4ame: Difference between revisions

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[[Image:4ame.gif|left|200px]]


<!--
==TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T18A==
The line below this paragraph, containing "STRUCTURE_4ame", creates the "Structure Box" on the page.
<StructureSection load='4ame' size='340' side='right'caption='[[4ame]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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>
-->
<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>
{{STRUCTURE_4ame|  PDB=4ame |  SCENE= }}
</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 ==
[[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/4ame_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/main_output.php?pdb_ID=4ame ConSurf].
<div style="clear:both"></div>


'''TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T18A'''
==See Also==
 
*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
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.
[[Category: Large Structures]]
 
[[Category: Zoarces americanus]]
==About this Structure==
[[Category: Baardsnes J]]
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].
[[Category: Davies PL]]
 
[[Category: Deluca CI]]
==Reference==
[[Category: Graether SP]]
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]
[[Category: Hill GA]]
[[Category: Macrozoarces americanus]]
[[Category: Jia Z]]
[[Category: Single protein]]
[[Category: Baardsnes, J.]]
[[Category: Davies, P L.]]
[[Category: Deluca, C I.]]
[[Category: Graether, S P.]]
[[Category: Hill, G A.]]
[[Category: Jia, Z.]]
[[Category: Antifreeze protein]]
[[Category: Ice binding protein]]
[[Category: Mutant]]
[[Category: Thermal hysteresis protein]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 22:20:43 2008''

Latest revision as of 14:28, 14 March 2024

TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T18A

4ame, resolution 2.05Å

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