Peptide

For peptides used medically, see Peptide therapeutics.

"Peptides" redirects here. For the journal, see Peptides (journal).

Drosomycin, an example of a peptide

Peptides are short chains of amino acids linked by peptide bonds. ^{[1] [2]} A polypeptide is a longer, continuous, unbranched peptide chain. ^[3] Polypeptides that have a molecular mass of 10,000 Da or more are called proteins. ^[4] Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. ^[5]

Amino acids comprise peptides as residues. ^[6] Peptides are usually "linear" with an N-terminal (amine group) and C-terminal (carboxyl group) residue at the ends. Cyclic peptides are a distinct class.

Classification

Peptides have been classified according to their sources and functions. ^[7] Some groups of peptides include plant peptides, bacterial/antibiotic peptides, fungal peptides, invertebrate peptides, amphibian/skin peptides, venom peptides, cancer/anticancer peptides, vaccine peptides, immune/inflammatory peptides, brain peptides, endocrine peptides, ingestive peptides, gastrointestinal peptides, cardiovascular peptides, renal peptides, respiratory peptides, opioid peptides, neurotrophic peptides, and blood–brain peptides. ^[8]

Some ribosomal peptides are subject to proteolysis. These function, typically in higher organisms, as hormones and signaling molecules. Some microbes produce peptides as antibiotics, such as microcins and bacteriocins. ^[9]

Peptides frequently have post-translational modifications such as phosphorylation, hydroxylation, sulfonation, palmitoylation, glycosylation, and disulfide formation. In general, peptides are linear, although lariat structures have been observed. ^[10] More exotic manipulations do occur, such as racemization of L-amino acids to D-amino acids in platypus venom. ^[11]

Nonribosomal peptides are assembled by enzymes, not the ribosome. A common non-ribosomal peptide is glutathione, a component of the antioxidant defenses of most aerobic organisms. ^[12] Other nonribosomal peptides are most common in unicellular organisms, plants, and fungi and are synthesized by modular enzyme complexes called nonribosomal peptide synthetases. ^[13]

These complexes are often laid out in a similar fashion, and they can contain many different modules to perform a diverse set of chemical manipulations on the developing product. ^[14] These peptides are often cyclic and can have highly complex cyclic structures, although linear nonribosomal peptides are also common. Since the system is closely related to the machinery for building fatty acids and polyketides, hybrid compounds are often found. The presence of oxazoles or thiazoles often indicates that the compound was synthesized in this fashion. ^[15]

Peptones are derived from animal milk or meat digested by proteolysis. ^[16] In addition to containing small peptides, the resulting material includes fats, metals, salts, vitamins, and many other biological compounds. Peptones are used in nutrient media for growing bacteria and fungi. ^[17]

Peptide fragments refer to fragments of proteins that are used to identify or quantify the source protein. ^[18] Often these are the products of enzymatic degradation performed in the laboratory on a controlled sample, but can also be forensic or paleontological samples that have been degraded by natural effects. ^{[19] [20]}

Chemical synthesis

Main article: Peptide synthesis

Solid-phase peptide synthesis on a rink amide resin using Fmoc-α-amine-protected amino acid

Protein–peptide interactions

Example of a protein (orange) and peptide (green) interaction. Obtained from Propedia: a peptide-protein interactions database.

Peptides can perform interactions with proteins and other macromolecules. They are responsible for numerous important functions in human cells, such as cell signaling, and act as immune modulators. ^[22] Indeed, studies have reported that 15-40% of all protein–protein interactions in human cells are mediated by peptides. ^[23] Additionally, it is estimated that at least 10% of the pharmaceutical market is based on peptide products. ^[22]

Applications of machine learning in peptide prediction

Machine learning and deep learning methods are increasingly used to classify, screen and design peptides from sequence- or structure-derived data, particularly when experimental screening is costly, slow or difficult to scale. ^{[24] [25] [26]} A typical computational pipeline includes the preparation of benchmark datasets, conversion of peptide sequences or structures into numerical representations, model training, and performance evaluation. ^[26] Common representations include amino acid composition, dipeptide composition, pseudo-amino acid composition, physicochemical descriptors, substitution matrices, molecular fingerprints and learned embeddings from protein or peptide language models. ^{[26] [27]}

These approaches have been applied to several peptide classes, including antimicrobial peptides, cell-penetrating peptides, blood–brain barrier-penetrating peptides, anticancer peptides, antiviral peptides and other functional peptide groups. ^[26] For example, BrainPepPass uses supervised dimensionality reduction and extreme gradient boosting to predict blood–brain barrier-penetrating peptides from molecular descriptors of natural and chemically modified peptides. ^[28] For cell-penetrating peptides, ConvBoost-CPP combines a convolutional neural network with XGBoost and uses descriptors such as nitrogen, oxygen and Eisenberg hydrophobicity; in the reported dataset, this descriptor combination increased independent-test accuracy from 82.6% to 91.3%. ^[29] In antimicrobial peptide research, artificial intelligence methods have expanded from classical machine-learning classifiers to large language models, graph neural networks, diffusion models and structure-guided design strategies. ^[25] Important limitations include small or biased datasets, inconsistent benchmarking protocols, uncertain negative samples, and limited interpretability of some predictive models. ^{[26] [25]}

Molecular properties and chemical space of peptides

The chemical space of peptides can be described as a multidimensional descriptor or fingerprint space in which distances between molecules approximate chemical or functional similarity. ^{[30] [31]} Peptide chemical space may be mapped from amino acid sequences, three-dimensional molecular structures, or both. Molecular properties used for this purpose include molecular weight, logP, logD, topological polar surface area, hydrogen-bond donors and acceptors, nitrogen and oxygen atom counts, charge, hydrophobicity, secondary-structure-related features and molecular fingerprints. ^{[28] [31]} Dimensionality-reduction methods such as principal component analysis, t-SNE, UMAP and supervised manifold learning, often combined with clustering or similarity networks, are used to visualize peptide libraries and identify groups with related properties or activities. ^{[32] [33] [34] [31]}

Peptides differ from many small molecules because their residue sequence, amide backbone, conformational flexibility and chemical modifications jointly influence bioactivity, bioavailability and membrane permeability. ^[31] Sequence-based notations, including FASTA, HELM and BILN, can encode canonical and modified peptides for computational analysis, whereas atom-based strings and graph representations can capture connectivity, stereochemistry and structural constraints. ^{[31] [27]} Chemical modifications such as cyclization, N-methylation, incorporation of non-natural amino acids and site-specific modifications can shift a peptide's position in chemical space and alter properties such as solubility, stability, permeability and target affinity. ^{[31] [27]} Because unrelated peptide classes may partially overlap in descriptor space, chemical-space analysis is also used to investigate shared regions of bioactivity and to support virtual screening, repurposing and peptide design. ^[31]

Example families

The peptide families in this section are ribosomal peptides, usually with hormonal activity. All of these peptides are synthesized by cells as longer "propeptides" or "proproteins" and truncated prior to exiting the cell. They are released into the bloodstream where they perform their signaling functions. ^[35]

Antimicrobial peptides

• Magainin family
• Cecropin family
• Cathelicidin family
• Defensin family

Tachykinin peptides

Main article: Tachykinin peptides

• Substance P
• Kassinin
• Neurokinin A
• Eledoisin
• Neurokinin B

Vasoactive intestinal peptides

Main article: Secretin family

• VIP (Vasoactive Intestinal Peptide; PHM27)
• PACAP Pituitary Adenylate Cyclase Activating Peptide
• Peptide PHI 27 (Peptide Histidine Isoleucine 27)
• GHRH 1-24 (Growth Hormone Releasing Hormone 1-24)
• Glucagon
• Secretin

Pancreatic polypeptide-related peptides

• NPY (NeuroPeptide Y)
• PYY (Peptide YY)
• APP (Avian Pancreatic Polypeptide)
• PPY (Pancreatic PolYpeptide)

Opioid peptides

Main article: Opioid peptide

• Proopiomelanocortin (POMC) peptides
• Enkephalin pentapeptides
• Prodynorphin peptides

Calcitonin peptides

• Calcitonin
• Amylin
• AGG01

Self-assembling peptides

• Aromatic short peptides ^{[36] [37]}
• Biomimetic peptides ^[38]
• Peptide amphiphiles ^{[39] [40] [41] [42]}
• Peptide dendrimers ^[43]

Other peptides

• B-type Natriuretic Peptide (BNP) – produced in the myocardium and useful in medical diagnosis
• Lactotripeptides – Lactotripeptides might reduce blood pressure, ^{[44] [45] [46]} although the evidence is mixed. ^[47]
• Peptidic components from traditional Chinese medicine Colla Corii Asini in hematopoiesis. ^[48]
• Jelleine – produced from royal jelly of honey bees.

Terminology

Length

Several terms related to peptides have no strict length definitions, and there is often overlap in their usage:^{[ citation needed ]}

• A polypeptide is a single linear chain of many amino acids (any length), held together by amide bonds.
• A protein consists of one or more polypeptides (more than about 50 amino acids long).
• An oligopeptide consists of only a few amino acids (between two and twenty).

Number of amino acids

A tripeptide (example Val-Gly-Ala) with
green marked amino end (L-valine) and
blue marked carboxyl end (L-alanine)

Peptides and proteins are often described by the number of amino acids in their chain, e.g. a protein with 158 amino acids may be described as a "158 amino-acid-long protein". Peptides of specific shorter lengths are named using IUPAC numerical multiplier prefixes:

• A monopeptide has one amino acid (not alone but combined with (an)other type(s) of molecule(s)).
• A dipeptide has two amino acids.
• A tripeptide has three amino acids.
• A tetrapeptide has four amino acids.
• A pentapeptide has five amino acids. (e.g., enkephalin).
• A hexapeptide has six amino acids. (e.g., angiotensin IV).
• A heptapeptide has seven amino acids. (e.g., spinorphin).
• An octapeptide has eight amino acids (e.g., angiotensin II).
• A nonapeptide has nine amino acids (e.g., oxytocin).
• A decapeptide has ten amino acids (e.g., gonadotropin-releasing hormone and angiotensin I).
• A undecapeptide has eleven amino acids (e.g., substance P).

The same words are also used to describe a group of residues in a larger polypeptide (e.g., RGD motif).

Function

• A neuropeptide is a peptide that is active in association with neural tissue.
• A lipopeptide is a peptide that has a lipid connected to it, and pepducins are lipopeptides that interact with GPCRs.
• A peptide hormone is a peptide that acts as a hormone.
• A proteose is a mixture of peptides produced by the hydrolysis of proteins. The term is somewhat archaic.
• A peptidergic agent (or drug) is a chemical which functions to directly modulate the peptide systems in the body or brain. An example is opioidergics, which are neuropeptidergics.
• A cell-penetrating peptide is a peptide able to penetrate the cell membrane.

See also

• Acetyl hexapeptide-3
• Beefy meaty peptide
• Collagen hybridizing peptide, a short peptide that can bind to denatured collagen in tissues
• Bis-peptide
• CLE peptide
• D-peptide
• Epidermal growth factor
• Journal of Peptide Science
• Lactotripeptides
• Micropeptide
• Neuropeptide
• Palmitoyl pentapeptide-4
• Pancreatic hormone
• peptide spectral library
• Peptide synthesis
• Peptidomimetics (such as peptoids and β-peptides) to peptides, but with different properties.
• Protein tag, describing addition of peptide sequences to enable protein isolation or detection
• Replikins
• Ribosome
• Translation (biology)

References

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External links

• Quotations related to Peptide at Wikiquote