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.

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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

    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

    Sulfation is the chemical reaction that entails the addition of SO3 group. In principle, many sulfations would involve reactions of sulfur trioxide (SO3). In practice, most sulfations are effected less directly. Regardless of the mechanism, the installation of a sulfate-like group on a substrate leads to substantial changes.

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Wiki: Sulfation

    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: Succinylation

    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-cysteinylation and S-sulfonation are the most common modifications in the blood and cerebrospinal fluid, which affect TTR stability and alter the propensity of TTR to form amyloid fibrils.

Reference
Pubmed: Duan G, Li Y, Ye M, Liu H, Wang N, Luo S. The Regulatory Mechanism of Transthyretin Irreversible Aggregation through Liquid-to-Solid Phase Transition. International journal of molecular sciences vol. 24,4 3729. 13 Feb. 2023, doi:10.3390/ijms24043729

    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

    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

    Redox (reduction¨Coxidation or oxidation¨Creduction) is a type of chemical reaction in which the oxidation states of a reactant change. Oxidation is the loss of electrons or an increase in the oxidation state, while reduction is the gain of electrons or a decrease in the oxidation state.

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Wiki: Oxidation

    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

    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

    Protein malonylation, a reversible post-translational modification of lysine residues, is associated with various biological functions, such as cellular regulation and pathogenesis. In proteomics, to improve our understanding of the mechanisms of malonylation at the molecular level, the identification of malonylation sites via an efficient methodology is essential. However, experimental identification of malonylated substrates via mass spectrometry is time-consuming, labor-intensive, and expensive.

Reference
Pubmed: Chung CR, Chang YP, Hsu YL, Chen S, Wu LC, Horng JT, Lee TY. Incorporating hybrid models into lysine malonylation sites prediction on mammalian and plant proteins. Sci Rep. 2020 Jun 29;10(1):10541. doi: 10.1038/s41598-020-67384-w.

    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

    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

    S-Glutathionylation is the posttranslational modification of protein cysteine residues by the addition of glutathione, the most abundant and important low-molecular-mass thiol within most cell types.

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Wiki: Glutathionylation

    Post-translational modifications (PTMs) dynamically regulate cellular processes. Lysine undergoes a range of acylations, including malonylation, succinylation (SucK) and glutarylation (GluK). These PTMs increase the size of the lysine side chain and reverse its charge from +1 to ?1 under physiological conditions, probably impacting protein structure and function. To understand the functional roles of these PTMs, homogeneously modified proteins are required for biochemical studies.

Reference
Pubmed: Weyh M, Jokisch ML, Nguyen TA, Fottner M, Lang K. Deciphering functional roles of protein succinylation and glutarylation using genetic code expansion. Nat Chem. 2024 Mar 26. doi: 10.1038/s41557-024-01500-5.

    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.

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Wiki: Dimethylation

    SUMO can be removed from its substrate, which is called deSUMOylation. Specific proteases mediate this procedure (SENP in human or Ulp1 and Ulp2 in yeast).

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Wiki: DeSUMOylation

    Deamidation is a chemical reaction in which an amide functional group in the side chain of the amino acids asparagine or glutamine is removed or converted to another functional group. Typically, asparagine is converted to aspartic acid or isoaspartic acid. Glutamine is converted to glutamic acid or pyroglutamic acid (5-oxoproline). In a protein or peptide, these reactions are important because they may alter its structure, stability or function and may lead to protein degradation. The net chemical change is the addition of a water group and removal of an ammonia group, which corresponds to a +1 (0.98402) Da mass increase. Although deamidation occurs on glutamine, glycosylated asparagine and other amides, these are negligible under typical proteolysis conditions.

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Wiki: Deamidation

    Citrullination or deimination is the conversion of the amino acid arginine in a protein into the amino acid citrulline. Citrulline is not one of the 20 standard amino acids encoded by DNA in the genetic code. Instead, it is the result of a post-translational modification. Citrullination is distinct from the formation of the free amino acid citrulline as part of the urea cycle or as a byproduct of enzymes of the nitric oxide synthase family.

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Wiki: Citrullination

    Carboxylation is a chemical reaction in which a carboxylic acid is produced by treating a substrate with carbon dioxide. The opposite reaction is decarboxylation. In chemistry, the term carbonation is sometimes used synonymously with carboxylation, especially when applied to the reaction of carbanionic reagents with CO2. More generally, carbonation usually describes the production of carbonates.

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Wiki: Carboxylation

    C-linked glycosylation is essential for the trafficking, folding and function of secretory and transmembrane proteins involved in cellular communication processes. The tryptophan C-mannosyltransferase (CMT) enzymes that install the modification attach a mannose to the first tryptophan of WxxW/C sequons in nascent polypeptide chains by an unknown mechanism.

Reference
Pubmed: Bloch JS, John A, Mao R, Mukherjee S, Boilevin J, Irobalieva RN, Darbre T, Scott NE, Reymond JL, Kossiakoff AA, Goddard-Borger ED, Locher KP. Structure, sequon recognition and mechanism of tryptophan C-mannosyltransferase. Nat Chem Biol. 2023 May;19(5):575-584. doi: 10.1038/s41589-022-01219-9.

    Lysine butyrylation (Kbu) is a novel PTM that is found in histone and nonhistone proteins8. Kbu has been identified in fungi, plants and animals9,10,11, but a global landscape of nonhistone protein Kbu modification in humans is lacking. More importantly, the writer and eraser responsible for Kbu deposition and removal in humans, respectively, have not been reported.

Reference
Pubmed: He Y, Zheng CC, Yang J, Li SJ, Xu TY, Wei X, Chen WY, Jiang ZL, Xu JJ, Zhang GG, Cheng C, Chen KS, Shi XY, Qin DJ, Liu JB, Li B. Lysine butyrylation of HSP90 regulated by KAT8 and HDAC11 confers chemoresistance. Cell Discov. 2023 Jul 18;9(1):74. doi: 10.1038/s41421-023-00570-y.

    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

    Adenylylation, more commonly known as AMPylation, is a process in which an adenosine monophosphate (AMP) molecule is covalently attached to the amino acid side chain of a protein. This covalent addition of AMP to a hydroxyl side chain of the protein is a post-translational modification. Adenylylation involves a phosphodiester bond between a hydroxyl group of the molecule undergoing adenylylation, and the phosphate group of the adenosine monophosphate nucleotide (i.e. adenylic acid). Enzymes that are capable of catalyzing this process are called AMPylators.

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Wiki: Ampylation

    Mycobacteria assemble a complex cell wall with cross-linked peptidoglycan (PG) which plays an essential role in maintenance of cell wall integrity and tolerance to osmotic pressure. We previously demonstrated that various hydrolytic enzymes are required to remodel PG during essential processes such as cell elongation and septal hydrolysis. Here, we explore the chemistry associated with PG cross-linking, specifically the requirement for amidation of the D-glutamate residue found in PG precursors.

Reference
Pubmed: Shaku MT, Ocius KL, Apostolos AJ, Pires MM, VanNieuwenhze MS, Dhar N, Kana BD. Amidation of glutamate residues in mycobacterial peptidoglycan is essential for cell wall cross-linking. Front Cell Infect Microbiol. 2023 Aug 24;13:1205829. doi: 10.3389/fcimb.2023.1205829.

    ADP-ribosylation is the addition of one or more ADP-ribose moieties to a protein. It is a reversible post-translational modification that is involved in many cellular processes, including cell signaling, DNA repair, gene regulation and apoptosis. Improper ADP-ribosylation has been implicated in some forms of cancer. It is also the basis for the toxicity of bacterial compounds such as cholera toxin, diphtheria toxin, and others.

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Wiki: ADP-ribosylation

    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