Biochemistry of signal transduction and regulation

Preface VI 1 The Regulation of Gene Expression 1 1.1 Regulation of Gene Expression: How and Where? A Schematic Overview 1 1.2 Protein-Nucleic Acid Interactions as a Basis for Specific Gene Regulation 3 1.2.1 Structural Motifs of DNA-binding Proteins 3 1.2.2 The Nature of the Specific Interactions in Protein-Nucleic Acid Complexes 9 1.2.3 The Role of the DNA Conformation in Protein-DNA Interactions 11 1.2.4 Structure of the Recognition Sequence and Quaternary Structure of DNA-binding Proteins 13 1.3 The Principles of Transcription Regulation 17 1.3.1 Elements of Transcription Regulation 17 1.3.2 Functional Requirements for Repressors and Transcriptional Activators 19 1.3.3 Mechanisms for the Control of the Activity of DNA-binding Proteins 20 1.3.3.1 Binding of Effector Molecules 21 1.3.3.2 Binding of Inhibitory Proteins 23 1.3.3.3 Modification of Regulatory Proteins 23 1.3.3.4 Changes in the Concentration of Regulatory DNA-binding Proteins 24 1.4 Regulation of Transcription in Eucaryotes 25 1.4.1 Overview of Transcription Initiation in Procaryotes 26 1.4.2 The Basic Features of Eukaryotic Transcription 28 1.4.3 The Eucaryotic Transcription Apparatus 30 1.4.3.1 Structure of the Transcription Start Site and Regulatory Sequences 30 1.4.3.2 Elementary Steps of Eucaryotic Transcription 32 1.4.3.3 Formation of a Basal Transcription Apparatus from General Transcription Factors and RNA Polymerase 33 1.4.3.4 Phosphorylation of RNA Polymerase II and the Onset of Transcription 36 1.4.3.5 TFIIH – a Pivotal Regulatory Protein Complex 38 IX 1.4.4 Regulation of Eucaryotic Transcription by DNA-binding Proteins 39 1.4.4.1 The Structure of Eucaryotic Transcriptional Activators 39 1.4.4.2 Concerted Action of Transcriptional Activators and Coactivators in the Regulation of Transcription 41 1.4.4.3 Interactions with the Transcription Apparatus 45 1.4.5 Regulation of the Activity of Transcriptional Activators 45 1.4.5.1 The Principal Pathways for the Regulation of Transcriptional Activators 46 1.4.5.2 Phosphorylation of Transcriptional Activators 46 1.4.5.3 Heterotypic Dimerization 50 1.4.5.4 Regulation by Binding of Effector Molecules 52 1.4.6 Specific Repression of Transcription 52 1.4.7 Chromatin Structure and Transcription Activation 55 14.7.1 Transcriptional Activity and Histone Acetylation 58 1.4.7.2 Transcriptional Activity and Histone Methylation 62 1.4.7.3 Enhanceosomes 63 1.4.8 Methylation of DNA 65 1.5 Post-transcriptional Regulation of Gene Expression 68 1.5.1 Modifications at the 5’ and 3’ Ends of the Pre-mRNA 69 1.5.2 Formation of Alternative mRNA by Alternative Polyadenylation and by Alternative Splicing 70 1.5.3 Regulation via Transport and Splicing of Pre-mRNA 73 1.5.4 Stability of the mRNA 75 1.5.5 Regulation at the Level of Translation 78 1.5.5.1 Regulation by binding of protein to the 5’ end of the mRNA 79 1.5.5.2 Regulation by Modification of Initiation Factors 80 2 The Regulation of Enzyme Activity 89 2.1 Enzymes as Catalysts 90 2.2 Regulation of Enzymes by Effector Molecules 91 2.3 Principal Features of Allosteric Regulation 93 2.4 Regulation of Enzyme Activity by Binding of Inhibitor and Activator Proteins 94 2.5 Regulation of Enzyme Activity by Phosphorylation 95 2.5.1 Regulation of Glycogen Phosphorylase by Phosphorylation 97 2.5.2 Regulation of Isocitrate Dehydrogenase (E. coli) by Phosphorylation 100 2.6 Regulation via the Ubiquitin-Proteasome Pathway 101 2.6.1 Components of the Ubiquitin System 102 2.6.2 Degradation in the Proteasome 107 2.6.3 Recognition of the Substrate in the Ubiquitin-Proteasome Degradation Pathway 108 2.6.4 Regulatory Function of Ubiquitin Conjugation and the Targeted Degradation of Proteins 110 2.7 Regulation of Proteins by Sumoylation 113 X Contents 3 Structure and Function of Signal Pathways 115 3.1 General Function of Signal Pathways 115 3.2 Structure of Signaling Pathways 117 3.2.1 The Mechanisms of Intercellular Communication 117 3.2.2 Principles of Intracellular Signal Transduction 119 3.2.3 Components of Intracellular Signal Transduction 120 3.2.4 Coupling of Proteins in Signaling Chains 122 3.2.4.1 Coupling by Specific Protein–Protein Interactions 122 3.2.4.2 Coupling by Protein Modules 122 3.2.4.3 Coupling by Reversible Docking Sites 123 3.2.4.4 Coupling by Colocalization 123 3.2.4.5 Linearity, Branching and Crosstalk 124 3.2.4.6 Variability and Specificity of Receptors and Signal Responses 126 3.3 Extracellular Signaling Molecules 128 3.3.1 The Chemical Nature of Hormones 128 3.3.2 Hormone Analogs: Agonists and Antagonists 131 3.3.3 Endocrine, Paracrine and Autocrine Signaling 133 3.3.4 Direct Modification of Protein by Signaling Molecules 133 3.4 Hormone Receptors 135 3.4.1 Recognition of Hormones by Receptors 135 3.4.2 The Interaction between Hormone and Receptor 135 3.5 Signal Amplification 139 3.6 Regulation of Inter- and Intracellular Signaling 141 3.7 Membrane Anchoring and Signal Transduction 142 3.7.1 Myristoylation 144 3.7.2 Palmitoylation 145 3.7.3 Farnesylation and Geranylation 146 3.7.4 The Glycosyl-Phosphatidyl-Inositol Anchor (GPI Anchor) 147 3.7.5 The Switch Function of Lipid Anchors 148 4 Signaling by Nuclear Receptors 151 4.1 Ligands of Nuclear Receptors 151 4.2 Principles of Signaling by Nuclear Receptors 153 4.3 Classification and Structure of Nuclear Receptors 156 4.3.1 DNA-Binding Elements of Nuclear Receptors, HREs 156 4.3.2 The DNA-Binding Domain of Nuclear Receptors 159 4.3.3 HRE Recognition and Structure of the HRE-Receptor Complex 161 4.3.4 Ligand-binding Domains 162 4.3.5 Transactivating Elements of the Nuclear Receptors 164 4.4 Mechanisms of Transcriptional Regulation by Nuclear Receptors 165 4.5 Regulation and Variability of Signaling by Nuclear Receptors 169 4.6 The Signaling Pathway of the Steroid Hormone Receptors 171 4.7 Signaling by Retinoids, Vitamin D3, and the T3-Hormone 173 4.7.1 Structure of the HREs of RXR Heterodimers 175 4.7.2 Complexity of the Interaction between HRE, Receptor and Hormone 175 Contents XI 5 G Protein-Coupled Signal Transmission Pathways 179 5.1 Transmembrane Receptors: General Structure and Classification 179 5.2 Structural Principles of Transmembrane Receptors 181 5.2.1 The Extracellular Domain of Transmembrane Receptors 181 5.2.2 The Transmembrane Domain 183 5.2.3 The Intracellular Domain of Membrane Receptors 185 5.2.4 Regulation of Receptor Activity 186 5.3 G Protein-Coupled Receptors 187 5.3.1 Structure of G Protein-Coupled Receptors 188 5.3.2 Ligand Binding 191 5.3.3 Mechanism of Signal Transmission 192 5.3.4 Switching Off and Desensitization of 7-Helix Transmembrane Receptors 192 5.3.5 Dimerization of GPCRs 196 5.4 Regulatory GTPases 197 5.4.1 The GTPase Superfamily: General Functions and Mechanism 197 5.4.2 Inhibition of GTPases by GTP Analogs 200 5.4.3 The G-domain as Common Structural Element of the GTPases 200 5.4.4 The Different GTPase Families 201 5.5 The Heterotrimeric G Proteins 202 5.5.1 Classification of the Heterotrimeric G Proteins 203 5.5.2 Toxins as Tools in the Characterization of Heterotrimeric G Proteins 205 5.5.3 The Functional Cycle of Heterotrimeric G Proteins 206 5.5.4 Structural and Mechanistic Aspects of the Switch Function of G Proteins 208 5.5.5 Structure and Function of the bc-Complex 215 5.5.6 Membrane Association of the G Proteins 217 5.5.7 Regulators of G Proteins: Phosducin and RGS Proteins 218 5.6 Effector Molecules of G Proteins 220 5.6.1 Adenylyl Cyclase and cAMP as Second Messenger 220 5.6.2 Phospholipase C 225 6 Intracellular Messenger Substances: Second Messengers 231 6.1 General Functions of Intracellular Messenger Substances 231 6.2 cAMP 233 6.3 cGMP 235 6.4 Metabolism of Inositol Phospholipids and Inositol Phosphates 237 6.5 Inositol 1,4,5-Triphosphate and Release of Ca2+ 240 6.5.1 Release of Ca2+ from Ca2+ Storage 241 6.5.2 Influx of Ca2+ from the Extracellular Region 245 6.5.3 Removal and Storage of Ca2+ 246 6.5.4 Temporal and Spatial Changes in Ca2+ Concentration 246 6.6 Phosphatidyl Inositol Phosphates and PI3-Kinase 248 6.6.1 PI3-Kinases 249 6.6.2 The Messenger Substance PtdIns(3,4,5)P3 250 XII Contents 6.6.3 Akt Kinase and PtdIns(3,4,5)P3 Signaling 252 6.6.4 Functions of PtIns(4,5)P2 253 6.7 Ca2+ as a Signal Molecule 253 6.7.1 Calmodulin as a Ca2+ Receptor 256 6.7.2 Target Proteins of Ca2+/Calmodulin 257 6.7.3 Other Ca2+ Receptors 258 6.8 Diacylglycerol as a Signal Molecule 259 6.9 Other Lipid Messengers 260 6.10 The NO Signaling Molecule 261 6.10.1 Reactivity and Stability of NO 262 6.10.2 Synthesis of NO 263 6.10.3 Physiological Functions and Attack Points of NO 264 7 Ser/Thr-specific Protein Kinases and Protein Phosphatases 269 7.1 Classification, Structure and Characteristics of Protein Kinases 269 7.1.1 General Classification and Function of Protein Kinases 269 7.1.2 Classification of Ser/Thr-specific Protein Kinases 272 7.2 Structure and Regulation of Protein Kinases 273 7.2.1 Main Structural Elements of Protein Kinases 274 7.2.2 Substrate Binding and Recognition 276 7.2.3 Control of Protein Kinase Activity 277 7.3 Protein Kinase A 280 7.3.1 Structure and Substrate Specificity of Protein Kinase A 280 7.3.2 Regulation of Protein Kinase A 281 7.4 Protein Kinase C 283 7.4.1 Characterization and Classification 283 7.4.2 Structure and Activation of Protein Kinase C 286 7.4.3 Regulation of Protein Kinase C 288 7.4.4 Functions and Substrates of Protein Kinase C 290 7.5 Ca2+/Calmodulin-dependent Protein Kinases 292 7.5.1 Importance and General Function 292 7.5.2 Structure and Autoregulation of CaM Kinase II 293 7.6 Ser/Thr-specific Protein Phosphatases 296 7.6.1 Structure and Classification of Ser/Thr Protein Phosphatases 296 7.6.2 Regulation of Ser/Thr Protein Phosphatases 297 7.6.3 Protein Phosphatase I, PPI 299 7.6.4 Protein Phosphatase 2A, PP2A 301 7.6.5 Protein Phosphatase 2B, Calcineurin 302 7.7 Regulation of Protein Phosphorylation by Subcellular Localization 305 8 Signal Transmission via Transmembrane Receptors with Tyrosine-Specific Protein Kinase Activity 311 8.1 Structure and Function of Receptor Tyrosine Kinases 311 8.1.1 General Structure and Classification 313 8.1.2 Ligand Binding and Activation 314 Contents XIII 8.1.3 Structure and Activation of the Tyrosine Kinase Domain 319 8.1.4 Effector Proteins of the Receptor Tyrosine Kinases 323 8.1.5 Attenuation and Termination of RTK Signaling 326 8.2 Protein Modules as Coupling Elements of Signal Proteins 328 8.2.1 SH2 Domains 329 8.2.2 Phosphotyrosine-binding Domain (PTB Domain) 332 8.2.3 SH3 Domains 332 8.2.4 Membrane-targeting Domains: Pleckstrin Homology (PH) Domains and FYVE Domains 334 8.2.5 Phosphoserine/Threonine-binding Domains 335 8.2.6 PDZ Domains 336 8.3 Nonreceptor Tyrosine-specific Protein Kinases 337 8.3.1 Structure and General Function of Nonreceptor Tyrosine Kinases 337 8.3.2 Src Tyrosine Kinase and Abl Tyrosine Kinase 338 8.4 Protein Tyrosine Phosphatases 342 8.4.1 Structure and Classification of Protein Tyrosine Phosphatases 343 8.4.2 Cooperation of Protein Tyrosine Phosphatases and Protein Tyrosine Kinases 346 8.4.3 Regulation of Protein Tyrosine Phosphatases 348 8.5 Adaptor Molecules of Intracellular Signal Transduction 351 9 Signal Transmission via Ras Proteins 355 9.1 The Ras Superfamily of Monomeric GTPases 355 9.2 General Importance of Ras Protein 358 9.3 Structure and Biochemical Properties of Ras Protein 360 9.3.1 Structure of the GTP- and GDP-bound Forms of Ras Protein 361 9.3.2 GTP Hydrolysis: Mechanism and Stimulation by GAP Proteins 363 9.3.3 Structure and Biochemical Properties of Transforming Mutants of Ras Protein 366 9.4 Membrane Localization of Ras Protein 366 9.5 GTPase-activating Protein (GAP) in Ras Signal Transduction 368 9.6 Guanine Nucleotide Exchange Factors (GEFs) in Signal Transduction via Ras Proteins 369 9.6.1 General Function of GEFs 369 9.6.2 Structure and Activation of GEFs 369 9.7 Raf Kinase as an Effector of Signal Transduction by Ras Proteins 373 9.7.1 Structure of Raf Kinase 373 9.7.2 Interaction of Raf Kinase with Ras Protein 374 9.7.3 Mechanism of Activation and Regulation of Raf Kinase 374 9.8 Reception and Transmission of Multiple Signals by Ras Protein 375 10 Intracellular Signal Transduction: the Protein Cascades of the MAP Kinase Pathways 383 10.1 Components of MAPK Pathways 385 10.2 The Major MAPK Pathways of Mammals 388 XIV Contents 10.2.1 The ERK Pathway 388 10.2.2 The JNK/SAPK, p38 and ERK5 MAPK Pathways 391 11 Membrane Receptors with Associated Tyrosine Kinase Activity 395 11.1 Cytokines and Cytokine Receptors 395 11.2 Structure and Activation of Cytokine Receptors 396 11.2.1 Activation of Cytoplasmic Tyrosine Kinases 401 11.2.2 The Jak-Stat Pathway 405 11.2.2.1 The Janus Kinases 405 11.2.2.2 The Stat Proteins 406 11.3 T and B Cell Antigen Receptors 409 11.3.1 Receptor Structure 410 11.3.2 Intracellular Signal Molecules of the T and B Cell Antigen Receptors 411 11.4 Signal Transduction via Integrins 413 12 Other Receptor Classes 417 12.1 Receptors with Intrinsic Ser/Thr Kinase Activity: the TGFb Receptor and the Smad Proteins 417 12.1.1 TGFb Receptor 417 12.1.2 Smad Proteins 418 12.2 Receptor Regulation by Intramembrane Proteolysis 422 12.3 Signal Transduction via the Two-Component Pathway 424 13 Regulation of the Cell Cycle 429 13.1 Overview of the Cell Cycle 429 13.1.1 Principles of Cell Cycle Control 429 13.1.2 Intrinsic Control Mechanisms 431 13.1.3 External Control Mechanisms 433 13.1.4 Critical Cell Cycle Events and Cell Cycle Transitions 434 13.2 Key Elements of the Cell Cycle Apparatus 434 13.2.1 Cyclin-dependent Protein Kinases, CDKs 435 13.2.2 Structure of CDKs and Regulation by Phosphorylation 437 13.2.3 Cyclins 439 13.2.4 Regulation of Cyclin Concentration 440 13.2.5 Structural Basis for CDK Activation 442 13.2.6 Inhibitors of CDKs: the CKIs 445 13.2.7 Substrates of CDKs 447 13.2.8 Multiple Regulation of CDKs 449 13.3 Regulation of the Cell Cycle by Proteolysis 449 13.3.1 Targeted Proteolysis by the SCF Complex 451 13.3.2 Proteolysis during Mitosis: the Anaphase-promoting Complex/ Cyclosome 452 13.4 The G1/S Phase Transition 453 13.4.1 Function of the D-type Cyclins 454 13.4.2 Function of pRb in the Cell Cycle 456 13.5 Cell Cycle Control of DNA Replication 461 Contents XV 13.6 The G2/M Transition and Cdc25 Phosphatase 463 13.7 Summary of Cell Cycle Progression 465 13.8 The DNA Damage Checkpoints 466 14 Malfunction of Signaling Pathways and Tumorigenesis: Oncogenes and Tumor Suppressor Genes 469 14.1 General Aspects of Tumor Formation 469 14.1.1 Characteristics of Tumor Cells 469 14.1.2 Genetic Changes in Tumor Cells 471 14.1.3 Epigenetic Changes in Tumor Cells 472 14.1.4 Causes of Oncogenic Mutations 473 14.1.5 DNA Repair, DNA Damage Checkpoints, and Tumor Formation 474 14.1.6 Cell Division and Tumor Formation 475 14.2 Cell Division Activity, Errors in Function of Signal Proteins, and Tumor Formation 475 14.2.1 The Fate of a Cell: Quiescence, Division, or Death 476 14.3 Definition and General Function of Oncogenes and Tumor Suppressor Genes 477 14.3.1 Oncogenes and Proto-Oncogenes 478 14.3.2 Mechanisms of Activation of Proto-Oncogenes 479 14.3.3 Examples of the Functions of Oncogenes 482 14.4 Tumor Suppressor Genes: General Functions 487 14.5 DNA Repair, DNA Integrity and Tumor Suppression 488 14.6 The Retinoblastoma Protein pRb in Cancer 490 14.7 The p16INK4a Gene Locus and ARF 493 14.8 The Tumor Suppressor Protein p53 494 14.8.1 Structure and Biochemical Properties of the p53 Protein 495 14.8.2 Sequence-Specific DNA Binding of p53 496 14.8.3 Genes Regulated by p53 498 14.8.4 Activation, Regulation and Modulation of the Function of p53 500 14.8.5 Overview of p53 Regulation 502 14.8.6 The MDM2-p53 Network and Cancer 505 14.9 The Tumor Suppressor APC and Wnt/b-Catenin Signaling 507 15 Apoptosis 511 15.1 Basic Functions of Apoptosis 511 15.2 Overview of Apoptosis 513 15.3 Caspases: Death by Proteolysis 515 15.4 The Family of Bcl-2 Proteins: Gatekeepers of Apoptosis 520 15.5 The Mitochondrial Pathway of Apoptosis 522 15.6 Death Receptor-triggered Apoptosis 524 15.6.1 The Fas/CD95 Signaling Pathway 525 15.6.2 Tumor Necrosis Factor-Receptor 1 and Apoptosis 527 15.7 Links of Apoptosis and Cellular Signaling Pathways 528 15.7.1 PI3-Kinase/Akt Kinase and Apoptosis 529 15.7.2 The Protein p53 and Apoptosis 530 Index 533 XVI Contents