ANTIFREEZE PROTEINS - RCSB Protein Data Bank

MOLECULE OF THE MONTH:
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ANTIFREEZE PROTEINS
10.2210/rcsb_pdb/mom_2009_12
Ice is a big problem for
organisms that live in cold
climates. Once the temperature
dips below freezing, ice
crystals steadily grow and
burst cells. This danger,
however, has not limited the
spread of life on Earth to
temperate regions.
Organisms of all types–
plants, animals, fungi and
bacteria–have developed
ways to combat the deadly
growth of ice crystals. In
some cases, they pack their
cells with small antifreeze
compounds like sugars or
glycerol. But in cases where
extra help is needed, cells
make specialized antifreeze
proteins to protect
themselves as the
temperature drops.
About the
RCSB PDB Molecule of the Month
Using selected molecules from the PDB
archive, each feature includes an
introduction to the structure and function
of the molecule, a discussion of its
relevance to human health and welfare,
and suggestions for viewing and
accessing further details.
The RCSB PDB Molecule of the Month
is read by students, teachers, and scientists
worldwide at www.pdb.org.
This December 2009 edition was
written and illustrated by
David S. Goodsell
(RCSB PDB and The Scripps
Research Institute).
1kdf
Nice Ice
Antifreeze proteins don't stop the growth of ice
crystals, but they limit the growth to manageable
sizes. For this reason, they are also known
as ice-restructuring proteins. This is necessary
because of an unusual property of ice called
recrystallization. When water begins to freeze,
many small crystals form, but then a few small
crystals dominate and grow larger and larger,
stealing water molecules from the surrounding
small crystals. Antifreeze proteins counteract
this recrystallization effect. They bind to the
surface of the small ice crystals and slow or prevent
the growth into larger dangerous crystals.
Supercooling
Antifreeze proteins lower the freezing point of
water by a few degrees, but surprisingly, they
don't change the melting point. This process of
depressing the freezing point while not effecting
the melting point is termed thermal hysteresis.
The most effective antifreeze proteins
are made by insects, which lower the freezing
point by about 6 degrees. However, antifreeze
proteins, even the ones from plants and bacteria
that have smaller effects on freezing point,
are useful in another way. They are placed outside
cells where they control the size of ice crystals
and prevent catastrophic ice crystal formation
when the temperature drops below the
(lowered) freezing point.
Icy Ice Cream
Antifreeze proteins have been useful in industry.
For instance, natural antifreeze proteins
purified from cold-water ocean pout (shown
here from PDB entry 1kdf) have been used as
a preservative in ice cream. They coat the fine
ice crystals that give ice cream its smooth texture,
and prevent it from recrystallizing
during storage and delivery into chunky, icy
ice cream. Researchers are also experimenting
with antifreeze proteins as a way to preserve
tissues and organs that are stored at low
temperatures, reducing the possible damage
from ice crystals.

ANTIFREEZE PROTEINS
RCSB Protein Data Bank
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(wwPDB; www.wwpdb.org).
1kdf 1wfb 1ezg 1eww 2pne
ocean pout
winter flounder
Many Solutions to the
Same Problem
Antifreeze proteins are a perfect example of
convergent evolution. Looking at the proteins
used by different organisms, we see that many
different proteins have been selected to serve
this same function. Several examples are
included above. All of these are small proteins
with a flat surface that is rich in threonine
(colored lighter blue here), which binds to the
surface of ice crystals. These include two proteins
from fish, the ocean pout (1kdf) and the
winter flounder (1wfb), and three very active
proteins from insects, the yellow mealworm
beetle (1ezg), the spruce budworm moth
(1eww), and the snow flea (2pne).
yellow
mealworm
beettle
spruce
budworm
moth
snow flea
Exploring the Structure
Antifreeze proteins bind to ice crystals, blocking
the surface and preventing growth of the
crystal. The structure of snow flea antifreeze
protein (2pne) will give you an idea of what
this recognition may be like. In the crystal
structure, the ice-binding surface of the protein
is covered with strings of water molecules
(shown here in red). These water molecules are
spaced similarly to the water molecules in ice
crystals. So you can imagine this protein binding
to the geometric lattice of water molecules
in ice in a similar way.
References:
1kdf: F.D. Sonnichsen, C.I. DeLuca, P.L. Davies,
B.D. Sykes (1996) Refined solution structure of type
III antifreeze protein: hydrophobic groups may be
involved in the energetics of the protein-ice interaction.
Structure 4: 1325-1337
1wfb: F. Sicheri, D.S. Yang (1995) Ice-binding structure
and mechanism of an antifreeze protein from
winter flounder. Nature 375: 427-431
1ezg: Y.C. Liou, A. Tocilj, P.L. Davies, Z. Jia (2000)
Mimicry of ice structure by surface hydroxyls and
water of a beta-helix antifreeze protein. Nature 406:
322-324
1eww: S.P. Graether, M.J. Kuiper, S.M., Gagne, V.K.
Walker, Z. Jia, B.D. Sykes, P.L. Davies (2000) Betahelix
structure and ice-binding properties of a hyperactive
antifreeze protein from an insect. Nature 406:
325-328
2pne: B.L. Pentelute, Z.P. Gates, V. Tereshko, J.L.
Dashnau, J.M. Vanderkooi, A.A. Kossiakoff, S.B.
Kent (2008) X-ray structure of snow flea antifreeze
protein determined by racemic crystallization of synthetic
protein enantiomers. J.Am.Chem.Soc. 130:
9695-9701
Topics for Further Exploration
1. Antifreeze proteins are examples of convergent evolution.
Can you find other examples in the PDB where two entirely
different proteins perform the same function?
2. The insect antifreeze proteins are examples of solenoidal
folds, where the protein chain loops around like a spring.
Compare the way the chain is folded in the beetle and
moth proteins with the entirely different type of looping
fold in the snow flea protein. Can you find other examples
of solenoidal folds in the PDB (hint: look at the SCOP
classification of these proteins, available at the bottom of
the structure browser page).
Additional Information on Antifreeze Proteins
• S. Venkatesh and C. Dayananda (2008) Properties, potentials, and prospects of antifreeze proteins. Critical Reviews in Biotechnology
28: 57-82.
• A. Regand and H. D. Goff (2006) Ice recrystallization inhibition in ice cream as affected by ice restructuring proteins from winter
wheat grass. Journal of Dairy Science 89: 49-57.
• Z. Jia and P. L. Davies (2002) Antifreeze proteins: an unusual receptor-ligand interaction. Trends in Biochemical Sciences 27: 101-106.