* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download GPI Anchor
Evolution of metal ions in biological systems wikipedia , lookup
Ancestral sequence reconstruction wikipedia , lookup
Point mutation wikipedia , lookup
Amino acid synthesis wikipedia , lookup
Gene expression wikipedia , lookup
Biochemical cascade wikipedia , lookup
Genetic code wikipedia , lookup
Biosynthesis wikipedia , lookup
Expression vector wikipedia , lookup
Paracrine signalling wikipedia , lookup
G protein–coupled receptor wikipedia , lookup
Magnesium transporter wikipedia , lookup
Metalloprotein wikipedia , lookup
Bimolecular fluorescence complementation wikipedia , lookup
Signal transduction wikipedia , lookup
Nuclear magnetic resonance spectroscopy of proteins wikipedia , lookup
Ribosomally synthesized and post-translationally modified peptides wikipedia , lookup
Interactome wikipedia , lookup
Protein purification wikipedia , lookup
Biochemistry wikipedia , lookup
Protein structure prediction wikipedia , lookup
Acetylation wikipedia , lookup
Protein–protein interaction wikipedia , lookup
Western blot wikipedia , lookup
蛋白質體學 Proteomics 2014 Post-translational Modifications (PTM) 陳威戎 2014.12.15 Classical Protein Biosynthesis 1. Proteins are synthesized in ribosomes and one trinucleotide specifies one amino acid. 2. Codons are universal and the starting codon (AUG) specifies Met or fMet. 3. Every protein should start with Met or fMet at the NH2-terminus. 4. Every protein should have no more than 20 amino acids. However, many exceptional amino acids were found in many naturally occurring proteins, therefore, proteins must be modified before, during or after ribosomal protein synthesis. Protein Biosynthesis at Three Levels of Modifications 20 Amino acids + 20 tRNAs Pre-translational Modifications 20 aa-tRNAs Co-translational Modifications ↓ ↓ Nascent polypeptide Post-translational Modifications ↓ Completed polypeptide Examples of Three Levels of Protein Modifications Levels 1. Pre-translational Examples a) Selenocysteine t-RNA b) Nonnatural amino acid t-RNA 2. Co-translational a) Signal sequence cleavage b) N-Glycosylation 3. Post-translational a) O-Glycosylation b) Peptide bond cleavage c) Protein splicing d) Lipidation e) Disulfide bond formation f) Ubiquitination, Sumoylation 以下內容感謝 “台灣大學 廖大修 名譽教授”、“長庚大學 游佳融 副教授”與 ”台灣大學 張世宗 副教授” 提供 N-Acetylation Reactions Acetylation Sites in Histones Hyperacetylated Chromatin Domains 1.In eukaryotes, the genome is packaged into two general types of chromatin: heterochromatin, which appears compact or condensed throughout the cell cycle, and euchromatin, which appears condensed only prior to mitosis. 2.A small number of loci that exhibit covalent histone modifications by histone acetyltransferases (HAT), such as hyperacetylation. 3.The hyperacetylated domains occur exclusively at loci containing highly expressed, tissue-specific genes, and that they are involved in the activation of these genes. Protein Acetylation in Prokaryotes 1. Protein acetylation plays a critical regulatory role in eukaryotes but prokaryotes also have the capacity to acetylate both the N-terminal residues and the side chain of Lys and is widespread for regulation of fundamental cellular processes. 2. Lys acetylation in particular can occur in proteins involved in transcription, translation, pathways associated with central metabolism and stress responses. 3. Like phosphorylation, acetylation appears to be an ancient reversible modification that can be present at multiple sites in proteins. 4. Acetylation is particularly important in regulating central metabolism in prokaryotes due to the requirement for acetyl-CoA and NAD+ for HAT and HDAC, respectively. Methylase-Catalyzed Reactions Protein Kinases and Their Preferred Substrate Specificities Substrate recognition at the catalytic site involves specific residues in the region near the site of phosphorylation. Protein Glycosylation Common in Eukaryotic Proteins Sugar–Peptide Bonds Sugar–Amino Acid Linkages of Glycoproteins Type of bond N-glycosyl O-glycosyl C-mannosylation Phosphoglycosyl Glypiation Linkage Sugar Configuration Asn GlcNAc Asn Glc Asn GalNAc Asn Rha Arg Glc Ser/Thr GalNAc Ser/Thr GlcNAc Ser/Thr Gal Ser/Thr Man Ser/Thr Fuc Ser/Thr Pse Ser Glc Ser FucNAc Ser Xyl Ser Gal Thr Man Thr GlcNAc Thr Glc Thr Gal Hyli Gal Hyp Ara Hyp Gal Hyp GlcNAc Tyr Glc Tyr Glc Tyr Gal Trp Man Ser GlcNAc Ser Man Ser Fuc Ser Xyl Pr-C-(O)-EthN-6-P-Man β β * * β α β α α α α β β β α α α * * β β β * α β β α α-1-P α-1-P β-1-P *-1-P Examples Ovalbumin, fetuin, insulin receptor Laminin, H. halobium S-layer H. halobium S-layer S. sanguis cell wall Sweet corn amylogenin Mucins, fetuin, glycophorin Nuclear and cytoplasmic proteins Earthworm collagen, B. cellulosoleum Yeast mannoproteins Coagulation and fibrinolytic factors C. jejuni flagellins Coagulation factors P. aeruginosa pili Proteoglycans Cell walls of plants M. tuberculosis secreted glycoproteins Dictyosteliumh, T. cruzi Rho proteins (GTPases) H. halobium S-layer, vent worm collagen Collagen, C1q complement Potato lectin Wheat endosperm Dictyostelium cytoplasmic proteins Muscle and liver glycogenin C. thermohydrosulfuricum S-layer T. thermohydrosulfuricus S-layer RNase 2, interleukin 12, properdin Dictyostelium proteinases L. mexicana acid phosphatase Dictyostelium proteins T. cruzi cell surface T. brucei VSG, Thy-1, Sulfolobus proteins Consensus Squences or Glycosylation Motifs for the Formation of Glycopeptide Bonds Glycopeptide bond GlcNAc-β-Asn Glc-β-Asn GalNAc-α-Ser/Thr GlcNAc-α-Thr GlcNAc-β-Ser/Thr Man-α-Ser/Thr Fuc-α-Ser/Thr Glc-β-Ser Xyl-β-Ser Glc/GlcNAc-Thr Gal-Thr Gal-β-Hyl Ara-α-Hyp GlcNAc-Hyp Glc-α-Tyr GlcNAc-α-1-P-Ser Man-α-1-P-Ser Man-α-Trpf Man-6-P-EthN-C(O)-Pr Consensus sequence or peptide domain Asn-X-Ser/Thr (X = any amino acid except Pro) Asn-X-Ser/Thr Repeat domains rich in Ser, Thr, Pro, Gly, Ala in no special sequence Thr rich domain near Pro residues Ser/Thr rich domains near Pro, Val, Ala, Gly Ser/Thr rich domains EGF modules (Cys-X-X-Gly-Gly-Thr/Ser-Cys) EGF modules (Cys-X-Ser-X-Pro-Cys) Ser-Gly (Ala) (in the vicinity of one or more acidic residues) Rho: Thr-37d; Ras, Rac and Cdc42: Thr-35 Gly-X-Thr (X = Ala, Arg, Pro, Hyp, Ser) (vent worm) Collagen repeats (X-Hyl-Gly) Repetitive Hyp rich domains (e.g., Lys-Pro-Hyp-Hyp-Val) Skp1: Hyp-143d Glycogenin: Tyr-194d Ser rich domains (e.g., Ala-Ser-Ser-Ala) Ser rich repeat domains Trp-X-X-Trp GPI attached after cleavage of C-terminal peptide Importance of Myristoylation 1.The myristate moiety participates in protein subcellular localization by facilitating protein-membrane interactions as well as protein-protein interactions. 2.Myristoylated proteins are crucial components of a wide variety of functions, including many signaling pathways, oncogenesis or viral replication. 3.Initially, myristoylation was described as a co-translational reaction that occurs after the removal of the initiator Met. It is now established that myristoylation can also occur post-translationally in apoptotic cells. 4.During apoptosis hundreds of proteins are cleaved by caspases and in many cases this cleavage exposes an N-terminal Gly within a cryptic myristoylation consensus sequence, which can be myristoylated. Co- and Post-translational Attachment of Myristate to Proteins Co-translational myristoylation: following removal of the initiator Met, the exposed N-terminal Gly is myristoylated. Post-translational myristoylation: following cleavage of a cryptic myristoylation site by caspase cleavage, the exposed Nterminl Gly is myristoylated. Biosynthesis of C-Terminal Isoprenyl Cysteine Methyl Ester 1. Proteins with a terminal Leu are modified by an isoprenyltransferase that transfers from geranylgeranyl pyrophosphate to Cys. Proteins with terminal residues, Ser, Ala, Met, or Gln are modified by another enzyme that adds farnesyl pyrophosphate to Cys. 2. Following the attachment of the isoprenyl moietis, the three terminal amino acids are cleaved by a protease. 3. Finally, an enzyme catalyzes the addition of a methyl group to the newly exposed carboxyl terminal Cys. Isoprenyl Proteins and Their Functions 1.Isoprenyl proteins include many G-proteins, many isoprenyl proteins function in signal transduction processes across the plasma membrane or in the control of cell division. 2.The increased hydrophobicity of the C-terminus can lead to interactions with the membrane bilayer that result in membrane association of these proteins. 3.Alternatively, the isoprenyl and methyl groups may be specific targets for binding by other membrane "receptor" proteins, leading to a specific alignment of protein partners in signaling pathways. S-Palmitoylation ︱ Structure: CH3(CH2)14CO-SCys ︱ 1. Protein S-palmitoylation is the thioester linkage of long-chain fatty acids to Cys in proteins. 2. Addition of palmitate to proteins facilitates their membrane interactions and trafficking, and it modulates protein-protein interactions and enzyme activity. 3. The reversibility of palmitoylation makes it a biological mechanism for regulating protein activity. 4. The regulation of palmitoylation occurs through the actions of acyltransferases and acylthioesterases. These molecules work in concert with thioesterases to regulate the palmitoylation status of numerous signaling molecules, ultimately influencing their function. Functions of Palmitoylation 1.Similar to other lipid modifications, palmitoylation promotes membrane association of otherwise soluble proteins. 2.The function of palmitoylation, however, ranges beyond that of a simple membrane anchor. 3.Trafficking of lipidated proteins from the early secretory pathway to the plasma membrane is dependent upon palmitoylation in many cases. 4.Modification with fatty acids impacts the lateral distribution of proteins on the plasma membrane by targeting them to lipid rafts. 5.Palmitoylation also functions in the regulation of protein activity. Glypiation 1. The process of adding glycosyl phosphatidyl inositol (GPI) to proteins, which has been termed glypiation, is carried out by a transamidase that cleaves the C-terminal peptide and concomitantly transfers the preassembled GPI anchor to the newly exposed carboxyterminal amino acid residue to establish an amide bond between the latter and the ethanolamine moiety of the glycolipid. 2. GPI assembly takes place entirely on the cytoplasmic side of the ER and followed by its translocation to the lumenal side, where attachment to the protein takes place. 3. The transamidase reaction is carried out by a multiprotein complex that has as yet not been isolated in its intact form. 4. The carboxy-terminal signal peptide which is cleaved prior to binding of the GPI, consisting 15–30 amino acids, has structural similarities to the NH2-terminal peptide that functions in general to direct nascent chains into the ER lumen. GPI Anchor The GPI anchor is a complex structure comprising a phosphoethanolamine linker, glycan core, and phospholipid tail. Membrane-Associated Proteins in a Lipid Bilayer Containing Lipid Raft Domains The GPI anchor anchors the modified protein in the outer leaflet of the cell membrane. Biosynthesis of GPI Anchor In trypanosomes In mammalian cells PI, phophatidylinositol; G, glucosamine; Ac, acetyl; M, mannose; pE, Phosphoehanolamine; (acyl), fatty acid linked to inositol. Functions of GPI-Anchored Proteins ──────────────────────────────────────────────────────────────── Biological role Protein Source ──────────────────────────────────────────────────────────────── enzymes alkaline phosphatase mammalian tissues, Schistosoma 5′-nucleotidase mammalian tissues dipeptidase pig and human kidney, sheep lung cell-cell interaction LFA-3 human blood cells PH-20 guinea pig sperm complement regulation CD55 (DAF) human blood cells CD59 human blood cells mammalian antigens Thy-1 mammalian brain and lymphocytes Qa-2 mouse lymphocytes CD14 human monocytes CD52 human lymphocytes protozoan antigens VSG T. brucei 1G7 T. cruzi procyclin T. brucei miscellaneous scrapie prion protein hamster brain CD16b human neutrophils folate-binding protein human epithelial cells ──────────────────────────────────────────────────────────────── ■ Steps involved in protein degradation 19S 20S Core Peptidases 6 ATPases Poly-ubiquitin chain 2-25 residues Antigenic peptides Cytosolic peptidases Amino acids ■ The ubiquitination cascade E2 E1 E3 Degradation ■ Comparison of ubiquitin and SUMO Small Ubiquitin-like Modifier (SUMO) C-terminal GG motif ■ The mechanism of reversible sumoylation SENP: sentrin- specific protease Sumoylation Processing E1 E2 Desumoylation E3 ■ Molecular consequences of sumoylation Interfere interaction Provide a binding site Conformational change More active or inactive ■ SUMO participates in diverse cellular processes DNA damage repair Chromosome segregation Nuclear transport Cell division Hypoxia Stress response Inflammatory response Oncogenesis Flowering time in plants Activation of Proteases 1. After trypsinogen enters the small intestine, it is converted into its active form, trypsin by enteropeptidase. 2. Now trypsin hydrolyzes more trypsinogen and starts to hydrolyze chymotrpsinogen to active their forms. Proteomic analysis of PTMs Mann and Jensen, Nature Biotech. 21, 255 (2003)