Proteases: Structure and Function (eBook)

Foreword 6
Contents 12
Chapter 1: Protease Families, Evolution and Mechanism of Action 14
1.1 Proteolytic Enzymes 14
1.1.1 Peptidases 15
1.1.1.1 Classification by Specificity 16
1.1.1.2 Classification by Catalytic Type 18
1.1.1.3 Classification by Homology 20
MEROPS Families 20
MEROPS Clans 21
MEROPS Identifiers 22
1.1.2 Catalytic Mechanisms 36
1.1.2.1 Serine Peptidases 37
1.1.2.2 Threonine Peptidases 37
1.1.2.3 Cysteine Peptidases 38
1.1.2.4 Aspartic Peptidases 38
1.1.2.5 Glutamic Peptidases 39
1.1.2.6 Metallopeptidases 39
1.1.3 Comparisons of Classifications 40
1.1.4 Integral Membrane Peptidases 41
1.1.5 Self-Cleaving Proteins 42
1.1.6 Relationships to Other Hydrolases 43
1.2 Other Proteolytic Enzymes 43
1.3 Conclusions 45
References 46
Chapter 2: Kinetics of the Interaction of Peptidases with Substrates and Modifiers 50
2.1 Introduction 50
2.2 Symbols, Nomenclature, Conventions and Software Used 51
2.3 Kinetics of Enzyme-Catalyzed Peptide Bond Hydrolysis 51
2.4 Basic Tools for Kinetic Data Analysis 54
2.4.1 Checking Enzyme Stability During Assays 54
2.4.2 Graphical Analysis 56
2.4.3 Regression Analysis 57
2.4.4 Numerical Integration and Global Fit of Progress Curves 58
2.5 Calculation of kcat and Km 60
2.5.1 Graphical Analysis 60
2.5.2 Non-linear Regression Analysis 62
2.5.3 First-Order Kinetics 63
2.5.4 The Integrated Michaelis-Menten Equation 64
2.5.5 Numerical Integration of the Differential Equation 65
2.6 Classical and Tight-Binding Enzyme Modification 65
2.6.1 The General Modifier Mechanism 67
2.6.2 The Specific Velocity Plot 69
2.6.3 A General Equation for Classical and Tight-Binding Systems 72
2.6.4 Non-productive Binding and Substrate Inhibition 74
2.7 Slow-Binding Inhibition 77
2.7.1 Integrated Rate Equations: Their Usefulness and Limits 79
2.7.2 Slow, Tight-Binding Inhibition 84
2.7.3 Numerical Integration Coupled to Non-linear Regression 84
2.7.4 The Serpin Inhibition Mechanism 87
2.8 Enzyme Inactivation 89
2.9 Further Concepts Relevant to Peptidases 93
2.9.1 Measuring `Invisible´ Kinetic Parameters 93
2.9.2 Double Enzyme-Modifier Interactions 94
2.9.3 Reporting Kinetic Results as IC50 94
References 94
Chapter 3: Compartmentalization of Proteolysis 98
3.1 Introduction 98
3.2 Sweet or Savoury-Salty or Tart: Biochemical Conditions of the Cleaving Environment 101
3.3 The Architectural Art of Compartmentalization of Proteolysis: Specified Rooms for Proteolytic Processing 107
3.4 Proteases Facing the Extracellular Space 110
3.5 Democracy as an Answer for Radical Decision-Making Processes 111
3.6 Debating Clubs: Proteases and Their Inhibitors 114
3.7 Speed-Dating of Proteolytic Enzymes and Their Substrates 116
3.8 How to Organise Proteolytic Actions in Busy Times Like Rapid Cell Cycle Progression, Remodelling of Cellular Components, o... 117
3.9 Themes Emerging from the Discovery of the New Kids on the Block 118
3.10 And Now, We Retire to the Study 119
References 120
Chapter 4: Cathepsins: Getting in Shape for Lysosomal Proteolysis 139
4.1 Introduction 139
4.2 Mannose 6-Phosphate Receptors: Key Cellular Interaction Partners of Lysosomal Cathepsins 140
4.3 Cysteine Cathepsins: Endopeptidases and Exopeptidases 142
4.4 Structures of Cysteine Cathepsin Precursors 144
4.5 Activation and Maturation of Cysteine Cathepsin Precursors 147
4.6 Unconventional Cysteine Cathepsin Gene Products 148
4.7 Biosynthesis and Molecular Forms of Cathepsin B 148
4.7.1 Proteolytic Maturation of Cathepsin B: A Lysosomal Proteinase as Catalyst and Substrate 149
4.7.2 Biosynthesis of Cathepsin B in Cancer Cells 150
4.7.3 Extracellular Forms of Cathepsin B and the Mechanisms of Its Release and Activation 151
4.8 Biosynthesis of Cathepsin L 152
4.8.1 Proteolytic Processing and Activation of Procathepsin L 154
4.8.2 Non-lysosomal Localization of Cathepsin L 155
4.8.3 M6P-Independent Intracellular Transport of Cathepsin L 157
4.9 Biosynthesis of Other Cysteine Cathepsins 159
4.10 Biosynthesis and Intracellular Transport of Cathepsin D 161
4.10.1 Biosynthesis of Rodent Cathepsin D 162
4.10.2 Biosynthesis and Molecular Forms of Cathepsin D in Non-mammalian Species 163
4.10.3 Maturation of Cathepsin D 165
4.10.4 Mechanism and Physiological Significance of the Single- to Double-Chain Processing of Cathepsin D 166
4.10.5 Structure and pH-Dependent Activation of Cathepsin D 167
4.10.6 Cathepsin D in Biological Fluids and Pathological Conditions 168
4.11 Cathepsins in Lysosomal Storage Disorders 169
4.12 Concluding Remarks 170
References 170
Chapter 5: Limited and Degradative Proteolysis in the Context of Posttranslational Regulatory Networks: Current Technical and Conceptional Advances 186
5.1 Introduction 186
5.2 Identification of Cleavage Sites by N- and C-Terminal Degradomics 189
5.2.1 Overview 189
5.2.2 Isolation of N-Termini: Positive Selection Procedures 191
5.2.2.1 Biotinylation of Protein N-Termini Using Subtiligase 191
5.2.2.2 Biotinylation of Protein N-Termini Post Lysine Guanidation 191
5.2.2.3 Labeling of Protein N-Termini with iTRAQ Reagents Post Lysine Guanidation 192
5.2.2.4 N-CLAP: Biotinylation of Protein N-Termini Using Edman Chemistry 193
5.2.3 Isolation of N-Termini: Negative Selection Procedures 194
5.2.3.1 Combined Fractional Diagonal Chromatography 194
5.2.3.2 Isolation of N-Termini by Phospho Tagging 195
5.2.3.3 Terminal Amine Isotope Labeling of Substrates 195
5.2.4 Isolation of C-Termini 197
5.2.4.1 COFRADIC-Based Enrichment of C-Terminal Peptides 197
5.2.4.2 C-Terminal Amine-Based Isotope Labeling of Substrates 197
5.2.5 Identification of Cleavage Sites by Non-selection Procedures 198
5.2.5.1 The Protein Topography and Migration Platform 198
5.3 Validation of Cleavage Sites 199
5.3.1 Overview 199
5.3.2 Proteomic Identification of Protease Cleavage Sites 200
5.3.3 Activity-Based Probes 201
5.4 Proteolysis Regulation Networks: Exemplary Studies 203
5.5 Interactions Between Proteolytic Processing and Post Translational Modification 207
5.6 Protein Turnover 212
5.6.1 Ubiquitin-Proteasome System 213
5.6.2 Autophagosomal-Lysosomal System 214
5.7 Outlook 214
References 216
Chapter 6: Exploring Systemic Functions of Lysosomal Proteases: The Perspective of Genetically Modified Mouse Models 228
6.1 Introduction 228
6.2 Cathepsin L in Epidermal Homeostasis and Regulation of Hair Cycling 229
6.2.1 Cathepsin L Deficiency as Molecular Cause of the Furless Phenotype 229
6.2.2 Cathepsin L Regulating Epidermal Proliferation and Carcinogenesis 231
6.2.3 Balanced Cathepsin Activity Required for Skin Barrier Function 232
6.3 Cysteine Cathepsins and Their Inhibitors in the Cardiovascular System 233
6.3.1 Atherosclerosis and Abdominal Aortic Aneurysm 233
6.3.2 Cardiac Homeostasis and Cardiomyopathy 235
6.4 Cathepsins in Lysosomal Neurodegenerative Disorders 236
6.4.1 Cathepsins in Neuronal Storage Disorders 236
6.4.2 Cathepsins as Executor Proteases in Neuronal Macroautophagy 238
6.4.3 Cystatin B a Critical Regulator of Neuronal Proteolytic Balance 238
6.5 Conclusions 239
References 240
Chapter 7: Astacins: Proteases in Development and Tissue Differentiation 245
7.1 Introduction 245
7.2 Structure of Astacin Proteases 246
7.2.1 Modular Composition of Astacins 246
7.2.2 Structure of Catalytic Domains and Metal Binding Sites 248
7.2.3 Buried N-Terminal Region in Mature Astacins 252
7.2.4 Active-Site Cleft and Substrate Specificity 253
7.2.5 Zymogen Structure and Activation Mechanism 254
7.2.6 Protein Inhibitors and Enhancers of Astacins 256
7.3 Distribution and Physiological Role of Astacins 257
7.3.1 BMP1/Tolloid Proteases (BTPs) 257
7.3.2 Meprin Proteases 259
7.3.3 Hatching Enzymes 261
7.3.4 Seminase Activated Astacin-Like Protease 262
References 262
Chapter 8: Proteases in Death Pathways 274
8.1 Introduction 275
8.2 Death Pathways 276
8.2.1 Nomenclature 276
8.2.2 Extrinsic Apoptosis 277
8.2.3 Intrinsic Apoptosis 277
8.2.4 Pyroptosis 278
8.2.5 Regulated Necrosis 278
8.2.6 Autophagy 279
8.2.7 Other Modalities 279
8.3 Caspases: The Essential Proteases in Death Pathways 279
8.3.1 Classification, Nomenclature and Family Members 280
8.3.1.1 Human Caspases 281
8.3.1.2 Caspases in Mammals 283
8.3.1.3 Non-mammalian Caspases and Metacaspases 283
8.3.2 The Caspase Fold 284
8.3.3 The Active Site, Substrate Recognition and Cleavage Mechanism 284
8.3.3.1 Active Site Architecture and Substrate Recognition 286
8.3.3.2 Catalytic Mechanism 287
8.3.4 Activation in Death Pathways 287
8.3.4.1 Caspase-Dependent Intrinsic Apoptosis: The Apoptosome 287
8.3.4.2 Extrinsic Apoptosis: Death Inducing Signaling Complex (DISC) 288
8.3.4.3 Pyroptosis: The Inflammasome 289
8.3.4.4 Caspase-2 Activation: The PIDDosome 290
8.3.4.5 Activation of Executioner Caspases 292
8.3.5 Caspase Substrates 293
8.3.5.1 Rho-Associated Kinase I (ROCK I) 293
8.3.5.2 Caspase-Activated DNAse (CAD) 293
8.3.5.3 Poly(ADP-Ribose) Polymerase (PARP) 294
8.3.5.4 Human Telomerase Reverse Transcriptase (hTERT) 294
8.3.5.5 Pro-interleukins and Interleukins 294
8.3.6 Morphological Changes upon Activation 295
8.3.7 Regulation and Specific Inhibition 297
8.3.7.1 X-Linked Inhibitor of Apoptosis Protein (XIAP) 299
8.3.7.2 c-FLIP: A Structural Homologue of Caspase-8 299
8.3.7.3 Non-natural Inhibition: Designed Ankyrin Repeat Proteins (DARPins) 300
8.4 Caspase-Related Diseases 302
8.5 Concluding Remarks 303
References 304
Chapter 9: ADAM Proteases in Physiology and Pathophysiology: Cleave to Function in Health or to Cause Disease 312
9.1 Introduction 312
9.2 ADAM17 Expression 313
9.3 In Vivo Function of the Major Sheddases 315
9.4 Structure 316
9.5 Shedding in Health and Disease 317
9.6 Substrate Recognition 318
9.7 Mechanisms of Activation 320
9.8 ADAM Proteases as Therapeutic Targets 322
References 323
Chapter 10: Proteases in the Nervous System 328
10.1 Proteases in Alzheimer´s Disease 328
10.1.1 ?-Secretase 329
10.1.2 beta-Secretase 331
10.1.3 Alternative beta-Secretases 332
10.1.3.1 Problems with BACE1 as Sole beta-Secretase 332
10.1.3.2 Cathepsins 333
10.1.3.3 Caspases 334
10.1.4 gamma-Secretase: A Hetero-tetrameric Intramembrane Protease Complex 335
10.1.5 Abeta-Degrading Proteases 337
10.1.5.1 Rationale 337
10.1.5.2 Neprilysin and Endothelin-Converting Enzymes 337
10.1.5.3 Insulin-Degrading Enzyme 338
10.1.5.4 Other Abeta-Degrading Proteases 338
10.2 Proline-Specific Peptidases in Brain and Neurodegeneration 340
10.2.1 Serine Peptidases of Clan SC 340
10.2.1.1 Prolyl Oligopeptidase Family S9 340
PEP Gene Family S9A 343
Dipeptidyl Peptidase 4 (DP4) Gene Family S9B 344
DP4 344
FAP 346
DP8 347
DP9 347
Dipetidyl Peptidase-Like Proteins 349
Ex-DP4-Like Enzymes 349
10.2.1.2 Family S28 350
Prolylcarboxypeptidase 350
Dipeptidyl Peptidase 2 (DP2) 351
10.2.2 Metallo-peptidases of Clan MG 352
10.2.2.1 X-Prolyl Aminopeptidases 353
AmpP1 353
AmpP2 353
AmpP3 354
10.2.2.2 Prolidase 355
10.2.3 Metallo-peptidase of Clan MH 356
10.2.3.1 Prolinase 356
References 357
Chapter 11: Proteases in the Mammalian Digestive System 381
11.1 Introduction 381
11.2 Distribution of Proteases in Anatomical Sections of the Digestive Tract 382
11.2.1 Salivary Proteases 382
11.2.2 Proteases of the Esophagus 383
11.2.3 Stomach Proteases 384
11.2.3.1 Pepsin 384
11.2.3.2 Chymosin 385
11.2.3.3 Gastricsin 385
11.2.4 Duodenum/Pancreas Proteases 386
11.2.5 Jejunum Proteases 387
11.2.6 Ileum Proteases 388
11.2.7 Large Intestine (Colon) Proteases 389
11.3 Protease Functions in Intestinal Pathobiology 390
11.3.1 Regulation of Proteases Under Physiological Condition 390
11.3.2 Dipeptidyl Peptidase IV (DDP4) and Diabetes, Celiac Disease 391
11.3.3 Tissue Remodeling and Wound Repair 392
11.3.4 Inflammatory Intestinal Diseases (e.g., IBD) and Proteases 393
11.3.5 Colon Cancer and Proteases 394
11.4 Conclusions 395
References 396
Chapter 12: Calpains in Health and Disease 402
12.1 Introduction 402
12.2 Conventional Calpains 404
12.2.1 Calpain-1/mu-Calpain and Calpain-2/m-Calpain 404
12.2.1.1 Discovery and Nomenclature 404
12.2.1.2 Structural Features 405
12.2.1.3 Biological Significance 406
12.2.1.4 Pathologic Role of Calpain 407
12.2.1.5 Conventional Calpain-Generated Biomarkers of CNS Injury 409
12.2.1.6 Calpain-Target-Based Theranostics for CNS Injury 409
12.3 Unconventional Calpains 412
12.3.1 Skeletal-Muscle-Specific Calpain 412
12.3.1.1 Discovery and Nomenclature 412
12.3.1.2 Structural Features 413
12.3.1.3 Proteolytic Activity 414
12.3.1.4 Biological Significance 415
12.3.2 Gastrointestinal-Tract-Specific Calpains 417
12.3.2.1 Discovery and Nomenclature 417
12.3.2.2 Structural Features 417
12.3.2.3 Activity and Substrates 419
12.3.2.4 Biological Significance 419
12.3.3 Other Calpains 420
12.3.3.1 PalB Homologs 420
12.3.3.2 The TRA-3 Homologs 421
12.3.3.3 The CAPN10 Homologs 422
12.3.3.4 The SOL Homologs 422
12.3.3.5 Phytocalpains 423
12.3.3.6 Other Calpain Members 423
12.4 Concluding Remarks 423
References 424
Chapter 13: Metalloproteinases in Cartilage Matrix Breakdown: The Roles in Rheumatoid Arthritis and Osteoarthritis 439
13.1 Introduction 439
13.2 MMPs and Metzincins 440
13.2.1 Three-Dimensional (3D) Structures of MMPs 444
13.2.1.1 Pro-domains 444
13.2.1.2 M Domain 444
13.2.1.3 Fibronectin Type II Domain 445
13.2.1.4 Linker Region 446
13.2.1.5 Hpx Domain 446
13.2.2 Mechanisms of Collagenolysis by MMPs 446
13.2.3 MMPs in Arthritis 449
13.3 ADAMTSs and Aggrecanases 450
13.3.1 3D Structures of ADAMTSs 451
13.3.1.1 M Domain 452
13.3.1.2 Dis Domain 453
13.3.1.3 TS Domain 453
13.3.1.4 CysR Domain 453
13.3.1.5 Sp Domain 454
13.3.2 The Role of Non-catalytic Domain of Aggrecanases (ADAMTS4 and ADAMTS5) in Aggrecanolysis 454
13.3.3 ADAMTSs in Arthritis 455
13.4 ADAMs 456
13.4.1 3D Structure of the ADAMs 457
13.4.1.1 M Domain 458
13.4.1.2 Dis Domain 459
13.4.1.3 CysR Domain 459
13.4.1.4 EGF Domain 460
13.4.2 ADAMs in Arthritis 460
13.5 Endogenous Inhibitors of MMPs, ADAMTSs and ADAMs 461
13.5.1 Inhibition Mechanisms of TIMPs 462
13.5.2 Pentosan Polysulfate Is an Exosite Inhibitor of ADAMTS4 and ADAMTS5 464
13.6 Future Prospects 464
References 465
Chapter 14: MMP-Mediated Collagen Remodeling and Vessel Functions 476
14.1 Introduction 476
14.2 Collagenolytic Activities of MMPs 477
14.3 MMP-Mediated Collagen Remodeling for Vessel Structure and Functions 479
14.3.1 Type IV Collagen Remodeling 479
14.3.2 Type I Collagen Remodeling 480
14.4 MMP-Mediated Proteolysis of Endothelial Cell-Cell Contact Molecules 481
14.5 MMP-Mediated Vessel Maturation Through Pericyte Recruitment 482
14.6 MT1-MMP: A Key Regulator of Vessel Function and Physiology 484
14.7 Concluding Remarks and Therapeutic Potentials 486
References 487
Chapter 15: Proteases in Cancer: Significance for Invasion and Metastasis 495
15.1 Introduction 495
15.2 Metalloproteases 496
15.2.1 Matrix Metalloproteases 496
15.2.1.1 The MMP Family 496
15.2.1.2 MMPs in Cancer 497
15.2.1.3 MMPs and Angiogenesis 500
15.2.1.4 MMPs and Inflammation 501
15.2.1.5 MMPs in Cancer Invasion 502
15.2.1.6 MMPs in Metastasis 503
15.2.2 ADAM and ADAM-TS Proteases 504
15.2.2.1 ADAMs and ADAM-TSs in Angiogenesis 506
15.2.2.2 ADAMs and ADAM-TSs in Invasion and Metastasis 507
15.2.2.3 ADAMs and ADAM-TSs in Inflammation and Immunity 507
15.2.2.4 ADAMs and ADAM-TSs as Markers or Therapeutic Targets in Cancer 508
15.3 Serine Proteases 509
15.3.1 Secreted Serine Proteases 509
15.3.1.1 The Plasminogen Activation System 509
15.3.1.2 Tissue Kallikreins 511
15.3.2 Membrane-Anchored Serine Proteases 513
15.3.2.1 GPI-Anchored Proteases: Testisin 513
15.3.2.2 GPI-Anchored Proteases: Prostasin 514
15.3.2.3 Type II Transmembrane Serine Proteases 515
TTSPs: Hepsin 515
TTSPs: Matriptase 516
TMPRSS2 518
15.3.3 Serine Protease Summary 518
15.4 Cysteine Proteases 519
15.4.1 Cysteine Cathepsins 519
15.4.1.1 Cathepsin B 520
15.4.1.2 Cathepsin X 522
15.4.1.3 Cathepsins L and V 523
15.4.1.4 Cathepsin H 524
15.4.1.5 Cathepsin C 524
15.4.1.6 Cathepsin K 524
15.4.1.7 Cathepsin S 525
15.4.1.8 Cathepsins F and W 525
15.4.1.9 Cathepsin O 526
15.4.1.10 Cysteine Cathepsins as Therapeutic Targets 526
15.5 Threonine Proteases 528
15.5.1 The Proteasome in Tumor Initiation/Promotion 528
15.5.2 The Proteasome in Angiogenesis 529
15.5.3 The Proteasome in Inflammation 530
15.5.4 The Proteasome in Drug Resistance 531
15.5.5 Proteasome Inhibitors in Cancer Therapy 531
15.6 Conclusions 532
References 535
Index 555