: Baardsnes, J.]]	+	[[Category: Baardsnes, J]]
-	[[Category: Davies, P L.]]	+	[[Category: Davies, P L]]
-	[[Category: Deluca, C I.]]	+	[[Category: Deluca, C I]]
-	[[Category: Graether, S P.]]	+	[[Category: Graether, S P]]
-	[[Category: Hill, G A.]]	+	[[Category: Hill, G A]]
-	[[Category: Jia, Z.]]	+	[[Category: Jia, Z]]
	[[Category: Antifreeze protein]]		[[Category: Antifreeze protein]]
	[[Category: Ice binding protein]]		[[Category: Ice binding protein]]
	[[Category: Mutant]]		[[Category: Mutant]]
	[[Category: Thermal hysteresis protein]]		[[Category: Thermal hysteresis protein]]

OCA at 17:55, 20 October 2012

OCA — Sat, 20 Oct 2012 17:55:57 GMT

←Older revision		Revision as of 17:55, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[8ame]] is a 1 chain structure ~~of [[Antifreeze protein]]~~ with sequence from [http://en.wikipedia.org/wiki/Zoarces_americanus Zoarces americanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AME OCA].	+	[[8ame]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Zoarces_americanus Zoarces americanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AME OCA].

	==See Also==		==See Also==

OCA: Protected "8ame" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 02:27:17 GMT

Protected "8ame" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:27, 27 July 2012

OCA at 02:27, 27 July 2012

OCA — Fri, 27 Jul 2012 02:27:16 GMT

←Older revision		Revision as of 02:27, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:8ame.png\|left\|200px]]		[[Image:8ame.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_8ame", 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.
-	-->
	{{STRUCTURE_8ame\| PDB=8ame \| SCENE= }}		{{STRUCTURE_8ame\| PDB=8ame \| SCENE= }}

	===TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N14SA16H===		===TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N14SA16H===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_10207002}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 10207002 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_10207002}}		{{ABSTRACT_PUBMED_10207002}}

	==About this Structure==		==About this Structure==
-	~~8AME~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/~~Macrozoarces_americanus Macrozoarces~~ americanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AME OCA].	+	[[8ame]] is a 1 chain structure of [[Antifreeze protein]] with sequence from [http://en.wikipedia.org/wiki/Zoarces_americanus Zoarces americanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AME OCA].
		+
		+	==See Also==
		+	*[[Antifreeze protein\|Antifreeze protein]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~10207002~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:010207002</ref><references group="xtra"/>
-	[[Category: ~~Macrozoarces~~ americanus]]	+	[[Category: Zoarces americanus]]
	[[Category: Baardsnes, J.]]		[[Category: Baardsnes, J.]]
	[[Category: Davies, P L.]]		[[Category: Davies, P L.]]
Line 35:		Line 26:
	[[Category: Mutant]]		[[Category: Mutant]]
	[[Category: Thermal hysteresis protein]]		[[Category: Thermal hysteresis protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:58:05 2009''

OCA at 16:58, 17 February 2009

OCA — Tue, 17 Feb 2009 16:58:06 GMT

←Older revision		Revision as of 16:58, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	8AME is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Macrozoarces_americanus Macrozoarces americanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AME OCA].	+	8AME is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Macrozoarces_americanus Macrozoarces americanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AME OCA].

	==Reference==		==Reference==
-	~~Quantitative and qualitative analysis of type III antifreeze protein structure and function., Graether SP, DeLuca CI, Baardsnes J, Hill GA, Davies PL, Jia Z, J Biol Chem. 1999 Apr 23;274(17):11842-7.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/10207002 10207002]~~	+	<ref group="xtra">PMID:10207002</ref><references group="xtra"/>
	[[Category: Macrozoarces americanus]]		[[Category: Macrozoarces americanus]]
-	[[Category: Single protein]]
	[[Category: Baardsnes, J.]]		[[Category: Baardsnes, J.]]
	[[Category: Davies, P L.]]		[[Category: Davies, P L.]]
Line 37:		Line 36:
	[[Category: Thermal hysteresis protein]]		[[Category: Thermal hysteresis protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri Jul 11 12~~:55:~~56 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:58:05 2009''

OCA at 09:55, 11 July 2008

OCA — Fri, 11 Jul 2008 09:55:56 GMT

←Older revision		Revision as of 09:55, 11 July 2008
Line 1:		Line 1:
-	[[Image:8ame.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:8ame.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_8ame\| PDB=8ame \| SCENE= }}		{{STRUCTURE_8ame\| PDB=8ame \| SCENE= }}

-	~~'''~~TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N14SA16H~~'''~~	+	===TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N14SA16H===


-	~~==Overview==~~	+	<!--
-	Some cold water marine fishes avoid cellular damage because of freezing by expressing antifreeze proteins (AFPs) that bind to ice and inhibit its growth; one such protein is the globular type III AFP from eel pout. Despite several studies, ~~the mechanism of ice binding remains unclear because of the difficulty in modeling the AFP-ice interaction. To further explore the mechanism~~, ~~we have determined~~ the ~~x-ray crystallographic structure of 10 type III AFP mutants and combined that information with 7 previously determined structures~~ to ~~mainly analyze specific AFP-ice interactions such as hydrogen bonds. Quantitative assessment of binding was performed using a neural network with properties of~~ the ~~structure~~ as ~~input and predicted antifreeze activity as output~~. ~~Using the cross-validation method, a correlation coefficient of 0~~.~~60 was obtained between measured and predicted activity~~, ~~indicating successful learning and good predictive power. A large loss in~~ the predictive power of the neural network occurred after properties related to the hydrophobic surface were left out, suggesting that van der Waal's interactions make a significant contribution to ice binding. ~~By combining the analysis of the neural network with antifreeze activity and x~~-~~ray crystallographic structures of the mutants, we extend the existing ice~~-binding model to a two-step process: 1) probing of the surface for the correct ice-binding plane by hydrogen-bonding side chains and 2) attractive van der Waal's interactions between the other residues of the ice-binding surface and the ice, which increases the strength of the protein-ice interaction.	+	The line below this paragraph, {{ABSTRACT_PUBMED_10207002}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 10207002 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_10207002}}

	==About this Structure==		==About this Structure==
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	[[Category: Mutant]]		[[Category: Mutant]]
	[[Category: Thermal hysteresis protein]]		[[Category: Thermal hysteresis protein]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 22~~:48:35 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Jul 11 12:55:56 2008''

OCA at 19:48, 4 May 2008

OCA — Sun, 04 May 2008 19:48:36 GMT

←Older revision		Revision as of 19:48, 4 May 2008
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	[[Image:8ame.gif\|left\|200px]]		[[Image:8ame.gif\|left\|200px]]

-	{{Structure	+	<!--
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-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	\|~~LIGAND~~=	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-	~~\|DOMAIN=~~	+	{{STRUCTURE_8ame\| PDB=8ame \| SCENE= }}
-	~~\|RELATEDENTRY=~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8ame FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ame OCA], [http://www.ebi.ac.uk/pdbsum/8ame PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=8ame RCSB]</span>	+
-	}}	+

	'''TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N14SA16H'''		'''TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 N14SA16H'''
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	[[Category: Hill, G A.]]		[[Category: Hill, G A.]]
	[[Category: Jia, Z.]]		[[Category: Jia, Z.]]
-	[[Category: ~~antifreeze~~ protein]]	+	[[Category: Antifreeze protein]]
-	[[Category: ~~ice~~ binding protein]]	+	[[Category: Ice binding protein]]
-	[[Category: ~~mutant~~]]	+	[[Category: Mutant]]
-	[[Category: ~~thermal~~ hysteresis protein]]	+	[[Category: Thermal hysteresis protein]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:48:35 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:45:02 2008''	+