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Post-translational modification

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Post-translational modification
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{{short description|Chemical changes in proteins following their translation from mRNA}}File:Insulin path.svg|right|thumb|upright=1.35|Post-translational modification of insulin. At the top, the ribosome translates a mRNA sequence into a protein, insulin, and passes the protein through the endoplasmic reticulum, where it is cut, folded, and held in shape by disulfide (-S-S-) bonds. Then the protein passes through the golgi apparatusgolgi apparatusIn molecular biology, post-translational modification (PTM) is the covalent process of changing proteins following protein biosynthesis. PTMs may involve enzymes or occur spontaneously. Proteins are created by ribosomes, which translate mRNA into polypeptide chains, which may then change to form the mature protein product. PTMs are important components in cell signalling, as for example when prohormones are converted to hormones.Post-translational modifications can occur on the amino acid side chains or at the protein's C- or N- termini.BOOK, Pratt, Charlotte W., Charlotte W. Pratt, Judith G. Voet, Donald Voet, Judith G., Voet, Voet, Donald,weblink Fundamentals of Biochemistry: Life at the Molecular Level, 2006, Wiley, Hoboken, NJ, 1280801548, 9780471214953, 13 July 2012,weblink 2nd, They can expand the chemical set of the 22 amino acids by changing an existing functional group or adding a new one such as phosphate. Phosphorylation is highly effective for controlling the enzyme activity and is the most common change after translation. JOURNAL, Khoury GA, Baliban RC, Floudas CA, Christodoulos Floudas, September 2011, Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database, Scientific Reports, 1, 90, 2011NatSR...1E..90K, 10.1038/srep00090, 3201773, 22034591, Many eukaryotic and prokaryotic proteins also have carbohydrate molecules attached to them in a process called glycosylation, which can promote protein folding and improve stability as well as serving regulatory functions. Attachment of lipid molecules, known as lipidation, often targets a protein or part of a protein attached to the cell membrane.Other forms of post-translational modification consist of cleaving peptide bonds, as in processing a propeptide to a mature form or removing the initiator methionine residue. The formation of disulfide bonds from cysteine residues may also be referred to as a post-translational modification.BOOK, Lodish H, Berk A, Zipursky SL, etal, 17.6, Post-Translational Modifications and Quality Control in the Rough ER, Molecular Cell Biology, 2000, W. H. Freeman, New York, 978-0-7167-3136-8, 4th,weblinkweblink For instance, the peptide hormone insulin is cut twice after disulfide bonds are formed, and a propeptide is removed from the middle of the chain; the resulting protein consists of two polypeptide chains connected by disulfide bonds.Some types of post-translational modification are consequences of oxidative stress. Carbonylation is one example that targets the modified protein for degradation and can result in the formation of protein aggregates.JOURNAL, Dalle-Donne I, Aldini G, Carini M, Colombo R, Rossi R, Milzani A, 2006, Protein carbonylation, cellular dysfunction, and disease progression, Journal of Cellular and Molecular Medicine, 10, 2, 389–406, 10.1111/j.1582-4934.2006.tb00407.x, 3933129, 16796807, JOURNAL, Grimsrud PA, Xie H, Griffin TJ, Bernlohr DA, August 2008, Oxidative stress and covalent modification of protein with bioactive aldehydes, The Journal of Biological Chemistry, 283, 32, 21837–41, 10.1074/jbc.R700019200, 2494933, 18445586, free, Specific amino acid modifications can be used as biomarkers indicating oxidative damage.JOURNAL, Gianazza E, Crawford J, Miller I, Detecting oxidative post-translational modifications in proteins, Amino Acids, 33, 1, 51–6, July 2007, 17021655, 10.1007/s00726-006-0410-2, 23819101, Sites that often undergo post-translational modification are those that have a functional group that can serve as a nucleophile in the reaction: the hydroxyl groups of serine, threonine, and tyrosine; the amine forms of lysine, arginine, and histidine; the thiolate anion of cysteine; the carboxylates of aspartate and glutamate; and the N- and C-termini. In addition, although the amide of asparagine is a weak nucleophile, it can serve as an attachment point for glycans. Rarer modifications can occur at oxidized methionines and at some methylene groups in side chains.BOOK, Walsh, Christopher T., Posttranslational modification of proteins : expanding nature's inventory, 2006, Roberts and Co. Publ., Englewood, 9780974707730, {{rp|12–14}}Post-translational modification of proteins can be experimentally detected by a variety of techniques, including mass spectrometry, Eastern blotting, and Western blotting. Additional methods are provided in the #External links section.

PTMs involving addition of functional groups

Addition by an enzyme in vivo

Hydrophobic groups for membrane localization

Cofactors for enhanced enzymatic activity

Modifications of translation factors

  • diphthamide formation (on a histidine found in eEF2)
  • ethanolamine phosphoglycerol attachment (on glutamate found in eEF1α)JOURNAL, Whiteheart SW, Shenbagamurthi P, Chen L, Cotter RJ, Hart GW, Murine elongation factor 1 alpha (EF-1 alpha) is posttranslationally modified by novel amide-linked ethanolamine-phosphoglycerol moieties. Addition of ethanolamine-phosphoglycerol to specific glutamic acid residues on EF-1 alpha, The Journal of Biological Chemistry, 264, 24, 14334–41, August 1989, 10.1016/S0021-9258(18)71682-7, 2569467, etal, free,
  • hypusine formation (on conserved lysine of eIF5A (eukaryotic) and aIF5A (archaeal))
  • beta-Lysine addition on a conserved lysine of the elongation factor P (EFP) in most bacteria.JOURNAL, Roy H, Zou SB, Bullwinkle TJ, Wolfe BS, Gilreath MS, Forsyth CJ, Navarre WW, Ibba M, The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-β-lysine, Nature Chemical Biology, 7, 10, 667–9, August 2011, 21841797, 3177975, 10.1038/nchembio.632, EFP is a homolog to eIF5A (eukaryotic) and aIF5A (archaeal) (see above).

Smaller chemical groups

Non-enzymatic modifications in vivo

Examples of non-enzymatic PTMs are glycation, glycoxidation, nitrosylation, oxidation, succination, and lipoxidation."The Advanced Lipoxidation End-Product Malondialdehyde-Lysine in Aging and Longevity" PMID 33203089 PMC7696601
  • glycation, the addition of a sugar molecule to a protein without the controlling action of an enzyme.
  • carbamylation the addition of Isocyanic acid to a protein's N-terminus or the side-chain of Lys.JOURNAL, Jaisson S, Pietrement C, Gillery P, Carbamylation-derived products: bioactive compounds and potential biomarkers in chronic renal failure and atherosclerosis, Clinical Chemistry, 57, 11, 1499–505, November 2011, 21768218, 10.1373/clinchem.2011.163188, free,
  • carbonylation the addition of carbon monoxide to other organic/inorganic compounds.
  • spontaneous isopeptide bond formation, as found in many surface proteins of Gram-positive bacteria.JOURNAL, Kang HJ, Baker EN, Intramolecular isopeptide bonds: protein crosslinks built for stress?, Trends in Biochemical Sciences, 36, 4, 229–37, April 2011, 21055949, 10.1016/j.tibs.2010.09.007,

Non-enzymatic additions in vitro

  • biotinylation: covalent attachment of a biotin moiety using a biotinylation reagent, typically for the purpose of labeling a protein.
  • carbamylation: the addition of Isocyanic acid to a protein's N-terminus or the side-chain of Lys or Cys residues, typically resulting from exposure to urea solutions.JOURNAL, Stark GR, Stein WH, Moore X, Reactions of the Cyanate Present in Aqueous Urea with Amino Acids and Proteins, J Biol Chem, 235, 11, 3177–3181, 1960, 10.1016/S0021-9258(20)81332-5, free,
  • oxidation: addition of one or more Oxygen atoms to a susceptible side-chain, principally of Met, Trp, His or Cys residues. Formation of disulfide bonds between Cys residues.
  • pegylation: covalent attachment of polyethylene glycol (PEG) using a pegylation reagent, typically to the N-terminus or the side-chains of Lys residues. Pegylation is used to improve the efficacy of protein pharmaceuticals.

Conjugation with other proteins or peptides

  • ubiquitination, the covalent linkage to the protein ubiquitin.
  • SUMOylation, the covalent linkage to the SUMO protein (Small Ubiquitin-related MOdifier)Van G. Wilson (Ed.) (2004). Sumoylation: Molecular Biology and Biochemistry {{webarchive|url=https://web.archive.org/web/20050209075122weblink |date=2005-02-09 }}. Horizon Bioscience. {{ISBN|0-9545232-8-8}}.
  • neddylation, the covalent linkage to the Nedd protein
  • ISGylation, the covalent linkage to the ISG15 protein (Interferon-Stimulated Gene 15)JOURNAL, Malakhova OA, Yan M, Malakhov MP, Yuan Y, Ritchie KJ, Kim KI, Peterson LF, Shuai K, Zhang DE, Protein ISGylation modulates the JAK-STAT signaling pathway, Genes & Development, 17, 4, 455–60, February 2003, 12600939, 195994, 10.1101/gad.1056303,
  • pupylation, the covalent linkage to the prokaryotic ubiquitin-like protein

Chemical modification of amino acids

Structural changes

Statistics

Common PTMs by frequency

In 2011, statistics of each post-translational modification experimentally and putatively detected have been compiled using proteome-wide information from the Swiss-Prot database.JOURNAL, Khoury GA, Baliban RC, Floudas CA, Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database, Scientific Reports, 1, 90, 90, September 2011, 22034591, 3201773, 10.1038/srep00090, 2011NatSR...1E..90K, The 10 most common experimentally found modifications were as follows:WEB,weblink Proteome-Wide Post-Translational Modification Statistics, selene.princeton.edu, 2011-07-22,weblink" title="web.archive.org/web/20120830234041weblink">weblink 2012-08-30, dead, {| class="wikitable"!Frequency!Modification|58383|Phosphorylation
|6751|Acetylation
|5526|N-linked glycosylation
|2844
#amidation>Amidation
|1619|Hydroxylation
|1523|Methylation
|1133|O-linked glycosylation
|878
Ubiquitin>Ubiquitylation
|826
Pyroglutamic acid>Pyrrolidone carboxylic acid
|504|Sulfation

Common PTMs by residue

Some common post-translational modifications to specific amino-acid residues are shown below. Modifications occur on the side-chain unless indicated otherwise.{| class="wikitable sortable" style="text-align: left" ! Amino Acid !! Abbrev. !! Modification
! Alanine| Ala or A
Acetylation>N-acetylation (N-terminus)
! Arginine| Arg or R
Citrullination>citrulline, methylation
! Asparagine| Asn or N
deamidation to Asp or iso(Asp), N-linked glycosylation, Isopeptide bond>spontaneous isopeptide bond formation
! Aspartic acid| Asp or D
deamidation>isomerization to isoaspartic acid, spontaneous isopeptide bond formation
! Cysteine| Cys or C
disulfide-bond formation, oxidation to sulfenic, sulfinic or sulfonic acid, palmitoylation, Acetylation>N-acetylation (N-terminus), S-nitrosylation
! Glutamine| Gln or Q| cyclization to pyroglutamic acid (N-terminus), deamidation to Glutamic acid or isopeptide bond formation to a lysine by a transglutaminase
! Glutamic acid| Glu or E| cyclization to Pyroglutamic acid (N-terminus), gamma-carboxylation
! Glycine| Gly or G
Myristoylation (N-terminus), Acetylation>N-acetylation (N-terminus)
! Histidine| His or H
Histidine kinase>Phosphorylation
! Isoleucine| Ile or I|
! Leucine| Leu or L|
! Lysine| Lys or K
acetylation, ubiquitylation, SUMO protein>SUMOylation, Protein methylation, hydroxylation leading to allysine, Isopeptide bond>spontaneous isopeptide bond formation
! Methionine| Met or M
Acetylation>N-acetylation (N-terminus), N-linked Ubiquitination, oxidation to sulfoxide or sulfone
! Phenylalanine| Phe or F|
! Proline| Pro or P| hydroxylation
! Serine| Ser or S
Phosphorylation, O-linked glycosylation, Acetylation>N-acetylation (N-terminus)
! Threonine| Thr or T
Phosphorylation, O-linked glycosylation, Acetylation>N-acetylation (N-terminus)
! Tryptophan| Trp or W| mono- or di-oxidation, formation of kynurenine, tryptophan tryptophylquinone
! Tyrosine| Tyr or Y
Tyrosine sulfation>sulfation, phosphorylation
! Valine| Val or V
Acetylation>N-acetylation (N-terminus)

Databases and tools

(File:Image for Wiki 2.jpg|alt=|thumb|Flowchart of the process and the data sources to predict PTMs.JOURNAL, Lee TY, Huang HD, Hung JH, Huang HY, Yang YS, Wang TH, dbPTM: an information repository of protein post-translational modification, Nucleic Acids Research, 34, Database issue, D622-7, January 2006, 16381945, 1347446, 10.1093/nar/gkj083, |440x440px)Protein sequences contain sequence motifs that are recognized by modifying enzymes, and which can be documented or predicted in PTM databases. With the large number of different modifications being discovered, there is a need to document this sort of information in databases. PTM information can be collected through experimental means or predicted from high-quality, manually curated data. Numerous databases have been created, often with a focus on certain taxonomic groups (e.g. human proteins) or other features.

List of resources

  • PhosphoSitePlusJOURNAL, Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E, PhosphoSitePlus, 2014: mutations, PTMs and recalibrations, Nucleic Acids Research, 43, Database issue, D512-20, January 2015, 25514926, 4383998, 10.1093/nar/gku1267, – A database of comprehensive information and tools for the study of mammalian protein post-translational modification
  • ProteomeScoutJOURNAL, Goel R, Harsha HC, Pandey A, Prasad TS, Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis, Molecular BioSystems, 8, 2, 453–63, February 2012, 22159132, 3804167, 10.1039/c1mb05340j, – A database of proteins and post-translational modifications experimentally
  • Human Protein Reference Database – A database for different modifications and understand different proteins, their class, and function/process related to disease causing proteins
  • PROSITEJOURNAL, Sigrist CJ, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N, PROSITE, a protein domain database for functional characterization and annotation, Nucleic Acids Research, 38, Database issue, D161-6, January 2010, 19858104, 2808866, 10.1093/nar/gkp885, – A database of Consensus patterns for many types of PTM's including sites
  • RESIDJOURNAL, Garavelli JS, The RESID Database of Protein Modifications: 2003 developments, Nucleic Acids Research, 31, 1, 499–501, January 2003, 12520062, 165485, 10.1093/nar/gkg038, – A database consisting of a collection of annotations and structures for PTMs.
  • iPTMnet JOURNAL, Huang H, Arighi CN, Ross KE, Ren J, Li G, Chen SC, Wang Q, Cowart J, Vijay-Shanker K, Wu CH, iPTMnet: an integrated resource for protein post-translational modification network discovery, Nucleic Acids Research, 46, 1, D542–D550, January 2018, 2914561, 5753337, 10.1093/nar/gkx1104, – A database that integrates PTM information from several knowledgbases and text mining results.
  • dbPTM – A database that shows different PTM's and information regarding their chemical components/structures and a frequency for amino acid modified site
  • Uniprot has PTM information although that may be less comprehensive than in more specialized databases.(File:Image for Wiki 1.jpg|alt=|thumb|Effect of PTMs on protein function and physiological processes.JOURNAL, Audagnotto M, Dal Peraro M, In silico prediction tools and molecular modeling, Computational and Structural Biotechnology Journal, 15, 307–319, 2017-03-31, 28458782, 5397102, 10.1016/j.csbj.2017.03.004, |440x440px)
  • The O-GlcNAc DatabaseJOURNAL, Wulff-Fuentes E, Berendt RR, Massman L, Danner L, Malard F, Vora J, Kahsay R, Olivier-Van Stichelen S, The human O-GlcNAcome database and meta-analysis, Scientific Data, 8, January 2021, 1, 25, 33479245, 7820439, 10.1038/s41597-021-00810-4, 2021NatSD...8...25W, JOURNAL, Malard F, Wulff-Fuentes E, Berendt RR, Didier G, Olivier-Van Stichelen S, Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database, Database (Oxford), 2021, July 2021, 1, 34279596, 10.1093/database/baab039, 8288053, - A curated database for protein O-GlcNAcylation and referencing more than 14 000 protein entries and 10 000 O-GlcNAc sites.

Tools

List of software for visualization of proteins and their PTMs
  • PyMOLJOURNAL, Warnecke A, Sandalova T, Achour A, Harris RA, PyTMs: a useful PyMOL plugin for modeling common post-translational modifications, BMC Bioinformatics, 15, 1, 370, November 2014, 25431162, 4256751, 10.1186/s12859-014-0370-6, free, – introduce a set of common PTM's into protein models
  • AWESOMEJOURNAL, Yang Y, Peng X, Ying P, Tian J, Li J, Ke J, Zhu Y, Gong Y, Zou D, Yang N, Wang X, Mei S, Zhong R, Gong J, Chang J, Miao X, AWESOME: a database of SNPs that affect protein post-translational modifications, Nucleic Acids Research, 47, D1, D874–D880, January 2019, 30215764, 6324025, 10.1093/nar/gky821, – Interactive tool to see the role of single nucleotide polymorphisms to PTM's
  • ChimeraJOURNAL, Morris JH, Huang CC, Babbitt PC, Ferrin TE, structureViz: linking Cytoscape and UCSF Chimera, Bioinformatics, 23, 17, 2345–7, September 2007, 17623706, 10.1093/bioinformatics/btm329, free, – Interactive Database to visualize molecules

Case examples

{{more citations needed section|date=January 2016}}

See also

References

{{reflist|30em}}

External links

  • weblink" title="web.archive.org/web/20190718064223weblink">dbPTM - database of protein post-translational modifications
(Wayback Machine copy) (Wayback Machine copy) {{Protein topics}}{{Protein primary structure}}{{Posttranslational modification}}{{Gene expression}}

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