Outline (huang)

Xin­Yun Huang Cornell

Signaling Molecules I: Kinases, Phosphatases, and G-proteins Oct. 10 –14, 2005

G-proteins: (Oct. 10 or 13)

I. Overview of cellular signaling: 1. Cell-to-cell communication by extracellular signaling usually involves six steps 2. Signaling molecules operate over various distances in animals 3. Hormones can be classed based on their solubility and receptor location 4. Cell-surface receptors belong to four major classes

II. Heterotrimeric G Proteins: 1. History of transmembrane signaling 2. Second messenger hypothesis 3. Reversible protein phosphorylation

4. Transducer model 5. Purification of G proteins 6. G-protein coupled receptors 7. Classification of GPCRs 8. Structures of GPCRs and G proteins

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Xin­Yun Huang Cornell

9. Demonstration of functional domains in GPCRs 10. Classification of Gα subunits 11. Gs links β-adrenergic receptors and adenylyl cyclases

12.Some bacterial toxins irreversibly modify G proteins 13.The structure of adenylyl cyclase 14. The structure of Gα s with adenylyl cyclase

15.Kinase cascades permit multi-enzyme regulation and amplify hormone signals 16. Cellular responses to cAMP vary among different cell types

17.Visual transduction 18.Gi 19.Gq 20. Hormone-induced release of Ca2+ from the ER is mediated by IP3 21. IP3-induced Ca2+ increases are used to trigger various responses in different cells

22.The effects of many hormones are mediated by second messengers 23. Effectors and interacting proteins of Gα subunits 24. Effectors of Gβγ subunits

25.From plasma membrane to nucleus 26.CREB links cAMP signals to transcription

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Xin­Yun Huang Cornell

III. Ras super-family small GTPases 1. Signaling through small GTPases 2. Five families 3. Ras family a. Lipid modification b. Anchoring to the plasma membrane c. Ras cycle d. Structure of Ras e. MAPK kinase pathway f. Adapter protein and GEF g. Various types of receptors transmit signals to MAPK kinase h. Yeast pheromone pathway i. Multiple MAPK pathways are found in yeast j. ERK, JNK, and p38 k. Ras targets multiple effectors 4. Rho family a. Rho cycle b. Dbl family GEFs c. Activation of RhoGEFs by extracellular signals d. Structure of Vav DH domain

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e. Translocation of Rho-GEF f. Effectors of Rho proteins g. Effectors of Rac and Cdc42 proteins h. Function of Rho family proteins i. Actin cytoskeletal reorganization j. Cell migration k. Stress fiber formation l. Focal adhesion m. Filopodia and Lamellipodia n. Gene expression 5. Rab family a. Endocytosis and exocytosis b. Secretory vesicles and lysosomes c. Yeast exocytosis and endocytosis d. Rab proteins and effectors e. V-SNARE and t-SNARE and docking factors 6. Arf family a. ER to Golgi and intra-Golgi transport 7. Ran family a. Ran cycle

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b. Protein nucleus export c. Protein nucleus import

Kinases and Phosphatases: (Oct. 12 or 14)

I. Protein Kinases: 1. Protein kinase Web resource 2. Classification of eukaryotic protein kinases 3. S. cerevisiae protein kinases 4. The human Kinome 5. PKA a. Structure of PKA catalytic domain b. Catalytic domain of lipid kinases is similar to protein kinases c. Dynamics of the glycine-rich loop of PKA with different ligands d. Substrate binding by PKA e. Structural features of the PKA activation segment f. Variation in size of the activation loop in different kinases g. Substrate binding by PKA 5

Xin­Yun Huang Cornell

6. MAPK a. Multiple MAPK pathways b. Phosphorylation of the ERK2 activation loop c. Structures of unphosphorylated and phosphorylated ERK2 7. Cyclin-dependent kinases a. Cdk2:CyclinA structure b. Structural comparison of Cdk2 and Cdk2:CyclinA c. Rotation of helix C d. Structure of cell cycle inhibitor p16INK4

e. Structure of Cdk6:p16 f. Comparison of Cdk2:CyclinA and Cdk6:p16 8. Src-family tyrosine kinases a. Structure of Src b. Comparison of Src activation and Cdk activation c. Bidirectional activation of non-receptor tyrosine kinases

II. Protein Phosphatases: 1. Protein Serine/Threonine Phosphatases a. PP1 b. PP2A

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Xin­Yun Huang Cornell

c. PP2B d. PP2C e. Structure of PP1 with an inhibitor f. Structure of PP2C 2. Protein Tyrosine Phosphatases a. Summary of PTPs b. Receptor PTPs c. Non-receptor PTPs d. Structure of PTP1B 3. Dual Specificity Protein Phosphatases: a. MKPs b. Cdc25

REFERENCES:

1. Chapter 20, Molecular Cell Biology, Fourth Edition, by Lodish et al. 2. Manning, G. et al. (2002) The protein kinase complement of the human

genome. Science 298: 1912-1934.

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Xin­Yun Huang Cornell 3. Alonso, A., et al. (2004) Protein tyrosine phosphatases in the human

genome. Cell 117: 699-711. 4. Takai, Y. et al., (2001) Small GTP-Binding Proteins. Physiological

Reviews 81: 153-208. 5. Johnson, S.A. and Hunter, T. (2005) Kinomics: methods for

deciphering the kinome. Nature Methods 2: 17-25.

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