Category: Proteins

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Proteins are amino acid polymers with myriad roles in creating and maintaining cell shape and structure, recognising molecules within cells or at the cell membrane and critically in catalysing biochemical reactions. More than half the dry weight of every cell is protein, with each individual protein composed of specific amino acids in a sequence and structural arrangement that confers properties vital for correct function.

Amino acids are small organic molecules characterised by an amine group (NH2), carboxylic acid group (COOH) and a specific side-group or 'residue' joined to a central or 'alpha' carbon atom. All living organisms share 20 common amino acids, each encoded within messenger RNA (mRNA) sequences (after transcription from DNA) by nucleotide base triplets called codons. A few organisms use an extra amino acid, selenocysteine, and some archaeal bacteria use pyrrolysine. mRNA sequences are read or 'transcribed' within ribosomes, RNA-protein complexes that bind to mRNA and move along it, recruiting transfer RNA (tRNA) molecules complementary to each codon, each tRNA bound to a specific amino acid. A polypeptide chain forms at the ribosome as each new amino acid is linked to the previous one before the corresponding tRNA is released and the ribosome moves to the next stretch of mRNA. Amino acids are linked by peptide bonds through condensation between amine and carboxylic acids groups, with resulting polypeptide sequences described from the amine or 'N' terminal on the left to the carboxylic acid or 'C' terminal on the right. Whereas the building blocks of DNA and RNA are chemically very similar, each amino acid is chemically distinct, which explains why proteins have evolved (from a primordial "RNA world" with few polypeptides) to become the main catalysts of cellular reactions.

The basic subunits (or monomers) of protein structure are termed 'domains' and consist of several distinct structural motifs (e.g. alpha-helix or beta-pleated sheet) combined in a single, highly folded globule. Amino acids have non-polar, acidic, basic or uncharged polar side-groups. Those with non-polar side-groups are hydrophobic and so orient themselves away from water, on the inside of the protein globule, while more polar, hydrophilic ones array themselves towards the external, aqueous environment. At binding sites, specific external residues are arranged to allow an exact fit with another molecule, termed a ligand. When catalytic proteins, or enzymes, subsequently modify the bound ligand (or substrate) they accelerate reactions, sometimes to astinishing rates. They owe this capacity to the close-fitting structure of the binding site and by using energy released at unstable intermediate stages of the reaction pathway. Protein subunits may assemble to form sheets, tubes, rings or helices, and functionally related proteins may also bind together to form 'multi-enzyme complexes', with the binding sites for substrates resulting from a chain of reactions all located in close proximity to localise relevant substrate concentrations and so promote optimal reaction rates.

Biochemical convergences

Chemically active proteins such as enzymes or respiratory proteins provide many examples of convergence. Among enzymes, identical active site structure may evolve, such as the serine-histidine-aspartate 'triad' in trypsin and subtilisin, or different routes may taken by structurally distinct proteins to catalyse an identical substrate (e.g. β-lactamases can function via serine protease or zinc 'metalloprotease' groups). Carbonic anhydrase (CA) converts CO2 + H20 → HCO3- (bicarbonate) + H+, a reversible reaction critical for processes as diverse as photosynthesis, respiration, biomineralisation and kidney function. Not surprisingly, therefore, CA enzymes are ubiquitous, and yet they appear to have evolved at least five (or six) times independently, and various CA families are known in animals, plants, bacteria and certain algae (e.g. diatoms, haptophytes). Peroxidases are typical anti-microbial enzymes, creating toxic oxidising conditions via generation of highly reactive hydrogen peroxide (H2O2) or organic hydroperoxidases. An array of peroxidases is known to have evolved in animals, plants, fungi and bacteria, variously depending on heme (iron-based) cofactors, active cysteine or selenocysteine to function. Luciferases have evolved at least 30 times to power bioluminescence, being recruited each time from pre-existing enzymes such as oxidases and synthetases. Astonishingly, the copper-based respiratory protein haemocyanin evolved independently in arthropods and molluscs, while iron-based β-haemoglobins show convergent gene duplication patterns in birds and mammals (as well as between monotreme and therian mammals). Lipocalin proteins have evolved independently in many animals, plants and gram negative bacteria, and in many cases act to bind with and transport hydrophobic molecules such as lipids and sterols. Lipocalins have been found in the milk secretions of placental mammals (e.g. ruminants) and marsupials (e.g. kangaroos, wallabies and possums) as well as insects such as the viviparous cockroach Diploptera punctata. Lipocalins are secreted in insects and some mammals (e.g. hamsters and mice) to carry critical pheromones, and have been observed to elicit allergenic activity in mammals and cockroaches.

Structural convergences

A range of proteins with key structural or anatomical roles demonstrate convergence clearly. Eye lenses are transparent due to the properties of crystallin proteins, independently recruited from microbes many times in animal evolution and co-opted from roles in stress resistance (e.g. heat shock proteins). Inriguingly, genes for crystallins made of very different proteins are driven by almost identical promoter regions in the genomes of scallops and vertebrates! Collagen is an essential structural protein in the ligaments and skin of animals, composed of three intertwined helices with frequent triplet-repeats of glycine-proline/hydroxyproline and a third residue. Surprisingly a collagen-like protein with proline-theronine-glycine triplets occurs in Bacillus anthracis (anthrax) spores, and a collagen gene was acquired by lateral gene transfer in the cyanobacterium Trichodesmium erythraeum, where its protein assists in cellular adhesion during blooms. Organised layers of high and lower refractive index collagen fibrils evolved independently at least 50 times in birds, resulting in structural colouration of feathers by 'thin film reflection' of incident light. Although fully reflective thin-film interfaces such as cats' eyes are typically built of insoluble guanine, collagen-based thin-film reflection is found in the deep-sea squid Vampyroteuthis whereas in the reverse-eye of the squid Euprymna convergence on reflective properties is based on entirely different proteins called reflectins. Proteins that form the celebrated bacterial flagellar motor are now well understood, in terms of the genes that code for them and their co-option to novel roles in the motor complex. Significantly, the flagellar motor has evolved more than once and is convergent in the eubacteria and archael bacteria. Proteins with elastic properties show convergences as various levels, from elastins in the vertebrate and cephalopod aorta to the shared characteristics of resilin, abductin, elastin and even gluten from plant seeds. Bivalves such as the well-known mussels have attachment structures with both elastic and more rigid silk fibroin-like regions, and the 'pen shell' Pinna has a byssus of 'sea-silk' threads, reminiscent of arthropod silk. Silk evolved for various functions at least three times in arachnids (spiders, spider-mites and some pseudoscorpions) and many more times in the insects, especially at larval stages. To name but a few examples: spiders, spider-mites and caddis fly larvae build webs; silk nests are built by weaver ants, leafhoppers, 'webspinners' and pseudoscorpions; the silk-worm Bombyx makes silk cocoons; a few (brave) spiders and hilarinid flies offer silken 'nuptial gifts', and spiders, spider mites and moth larvae use silk lines for 'ballooning' into the air.

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Topic Title Teaser text Availablity

Flying through the air on a summer's evening or sparkling in the ocean you may see magical flashes of light that signal some of nature's most enchanting creatures, those that are bioluminescent.

Antifreeze proteins n/a Not Available
Monochromacy in mammals

Underwater environments are dominated by blue light. Ironically, whales and seals cannot see blue, because they have independently lost their short-wavelength opsins.

Luciferases n/a Not Available
Foam nests in animals

Nests crop up everywhere, but one made out of foam? Might not sound like a great idea, but it is. And no surprise, it has evolved several times...

Peroxidases and oxidases n/a Not Available
Muts proteins in plants and corals n/a Not Available
Mitochondrial genome convergences

Most likely, mitochondria have a single evolutionary origin, but that doesn't mean they are immune to convergence...

Collagen in animals and bacteria n/a Available
SNARE protein receptors and the evolution of multicellularity

There is an intriguing correlation with larger numbers of SNAREs and multicellularity, at least in plants and animals.

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Membrane transport in eukaryotes

Dense core granules (DCGs) are very similar in ciliates and animals, but the systems are clearly convergent, and in particular the recruitment of a key group of proteins (known as dynamins) is independent.

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Extremophiles: Archaea and Bacteria

Surely, no organism can survive in boiling water or brines nine times the salinity of seawater? Wrong - some archaea and bacteria have independently evolved adaptations to such extreme environments...

Trichromatic vision in mammals

Who has not enjoyed the splash of colour in a market: gorgeous red peppers, the green of basil and what on earth are these purple vegetables over there? All thanks to trichromatic vision, another story of convergence.

Olfaction: insights into convergence

Although olfaction is very widespread, there is abundant evidence for repeated convergence of key features, strongly suggesting that there really is an optimal solution to detecting smells.

Ancient opsins and vision in extinct animals

Spectral tuning of the eye generally depends on key substitutions of amino acid sites in opsin proteins.

Hearts in cephalopods and vertebrates

There is a striking convergence between the aorta of the cephalopod and vertebrate heart, notably in its structure and the employment of elastic proteins.

Milk production in tsetse flies and cockroaches

In at least some cases the cycle of milk secretory activity in tsetse flies and coackroaches is strikingly similar to that found in the mammary glands of mammals.

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Lipocalins for milk and pheromone transport

Lipocalins are proteins that bind to and transport small hydrophobic molecules such as lipids and steroids, and have been associated with biological processes such as milk production, pheromone transport and immune responses.

Haptoglobins: convergence of Hp2 allele

One of the allelic forms of haptoglobin, known as Hp2, in the case of humans and cow shows a striking convergence, notably in the so-called complement control protein (CCP) domain.

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Animal haemoglobins

There is good evidence for convergence in animal haemoglobins because even though the protein itself is ancestral to all animals, during its evolution various episodes of gene duplication have led to a number of different varieties, notably the β-globins.

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Innate and adaptive immune systems

A vile cough, soaring temperature? When attacked by nasty microbes, our immune system comes in handy. Surprisingly (or not), plants have come up with a very similar solution to dealing with pathogens, but independently...



Silk production and use in arthropods

Remarkably, fossil silk is known, especially from amber of Cretaceous age. Material includes both silk with trapped insects, possibly from an orb-web, and strands with the characteristic viscid droplets that are the key in trapping prey.

Mussel attachment and the Pinna byssus

It is clear that the Pinna byssus has unusual properties in comparison to its equivalent in the bivalve mussel, and is conspicuously different in terms of crystallinity.

Biological uses of silk: from webs to ballooning

What material is so versatile that it can be used for capturing prey, building nests, communication and even cleaning? The answer: that most remarkable of biomaterials - silk.


Lysozymes are common antibacterial enzymes that protect our eyes and nose from infection, but some animals have recruited them for a rather different purpose...

Enzymes: convergence on active sites and reaction types

Enzymes make the world go round, each an evolutionary marvel - and convergent.

Evolution of insecticide resistance

There are several varieties of insecticide, and each one is designed to knock out some metabolic or physiological capability of the insect, targeting a specific system.

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Structural colouration in birds

In the great majority of birds both the colour of the feathers (plumage) and the skin is a result of so-called structural colouration which arises from the interaction of the light with ordered biological tissue

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Pigmentation in birds

The striking plumage of the turaco owes its colour to turacoverdin. Interestingly, this is a copper based pigment and is also convergent in the jacanas, a group of wading birds.

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Carbonic anhydrase in vertebrates, plants, algae and bacteria

Carbonic anhydrase is extremely convergent and may have evolved as many as six times. The most familiar variants are α, β and γ carbonic anhydrases.

Bacterial flagellar motors

The bacterial flagellum has proved to be a cause celebre because of its high-jacking by the “intelligent design” movement who argue that it is “irreducibly complex” and therefore could not have evolved by Darwinian processes.

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Gene regulation and cell cycles in bacteria and eukaryotes

Regulation of gene networks and cell cycles are of particular importance for convergence because genomic organization in bacteria shows significant differences from the eukaryotes.

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Haemocyanin in arthropods and molluscs

The degree of similarity between the active sites in arthropod and molluscan haemocyanin has been called “remarkable” and “startling”, but actually suggests that wherever in the universe life employs copper for aerobic respiration it will call upon haemocyanin.

Elastic proteins

What do rubber bands and fleas have in common?

Crystallins: eye lens proteins

Whereas typically technology demands furnaces, so that the glass for a lens is produced at hundreds of degrees Celsius and then requires most careful grinding, so nature calls upon proteins known as crystallins.

Moulting in arthopods, annelids and other animals

Moulting has, however, evolved independently in other groups, including the annelids where some polychaetes shed their jaws.

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Reflective tissues

Other cephalopods achieve reflectivity by employing collagen fibrils, of which the deep-sea Vampyroteuthis is perhaps the most striking example.

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