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PDBsum entry 1ops
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Antifreeze protein
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PDB id
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1ops
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References listed in PDB file
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Key reference
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Title
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Identification of the ice-Binding surface on a type III antifreeze protein with a "flatness function" algorithm.
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Authors
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D.S.Yang,
W.C.Hon,
S.Bubanko,
Y.Xue,
J.Seetharaman,
C.L.Hew,
F.Sicheri.
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Ref.
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Biophys J, 1998,
74,
2142-2151.
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
88%.
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Abstract
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Antifreeze proteins (AFPs) adsorb to surfaces of growing ice crystals, thereby
arresting their growth. The prevailing hypothesis explains the nature of
adsorption in terms of a match between the hydrophilic side chains on the AFP's
ice-binding surface (IBS) and the water molecules on the ice surface. The number
and spatial arrangement of hydrogen bonds thus formed have been proposed to
account, respectively, for the binding affinity and specificity. The crystal
structure of a type III AFP from ocean pout (isoform HPLC-3) has been determined
to 2.0-A resolution. The structure reveals an internal dyad motif formed by two
19-residue, loop-shaped elements. Based on of the flatness observed on the type
I alpha-helical AFP's IBS, an automated algorithm was developed to analyze the
surface planarity of the globular type III AFP and was used to identify the IBS
on this protein. The surface with the highest flatness score is formed by one
loop of the dyad motif and is identical to the IBS deduced from earlier
mutagenesis studies. Interestingly, 67% of this surface contains nonpolar
solvent-accessible surface area. The success of our approach to identifying the
IBS on an AFP, without considering the presence of polar side chains, indicates
that flatness is the first approximation of an IBS. We further propose that the
specificity of interactions between an IBS and a particular ice-crystallographic
plane arises from surface complementarity.
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