The trefoil knot fold is a

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

fold in which the protein backbone is twisted into a

trefoil knot In knot theory, a branch of mathematics, the trefoil knot is the simplest example of a nontrivial knot (mathematics), knot. The trefoil can be obtained by joining the two loose ends of a common overhand knot, resulting in a knotted loop (topology ...

shape. "Shallow" knots in which the tail of the polypeptide chain only passes through a loop by a few residues are uncommon, but "deep" knots in which many residues are passed through the loop are extremely rare. Deep trefoil knots have been found in the SPOUT superfamily. including

methyltransferase Methyltransferases are a large group of enzymes that all methylate their substrates but can be split into several subclasses based on their structural features. The most common class of methyltransferases is class I, all of which contain a Ro ...

proteins involved in posttranscriptional

RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...

modification in all

three domains of life The three-domain system is a taxonomic classification system that groups all cellular life into three domains, namely Archaea, Bacteria and Eukarya, introduced by Carl Woese, Otto Kandler and Mark Wheelis in 1990. The key difference from earli ...

, including

bacterium Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the ...

Thermus thermophilus ''Thermus thermophilus'' is a gram stain, Gram-negative bacterium used in a range of biotechnological applications, including as a model organism for genetic manipulation, structural genomics, and systems biology. The bacterium is extremely therm ...

'' and proteins, in

archaea Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...

and in

eukaryota The eukaryotes ( ) constitute the Domain (biology), domain of Eukaryota or Eukarya, organisms whose Cell (biology), cells have a membrane-bound cell nucleus, nucleus. All animals, plants, Fungus, fungi, seaweeds, and many unicellular organisms ...

. In many cases the trefoil knot is part of the

active site In biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the ''binding s ...

or a ligand-binding site and is critical to the activity of the

enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...

in which it appears. Before the discovery of the first knotted protein, it was believed that the process of

protein folding Protein folding is the physical process by which a protein, after Protein biosynthesis, synthesis by a ribosome as a linear chain of Amino acid, amino acids, changes from an unstable random coil into a more ordered protein tertiary structure, t ...

could not efficiently produce deep knots in protein backbones. Studies of the folding kinetics of a dimeric protein from ''

Haemophilus influenzae ''Haemophilus influenzae'' (formerly called Pfeiffer's bacillus or ''Bacillus influenzae'') is a Gram-negative, Motility, non-motile, Coccobacillus, coccobacillary, facultative anaerobic organism, facultatively anaerobic, Capnophile, capnophili ...

'' have revealed that the folding of trefoil knot proteins may depend on

proline Proline (symbol Pro or P) is an organic acid classed as a proteinogenic amino acid (used in the biosynthesis of proteins), although it does not contain the amino group but is rather a secondary amine. The secondary amine nitrogen is in the p ...

isomerization. Computational algorithms have been developed to identify knotted protein structures, both to canvas the

Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained a ...

for previously undetected natural knots and to identify knots in

protein structure prediction Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its Protein secondary structure, secondary and Protein tertiary structure, tertiary structure ...

s, where they are unlikely to accurately reproduce the native-state structure due to the rarity of knots in known proteins. Knottins are small, diverse and stable proteins with important drug design potential. They can be classified in 30 families which cover a wide range of sequences (1621 sequenced), three-dimensional structures (155 solved) and functions (> 10). Inter knottin similarity lies mainly between 20% and 40% sequence identity and 1.5 to 4 A backbone deviations although they all share a tightly knotted disulfide core. This important variability is likely to arise from the highly diverse loops which connect the successive knotted

cysteine Cysteine (; symbol Cys or C) is a semiessential proteinogenic amino acid with the chemical formula, formula . The thiol side chain in cysteine enables the formation of Disulfide, disulfide bonds, and often participates in enzymatic reactions as ...

s. The prediction of structural models for all knottin sequences would open new directions for the analysis of interaction sites and to provide a better understanding of the structural and functional organization of proteins sharing this scaffold.

Trefoil domain

Trefoil (P-type) domain is a cysteine-rich

domain A domain is a geographic area controlled by a single person or organization. Domain may also refer to: Law and human geography * Demesne, in English common law and other Medieval European contexts, lands directly managed by their holder rather ...

of approximately forty five amino-acid residues has been found in some extracellular eukaryotic proteins. It is known as either the 'P', 'trefoil' or 'TFF' domain, and contains six cysteines linked by three disulphide bonds with connectivity 1–5, 2–4, 3–6. The domain has been found in a variety of extracellular eukaryotic proteins, including protein pS2 ( TFF1) a protein secreted by the stomach mucosa; spasmolytic polypeptide (SP) ( TFF2), a protein of about 115 residues that inhibits gastrointestinal

motility Motility is the ability of an organism to move independently using metabolism, metabolic energy. This biological concept encompasses movement at various levels, from whole organisms to cells and subcellular components. Motility is observed in ...

and

gastric acid Gastric acid or stomach acid is the acidic component – hydrochloric acid – of gastric juice, produced by parietal cells in the gastric glands of the stomach lining. In humans, the pH is between one and three, much lower than most other a ...

secretion Secretion is the movement of material from one point to another, such as a secreted chemical substance from a cell or gland. In contrast, excretion is the removal of certain substances or waste products from a cell or organism. The classical mec ...

; intestinal trefoil factor (ITF) ( TFF3); ''

Xenopus laevis The African clawed frog (''Xenopus laevis''), also known as simply xenopus, African clawed toad, African claw-toed frog or the ''platanna'') is a species of African aquatic frog of the family Pipidae. Its name is derived from the short black ...

'' stomach proteins xP1 and xP4; xenopus integumentary

mucin Mucins () are a family of high molecular weight, heavily glycosylated proteins ( glycoconjugates) produced by epithelial tissues in most animals. Mucins' key characteristic is their ability to form gels; therefore they are a key component in ...

s A.1 (preprospasmolysin) and C.1, proteins which may be involved in defense against microbial infections by protecting the epithelia from the external environment; xenopus skin protein xp2 (or APEG);

Zona pellucida The ''zona pellucida'' (Latin meaning "transparent zone") is the specialized area surrounding mammalian oocytes (eggs). It is also known as an egg coat. The ''zona pellucida'' is essential for oocyte growth and fertilization. The ''zona pelluc ...

sperm-binding protein B (ZP-B); intestinal

sucrase-isomaltase Sucrase-isomaltase is a bifunctional glucosidase (sugar-digesting enzyme) located on the brush border of the small intestine, encoded by the human gene ''SI''. It is a dual-function enzyme with two GH31 domains, one serving as the isomaltase, the ...

( / ), a vertebrate membrane bound, multifunctional enzyme complex which hydrolyzes sucrose, maltose and isomaltose; and lysosomal alpha-glucosidase ().

Examples

Human gene encoding proteins containing the trefoil domain include: *

acid alpha-glucosidase Acid alpha-glucosidase, also called acid maltase, is an enzyme that helps to break down glycogen in the lysosome. It is functionally similar to glycogen debranching enzyme, but is on a different chromosome, processed differently by the cell and is ...

, MGAM, TFF1, TFF2, TFF3, and ZP4.

History

There was a web server pKNOT available to detect knots in proteins as well as to provide information on knotted proteins in the

References

External links

SCOP alpha/beta knot fold

CATH alpha/beta knot topology

Bibliography

*Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM. (2007). Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. ''BMC Bioinformatics''. 8:73 {{Protein tertiary structure Protein folds Protein tandem repeats Protein domains