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PDBsum entry 1kdf
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Antifreeze protein
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PDB id
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1kdf
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References listed in PDB file
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Key reference
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Title
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Refined solution structure of type III antifreeze protein: hydrophobic groups may be involved in the energetics of the protein-Ice interaction.
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Authors
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F.D.Sönnichsen,
C.I.Deluca,
P.L.Davies,
B.D.Sykes.
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Ref.
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Structure, 1996,
4,
1325-1337.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: Antifreeze proteins are found in certain fish inhabiting polar sea
water. These proteins depress the freezing points of blood and body fluids below
that of the surrounding sea water by binding to and inhibiting the growth of
seed ice crystals. The proteins are believed to bind irreversibly to growing ice
crystals in such a way as to change the curvature of the ice-water interface,
leading to freezing point depression, but the mechanism of high-affinity ice
binding is not yet fully understood. RESULTS: The solution structure of the type
III antifreeze protein was determined by multidimensional NMR spectroscopy.
Twenty-two structures converged and display a root mean square difference from
the mean of 0.26 A for backbone atoms and 0.62 A for all non-hydrogen atoms. The
protein exhibits a compact fold with a relatively large hydrophobic core,
several short and irregular beta sheets and one helical turn. The ice-binding
site, which encompasses parts of the C-terminal sheet and a loop, is planar and
relatively nonpolar. The site is further characterized by the low solvent
accessibilities and the specific spatial arrangement of the polar side-chain
atoms of the putative ice-binding residues Gln9, Asn14, Thr15, Thr18 and Gln44.
CONCLUSIONS: In agreement with the adsorption-inhibition mechanism of action,
interatomic distances between active polar protein residues match the spacing of
water molecules in the prism planes (¿10&1macr;0¿) of the hexagonal ice
crystal. The particular side-chain conformations, however, limit the number and
strength of possible proten-ice hydrogen bonds. This suggests that other
entropic and enthalpic contributions, such as those arising from hydrophobic
groups, could play a role in the high-affinity protein-ice adsorption.
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Figure 6.
Figure 6. Solvent accessible surface of type III AFP. The
surface was calculated for the restrained minimized average
structure. The view shows the ice-binding site with the surface
colored by atom type (O=red, N=blue, C/S=white) and labeling of
the polar areas with the corresponding residue or atom.
Figure 6. Solvent accessible surface of type III AFP. The
surface was calculated for the restrained minimized average
structure. The view shows the ice-binding site with the surface
colored by atom type (O=red, N=blue, C/S=white) and labeling of
the polar areas with the corresponding residue or atom. (Figure
generated using the program InsightII [Biosym, Palo Alto, CA].)
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Figure 8.
Figure 8. Model for the type III AFP bound to the {10 Image 0}
plane of ice. (a) View nearly parallel to the ice surface, with
the c-axis of the hexagonal ice vertical. Ice water molecules
(including protons) are in CPK presentation, and the protein
backbone is shown in stick presentation. The polar contacts or
hydrogen bonds between protein atoms and ice surface atoms are
indicated by yellow lines. (Figure generated using the program
InsightII [Biosym, Palo Alto, CA].) (b) Presentation of the
excluded molecular surface. The ice surface and protein surface
is shown on the left and right, respectively. The applied color
gradient from white via blue to red represents distances
between the protein and ice surface in the complex from 0
å (direct contact) over 1.4 å (water inaccessible)
to 3 å. Figure 8. Model for the type III AFP bound to
the {10 [3]Image 0} plane of ice. (a) View nearly parallel to
the ice surface, with the c-axis of the hexagonal ice vertical.
Ice water molecules (including protons) are in CPK presentation,
and the protein backbone is shown in stick presentation. The
polar contacts or hydrogen bonds between protein atoms and ice
surface atoms are indicated by yellow lines. (Figure generated
using the program InsightII [Biosym, Palo Alto, CA].) (b)
Presentation of the excluded molecular surface. The ice surface
and protein surface is shown on the left and right,
respectively. The applied color gradient from white via blue to
red represents distances between the protein and ice surface in
the complex from 0 å (direct contact) over 1.4 å
(water inaccessible) to 3 å. (Figure generated using the
program GRASP [[4]55].)
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The above figures are
reprinted
by permission from Cell Press:
Structure
(1996,
4,
1325-1337)
copyright 1996.
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Secondary reference #1
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Title
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Structure-Function relationship in the globular type III antifreeze protein: identification of a cluster of surface residues required for binding to ice.
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Authors
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H.Chao,
F.D.Sönnichsen,
C.I.Deluca,
B.D.Sykes,
P.L.Davies.
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Ref.
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Protein Sci, 1994,
3,
1760-1769.
[DOI no: ]
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PubMed id
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Figure 3.
Fig. 3. ibbon presentation of the globular
Type 11 AFP showing the disposition ofse-
lected idechains on andaroundthe C-t&
&sheet. The N- and C-terminal0-sheets are
colored red and blue, respectively. Side
chains of selectedresidues are illustrated in
a stick presenetion, labeledwithresidue ype
andsequencenumber.Thecolorcode the
variousresiduesis T, yellow;Q and N,
purple; A, reen.
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Figure 4.
Fig. 4. Antifreeze activityofType In AFP mutants. Thermal hyster-
esivalues for Type 111 mutants and rQAE ml.1 t various concen-
trations were compared. Assayswere performed in 0.1 M NH4HC03
(pH 7.9). Each data pointrepresentsthemean of 3determintions.Stan-
dard deviations are shown as verticalbars. A: Activitycurves for rQAE
ml.1 (M), T18 (FT), and T18N (H). : Activitycurves for
rQAE ml.1 (O-O), 14Q (F), and N14S (H). C: Activitycurves
for rQAE ml.1 (M), Q44T (FT), N14S/Q44T (H), and
N14S/T18N/Q44T H). D Activitycurves for rQAE ml.1 (M),
S42G (FT), and N46S (H).
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by the Protein Society
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Secondary reference #2
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Title
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The nonhelical structure of antifreeze protein type III.
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Authors
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F.D.Sönnichsen,
B.D.Sykes,
H.Chao,
P.L.Davies.
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Ref.
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Science, 1993,
259,
1154-1157.
[DOI no: ]
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PubMed id
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