Post-translational modification

Short description: Biological processes

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 apparatus, where it is packaged into a vesicle. In the vesicle, more parts are cut off, and it turns into mature insulin.

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 translating 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.[1] 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. [2] 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.[3] 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.[4][5] Specific amino acid modifications can be used as biomarkers indicating oxidative damage.[6]

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.[7]

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.

## Contents

* 1 PTMs involving addition of functional groups
* 1.1 Addition by an enzyme in vivo
* 1.1.1 Hydrophobic groups for membrane localization
* 1.1.2 Cofactors for enhanced enzymatic activity
* 1.1.3 Modifications of translation factors
* 1.1.4 Smaller chemical groups
* 1.2 Non-enzymatic modifications in vivo
* 1.3 Non-enzymatic additions in vitro
* 2 Conjugation with other proteins or peptides
* 3 Chemical modification of amino acids
* 4 Structural changes
* 5 Statistics
* 5.1 Common PTMs by frequency
* 5.2 Common PTMs by residue
* 6 Databases and tools
* 6.1 List of resources
* 6.2 Tools
* 7 Case examples
* 8 See also
* 9 References
* 10 External links

## PTMs involving addition of functional groups

### Addition by an enzyme in vivo

#### Hydrophobic groups for membrane localization

* myristoylation (a type of acylation), attachment of myristate, a C14 saturated acid
* palmitoylation (a type of acylation), attachment of palmitate, a C16 saturated acid
* isoprenylation or prenylation, the addition of an isoprenoid group (e.g. farnesol and geranylgeraniol)
* farnesylation
* geranylgeranylation
* glypiation, glycosylphosphatidylinositol (GPI) anchor formation via an amide bond to C-terminal tail

#### Cofactors for enhanced enzymatic activity

* lipoylation (a type of acylation), attachment of a lipoate (C8) functional group
* flavin moiety (FMN or FAD) may be covalently attached
* heme C attachment via thioether bonds with cysteines
* phosphopantetheinylation, the addition of a 4'-phosphopantetheinyl moiety from coenzyme A, as in fatty acid, polyketide, non-ribosomal peptide and leucine biosynthesis
* retinylidene Schiff base formation

#### Modifications of translation factors

* diphthamide formation (on a histidine found in eEF2)
* ethanolamine phosphoglycerol attachment (on glutamate found in eEF1α)[8]
* 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.[9] EFP is a homolog to eIF5A (eukaryotic) and aIF5A (archaeal) (see above).

#### Smaller chemical groups

* acylation, e.g. O-acylation (esters), N-acylation (amides), S-acylation (thioesters)
* acetylation, the addition of an acetyl group, either at the N-terminus of the protein or at lysine residues.[10] The reverse is called deacetylation.
* formylation
* alkylation, the addition of an alkyl group, e.g. methyl, ethyl
* methylation the addition of a methyl group, usually at lysine or arginine residues. The reverse is called demethylation.
* amidation at C-terminus. Formed by oxidative dissociation of a C-terminal Gly residue.[11]
* amide bond formation
* amino acid addition
* arginylation, a tRNA-mediation addition
* polyglutamylation, covalent linkage of glutamic acid residues to the N-terminus of tubulin and some other proteins.[12] (See tubulin polyglutamylase)
* polyglycylation, covalent linkage of one to more than 40 glycine residues to the tubulin C-terminal tail
* butyrylation
* gamma-carboxylation dependent on Vitamin K[13]
* glycosylation, the addition of a glycosyl group to either arginine, asparagine, cysteine, hydroxylysine, serine, threonine, tyrosine, or tryptophan resulting in a glycoprotein. Distinct from glycation, which is regarded as a nonenzymatic attachment of sugars.
* O-GlcNAc, addition of N-acetylglucosamine to serine or threonine residues in a β-glycosidic linkage
* polysialylation, addition of polysialic acid, PSA, to NCAM
* malonylation
* hydroxylation: addition of an oxygen atom to the side-chain of a Pro or Lys residue
* iodination: addition of an iodine atom to the aromatic ring of a tyrosine residue (e.g. in thyroglobulin)
* nucleotide addition such as ADP-ribosylation
* phosphate ester (O-linked) or phosphoramidate (N-linked) formation
* phosphorylation, the addition of a phosphate group, usually to serine, threonine, and tyrosine (O-linked), or histidine (N-linked)
* adenylylation, the addition of an adenylyl moiety, usually to tyrosine (O-linked), or histidine and lysine (N-linked)
* uridylylation, the addition of an uridylyl-group (i.e. uridine monophosphate, UMP), usually to tyrosine
* propionylation
* pyroglutamate formation
* S-glutathionylation
* S-nitrosylation
* S-sulfenylation (aka S-sulphenylation), reversible covalent addition of one oxygen atom to the thiol group of a cysteine residue[14]
* S-sulfinylation, normally irreversible covalent addition of two oxygen atoms to the thiol group of a cysteine residue[14]
* S-sulfonylation, normally irreversible covalent addition of three oxygen atoms to the thiol group of a cysteine residue, resulting in the formation of a cysteic acid residue[14]
* succinylation addition of a succinyl group to lysine
* sulfation, the addition of a sulfate group to a tyrosine.

### Non-enzymatic modifications in vivo

Examples of non-enzymatic PTMs are glycation, glycoxidation, nitrosylation, oxidation, succination, and lipoxidation.[15]

* 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.[16]
* 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.[17]

### 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.[18]
* 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)[19]
* neddylation, the covalent linkage to the Nedd protein
* ISGylation, the covalent linkage to the ISG15 protein (Interferon-Stimulated Gene 15)[20]
* pupylation, the covalent linkage to the prokaryotic ubiquitin-like protein

## Chemical modification of amino acids

* citrullination, or deimination, the conversion of arginine to citrulline[21]
* deamidation, the conversion of glutamine to glutamic acid or asparagine to aspartic acid
* eliminylation, the conversion to an alkene by beta-elimination of phosphothreonine and phosphoserine, or dehydration of threonine and serine[22]

## Structural changes

* disulfide bridges, the covalent linkage of two cysteine amino acids
* lysine-cysteine bridges, the covalent linkage of 1 lysine and 1 or 2 cystine residues via an oxygen atom (NOS and SONOS bridges)[23]
* proteolytic cleavage, cleavage of a protein at a peptide bond
* isoaspartate formation, via the cyclisation of asparagine or aspartic acid amino-acid residues
* racemization
* of serine by protein-serine epimerase
* of alanine in dermorphin, a frog opioid peptide
* of methionine in deltorphin, also a frog opioid peptide
* protein splicing, self-catalytic removal of inteins analogous to mRNA processing

## 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.[24] The 10 most common experimentally found modifications were as follows:[25]

Frequency  | Modification

|

58383  | Phosphorylation
6751  | Acetylation
5526  | N-linked glycosylation
2844  | Amidation
1619  | Hydroxylation
1523  | Methylation
1133  | O-linked glycosylation
878  | Ubiquitylation
826  | 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.

Amino Acid | Abbrev. | Modification

|
|

Alanine | Ala or A  | N-acetylation (N-terminus)
Arginine | Arg or R  | deimination to citrulline, methylation
Asparagine | Asn or N  | deamidation to Asp or iso(Asp), N-linked glycosylation, spontaneous isopeptide bond formation
Aspartic acid | Asp or D  | isomerization to isoaspartic acid, spontaneous isopeptide bond formation
Cysteine | Cys or C  | disulfide-bond formation, oxidation to sulfenic, sulfinic or sulfonic acid, palmitoylation, 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  | N-Myristoylation (N-terminus), N-acetylation (N-terminus)
Histidine | His or H  | Phosphorylation
Isoleucine | Ile or I  |
Leucine | Leu or L  |
Lysine | Lys or K  | acetylation, ubiquitylation, SUMOylation, methylation, hydroxylation leading to allysine, spontaneous isopeptide bond formation
Methionine | Met or M  | 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, N-acetylation (N-terminus)
Threonine | Thr or T  | Phosphorylation, O-linked glycosylation, N-acetylation (N-terminus)
Tryptophan | Trp or W  | mono- or di-oxidation, formation of kynurenine, tryptophan tryptophylquinone
Tyrosine | Tyr or Y  | sulfation, phosphorylation
Valine | Val or V  | N-acetylation (N-terminus)

## Databases and tools

Flowchart of the process and the data sources to predict PTMs.[26]

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

* PhosphoSitePlus[27] – A database of comprehensive information and tools for the study of mammalian protein post-translational modification
* ProteomeScout[28] – A database of proteins and post-translational modifications experimentally
* Human Protein Reference Database[28] – A database for different modifications and understand different proteins, their class, and function/process related to disease causing proteins
* PROSITE[29] – A database of Consensus patterns for many types of PTM's including sites
* RESID[30] – A database consisting of a collection of annotations and structures for PTMs.
* iPTMnet [31]– A database that integrates PTM information from several knowledgbases and text mining results.
* dbPTM[26] – 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.

Effect of PTMs on protein function and physiological processes.[32]

* The O-GlcNAc Database[33][34] \- 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

* PyMOL[35] – introduce a set of common PTM's into protein models
* AWESOME[36] – Interactive tool to see the role of single nucleotide polymorphisms to PTM's
* Chimera[37] – Interactive Database to visualize molecules

## Case examples

* Cleavage and formation of disulfide bridges during the production of insulin
* PTM of histones as regulation of transcription: RNA polymerase control by chromatin structure
* PTM of RNA polymerase II as regulation of transcription
* Cleavage of polypeptide chains as crucial for lectin specificity[38]

## See also

* Protein targeting
* Post-translational regulation

## References

1. ↑ Pratt, Charlotte W.; Voet, Judith G.; Voet, Donald (2006). Fundamentals of Biochemistry: Life at the Molecular Level (2nd ed.). Hoboken, NJ: Wiley. ISBN 9780471214953. OCLC 1280801548. https://books.google.com/books?id=h0FCAQAAIAAJ.
2. ↑ "Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database". Scientific Reports 1: 90. September 2011. doi:10.1038/srep00090. PMID 22034591. Bibcode: 2011NatSR...1E..90K.
3. ↑ "17.6, Post-Translational Modifications and Quality Control in the Rough ER". Molecular Cell Biology (4th ed.). New York: W. H. Freeman. 2000. ISBN 978-0-7167-3136-8. https://www.ncbi.nlm.nih.gov/books/NBK21741/.
4. ↑ "Protein carbonylation, cellular dysfunction, and disease progression". Journal of Cellular and Molecular Medicine 10 (2): 389–406. 2006. doi:10.1111/j.1582-4934.2006.tb00407.x. PMID 16796807.
5. ↑ "Oxidative stress and covalent modification of protein with bioactive aldehydes". The Journal of Biological Chemistry 283 (32): 21837–41. August 2008. doi:10.1074/jbc.R700019200. PMID 18445586.
6. ↑ "Detecting oxidative post-translational modifications in proteins". Amino Acids 33 (1): 51–6. July 2007. doi:10.1007/s00726-006-0410-2. PMID 17021655.
7. ↑ Walsh, Christopher T. (2006). Posttranslational modification of proteins : expanding nature's inventory. Englewood: Roberts and Co. Publ.. ISBN 9780974707730. :12–14
8. ↑ "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. doi:10.1016/S0021-9258(18)71682-7. PMID 2569467.
9. ↑ "The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-β-lysine". Nature Chemical Biology 7 (10): 667–9. August 2011. doi:10.1038/nchembio.632. PMID 21841797.
10. ↑ "Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics". Chem Rev 118 (3): 1216–1252. February 2018. doi:10.1021/acs.chemrev.7b00181. PMID 29405707.
11. ↑ "Peptide amidation". Trends in Biochemical Sciences 16 (3): 112–5. March 1991. doi:10.1016/0968-0004(91)90044-v. PMID 2057999.
12. ↑ "Posttranslational glutamylation of alpha-tubulin". Science 247 (4938): 83–5. January 1990. doi:10.1126/science.1967194. PMID 1967194. Bibcode: 1990Sci...247...83E.
13. ↑ "On a potential global role for vitamin K-dependent gamma-carboxylation in animal systems. Evidence for a gamma-glutamyl carboxylase in Drosophila". The Journal of Biological Chemistry 276 (11): 7769–74. March 2001. doi:10.1074/jbc.M009576200. PMID 11110799.
14. ↑ 14.0 14.1 14.2 "Cysteine oxidative posttranslational modifications: emerging regulation in the cardiovascular system". Circulation Research 112 (2): 382–92. January 2013. doi:10.1161/CIRCRESAHA.112.268680. PMID 23329793.
15. ↑ "The Advanced Lipoxidation End-Product Malondialdehyde-Lysine in Aging and Longevity" PMID 33203089 PMC7696601
16. ↑ "Carbamylation-derived products: bioactive compounds and potential biomarkers in chronic renal failure and atherosclerosis". Clinical Chemistry 57 (11): 1499–505. November 2011. doi:10.1373/clinchem.2011.163188. PMID 21768218.
17. ↑ "Intramolecular isopeptide bonds: protein crosslinks built for stress?". Trends in Biochemical Sciences 36 (4): 229–37. April 2011. doi:10.1016/j.tibs.2010.09.007. PMID 21055949.
18. ↑ "Reactions of the Cyanate Present in Aqueous Urea with Amino Acids and Proteins". J Biol Chem 235 (11): 3177–3181. 1960. doi:10.1016/S0021-9258(20)81332-5.
19. ↑ Van G. Wilson (Ed.) (2004). Sumoylation: Molecular Biology and Biochemistry . Horizon Bioscience. ISBN:0-9545232-8-8.
20. ↑ "Protein ISGylation modulates the JAK-STAT signaling pathway". Genes & Development 17 (4): 455–60. February 2003. doi:10.1101/gad.1056303. PMID 12600939.
21. ↑ "Immunity to citrullinated proteins in rheumatoid arthritis". Annual Review of Immunology 26: 651–75. 2008. doi:10.1146/annurev.immunol.26.021607.090244. PMID 18173373. https://zenodo.org/record/894124.
22. ↑ "Eliminylation: a post-translational modification catalyzed by phosphothreonine lyases". Trends in Biochemical Sciences 34 (3): 108–14. March 2009. doi:10.1016/j.tibs.2008.11.005. PMID 19233656.
23. ↑ Rabe von Pappenheim, Fabian; Wensien, Marie; Ye, Jin; Uranga, Jon; Irisarri, Iker; de Vries, Jan; Funk, Lisa-Marie; Mata, Ricardo A. et al. (April 2022). "Widespread occurrence of covalent lysine–cysteine redox switches in proteins". Nature Chemical Biology 18 (4): 368–375. doi:10.1038/s41589-021-00966-5.
24. ↑ "Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database". Scientific Reports 1 (90): 90. September 2011. doi:10.1038/srep00090. PMID 22034591. Bibcode: 2011NatSR...1E..90K.
25. ↑ "Proteome-Wide Post-Translational Modification Statistics". http://selene.princeton.edu/PTMCuration/.
26. ↑ 26.0 26.1 "dbPTM: an information repository of protein post-translational modification". Nucleic Acids Research 34 (Database issue): D622-7. January 2006. doi:10.1093/nar/gkj083. PMID 16381945.
27. ↑ "PhosphoSitePlus, 2014: mutations, PTMs and recalibrations". Nucleic Acids Research 43 (Database issue): D512-20. January 2015. doi:10.1093/nar/gku1267. PMID 25514926.
28. ↑ 28.0 28.1 "Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis". Molecular BioSystems 8 (2): 453–63. February 2012. doi:10.1039/c1mb05340j. PMID 22159132.
29. ↑ "PROSITE, a protein domain database for functional characterization and annotation". Nucleic Acids Research 38 (Database issue): D161-6. January 2010. doi:10.1093/nar/gkp885. PMID 19858104.
30. ↑ "The RESID Database of Protein Modifications: 2003 developments". Nucleic Acids Research 31 (1): 499–501. January 2003. doi:10.1093/nar/gkg038. PMID 12520062.
31. ↑ "iPTMnet: an integrated resource for protein post-translational modification network discovery". Nucleic Acids Research 46 (1): D542–D550. January 2018. doi:10.1093/nar/gkx1104. PMID 2914561.
32. ↑ "In silico prediction tools and molecular modeling". Computational and Structural Biotechnology Journal 15: 307–319. 2017-03-31. doi:10.1016/j.csbj.2017.03.004. PMID 28458782.
33. ↑ "The human O-GlcNAcome database and meta-analysis". Scientific Data 8 (1): 25. January 2021. doi:10.1038/s41597-021-00810-4. PMID 33479245. Bibcode: 2021NatSD...8...25W.
34. ↑ "Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database". Database (Oxford) 2021: 1. July 2021. doi:10.1093/database/baab039. PMID 34279596.
35. ↑ "PyTMs: a useful PyMOL plugin for modeling common post-translational modifications". BMC Bioinformatics 15 (1): 370. November 2014. doi:10.1186/s12859-014-0370-6. PMID 25431162.
36. ↑ "AWESOME: a database of SNPs that affect protein post-translational modifications". Nucleic Acids Research 47 (D1): D874–D880. January 2019. doi:10.1093/nar/gky821. PMID 30215764.
37. ↑ "structureViz: linking Cytoscape and UCSF Chimera". Bioinformatics 23 (17): 2345–7. September 2007. doi:10.1093/bioinformatics/btm329. PMID 17623706.
38. ↑ "1tp8 - Proteopedia, life in 3D". http://www.proteopedia.org/wiki/index.php/1tp8.

## External links

* dbPTM - database of protein post-translational modifications

(Wayback Machine copy)

* List of posttranslational modifications in ExPASy
* Browse SCOP domains by PTM — from the dcGO database
* Statistics of each post-translational modification from the Swiss-Prot database

(Wayback Machine copy)

* AutoMotif Server \- A Computational Protocol for Identification of Post-Translational Modifications in Protein Sequences
* Functional analyses for site-specific phosphorylation of a target protein in cells
* Detection of Post-Translational Modifications after high-accuracy MSMS
* Overview and description of commonly used post-translational modification detection techniques

* v
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Proteins

Processes|

* Protein biosynthesis
* Post-translational modification
* Protein folding
* Protein targeting
* Proteome
* Protein methods

Structures|

* Protein structure
* Protein structural domains
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Types|

* List of types of proteins
* List of proteins
* Membrane protein
* Globular protein
* Globulin
* Edestin
* Albumin
* Fibrous protein

* v
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Proteins: key methods of study

Experimental|

* Protein purification
* Green fluorescent protein
* Western blot
* Protein immunostaining
* Protein sequencing
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* Peptide mass fingerprinting/Protein mass spectrometry
* Dual-polarization interferometry
* Microscale thermophoresis
* Chromatin immunoprecipitation
* Surface plasmon resonance
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* Protein NMR
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* Freeze-fracture electron microscopy

Bioinformatics|

* Protein structure prediction
* Protein–protein docking
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Assay|

* Enzyme assay
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Display techniques|

* Bacterial display
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* Ribosome display
* Yeast display

Super-resolution microscopy|

* Photoactivated localization microscopy
* Vertico SMI

* v
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Protein primary structure and posttranslational modifications

General|

* Peptide bond
* Protein biosynthesis
* Proteolysis
* Racemization
* N-O acyl shift

N terminus|

* Acetylation
* Carbamylation
* Formylation
* Glycation
* Methylation
* Myristoylation (Gly)

C terminus|

* Amidation
* Glycosyl phosphatidylinositol (GPI)
* O-methylation
* Detyrosination

Single specific AAs|

| Serine/Threonine|

* Phosphorylation
* Dephosphorylation
* Glycosylation
* ADP-ribosylation
* Methylidene-imidazolone (MIO) formation

|

Tyrosine|

* Phosphorylation
* Dephosphorylation
* ADP-ribosylation
* Sulfation
* Porphyrin ring linkage
* Adenylylation
* Flavin linkage
* Topaquinone (TPQ) formation
* Detyrosination

Cysteine|

* Palmitoylation
* Prenylation

Aspartate|

* Succinimide formation
* ADP-ribosylation

Glutamate|

* Carboxylation
* ADP-ribosylation
* Methylation
* Polyglutamylation
* Polyglycylation

Asparagine|

* Deamidation
* Glycosylation

Glutamine|

* Transglutamination

Lysine|

* Methylation
* Acetylation
* Acylation
* Adenylylation
* Hydroxylation
* Ubiquitination
* Sumoylation
* ADP-ribosylation
* Deamination
* Oxidative deamination to aldehyde
* O-glycosylation
* Imine formation
* Glycation
* Carbamylation
* Succinylation

Arginine|

* Citrullination
* Methylation
* ADP-ribosylation

Proline|

* Hydroxylation

Histidine|

* Diphthamide formation
* Adenylylation

Tryptophan|

* C-mannosylation

Crosslinks between two AAs|

| Cysteine-Cysteine|

* Disulfide bond
* ADP-ribosylation

|

Methionine-Hydroxylysine|

* Sulfilimine bond

Lysine-Tyrosylquinone|

* Lysine tyrosylquinone (LTQ) formation

Tryptophan-Tryptophylquinone|

* Tryptophan tryptophylquinone (TTQ) formation

Three consecutive AAs
(chromophore formation)|

| Serine–Tyrosine–Glycine|

* p-Hydroxybenzylidene-imidazolinone formation

|

Histidine–Tyrosine–Glycine|

* 4-(p-hydroxybenzylidene)-5-imidazolinone formation

Crosslinks between four AAs|

| Allysine-Allysine-Allysine-Lysine|

* Desmosine

|

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Gene expression

Introduction
to genetics|

* Genetic code
* Central dogma
* DNA → RNA → Protein
* Special transfers
* RNA→RNA
* RNA→DNA
* Protein→Protein

Transcription|

| Types|

* Bacterial
* Eukaryotic

|

Key elements|

* Transcription factor
* RNA polymerase
* Promoter

Post-transcription|

* Precursor mRNA (pre-mRNA / hnRNA)
* 5' capping
* Splicing
* Polyadenylation
* Histone acetylation and deacetylation

Translation|

| Types|

* Prokaryotic
* Eukaryotic

|

Key elements|

* Ribosome
* Transfer RNA (tRNA)
* Ribosome-nascent chain complex (RNC)
* Post-translational modification

Regulation|

* Epigenetic
* imprinting
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* Gene regulatory network
* cis-regulatory element
* lac operon
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* sequestration (P-bodies)
* alternative splicing
* microRNA
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* reversible
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Influential people|

* François Jacob
* Jacques Monod

* Portal

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