Antifreeze proteins (AFPs) or ice structuring proteins refer to a class of
polypeptides produced by certain
animal
Animals are multicellular, eukaryotic organisms in the Biology, biological Kingdom (biology), kingdom Animalia (). With few exceptions, animals heterotroph, consume organic material, Cellular respiration#Aerobic respiration, breathe oxygen, ...
s,
plant
Plants are the eukaryotes that form the Kingdom (biology), kingdom Plantae; they are predominantly Photosynthesis, photosynthetic. This means that they obtain their energy from sunlight, using chloroplasts derived from endosymbiosis with c ...
s,
fungi
A fungus (: fungi , , , or ; or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and mold (fungus), molds, as well as the more familiar mushrooms. These organisms are classified as one ...
and
bacteria
Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
that permit their survival in temperatures below the freezing point of water. AFPs bind to small
ice crystals
Ice crystals are solid water (known as ice) in crystal structure, symmetrical shapes including hexagonal crystal family, hexagonal columns, hexagonal plates, and dendrite (crystal), dendritic crystals. Ice crystals are responsible for various at ...
to inhibit the growth and
recrystallization of ice that would otherwise be fatal.
There is also increasing evidence that AFPs interact with mammalian cell membranes to protect them from cold damage. This work suggests the involvement of AFPs in cold
acclimatization
Acclimatization or acclimatisation ( also called acclimation or acclimatation) is the process in which an individual organism adjusts to a change in its environment (such as a change in altitude, temperature, humidity, photoperiod, or pH), ...
.
Non-colligative properties
Unlike the widely used automotive antifreeze,
ethylene glycol, AFPs do not lower freezing point in proportion to concentration. Rather, they work in a non
colligative manner. This phenomenon allows them to act as an antifreeze at concentrations 1/300th to 1/500th of those of other dissolved solutes. Their low concentration minimizes their effect on
osmotic pressure
Osmotic pressure is the minimum pressure which needs to be applied to a Solution (chemistry), solution to prevent the inward flow of its pure solvent across a semipermeable membrane.
It is also defined as the measure of the tendency of a soluti ...
.
The unusual properties of AFPs are attributed to their selective affinity for specific crystalline ice forms and the resulting blockade of the ice-nucleation process.
Thermal hysteresis
AFPs create a difference between the melting point and freezing point (busting temperature of AFP bound ice crystal) known as thermal hysteresis. The addition of AFPs at the interface between solid ice and liquid water inhibits the thermodynamically favored growth of the ice crystal. Ice growth is kinetically inhibited by the AFPs covering the water-accessible surfaces of ice.
Thermal hysteresis is easily measured in the lab with a
nanolitre osmometer. Organisms differ in their values of thermal hysteresis. The maximum level of thermal hysteresis shown by fish AFP is approximately −3.5 °C (Sheikh Mahatabuddin et al., SciRep)(29.3 °F). In contrast, aquatic organisms are exposed only to −1 to −2 °C below freezing. During the extreme winter months, the
spruce budworm resists freezing at temperatures approaching −30 °C.
The rate of cooling can influence the thermal hysteresis value of AFPs. Rapid cooling can substantially decrease the nonequilibrium freezing point, and hence the thermal hysteresis value. Consequently, organisms cannot necessarily adapt to their subzero environment if the temperature drops abruptly.
Freeze tolerance versus freeze avoidance
Species containing AFPs may be classified as
Freeze avoidant: These species are able to prevent their body fluids from freezing altogether. Generally, the AFP function may be overcome at extremely cold temperatures, leading to rapid ice growth and death.
Freeze tolerant: These species are able to survive body fluid freezing. Some freeze tolerant species are thought to use AFPs as cryoprotectants to prevent the damage of freezing, but not freezing altogether. The exact mechanism is still unknown. However, it is thought AFPs may inhibit recrystallization and stabilize cell membranes to prevent damage by ice.
They may work in conjunction with ice
nucleating proteins (INPs) to control the rate of ice propagation following freezing.
Diversity
There are many known
nonhomologous types of AFPs.
Fish AFPs
Antifreeze
glycoproteins
Glycoproteins are proteins which contain oligosaccharide (sugar) chains covalently attached to amino acid side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known a ...
or AFGPs are found in
Antarctic
The Antarctic (, ; commonly ) is the polar regions of Earth, polar region of Earth that surrounds the South Pole, lying within the Antarctic Circle. It is antipodes, diametrically opposite of the Arctic region around the North Pole.
The Antar ...
notothenioids and
northern cod. They are 2.6-3.3 kD.
AFGPs evolved separately in notothenioids and northern cod. In notothenioids, the AFGP gene arose from an ancestral trypsinogen-like serine protease gene.
*Type I AFP is found in
winter flounder
The winter flounder (''Pseudopleuronectes americanus''), also known as the black back, is a right-eyed ("Sinistral and dextral, dextral") flatfish of the family Pleuronectidae. It is native to coastal waters of the western north Atlantic Ocean, A ...
,
longhorn sculpin and
shorthorn sculpin. It is the best documented AFP because it was the first to have its three-dimensional structure determined.
Type I AFP consists of a single, long, amphipathic alpha helix, about 3.3-4.5 kD in size. There are three faces to the 3D structure: the hydrophobic, hydrophilic, and Thr-Asx face.
**Type I-hyp AFP (where hyp stands for hyperactive) are found in several righteye flounders. It is approximately 32 kD (two 17 kD dimeric molecules). The protein was isolated from the blood plasma of winter flounder. It is considerably better at depressing freezing temperature than most fish AFPs.
The ability is partially derived from its many repeats of the Type I ice-binding site.
*Type II AFPs (e.g. ) are found in
sea raven,
smelt and
herring
Herring are various species of forage fish, belonging to the Order (biology), order Clupeiformes.
Herring often move in large Shoaling and schooling, schools around fishing banks and near the coast, found particularly in shallow, temperate wate ...
. They are cysteine-rich globular proteins containing five
disulfide bonds.
Type II AFPs likely evolved from calcium dependent (c-type) lectins.
Sea ravens, smelt, and herring are quite divergent lineages of
teleost
Teleostei (; Ancient Greek, Greek ''teleios'' "complete" + ''osteon'' "bone"), members of which are known as teleosts (), is, by far, the largest group of ray-finned fishes (class Actinopterygii), with 96% of all neontology, extant species of f ...
. If the AFP gene were present in the most recent common ancestor of these lineages, it is peculiar that the gene is scattered throughout those lineages, present in some orders and absent in others. It has been suggested that lateral gene transfer could be attributed to this discrepancy, such that the smelt acquired the type II AFP gene from the herring.
[ ]
*Type III AFPs are found in Antarctic
eelpout. They exhibit similar overall hydrophobicity at ice binding surfaces to type I AFPs. They are approximately 6kD in size.
Type III AFPs likely evolved from a sialic acid synthase (SAS) gene present in Antarctic eelpout. Through a gene duplication event, this gene—which has been shown to exhibit some ice-binding activity of its own—evolved into an effective AFP gene by loss of the N-terminal part.
*Type IV AFPs () are found in longhorn sculpins. They are alpha helical proteins rich in glutamate and glutamine.
This protein is approximately 12KDa in size and consists of a 4-helix bundle.
Its only posttranslational modification is a
pyroglutamate residue, a cyclized
glutamine residue at its
N-terminus
The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the amin ...
.
Plant AFPs
The classification of AFPs became more complicated when antifreeze proteins from plants were discovered.
Plant AFPs are rather different from the other AFPs in the following aspects:
#They have much weaker thermal hysteresis activity when compared to other AFPs.
#Their physiological function is likely in inhibiting the recrystallization of ice rather than in preventing ice formation.
#Most of them are evolved
pathogenesis-related proteins, sometimes retaining
antifungal
An antifungal medication, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis (thrush), serious systemic infections such as ...
properties.
Insect AFPs
There are a number of AFPs found in insects, including those from ''Dendroides'', ''Tenebrio'' and ''Rhagium'' beetles, spruce budworm and pale beauty moths, and midges (same order as flies). Insect AFPs share certain similarities, with most having higher activity (i.e. greater thermal hysteresis value, termed hyperactive) and a repetitive structure with a flat ice-binding surface. Those from the closely related ''Tenebrio'' and ''Dendroides'' beetles are homologous and each 12–13 amino-acid repeat is stabilized by an internal disulfide bond. Isoforms have between 6 and 10 of these repeats that form a coil, or beta-solenoid. One side of the solenoid has a flat ice-binding surface that consists of a double row of threonine residues.
Other beetles (genus ''Rhagium'') have longer repeats without internal disulfide bonds that form a compressed beta-solenoid (beta sandwich) with four rows of threonine residus, and this AFP is structurally similar to that modelled for the non-homologous AFP from the pale beauty moth. In contrast, the AFP from the spruce budworm moth is a solenoid that superficially resembles the ''Tenebrio'' protein, with a similar ice-binding surface, but it has a triangular cross-section, with longer repeats that lack the internal disulfide bonds. The AFP from midges is structurally similar to those from ''Tenebrio'' and ''Dendroides'', but the disulfide-braced beta-solenoid is formed from shorter 10 amino-acids repeats, and instead of threonine, the ice-binding surface consists of a single row of tyrosine residues. Springtails (Collembola) are not insects, but like insects, they are arthropods with six legs. A species found in Canada, which is often called a "snow flea", produces hyperactive AFPs.
Although they are also repetitive and have a flat ice-binding surface, the similarity ends there. Around 50% of the residues are glycine (Gly), with repeats of Gly-Gly- X or Gly-X-X, where X is any amino acid. Each 3-amino-acid repeat forms one turn of a polyproline type II helix. The helices then fold together, to form a bundle that is two helices thick, with an ice-binding face dominated by small hydrophobic residues like alanine, rather than threonine. Other insects, such as an Alaskan beetle, produce hyperactive antifreezes that are even less similar, as they are polymers of sugars (
xylomannan) rather than polymers of amino acids (proteins).
Taken together, this suggests that most of the AFPs and antifreezes arose after the lineages that gave rise to these various insects diverged. The similarities they do share are the result of convergent evolution.
Sea ice organism AFPs
Many microorganisms living in
sea ice possess AFPs that belong to a single family. The
diatom
A diatom (Neo-Latin ''diatoma'') is any member of a large group comprising several Genus, genera of algae, specifically microalgae, found in the oceans, waterways and soils of the world. Living diatoms make up a significant portion of Earth's B ...
s ''Fragilariopsis cylindrus'' and ''F. curta'' play a key role in polar sea ice communities, dominating the assemblages of both platelet layer and within pack ice. AFPs are widespread in these species, and the presence of AFP
genes
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
as a multigene family indicates the importance of this group for the genus ''Fragilariopsis''.
AFPs identified in ''F. cylindrus'' belong to an AFP family which is represented in different taxa and can be found in other organisms related to sea ice (''
Colwellia'' spp., ''Navicula glaciei'', ''Chaetoceros neogracile'' and ''Stephos longipes and Leucosporidium antarcticum'')
and Antarctic inland ice bacteria (
Flavobacteriaceae
Flavobacteriaceae is a family of rod-shaped gram negative bacteria. The family contains many environmental bacteria, with some species being potential pathogens.
History
The family of ''Flavobacteriaceae'' was first proposed by Reichenbach in 1 ...
),
as well as in cold-tolerant fungi (''
Typhula ishikariensis'', ''
Lentinula edodes'' and ''
Flammulina populicola'').
Several structures for sea ice AFPs have been solved. This family of proteins fold into a
beta helix that form a flat ice-binding surface. Unlike the other AFPs, there is not a singular sequence motif for the ice-binding site.
AFP found from the metagenome of the
ciliate
The ciliates are a group of alveolates characterized by the presence of hair-like organelles called cilia, which are identical in structure to flagellum, eukaryotic flagella, but are in general shorter and present in much larger numbers, with a ...
''Euplotes focardii'' and psychrophilic bacteria has an efficient ice re-crystallization inhibition ability.
1 μM of ''Euplotes focardii'' consortium ice-binding protein (''Efc''IBP) is enough for the total inhibition of ice re-crystallization in –7.4 °C temperature. This ice-recrystallization inhibition ability helps bacteria to tolerate ice rather than preventing the formation of ice. ''Efc''IBP produces also thermal hysteresis gap, but this ability is not as efficient as the ice-recrystallization inhibition ability. ''Efc''IBP helps to protect both purified proteins and whole bacterial cells in freezing temperatures.
Green fluorescent protein is functional after several cycles of freezing and melting when incubated with ''Efc''IBP. ''
Escherichia coli
''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Escherichia'' that is commonly fo ...
'' survives longer periods in 0 °C temperature when the ''efcIBP'' gene was inserted to ''E. coli'' genome.
''Efc''IBP has a typical AFP structure consisting of multiple
beta-sheet
The beta sheet (β-sheet, also β-pleated sheet) is a common structural motif, motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone chain, backbon ...
s and an
alpha-helix. Also, all the ice-binding polar residues are at the same site of the protein.
Evolution
The remarkable diversity and distribution of AFPs suggest the different types evolved recently in response to sea level
glaciation
A glacial period (alternatively glacial or glaciation) is an interval of time (thousands of years) within an ice age that is marked by colder temperatures and glacier advances. Interglacials, on the other hand, are periods of warmer climate be ...
occurring 1–2 million years ago in the Northern hemisphere and 10-30 million years ago in Antarctica. Data collected from deep sea ocean drilling has revealed that the development of the Antarctic Circumpolar Current was formed over 30 million years ago.
The cooling of Antarctic imposed from this current caused a mass extinction of teleost species that were unable to withstand freezing temperatures.
Notothenioids species with the antifreeze glycoprotein were able to survive the glaciation event and diversify into new niches.
This independent development of similar adaptations is referred to as
convergent evolution
Convergent evolution is the independent evolution of similar features in species of different periods or epochs in time. Convergent evolution creates analogous structures that have similar form or function but were not present in the last comm ...
.
Evidence for convergent evolution in Northern cod (
Gadidae) and Notothenioids is supported by the findings of different spacer sequences and different organization of introns and exons as well as unmatching AFGP tripeptide sequences, which emerged from duplications of short ancestral sequences which were differently permuted (for the same tripeptide) by each group. These groups diverged approximately 7-15 million years ago. Shortly after (5-15 mya), the AFGP gene evolved from an ancestral pancreatic trypsinogen gene in Notothenioids. AFGP and trypsinogen genes split via a sequence divergence - an adaptation which occurred alongside the cooling and eventual freezing of the Antarctic Ocean. The evolution of the AFGP gene in Northern cod occurred more recently (~3.2 mya) and emerged from a noncoding sequence via tandem duplications in a Thr-Ala-Ala unit. Antarctic notothenioid fish and arctic cod,
Boreogadus saida, are part of two distinct orders and have very similar antifreeze glycoproteins.
Although the two fish orders have similar antifreeze proteins, cod species contain arginine in AFG, while Antarctic notothenioid do not.
[ The role of arginine as an enhancer has been investigated in Dendroides canadensis antifreeze protein (DAFP-1) by observing the effect of a chemical modification using 1-2 cyclohexanedione.] Previous research has found various enhancers of this bettles' antifreeze protein including a thaumatin-like protein and polycarboxylates. Modifications of DAFP-1 with the arginine specific reagent resulted in the partial and complete loss of thermal hysteresis in DAFP-1, indicating that arginine plays a crucial role in enhancing its ability. Different enhancer molecules of DAFP-1 have distinct thermal hysteresis activity. Amornwittawat et al. 2008 found that the number of carboxylate groups in a molecules influence the enhancing ability of DAFP-1. Optimum activity in TH is correlated with high concentration of enhancer molecules. Li et al. 1998 investigated the effects of pH and solute on thermal hysteresis in Antifreeze proteins from Dendrioides canadensis. TH activity of DAFP-4 was not affected by pH unless the there was a low solute concentration (pH 1) in which TH decreased. The effect of five solutes; succinate, citrate, malate, malonate, and acetate, on TH activity was reported. Among the five solutes, citrate was shown to have the greatest enhancing effect.
This is an example of a proto-ORF model, a rare occurrence where new genes pre exist as a formed open reading frame before the existence of the regulatory element needed to activate them.
In fishes, horizontal gene transfer is responsible for the presence of Type II AFP proteins in some groups without a recently shared phylogeny. In Herring and smelt, up to 98% of introns for this gene are shared; the method of transfer is assumed to occur during mating via sperm cells exposed to foreign DNA. The direction of transfer is known to be from herring to smelt as herring have 8 times the copies of AFP gene as smelt (1) and the segments of the gene in smelt house transposable elements which are otherwise characteristic of and common in herring but not found in other fishes.
There are two reasons why many types of AFPs are able to carry out the same function despite their diversity:
# Although ice is uniformly composed of water molecules, it has many different surfaces exposed for binding. Different types of AFPs may interact with different surfaces.
# Although the five types of AFPs differ in their primary structure
Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthe ...
of amino acids, when each folds into a functioning protein they may share similarities in their three-dimensional or tertiary structure
Protein tertiary structure is the three-dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains and the ...
that facilitates the same interactions with ice.
Antifreeze glycoprotein activity has been observed across several ray-finned species including eelpouts, sculpins, and cod species. Fish species that possess the antifreeze glycoprotein express different levels of protein activity. Polar cod (''Boreogadus saida)'' exhibit similar protein activity and properties to the Antarctic species, ''T. borchgrevinki''.[ Both species have higher protein activity than saffron cod (''Eleginus gracilis'').][ Ice antifreeze proteins have been reported in diatom species to help decrease the freezing point of organism's proteins.] Bayer-Giraldi et al. 2010 found 30 species from distinct taxa with homologues of ice antifreeze proteins. The diversity is consistent with previous research that has observed the presence of these genes in crustaceans, insects, bacteria, and fungi. Horizontal gene transfer is responsible for the presence of ice antifreeze proteins in two sea diatom species, F. cylindrus and F. curta.
Mechanisms of action
AFPs are thought to inhibit ice growth by an adsorption
Adsorption is the adhesion of atoms, ions or molecules from a gas, liquid or dissolved solid to a surface. This process creates a film of the ''adsorbate'' on the surface of the ''adsorbent''. This process differs from absorption, in which a ...
–inhibition mechanism. They adsorb to non basal planes of ice, inhibiting thermodynamically-favored ice growth. The presence of a flat, rigid surface in some AFPs seems to facilitate its interaction with ice via Van der Waals force
In molecular physics and chemistry, the van der Waals force (sometimes van der Waals' force) is a distance-dependent interaction between atoms or molecules. Unlike ionic or covalent bonds, these attractions do not result from a chemical elec ...
surface complementarity.
Binding to ice
Normally, ice crystals grown in solution only exhibit the basal (0001) and prism faces (1010), and appear as round and flat discs. However, it appears the presence of AFPs exposes other faces. It now appears the ice surface 2021 is the preferred binding surface, at least for AFP type I. Through studies on type I AFP, ice and AFP were initially thought to interact through hydrogen bonding (Raymond and DeVries, 1977). However, when parts of the protein thought to facilitate this hydrogen bonding were mutated, the hypothesized decrease in antifreeze activity was not observed. Recent data suggest hydrophobic interactions could be the main contributor. It is difficult to discern the exact mechanism of binding because of the complex water-ice interface. Currently, attempts to uncover the precise mechanism are being made through use of molecular modelling
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials scien ...
programs (molecular dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamics ( ...
or the Monte Carlo method
Monte Carlo methods, or Monte Carlo experiments, are a broad class of computational algorithms that rely on repeated random sampling to obtain numerical results. The underlying concept is to use randomness to solve problems that might be ...
).
Binding mechanism and antifreeze function
According to the structure and function study on the antifreeze protein from '' Pseudopleuronectes americanus'', the antifreeze mechanism of the type-I AFP molecule was shown to be due to the binding to an ice nucleation structure in a zipper-like fashion through hydrogen bonding of the hydroxyl group
In chemistry, a hydroxy or hydroxyl group is a functional group with the chemical formula and composed of one oxygen atom covalently bonded to one hydrogen atom. In organic chemistry, alcohols and carboxylic acids contain one or more hydroxy ...
s of its four Thr residues to the oxygens along the