www.pdb.org [email protected]About the RCSB PDB Molecule of the MonthUsing selected molecules from the PDB archive, each feature includes an introduction to the structure and func- tion 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 Monthis read by students, teachers, and scien- tists worldwide atwww.pdb.org. This December 2009 edition was written and illustrated byDavid S. Goodsell (RCSB PDB and The Scripps Research Institute). MOLECULE OF THE MONTH: ANTIFREEZE PROTEINS Nice Ice Antifreeze proteins don't stop the growth of ice crystals, but they limit the growth to manage- able sizes. For this reason, they are also known as ice-restructuring proteins. This is necessarybecause 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 pre- vent the growth into larger dangerous crystals. Supercooling Antifreeze proteins lower the freezing point ofwater by a few degrees, but surprisingly, theydon't change the melting point. This process ofdepressing the freezing point while not effect- ing the melting point is termed thermal hys- teresis. 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 bacte- ria that have smaller effects on freezing point, are useful in another way. They are placed out- side cells where they control the size of ice cr ys- tals and prevent catastrophic ice crystal forma- tion when the temperature drops below the (lowered) freezing point. Icy Ice Cream Antifreeze proteins have been useful in indus- try. For instance, natural antifreeze proteins purified from cold-water ocean pout (shown here from PDB entry1kdf) have been used as a preservative in ice cream. They coat the fine ice crystals that give ice cream its smooth tex- ture, and prevent it from recrystallizing during storage and delivery into chunky, icyice cream. Researchers are also experimenting with antifreeze proteins as a way to preserve tissues and organs that are stored at lowtemperatures, reducing the possible damage from ice crystals. 10.2210/rcsb_pdb/mom_2009_12 Ice is a big problem for organisms that live in cold climates. Once the tempera- ture 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 deadlygrowth 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. 1kdf
archive, each feature includes anintroduction to the structure and func-tion of the molecule, a discussion of itsrelevance to human health and welfare,
and suggestions for viewing andaccessing further details.
The RCSB PDB Molecule of the Month is read by students, teachers, and scien-
tists worldwide at www.pdb.org.
This December 2009 edition was written and illustrated by
David S. Goodsell(RCSB PDB and The Scripps
Research Institute).
MOLECULE OF THE MONTH:
ANTIFREEZE PROTEINS
Nice Ice Antifreeze proteins don't stop the growth of icecrystals, but they limit the growth to manage-able sizes. For this reason, they are also knownas ice-restructuring proteins. This is necessary because of an unusual property of ice calledrecrystallization. When water begins to freeze,many small crystals form, but then a few smallcrystals dominate and grow larger and larger,stealing water molecules from the surroundingsmall crystals. Antifreeze proteins counteractthis recrystallization effect. They bind to the
surface of the small ice crystals and slow or pre-vent 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 effect-ing the melting point is termed thermal hys-teresis. The most effective antifreeze proteinsare made by insects, which lower the freezing
point by about 6 degrees. However, antifreezeproteins, even the ones from plants and bacte-ria that have smaller effects on freezing point,are useful in another way. They are placed out-side cells where they control the size of ice crys-tals and prevent catastrophic ice crystal forma-tion when the temperature drops below the(lowered) freezing point.
Icy Ice Cream Antifreeze proteins have been useful in indus-try. For instance, natural antifreeze proteinspurified from cold-water ocean pout (shownhere from PDB entry 1kdf ) have been used asa preservative in ice cream. They coat the fineice crystals that give ice cream its smooth tex-ture, and prevent it from recrystallizingduring storage and delivery into chunky, icy ice cream. Researchers are also experimenting
with antifreeze proteins as a way to preservetissues and organs that are stored at low temperatures, reducing the possible damagefrom ice crystals.
10.2210/rcsb_pdb/mom_2009_12
Ice is a big problem fororganisms that live in cold
climates. Once the tempera-ture dips below freezing, ice
crystals steadily grow andburst cells. This danger,
however, has not limited thespread of life on Earth to
temperate regions.Organisms of all types–
plants, animals, fungi andbacteria–have developed
ways to combat the deadly growth of ice crystals. In
some cases, they pack theircells with small antifreezecompounds like sugars or
glycerol. But in cases whereextra help is needed, cells
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It is supported by funds from theNational Science Foundation, the
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Cancer Institute, the National Instituteof Neurological Disorders and Stroke
and the National Institute of Diabetes& Digestive & Kidney Diseases.
The RCSB PDB is a member of the worldwide PDB
( wwPDB; www.wwpdb.org).
References:1kdf: F.D. Sonnichsen, C.I. DeLuca, P.L. Davies,B.D. Sykes (1996) Refined solution structure of typeIII antifreeze protein: hydrophobic groups may beinvolved in the energetics of the protein-ice interac-tion. Structure 4: 1325-1337
1wfb: F. Sicheri, D.S. Yang (1995) Ice-binding struc-ture 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) Beta-helix structure and ice-binding properties of a hyper-active 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 antifreezeprotein determined by racemic crystallization of syn-thetic protein enantiomers. J.Am.Chem.Soc.130:9695-9701
ANTIFREEZE PROTEINS
Topics for Further Exploration1. 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 solenoidalfolds, where the protein chain loops around like a spring.Compare the way the chain is folded in the beetle andmoth proteins with the entirely different type of loopingfold in the snow flea protein. Can you find other examplesof solenoidal folds in the PDB (hint: look at the SCOPclassification of these proteins, available at the bottom of the structure browser page).
Exploring the Structure Antifreeze proteins bind to ice crystals, block-ing the surface and preventing growth of thecrystal. The structure of snow flea antifreezeprotein (2pne) will give you an idea of whatthis recognition may be like. In the crystalstructure, the ice-binding surface of the pro-tein is covered with strings of water molecules(shown here in red). These water molecules arespaced similarly to the water molecules in icecrystals. So you can imagine this protein bind-ing to the geometric lattice of water moleculesin ice in a similar way.
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.
ocean pout
winter flounder
yellow mealwormbeettle
sprucebudwormmoth
snow flea
1kdf 1wfb 1ezg 1eww 2pne
Many Solutions to theSame Problem
Antifreeze proteins are a perfect example of convergent evolution. Looking at the proteinsused by different organisms, we see that many different proteins have been selected to servethis same function. Several examples areincluded above. All of these are small proteins
with a flat surface that is rich in threonine(colored lighter blue here), which binds to thesurface of ice crystals. These include two pro-teins from fish, the ocean pout (1kdf ) and the
winter flounder (1wfb), and three very activeproteins from insects, the yellow mealwormbeetle (1ezg), the spruce budworm moth(1eww ), and the snow flea (2pne).
