3ame

From Proteopedia

(Difference between revisions)

Current revision

TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 Q9TQ44T

Structural highlights

3ame is a 1 chain structure with sequence from Zoarces americanus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[1]

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

References

↑ Graether SP, DeLuca CI, Baardsnes J, Hill GA, Davies PL, Jia Z. Quantitative and qualitative analysis of type III antifreeze protein structure and function. J Biol Chem. 1999 Apr 23;274(17):11842-7. PMID:10207002

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ame"

@@ Line 1: / Line 1: @@
 ==TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 Q9TQ44T==
-<StructureSection load='3ame' size='340' side='right' caption='[[3ame]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='3ame' size='340' side='right'caption='[[3ame]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ame]] 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=3AME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AME FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ame]] 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=3AME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AME FirstGlance]. <br>
-</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=3ame FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ame OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ame RCSB], [http://www.ebi.ac.uk/pdbsum/3ame PDBsum]</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]] 2.3&#8491;</td></tr>
-<table>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ame FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ame OCA], [https://pdbe.org/3ame PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ame RCSB], [https://www.ebi.ac.uk/pdbsum/3ame PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ame ProSAT]</span></td></tr>
+</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/3ame_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/am/3ame_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].
+</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=3ame ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 23: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3ame" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Antifreeze protein|Antifreeze protein]]
+*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Zoarces americanus]]
-[[Category: Baardsnes, J.]]
+[[Category: Baardsnes J]]
-[[Category: Davies, P L.]]
+[[Category: Davies PL]]
-[[Category: Deluca, C I.]]
+[[Category: Deluca CI]]
-[[Category: Graether, S P.]]
+[[Category: Graether SP]]
-[[Category: Hill, G A.]]
+[[Category: Hill GA]]
-[[Category: Jia, Z.]]
+[[Category: Jia Z]]
-[[Category: Antifreeze protein]]
-[[Category: Ice binding protein]]
-[[Category: Mutant]]
-[[Category: Thermal hysteresis protein]]

3ame

From Proteopedia

Current revision

TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 Q9TQ44T

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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