Ubiquitination (also known as ubiquitylation) is an enzymatic, post-translational modification (PTM) process in which a ubiquitin protein is attached to a substrate protein. This process most commonly binds the last amino acid of ubiquitin (glycine 76) to a lysine residue on the substrate. An isopeptide bond is formed between the carboxylic acid group of the ubiquitin's glycine and the epsilon amino group of the substrate's lysine. Cases are known in which the amine group of a protein's N-terminus is used for ubiquitination, rather than a lysine residue. In a few rare cases nonlysine residues have been identified as ubiquitination targets, such as cysteine, threonine and serine. The end result of this process is the addition of one ubiquitin molecule (monoubiquitination) or a chain of ubiquitin molecules (polyubiquitination) to the substrate protein.

Reference
Wiki: Ubiquitination

    Tyrosine phosphorylation is the addition of a phosphate (PO43?) group to the amino acid tyrosine on a protein. It is one of the main types of protein phosphorylation. This transfer is made possible through enzymes called tyrosine kinases. Tyrosine phosphorylation is a key step in signal transduction and the regulation of enzymatic activity.

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Wiki: Tyrosine phosphorylation

    In particular, dimethylation and trimethylation of lysine side chains in proteins increase both hydrophobicity and steric bulk and can affect protein¨Cprotein interactions if they are in an interacting surface.

Reference
Wiki: Trimethylation

    Protein phosphorylation is a post-translational modification of proteins in which a serine, a threonine or a tyrosine residue is phosphorylated by a protein kinase by the addition of a covalently bound phosphate group. Regulation of proteins by phosphorylation is one of the most common modes of regulation of protein function, and is often termed "phosphoregulation". In almost all cases of phosphoregulation, the protein switches between a phosphorylated and an unphosphorylated form, and one of these two is an active form, while the other one is an inactive form. A serine/threonine protein kinase is a kinase enzyme that phosphorylates the OH group of serine or threonine (which have similar sidechains). At least 125 of the 500+ human protein kinases are serine/threonine kinases (STK). Serine/Threonine Kinase receptors play a role in the regulation of cell proliferation, programmed cell death (apoptosis), cell differentiation, and embryonic development.

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Wiki: Threonine phosphorylation

    SUMO proteins are similar to ubiquitin, and SUMOylation is directed by an enzymatic cascade analogous to that involved in ubiquitination. In contrast to ubiquitin, SUMO is not used to tag proteins for degradation. Mature SUMO is produced when the last four amino acids of the C-terminus have been cleaved off to allow formation of an isopeptide bond between the C-terminal glycine residue of SUMO and an acceptor lysine on the target protein.

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Wiki: SUMOylation

    Serotonylation is a receptor independent signaling mechanism by which serotonin activates intracellular processes by creating long lasting covalent bonds upon proteins. It occurs through the modification of proteins by the attachment of serotonin on their glutamine residues. This happens through the enzyme transglutaminase and the creation of glutamyl-amide bonds. This process occurs following serotonin transportation into the cell rather on plasma membranes as with the brief interactions that serotonin has when it activates 5-HT receptors.

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Wiki: Serotonylation

    Protein phosphorylation is a reversible post-translational modification of proteins in which an amino acid residue is phosphorylated by a protein kinase by the addition of a covalently bound phosphate group. Phosphorylation alters the structural conformation of a protein, causing it to become activated, deactivated, or otherwise modifying its function.[1] Approximately 13,000 human proteins have sites that are phosphorylated.

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Wiki: Serine phosphorylation

    S-palmitoylation is generally done by proteins with the DHHC domain. Exceptions exist in non-enzymatic reactions. Acyl-protein thioesterase (APT) catalyses the reverse reaction. Other acyl groups such as stearate (C18:0) or oleate (C18:1) are also frequently accepted, more so in plant and viral proteins, making S-acylation a more useful name.

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Wiki: S-palmitoylation

    In biochemistry, S-nitrosylation is the covalent attachment of a nitric oxide group (?NO) to a cysteine thiol within a protein to form an S-nitrosothiol (SNO). S-Nitrosylation has diverse regulatory roles in bacteria, yeast and plants and in all mammalian cells. It thus operates as a fundamental mechanism for cellular signaling across phylogeny and accounts for the large part of NO bioactivity.

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Wiki: S-Nitrosylation

    Polyubiquitination is the formation of a ubiquitin chain on a single lysine residue on the substrate protein. Following addition of a single ubiquitin moiety to a protein substrate, further ubiquitin molecules can be added to the first, yielding a polyubiquitin chain. These chains are made by linking the glycine residue of a ubiquitin molecule to a lysine of ubiquitin bound to a substrate. Ubiquitin has seven lysine residues and an N-terminus that may serve as points of ubiquitination; they are K6, K11, K27, K29, K33, K48, and K63. Lysine 48-linked chains were the first identified and are the best-characterised type of ubiquitin chain. K63 chains have also been well-characterised, whereas the function of other lysine chains, mixed chains, branched chains, N-terminal linear chains, and heterologous chains (mixtures of ubiquitin and other ubiquitin-like proteins) remains more unclear.

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Wiki: Polyubiquitination

    In biochemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology. Protein phosphorylation often activates (or deactivates) many enzymes.

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Wiki: Phosphorylation

    Palmitoylation is the covalent attachment of fatty acids, such as palmitic acid, to cysteine (S-palmitoylation) and less frequently to serine and threonine (O-palmitoylation) residues of proteins, which are typically membrane proteins. The precise function of palmitoylation depends on the particular protein being considered. Palmitoylation enhances the hydrophobicity of proteins and contributes to their membrane association. Palmitoylation also appears to play a significant role in subcellular trafficking of proteins between membrane compartments, as well as in modulating protein¨Cprotein interactions. In contrast to prenylation and myristoylation, palmitoylation is usually reversible (because the bond between palmitic acid and protein is often a thioester bond). The reverse reaction in mammalian cells is catalyzed by acyl-protein thioesterases (APTs) in the cytosol and palmitoyl protein thioesterases in lysosomes. Because palmitoylation is a dynamic, post-translational process, it is believed to be employed by the cell to alter the subcellular localization, protein¨Cprotein interactions, or binding capacities of a protein.

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Wiki: Palmitoylation

    O-linked glycosylation is the attachment of a sugar molecule to the oxygen atom of serine (Ser) or threonine (Thr) residues in a protein. O-glycosylation is a post-translational modification that occurs after the protein has been synthesised. In eukaryotes, it occurs in the endoplasmic reticulum, Golgi apparatus and occasionally in the cytoplasm; in prokaryotes, it occurs in the cytoplasm.Several different sugars can be added to the serine or threonine, and they affect the protein in different ways by changing protein stability and regulating protein activity. O-glycans, which are the sugars added to the serine or threonine, have numerous functions throughout the body, including trafficking of cells in the immune system, allowing recognition of foreign material, controlling cell metabolism and providing cartilage and tendon flexibility.Because of the many functions they have, changes in O-glycosylation are important in many diseases including cancer, diabetes and Alzheimer's. O-glycosylation occurs in all domains of life, including eukaryotes, archaea and a number of pathogenic bacteria including Burkholderia cenocepacia,Neisseria gonorrhoeae and Acinetobacter baumannii.

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Wiki: O-linked glycosylation

    In organic chemistry, nitration is a general class of chemical processes for the introduction of a nitro group (?NO2) into an organic compound. The term also is applied incorrectly to the different process of forming nitrate esters (?ONO2) between alcohols and nitric acid (as occurs in the synthesis of nitroglycerin). The difference between the resulting molecular structures of nitro compounds and nitrates (NO?3) is that the nitrogen atom in nitro compounds is directly bonded to a non-oxygen atom (typically carbon or another nitrogen atom), whereas in nitrate esters (also called organic nitrates), the nitrogen is bonded to an oxygen atom that in turn usually is bonded to a carbon atom (nitrito group).

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Wiki: Nitration

    Neddylation (also NEDDylation) is the process by which the ubiquitin-like protein NEDD8 is conjugated to its target proteins. This process is analogous to ubiquitination, although it relies on its own E1 and E2 enzymes. No NEDD8-specific E3 has yet been identified and it is possible that the Neddylation system relies on E3 ligases with dual specificity.

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Wiki: Neddylation

    Protein N-myristoylation is an important fatty acylation catalyzed by N-myristoyltransferases (NMTs), which are ubiquitous enzymes in eukaryotes. Specifically, attachment of a myristoyl group is vital for proteins participating in various biological functions, including signal transduction, cellular localization, and oncogenesis. Recent studies have revealed unexpected mechanisms indicating that protein N-myristoylation is involved in host defense against microbial and viral infections.

Reference
Pubmed: Wang B, Dai T, Sun W, Wei Y, Ren J, Zhang L, Zhang M, Zhou F. Protein N-myristoylation: functions and mechanisms in control of innate immunity. Cell Mol Immunol. 2021 Apr;18(4):878-888. doi: 10.1038/s41423-021-00663-2.

    N-linked glycosylation, is the attachment of an oligosaccharide, a carbohydrate consisting of several sugar molecules, sometimes also referred to as glycan, to a nitrogen atom (the amide nitrogen of an asparagine (Asn) residue of a protein), in a process called N-glycosylation, studied in biochemistry. The resulting protein is called an N-linked glycan, or simply an N-glycan.

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Wiki: N-linked glycosylation

    Monoubiquitination is the addition of one ubiquitin molecule to one substrate protein residue. Multi-monoubiquitination is the addition of one ubiquitin molecule to multiple substrate residues. The monoubiquitination of a protein can have different effects to the polyubiquitination of the same protein. The addition of a single ubiquitin molecule is thought to be required prior to the formation of polyubiquitin chains. Monoubiquitination affects cellular processes such as membrane trafficking, endocytosis and viral budding.

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Wiki: Monoubiquitination

    Methylation, in the chemical sciences, is the addition of a methyl group on a substrate, or the substitution of an atom (or group) by a methyl group. Methylation is a form of alkylation, with a methyl group replacing a hydrogen atom. These terms are commonly used in chemistry, biochemistry, soil science, and biology. In biological systems, methylation is catalyzed by enzymes; such methylation can be involved in modification of heavy metals, regulation of gene expression, regulation of protein function, and RNA processing. In vitro methylation of tissue samples is also a way to reduce some histological staining artifacts. The reverse of methylation is demethylation.

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Wiki: Methylation

    In chemistry, sulfoxidation refers to two distinct reactions.In one meaning, sulfoxidation refers to the reaction of alkanes with a mixture of sulfur dioxide and oxygen. This reaction is employed industrially to produce alkyl sulfonic acids, which are used as surfactants. The reaction requires UV-radiation. The reaction favors secondary positions in accord with its free-radical mechanism. Mixtures are produced. Semiconductor-sensitized variants have been reported. Sulfoxidation can also refer to the oxidation of a thioether to a sulfoxide. A typical source of "O" is hydrogen peroxide.

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Wiki: Methionine sulfoxidation

    Protein lysine methylation, is a PTM involving the transfer of one, two or three methyl groups to the epsilon - amine of a lysine side chain. Lysine methylation represents a complex and often elusive PTM that has nonetheless the potential to alter the function of the modified protein. lysine methylation has been observed in both nuclear and cytoplasmic proteins and is now considered a prevalent modification in eukaryotes, prokaryotes and archaea. Two groups of enzymes, both using S - adenosyl - L - methionine (SAM) as a methyl donor, catalyze the addition of a methyl group to the epsilon - amine group of a lysine side chain. The first type of protein lysine methyltransferase regroups the enzymes containing a catalytic SET domain and the second class of PKMTs, the seven beta - strand methyltransferases (class I methyltransferases), belongs to an extended superfamily of methyltransferases found throughout eukaryotes, prokaryotes and archaea.

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Wiki: Lysine methylation

    Methylation on leucine was first observed in 1999, the carboxyl methyltransferase, which is claimed to exclusively methylate the carboxyl group of the C-terminal leucine residue of the catalytic subunit of protein phosphatase 2A (Leu(309)), was purified from porcine brain. The cDNA encoding the human homologue was also cloned. The cDNA of this gene encodes for a protein of 334 amino acids with a calculated M(r) of 38 305 and a predicted pI of 5.72. Database screening reveals the presence of this protein in diverse phyla. Recent studies revealed that PP2A methylation is associated with "PP2A" dysfunction which has been linked to tau hyperphosphorylation, amyloidogenesis and synaptic deficits that are pathological hallmarks of this neurodegenerative disorder.

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Wiki: Leucine methylation

    Histone lactylation is the addition of a lactyl group to lysine residues in histone proteins, derived from the metabolite lactate.

Reference
Pubmed: Izzo LT, Wellen KE. Histone lactylation links metabolism and gene regulation. Nature. 2019 Oct;574(7779):492-493. doi: 10.1038/d41586-019-03122-1.

    Protein hydroxylation is a post-translational modification catalyzed by 2-oxoglutarate-dependent dioxygenases. The hydroxylation modification can take place on various amino acids, including but not limited to proline, lysine, asparagine, aspartate and histidine.

Reference
Pubmed: Zurlo G, Guo J, Takada M, Wei W, Zhang Q. New Insights into Protein Hydroxylation and Its Important Role in Human Diseases. Biochim Biophys Acta. 2016 Dec;1866(2):208-220. doi: 10.1016/j.bbcan.2016.09.004.

    Glycosylation is the reaction in which a carbohydrate (or 'glycan'), i.e. a glycosyl donor, is attached to a hydroxyl or other functional group of another molecule (a glycosyl acceptor) in order to form a glycoconjugate. In biology (but not always in chemistry), glycosylation usually refers to an enzyme-catalysed reaction, whereas glycation (also 'non-enzymatic glycation' and 'non-enzymatic glycosylation') may refer to a non-enzymatic reaction.

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Wiki: Glycosylation

    Prenylation (also known as isoprenylation or lipidation) is the addition of hydrophobic molecules to a protein or a biomolecule. It is usually assumed that prenyl groups (3-methylbut-2-en-1-yl) facilitate attachment to cell membranes, similar to lipid anchors like the GPI anchor, though direct evidence of this has not been observed. Prenyl groups (also called isoprenyl groups, having one hydrogen atom more than isoprene) have been shown to be important for protein¨Cprotein binding through specialized prenyl-binding domains.Farnesylation is a type of prenylation, a post-translational modification of proteins by which an isoprenyl group is added to a cysteine residue. It is an important process to mediate protein¨Cprotein interactions and protein¨Cmembrane interactions.

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Wiki: Farnesylation

    In particular, dimethylation and trimethylation of lysine side chains in proteins increase both hydrophobicity and steric bulk and can affect protein¨Cprotein interactions if they are in an interacting surface.

Reference
Wiki: Dimethylation

    Deubiquitinating enzymes (deubiquitinases; DUBs) oppose the role of ubiquitylation by removing ubiquitin from substrate proteins. They are cysteine proteases that cleave the amide bond between the two proteins. They are highly specific, as are the E3 ligases that attach the ubiquitin, with only a few substrates per enzyme. They can cleave both isopeptide (between ubiquitin and lysine) and peptide bonds (between ubiquitin and the N-terminus). In addition to removing ubiquitin from substrate proteins, DUBs have many other roles within the cell. Ubiquitin is either expressed as multiple copies joined in a chain (polyubiquitin) or attached to ribosomal subunits. DUBs cleave these proteins to produce active ubiquitin. They also recycle ubiquitin that has been bound to small nucleophilic molecules during the ubiquitylation process. Monoubiquitin is formed by DUBs that cleave ubiquitin from free polyubiquitin chains that have been previously removed from proteins.

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Wiki: Deubiquitination

    In biochemistry, succinylation is a posttranslational modification where a succinyl group (?CO?CH2?CH2?CO2H) is added to a lysine residue of a protein molecule. This modification is found in many proteins, including histones. The potential role of succinylation is under investigation, but as addition of succinyl group changes lysine's charge from +1 to ?1 (at physiological pH) and introduces a relatively large structural moiety (100 Da), bigger than acetylation (42 Da) or methylation (14 Da), it is expected to lead to more significant changes in protein structure and function. By analogy to acetylation, it has been suggested that succinyl-CoA is the cofactor of enzyme-mediated lysine succinylation.

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Wiki: Desuccinylation

    In biochemistry, dephosphorylation is the removal of a phosphate (PO43?) group from an organic compound by hydrolysis. It is a reversible post-translational modification. Dephosphorylation and its counterpart, phosphorylation, activate and deactivate enzymes by detaching or attaching phosphoric esters and anhydrides. A notable occurrence of dephosphorylation is the conversion of ATP to ADP and inorganic phosphate. Dephosphorylation employs a type of hydrolytic enzyme, or hydrolase, which cleaves ester bonds. The prominent hydrolase subclass used in dephosphorylation is phosphatase, which removes phosphate groups by hydrolysing phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxyl (-OH) group. The reversible phosphorylation-dephosphorylation reaction occurs in every physiological process, making proper function of protein phosphatases necessary for organism viability. Because protein dephosphorylation is a key process involved in cell signalling, protein phosphatases are implicated in conditions such as cardiac disease, diabetes, and Alzheimer's disease.

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Wiki: Dephosphorylation

    In chemistry, acetylation is an organic esterification reaction with acetic acid. It introduces an acetyl group into a chemical compound. Such compounds are termed acetate esters or simply acetates. Deacetylation is the opposite reaction, the removal of an acetyl group from a chemical compound.

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Wiki: Deacetylation

    Cysteine carboxyethylation is an in vivo protein modification induced by the metabolite 3-HPA, which is commonly released from gut microbes. Carboxyethylated ITGA2B then induces autoantibody production and autoimmune response in AS. Our work provides a systematic workflow to identify differentially modified proteins that are important for neoantigen production in immune disorders. This approach furthers our understanding of AS pathogenesis and may aid in the development of neoantigen-based diagnosis and treatment for AS and other autoimmune diseases.

Reference
Pubmed: Zhai Y, Chen L, Zhao Q, Zheng ZH, Chen ZN, Bian H, Yang X, Lu HY, Lin P, Chen X, Chen R, Sun HY, Fan LN, Zhang K, Wang B, Sun XX, Feng Z, Zhu YM, Zhou JS, Chen SR, Zhang T, Chen SY, Chen JJ, Zhang K, Wang Y, Chang Y, Zhang R, Zhang B, Wang LJ, Li XM, He Q, Yang XM, Nan G, Xie RH, Yang L, Yang JH, Zhu P. Cysteine carboxyethylation generates neoantigens to induce HLA-restricted autoimmunity. Science. 2023 Mar 17;379(6637):eabg2482. doi: 10.1126/science.abg2482.

    Autophosphorylation is a type of post-translational modification of proteins. It is generally defined as the phosphorylation of the kinase by itself. In eukaryotes, this process occurs by the addition of a phosphate group to serine, threonine or tyrosine residues within protein kinases, normally to regulate the catalytic activity. Autophosphorylation may occur when a kinases' own active site catalyzes the phosphorylation reaction (cis autophosphorylation), or when another kinase of the same type provides the active site that carries out the chemistry (trans autophosphorylation). The latter often occurs when kinase molecules dimerize. In general, the phosphate groups introduced are gamma phosphates from nucleoside triphosphates, most commonly ATP.

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Wiki: Autophosphorylation

    Arginine methylation is a prevalent post-translational modification found on both nuclear and cytoplasmic proteins. The methylation of arginine residues is catalyzed by the protein arginine Nmethyltransferase (PRMT) family of enzymes. Proteins that are arginine methylated are involved in a number of different cellular processes, including transcriptional regulation, RNA metabolism and DNA damage repair (Bedford and Richard, 2005). Most PRMTs methylate glycine- and arginine-rich patches (GAR motifs) within their substrates.

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Wiki: Arginine methylation

    In chemistry, acetylation is an organic esterification reaction with acetic acid. It introduces an acetyl group into a chemical compound. Such compounds are termed acetate esters or simply acetates. Deacetylation is the opposite reaction, the removal of an acetyl group from a chemical compound.

Reference
Wiki: Acetylation