Intrachain (with no prosthetic group) every amino acid in the chain (also not contiguous) intrachain disulfide bond in globular preproprotein  RNAase, insulin, Ig 2 Cys => cystin  usually uncatalyzed, except for protein disulfide isomerases (PDI)
deamidation CaM
Asn + H2O => isoAsp or D-Asp + NH4+
Gln + H2O => Glu + NH4+
thyronin formation thyroglobulin DIT + MIT (or DIT) => dehydroAla + (r)T3 (or T4) uncatalyzed (hypothetical role for TPo ?)
isomerization PIN1 Pro peptidyl-prolyl cis-trans isomerase (PPI)
dehydratation   Asp => dehydroAsp 
Ala => dehydroAla
oxidation SERCA1, SERCA2a, CaM, b-amyloid, collagen, elastin Cys => Cya 
Met => Met sulphoxide 
Lys, Pro, Arg, Thr => aldehyde and ketons
R.O.S. <=> Msr 
Lys oxidase
N-terminal amino acid cyclization neurotensin, TSH, TRH, GnRH Glu => pyroGlu or 5-oxoPro or Glp  
C-terminal amino acid cyclization   Hse => Hsl  
Intrachain with covalently bound prosthetic groups :
1) as coenzymes
every amino acid in the chain thiamine PP   ?  
FMN / FAD   e-Lys amide (other ?)  
ACP   e-Lys amide  
PyP   Schiff's base  with e-Lys  
biotin   e-Lys amide  
5'dA-B12   ?  
methyl-B12   ?  
rhodopsin   Schiff's base with e-Lys  
naphtoquinone   ?  
lipoic acid   e-Lys amide  
heme c   2 Cys  
heme P460   2 Cys  
2) in conjugated proteins with no enzymatic activity every amino acid in the chain cotranslational N-glycosylation in ER and Golgi apparatus   Asn in NX(no P)S/T box => 1st sugar  GlcNAc specific glycosyltransferase and UDP-, GDP- or CMP-sugars
O-glycosylation in Golgi apparatus (via dolichol phosphate) collagen Ser, Thr  5-Hyl => 1st sugar GalNAc  
diphtamidation eEF2 NtHis Corynebacterium diphteriae toxin
methylation = charge neutralization CheR, CaM, cyt c, H3 Glu, Asp, Lys, Nt/pHis, Arg specific methyltransferase and S-AdoMet
acetylation (C2) = charge neutralization a-tubulin, H2A, H2B, H3, H4 Lys + acetylCoA histone acetyltransferase (HAT) and histone deacetylase (HD or HDAC)
palmytoylation (C16) some GPCRs' CTD => Cys thioester  
isoprenylations or terpenylations [cytosol-side anchors] => direction to cellular membranes and protein-protein interactions
farnesylation (C15) Ras familyref1, ref2, ref3, g-subunit of some heterotrimeric G proteins (e.g. transducins) attachment of the prenyl moiety to the cystein resiude of the carboxy-terminal CAA(aliphatic, no Ala)X(preferably Ser or Met) motif by protein farnesyl transferase (FTase)ref1, ref2 or protein geranylgeranyltransferase-I (GGTase-I), respectively. Folowing the attachment of the isoprenoid, the AAX tripeptide is removed in a reaction that is catalysed by a prenyl-protein-specific protease known as RCE1ref, whereas in the third processing step a methyl group is transferred to the now C-terminal prenylcysteine by the enzyme isoprenylcysteine carboxyl methylatransferase (ICMT) (activation !) => Cys thioether
geranylgeranylation (C20) CDC42, g-subunit of some heterotrimeric G-proteins, RHO family (which includes RAC and CDC42), RAB family, RAC family, RAP family

nuclear lamins A and B
centromeric proteins CENPE and CENPF

adenilylation Gln synthetase Ser-, Thr-, Tyr-OH  
uridilylation PII Ser-, Thr-, Tyr-OH  
mono-(in Prokarya) or poly-(in Eukarya) ADP-ribosylation H1, 
G-protein as and ai-subunit, 
Asn, Nt-diphtamideHis, Arg PARP
Vibrio cholerae toxin (+ARF), 
Corynebacterium diphteriae toxin, 
Pseudomonas aeruginosa toxin, 
Clostridium botulinum toxin, 
Bordetella pertussis toxin, 
Escherichia coli LT toxin
hypusination eIF5A / eIF4D Lys + butylamino group from spermidine (=> putrescine) + OH- => hypusine
sulphonation fibrinopeptides, chromogranin B, gastrin II or 17, CCK Tyr-OH specific sulphotransferase and PAPS (irreversible !)
nitrosylation RYR, glutathione Cys + NO. => Cys-S-N=O uncatalyzed
nitration SERCA2a Tyr + ONOO- => 3-nitro-Tyr uncatalyzed
carboxylation osteocalcin
factor II
factor VII
factor IX 
factor X
matrix Gla protein
protein C
protein S
protein Z
Glu => Gla (Ca2+ chelating !) g-glutamyl carboxylase
halogenations thyroglobulin Tyr + I2 => MIT (or DIT) uncatalyzed (hypothetical role for TPo ?)
phosphorylation many proteins ! Ser/Thr-, Tyr-, Hyp-, His-, Asp-OH specific protein kinases (sometimes autophosphorylation occurs !) and phosphatases
The discovery in the 1940s and 50s that adding a phosphate group can change a protein's activity won its discoverers, Edmond Fischer and Edwin Krebs, a Nobel prize in 1992. Instead of ATP, Snyder and his team propose that a molecule called IP7 transfers one of its 7 phosphate groups to another protein, without the help of an enzyme. To demonstrate this, they radioactively tagged one of the phosphates on IP7, before mixing it with a slurry of proteins extracted from yeast, mice or flies. They showed that the radioactive phosphate wound up attached to a plethora of other proteins, and went on to identify a handful of themref.
cotranslational hydroxylation collagen type I and type II
Lys => 5-Hyl (=> glycosylation) 
Pro => 3- or 4-Hyp, 
Asp, Asn
specific ER hydroxylase :  + aKG + vitamin C => CO2 + succinate + hydroxy-Xaa (more hydrogen bonds !)
N-terminal amino acid formylation all proteins in Bacteria Met (pretranslational in Bacteria !) Met-tRNAMet transformylase and peptide deformylase
methylation fimbrial protein in Neisseria, Pseudomonas and Vibrio spp. Phe ?
acetylation H1, H4 Ser cytosolic histone acetyltransferase (HAT) : irreversible ! 
miristoylation [cytosol-side anchor] C subunit of PKAs, a subunit of G proteins, c-Src SH4 domain Gly  
carboxylation Hb and other serum proteins Any uncatalyzed => Hb carbammates 
C-terminal amino acid PE-amide Apg8 Gly Apg4
primary amide a-MSH, secretin0
gastrin II or 17, CCK
oxytocin, ADH, GnRH, chromogranin A
TSH, TRH, calcitonin
substance P


-NH2 donor = Gly 
cofactor = vitamin C
glypiation [GPI ECM-side anchor] AChE
CD14 / LPS-R
CD16b / FcgRIIIB
CD24 / BA-1 / HSA
CD48 / BCM1 / Blast-1 / Hu Lym3 / OX-45
CD55 / DAF
CD58 / LFA-3
CD59 / 1F-5Ag / H19 / HRF20 / MACIF / MIRL / P-18 / Protectin
CD73 / 5'-nucleotidase
CD87 / uPAR,
CD90 / Thy-1
CD230 / PrP
 Gly, Asp -COO-ethanolamine 
Man-Man- GlcNAc-Ins-PA
methylation PP2A Leu  
Anabolic partial proteolysis N-terminal amino acid(s) fMet and other amino acid(s) removal many proteins many amino acids aminoexopeptidases => t1/2 variation
signal sequence removal from preproteins or from preproproteins preproinsulin
  signal recognition particle (SRP) (9 kDa, 14 kDa / homologous Alu RNA binding protein, 19 kDa, 54 kDa, 68 kDa, 72 kDa) and signal peptidase (12 kDa and 18 kDa)
inactivating sequence removal from proproteins zymogens/proenzymes, prohormones, fibrin (fibrinopeptides), NFkB, collagen (telopeptides)   endopeptidases (telopeptidase, ...)
creation of different proteins from a polyprotein POMC, prodynorphin, protachykinin, ubiquitin/S?, gag-pol, dentin syalophosphoprotein (DSPP)   Ub C-terminal hydrolase, Pro, ...
creation of more copies of a same protein from a polyprotein poliUb   Ub C-terminal hydrolase
protein splicing Hedgehog homologs   intein removal and extein splicing
peptide bond hydrolysis with no contiguity alteration thanks to disulfide bond(s) thrombin, insulin, insulin receptor, Clostridium botulinum neurotoxin   endopeptidases
Olygomers formation bond between 2 chains interchains disulfide bond Ig 2 Cys => cystin uncatalyzed (except for protein disulfide isomerase or PDI)
lysylnorleucinylation collagen, elastin Lys + oxidized Lys => LysNle  
desammonification fibrin Gln + e-Lys => NH4+ + ? transglutaminase/factor XIII
bond among till to 4 chains His merodesmosin formation collagen Lys + 2 oxidized Lys + His => His-meroDes  
desmosin and isodesmosin formation elastin Lys + 3 oxidized Lys => Des or isoDes  
Olygopeptide addition mono- (<4) or poly- (>/=4) ubiquitylation or ubiquitination (= ubiquitin (UB) A, B, C or D addition) 
In polyubiquitinylation E3s mediate isopeptidic bonds between a target-bound-Ub e-Lys and the -OOC-Gly of another target-bound Ub molecule. The e-Lys in the first Ub molecule may be K11, K29, K48 (=> 26S proteasome, except for p21CIP1/WAF1 and ornithine decarboxylase (ODC), for which an antizyme system (OAZ1, OAZ2, OAZ3, and inhibitor) occurs) or K68 (=> DNA repair, IKK)
intra chain e-Lys (N-terminal amino acid for MyoD1 ubiquitylation !) + Ub => isopeptidic bond 
E1s (ubiquitin-activating ATPase) 
E2s/UBCs (carrier) : Ubc7 in S.cerevisiae, UBE2G1 and UBE2G2 in humans
E3s DUBs (UDP don't modify covalently their interacting proteins)
(no Ks on UBLs for isopeptidic bonds between them !) : ubiquitin-like proteins (UBLs) are conjugated by dynamic E1E2E3 enzyme cascades. E1 enzymes activate UBLs by catalysing UBL carboxy-terminal adenylation, forming a covalent E1~UBL thioester intermediate, and generating a thioester-linked E2~UBL product, which must be released for subsequent reactions.
sumoylation (= SUMO1/sentrin addition) H4 

If on the same Lys residues used for ubiquitylation, sumoylation prevents it ! If on other K it may stabilize or address the target 
E1s : AOS1 /SAE1 + UBA2
E2s : UBC9 in S.cerevisiae, UBE2I in humans 
E3s : 1) RING : protein inhibitor of activated STAT, 4 (PIAS4 / PIASg) (on LEF1

rubylation / neddylation (= Rub1/Nedd8 addition), the process that conjugates the ubiquitin-like polypeptide Nedd8 to the conserved lysines of cullins, is essential for in vivo cullin-organized E3 activities. Cullin family proteins organize ubiquitin ligase (E3) complexes to target numerous cellular proteins for proteasomal degradation. Deneddylation, which removes the Nedd8 moiety, requires the isopeptidase activity of the COP9 signalosome (CSN)3, 4. In cells deficient for CSN activity, cullin1 (Cul1) and cullin3 (Cul3) proteins are unstable, and that to preserve their normal cellular levels, CSN isopeptidase activity is required. Neddylated Cul1 and Cul3 are unstable as suggested by the evidence that Nedd8 promotes the instability of both cullins and that the unneddylatable forms of cullins are stable. The protein stability of Nedd8 is also subject to CSN regulation and this regulation depends on its cullin-conjugating ability, suggesting that Nedd8-conjugated cullins are degraded en bloc. While Nedd8 promotes cullin activation through neddylation, neddylation also renders cullins unstable. Thus, CSN deneddylation recycles the unstable, neddylated cullins into stable, unneddylated ones, and promotes cullin-organized E3 activity in vivoref. The activation complex contains NEDD8's heterodimeric E1 (APPBP1UBA3), 2 NEDD8s (one thioester-linked to E1, one noncovalently associated for adenylation), a catalytically inactive E2 (Ubc12), and MgATP. The results suggest that a thioester switch toggles E1E2 affinities. 2 E2 binding sites depend on NEDD8 being thioester-linked to E1. One is unmasked by a striking E1 conformational change. The other comes directly from the thioester-bound NEDD8. After NEDD8 transfer to E2, reversion to an alternate E1 conformation would facilitate release of the E2~NEDD8 thioester product. Thus, transferring the UBL's thioester linkage between successive conjugation enzymes can induce conformational changes and alter interaction networks to drive consecutive steps in UBL cascadesref Apg8 (reversible) 
Apg12 (irreversible)
Aminoacylation N-terminal aminoacid arginylation      
amide bonds to e-amino group of Lys N-homocysteinylation fibrillin 1 spontaneous
PEGylation to couple PEG to a protein, it is first necessary to activate the polymer by converting the hydroxyl terminus to a functional group capable of reacting typically with lysine and N-terminal amino groups of proteins. Each ethylene oxide unit of PEG associates with two to three water molecules, which results in the molecule behaving as if it were five to ten times as large as a protein of comparable molecular weightref. The clearance rate of PEGylated proteins is inversely proportional to molecular weight. Below a molecular weight of approximately 20,000, the molecule is cleared in the urine. Higher-molecular-weight PEG proteins are cleared more slowly in the urine and the fecesref       synthetic PEG addition ! => 
increased serum half-life and reduced antigenicityref, enhanced solubility, decreased proteolysis, and reduced rates of kidney clearance as well as enhanced selective tumor targeting :
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