4ame

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[[Image:4ame.gif|left|200px]]
 
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{{Structure
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==TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T18A==
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|PDB= 4ame |SIZE=350|CAPTION= <scene name='initialview01'>4ame</scene>, resolution 2.05&Aring;
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<StructureSection load='4ame' size='340' side='right'caption='[[4ame]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<table><tr><td colspan='2'>[[4ame]] 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=4AME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AME FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
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|GENE=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ame FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ame OCA], [https://pdbe.org/4ame PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ame RCSB], [https://www.ebi.ac.uk/pdbsum/4ame PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ame ProSAT]</span></td></tr>
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|DOMAIN=
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</table>
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|RELATEDENTRY=
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== Function ==
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ame FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ame OCA], [http://www.ebi.ac.uk/pdbsum/4ame PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=4ame RCSB]</span>
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[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.
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}}
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/am/4ame_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=4ame ConSurf].
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<div style="clear:both"></div>
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'''TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T18A'''
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==See Also==
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*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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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.
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[[Category: Large Structures]]
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[[Category: Zoarces americanus]]
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==About this Structure==
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[[Category: Baardsnes J]]
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4AME 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=4AME OCA].
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[[Category: Davies PL]]
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[[Category: Deluca CI]]
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==Reference==
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[[Category: Graether SP]]
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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]
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[[Category: Hill GA]]
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[[Category: Macrozoarces americanus]]
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[[Category: Jia Z]]
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[[Category: Single protein]]
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[[Category: Baardsnes, J.]]
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[[Category: Davies, P L.]]
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[[Category: Deluca, C I.]]
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[[Category: Graether, S P.]]
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[[Category: Hill, G A.]]
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[[Category: Jia, Z.]]
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[[Category: antifreeze protein]]
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[[Category: ice binding protein]]
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[[Category: mutant]]
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[[Category: thermal hysteresis protein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:37:55 2008''
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Current revision

TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T18A

PDB ID 4ame

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