Protein: Post-translational Modification

Gene encoding region (ORF) transcription mRNA translation Protein (nascent protein, precursor protein) protein processing, post-translational modification Mature protein

folding
Biological active protein

Post-translational Modification

1. numerous and diverse 2. change the charge, conformation or size of protein molecule

Effects of Post-translational Modification

1. stability of protein 2. biochemical activity (activity regulation) 3. protein targeting (protein localization) 4. protein signaling (protein-protein interaction,cascade amplification)

Why protein post-translational modifications are made? (Biological functions)

A. Regulation (interconvertable modifications)

Monocyclic cascade (allosteric effectors) -P/de-P receptor-associated Tyr-Kinase coupled cascade

Cyclic cascade ADP-ribosylation / poly-ADP-ribosylation Coordinated Glycogen phosphorylase / Glycogen synthase

Unidirectional cascade Proteolytic activation

B. Cross-links
Stabilize or fix certain folded str. (Cofactors covalent binding)

Disulfide bond-cross links (Cys-Cys) Isopeptide (N-(-Gln)-Lys Transamidation (GlnLys or Ornithine--NH2) (Transglutaminases)

Blood clotting factor VIII coagulation Tissue Transglutaminase reaction Cell proliferation, aging, endocytosis, secretion, differentiation, apotosis, programmed cell death

C.

Covalent Cofactors
Biotinyl lysine (Carboxylase, transcarboxylases) Cys-bound linear tetrapyrrole (phycobiliproteins lightharvesting system of photosynthetic microorganisms)

FAD-linked His, Cys, or Tyr (DHase, Oxidase)

FMN-linked Cys

Heme-covalent bound (Cyt. C)

D.

Membrane Anchors

-NH2 myristoyl Cys- fattyacyl thioether Ser- palmitate or other fatty acids esters ThrC-terminal glycophospholipids C-terminal Cys prenylated group Farnesyl C15, Geranylgeranyl C20

E. Signaling, Recognition and Structural Amplification

F.

Protein Turnover (Protein Degradation)

Spontaneous Oxidation: Cys, His, Tyr, Met Ubiquitination: Lys

G. Others

Iodination: Tyr, (Thyroid hormones) Sulfation or methylation; Tyr / secreted proteins

Types of Post-translational Modification

A. Modification Involving Peptide Bonds Cleavage (limited proteolysis)

1. Peptide Bonds Cleavage (limited proteolysis, specific and well-regulated )

Signal leader peptide removed by signal peptidase (both in prokaryotes and eukaryotes) Precursor protein mature protein (Insulin) Zymogen active enzyme Trypsinogen Trypsin Pepsinogen Pepsin Prohormone Hormone Polyprotein neuropeptides (peptide hormone ) conversion

2. Peptide Bond Isomerization (Intramolecular)

Ser esters Cys thioesters Asp or Asn isoaspartate Prolyl peptide cis-trans isomerization (prolyl isomerase catalyzed)

3. Peptide Bond Formation, Transpeptidation

peptide bond splicing with peptide deletion and/or permutation Plant lectin Concanvalin A

B. Modifications Involving Amino and Carboxyl Termini

1. The N terminusH3N+

N-Formyl- (C1) N-Acetyl- (C2) N-Acyl- (C2, C4, C6, C8, C10) N-Lauroyl- (C12) N-Myristoyl- (C14) N-Tetradeca (mono and di)enoyl- (C141 C142)

N-AminoacylN--KetoacylN-MethylN-Pyrrolidone carboxylN-GlucuronylN-Glycosyl-

2. The C Terminus

Amide O-(ADP-ribosyl)O-Methyl-(N-Ethanolamine-glycan-phosphoinositides) -(N-TyT)

C. Modifications Involving Individual Amino Acid (Side Chains)

1. Arginine

N-(ADP-ribosyl)N-MethylN-DimethylN-N-Dimethyl-

Ornithine Citrulline N-Phosphoryl-

2. Asparagine

N-GlycosylAspartate N-Methyl-

N-(-Aspartyl)lysine erythro--HydroxyN-(ADP-ribosyl)-

3. Aspartate

D-Asp (racemization) -Carboxyerythro--Hydroxy-

-MethylthioO-PhosphorylO-Methyl-

4. CysteineHS-CH2

Cystine S--GlutamylS-(2-Histidyl)S-(3-Tyr) S-(sn-1-Glyceryl)S-(sn-1-Diacylglyceryl)S-(sn-1-{2,3,-Di-O-[3 ,7 ,11 .15tetramethylhexadecyl]}glyceryl)S-PalmitoylS-FarnesylS-GeranylgeranylS-Heme

S-Phycocyanobilin S-p-Coumaroyl S-(6-Flavin [FMN]) S-(8-Flavin [FAD]) S-Coenzyme A S-(ADP-ribosyl)S-GlycosylDehydroalanine Lysinoalanine Lanthionine Selenocysteine

5. Glutamate

O-(ADP-ribosyl) -CarboxyO-MethylN-(-Glutamyl)-Glu1-5 N-(-Glutamyl)-Glu3-34 N- (-Glutamyl)ethanolaminephosphate) S--Glutamyl-Cys is listed under Cys

6. Glutamine

Glutamate N-(-Glutamyl)lysine N-(-Glutamyl)-L-ornithine N-(-Glutamyl)polyamine N,N-(Bis--glutamyl)polyamine N5-Methyl-

7. Histidine

Diphthamide N-(ADP-ribosyl)diphthamide N-PhosphorylN-Methyl4-Iodo-and diiodoN- and N (8-flavin [FAD]) N-(8-Flavin[FMN])

8. Lysine

N-AcetylN-( N-Monomethylalanyl)N-Murein (peptidoglycan) N-LipoylN-BiotinylN-UbiquitinylN-PhosphorylN-PhosphopyridoxylN-Retinyl-

N-GlycosylN-Mono-, di- , trimethylHypusineN-(4-amino-2-hydroxybutyl)Allysine -Hydroxy-Hydroxyallysine Cross-links (desmosines, syndesines, pyridinolines) -Glyxosyloxy-

9. Methionine

Sulfoxide

10. Phenylalanine

-Glycosyloxy-

11. Proline

3-Hydroxy4-Hydroxy3,4-DihydroxyO4-ArabinosylhydroxyO4-GalactosylhydroxyO4-Glucosylhydroxy-

12. SerineHO-CH2

Selenocysteine O-PhosphorylO-PantetheinephosphorylO-(GlcNAc-1-phosphoryl)O-(Glycerol-1-phosphoryl)O-Methyl-

O-GlycosylAlanino(- or -histidine) Lanthionine O-AcetylO-Fatty acyl-

How modifications are made ?

A. Nonenzymatic Reaction

deamidationAsn, Gln racemizationAsp, Ser dehydroalanineCys, phosphor-Ser slow oxidationCys, His, Met slow cleavage and permutation of peptide bonds reducing sugar reaction with NH2-group of aas or side chains (Lys)Maillard reaction (Browing reaction) Schiffs base reaction.

B. Enzymatic Reaction
1. Irrversible, Unidirectional Reaction (permanently modified)

N-linked glycosylation Carboxyl methylation S-isoprenylation-Cys

2. Irrversible, Bi-directional Reaction. (Signal Amplificaion) Phosphorylation (protein kinase) / Dephosphorylation (phosphatase)Ser, Tyr, Thr.

Uridylyl and adenylyl transfer in bacterial glutamine synthetase

3. Reversible Reaction

RS-SR + R-SH R-S-S-R + RSH(disulfide isomerase) Coupled with protein-folding process