1. CZ5225: Modeling and Simulation in Biology Lecture 10: Biological Pathways II: Signaling Pathways Prof. Chen Yu Zong Tel: 6874-6877 Email: yzchen@cz3.nus.edu.sg http://xin.cz3.nus.edu.sg Room 07-24, level 7, SOC1, NUS yzchen@cz3.nus.edu.sg http://xin.cz3.nus.edu.sgyzchen@cz3.nus.edu.sg http://xin.cz3.nus.edu.sg

2. 2 What is Signal Transduction? Signal Transduction is the process by which a cell converts an extracellular signal into a response. Involved in: Cell-cell communication Cell’s response to environment Intracellular homeostasis- internal communication

3. 3 Generic Signaling Pathway Signal Receptor (sensor) Transduction Cascade Targets Response Altered Metabolism Metabolic Enzyme Gene Regulator Cytoskeletal Protein Altered Gene Expression Altered Cell Shape or Motility

4. 4 Components of Signaling What can be the Signal? External message to the cell Peptides / Proteins- Growth Factors Amino acid derivatives - epinephrine, histamine Other small biomolecules - ATP Steroids, prostaglandins Gases - Nitric Oxide (NO) Photons Damaged DNA Odorants, tastants Signal = LIGAND Ligand- A molecule that binds to a specific site on another molecule, usually a protein, ie receptor

5. 5 Components of Signaling What are Receptors? Sensors, what the signal/ligand binds to initiate ST Cell surface Intracellular Hydrophillic Ligand Cell-Surface Receptor Plasma membrane Hydrophobic Ligand Carrier Protein Intracellular Receptor Nucleus

6. 6 Cell Surface Receptor Types: 1)Ligand-gated ion channel

7. 7 Cell Surface Receptor Types: 2) G-Protein Coupled Receptor

8. 8 Cell Surface Receptor Types: 3) Enzyme-linked Receptor eg Growth Factor Receptors

9. 9 Growth Factors Ligands which bind enzyme linked receptors Signaling diverse cellular responses including: Proliferation Differentiation Growth Survival Angiogenesis Capable of sending signal to multiple cell types or be specific

10. 10 FactorPrincipal Source Primary ActivityComments PDGFplatelets, endothelial cells, placenta promotes proliferation of connective tissue, glial and smooth muscle cells two different protein chains form 3 distinct dimer forms; AA, AB and BB EGFsubmaxillary gland, Brunners gland promotes proliferation of mesenchymal, glial and epithelial cells TGF-  common in transformed cells may be important for normal wound healing related to EGF FGFwide range of cells; protein is associated with the ECM promotes proliferation of many cells; inhibits some stem cells; induces mesoderm to form in early embryos at least 19 family members, 4 distinct receptors NGF promotes neurite outgrowth and neural cell survival several related proteins first identified as proto-oncogenes; trkA (trackA), trkB, trkC Erythropoietinkidneypromotes proliferation and differentiation of erythrocytes TGF-  activated TH 1 cells (T-helper) and natural killer (NK) cells anti-inflammatory (suppresses cytokine production and class II MHC expression), promotes wound healing, inhibits macrophage and lymphocyte proliferation at least 100 different family members IGF-Iprimarily liverpromotes proliferation of many cell types related to IGF-II and proinsulin, also called Somatomedin C IGF-IIvariety of cellspromotes proliferation of many cell types primarily of fetal origin related to IGF-I and proinsulin Growth Factors

11. 11 Growth Factor Receptors

12. 12 Most growth factors bind Receptor Tyrosine Kinases

13. 13

14. 14 Growth Factor Receptor Activation I RTKRS/TK

15. 15 Growth Factor Receptor Activation II

16. 16 Growth signal autonomy, Insensitivity to anti-growth signals, Resistance to apoptosis: Uncouple cell’s growth program from signals in the environment. Growth factors in normal cells serve as environmental signals. Growth Factor ST and Cancer Growth factors regulate growth, proliferation, and survival. These are all deregulated in cancer.

17. 17 GF Receptors with Oncogenic Potential EGFR, kinase activity stimulated by EGF-1 and TGF-a involved in cell growth and differentiation, was linked via sequence homology to a known avian erythroblastosis virus onocgene, v-erbB. Since then, many oncogenes have been shown to encode for GFRs. EGFR familyInsulin Receptor family erbB1 (c-erbB)IGF-1 (c-ros) erbB2 (neu) Neurotrophins FGF FamilyNGFR (trk) FGFR-1(fig)BDNFR (trk-B) FGFR-2(K-sam)NT3 R (trk-C) PDGFR Family CSF-1R (c-fms) SLF R (c-kit)

18. 18 Growth factors with Oncogenic Potential PDGF, originally shown to regulate proliferation, was also shown to have homology to v-sis, the simian sarcoma virus. Other viral oncogenes encoded protein products that were growth factors that often over-expressed in cancer such as TGF-a. Autocrine signalling leads to deregulated growth. PDGF familyNeurotrophins A chainNGF B chain (c-sis)BDNF FGF FamilyNT3 acidic FGFCytokines (Hematopoietic) basic FGFIL-2 EGF Family IL-3 EGFM-CSF TGF-aGM-CSF

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23. 23 Induction of cancer by alternations in several types of proteins involved in cell growth control

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25. 25 Generic Signal Transduction

26. 26 RTK Signal Transduction

27. 27 Signal Transduction Downstream effectors Protein Signaling Modules (Domains) SH2 and PTB bind to tyrosine phosphorylated sites SH3 and WW bind to proline-rich sequences PDZ domains bind to hydrophobic residues at the C-termini of target proteins PH domains bind to different phosphoinositides FYVE domains specifically bind to Pdtlns(3)P (phosphatidylinositol 3-phosphate)

28. 28 Mechanisms for Activation of Signaling Proteins by RTKs Activation by membrane translocation Activation by a conformational change Activation by tyrosine phosphorylation

29. 29 Mechanisms for Attenuation & Termination of RTK Activation 1) Ligand antagonists 2) Receptor antagonists 3) Phosphorylation and dephosphorylation 4) Receptor endocytosis 5) Receptor degradation by the ubiquitin-proteosome pathway

30. 30 Activation of MAPK Pathways by Multiple Signals Growth, differentiation, inflammation, apoptosis -> tumorigenesis

31. 31 Overview of MAPK Signaling Pathways

32. 32 The MAPK Pathway Activated by RTK

33. 33 RTK ST- PI3K pathway P

34. 34 Apoptosis Pathways

35. 35 TGF Pathway

36. 36 Proto-Oncogenes that Encode for Signaling Proteins Serine/Threonine Kinases c-raf family akt Non-receptor Tyrosine Kinases src abl Receptor associated binding proteins c-ras family

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39. 39 Ras recruits Raf to the membrane

40. 40 Activation Pathways for c-Src

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42. 42 ST intermediates can be targets for anti-cancer drugs Kinases: Raf

43. 43 ST intermediates can be targets for anti-cancer drugs Kinases: Bcr-Abl

44. 44 On-Line Resources Mechanisms of Signal Transduction http://www-isu.indstate.edu/thcme/mwking/signal-transduction.html Clear, illustrated summaries of the various mechanisms of signal transduction Pathways http://www.genome.ad.jp/kegg/kegg4.html KEGG: Kyoto Encyclopedia of Genes and Genomes. Site contains Pathway Info, Disease Catalogs, Cell Catalogs, Molecule Catalog, and Genomic Info. It also provides Links to Pathway and Other Databases. http://www.biocarta.com/genes/PathwayGeneSearch.asp?geneValue=g Comprehensive illustrations of signaling pathways Extracellular Signal Molecules http://www.grt.kyushu-u.ac.jp/spad/menu.html Signals and the pathways stimulated by each Kinetic constants http://bidd.nus.edu.sg/group/kdbi/kdbi.asp Kinetic Data of Biomolecular Interactions, a collection of experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligandbinding or reaction events described in the literature.

45. 45 On-Line Resources Viruses and Cancer http://www.geocities.com/tumorbio/vir/vir.htm History and current summary of viruses and human cancer Science Maagazine Signal Tansduction Knowledge Environment-Pathways http://stke.sciencemag.org/cm/index.dtl Mammalian MAPK signalling pathways http://kinase.oci.utoronto.ca/signallingmap.html MAPK signaling pathway, with information on each component Small Molecule Platform http://www.onyx- pharm.com/onyxtech/small_molecule_platform.html The development of anti-cancer drugs that act on the ras signaling pathway Signal Transduction http://www.kumc.edu/biochemistry/bioc800/siglofra.htm Signal transduction from a medical viewpoint