Fibrous Proteins: Structures and Mechanisms (eBook)

Preface 6
Contents 8
Chapter 1: Fibrous Protein Structures: Hierarchy, History and Heroes 10
1.1 Introduction: Early History and Key Players 12
1.1.1 Simplicity and Complexity in Amino Acids 12
1.1.2 The ?-Helix 14
1.1.3 The Coiled Coil and Heptads 19
1.1.4 Features of the Heptad 22
1.1.5 Multi-stranded Coiled-Coils 22
1.1.6 Stutters, Stammers and Coiled Coils with Specific Discontinuities 26
1.2 Beta Structures 26
1.3 The Collagen Fold 30
1.4 Assembly of Building Blocks 31
1.4.1 Globular Proteins 31
1.4.2 Packing of Coiled Coils 33
1.4.3 Assembly of ?-Sheets 34
1.4.4 Collagen Fibrils 36
1.5 New Approaches to Solving Fibrous Protein Structures 37
1.6 The Future: Protein Engineering 39
References 39
Chapter 2: Coiled-Coil Design: Updated and Upgraded 43
2.1 Scope of This Review 44
2.2 The Basics of Coiled-Coil Sequence and Structure 45
2.3 Computational Tools for Analysing Coiled-Coil Sequences and Structures 46
2.4 Straightforward Rules for Coiled-Coil Prediction and Design 48
2.5 A Heptad of Completely de novo Helical Assemblies 50
2.5.1 Rationally Designed Dimers, Trimers and Tetramers 50
2.5.2 Expanding de novo Coiled Coils Past Tetramer 51
2.5.3 Structural Rationale for Higher-Order Oligomerization 53
2.6 Parametric and Computational Coiled-Coil Design 55
2.6.1 Background: Computational Methods Old and New 55
2.6.2 Parametric Coiled-Coil Designs Achieved to Date 56
2.7 Improving Heterospecificity in Coiled-Coil Design 57
2.8 Adding Antiparallel Coiled Coils to the Mix 59
2.9 Building with Coiled-Coil Modules: Protein Origami, Synthetic Biology and Materials 59
2.10 Concluding Remarks 62
References 63
Chapter 3: Functional and Structural Roles of Coiled Coils 70
3.1 The Basic Architecture of Coiled Coils 71
3.2 Classical Roles of Coiled Coils 73
3.2.1 Filament-Forming Coiled-Coil Proteins 73
3.2.2 From Static Oligomerization to Dynamic Molecular Recognition 75
3.2.3 Intra-chain Coiled Coils 77
3.3 Molecular Spacers – Dynamic and Resilient 78
3.3.1 The Complex Nature of Trimeric Autotransporter Adhesins 78
3.3.2 Polar Core Residues – Between Specificity, Stability, and Foldability 80
3.3.3 Resilience Towards Insertions and Deletions – Boosting Evolvability 82
3.4 Non-specific Molecular Recognition 84
3.4.1 Molecular Recognition in Protein Folding and Disaggregation 85
3.4.2 Molecular Recognition in Protein Unfolding and Degradation 86
3.5 Coiled Coils in Signal Transduction 87
3.5.1 Basic Architecture and Signal Propagation in Histidine Kinases 89
3.5.2 Signal Propagation Through HAMP Domains 90
3.5.3 The Role of Asymmetry 92
3.6 Concluding Remarks 93
References 94
Chapter 4: The Structure and Topology of ?-Helical Coiled Coils 101
4.1 Introduction 102
4.2 Structural Parameters 105
4.2.1 The Standard Model 105
4.2.2 Prediction and Analysis Programs 106
4.2.3 Coiled Coils with Variant Core Geometry 108
4.2.4 Non-heptad Coiled Coils 110
4.3 Structural Determinants of Folding and Stability 117
4.3.1 Number and Orientation of Helices 117
4.3.2 Folding and Stability 120
4.4 Structural Diversity 123
4.4.1 Fibres and Zippers 123
4.4.2 Tubes, Sheets, Spirals, and Rings 127
4.5 Evolution and Phylogenetic Diversity 128
References 131
Chapter 5: Structural Transition of Trichocyte Keratin Intermediate Filaments During Development in the Hair Follicle 136
5.1 Introduction 137
5.2 Axial Structure of the IF 141
5.2.1 X-Ray Diffraction 141
5.2.2 Crosslinking 141
5.3 Lateral Structure of the IF 147
5.4 Radial Projection and Surface Lattice of Trichocyte IF 148
5.5 Summary 151
References 151
Chapter 6: Crystallographic Studies of Intermediate Filament Proteins 155
6.1 Introduction 156
6.2 Primary Structure of IF Proteins 159
6.3 Experimental Studies of the Elementary Dimer 162
6.4 Crystallographic Challenges of Coiled-Coil Fragments 165
6.5 Elementary Dimer Structure 167
6.6 Conclusions and Outlook 170
References 171
Chapter 7: Lessons from Animal Models of Cytoplasmic Intermediate Filament Proteins 175
7.1 Introduction 177
7.2 Analysis of Keratins 179
7.2.1 Simple Epithelial Keratins 180
7.2.1.1 Expression and Architectural Functions of Simple Epithelial Keratins 180
7.2.1.2 Scaffolding and Regulatory Functions of Simple Epithelial Keratins 183
7.2.2 Epidermal Keratins 189
7.2.2.1 Expression and Architectural Functions of Epidermal Keratins 189
Analysis of K5, K14 and K15 in the Basal Epidermis 189
Analysis of Suprabasal Epidermal Keratins 190
Analysis of Keratins Expressed in Corneal Epithelia 191
7.2.2.2 Regulatory Functions of Epidermal Keratins 191
Deletion of the Entire Keratin Protein Family 194
7.3 Analysis of Type III Intermediate Filament Proteins 195
7.3.1 Vimentin 195
7.3.2 Desmin 201
7.3.3 GFAP 203
7.3.4 Syncoilin and peripherin 205
7.4 Analysis of Type IV Intermediate Filaments 205
7.4.1 Neuronal Type IV IFs 205
7.4.2 Synemin 211
7.4.3 Nestin 212
7.5 Type VI Intermediate Filaments 213
7.5.1 Filensin (BFSP1) and Phakinin (BFSP2) 213
7.6 Caenorhabditis elegans cytoplasmic IFs 213
7.7 Conclusion 216
References 217
Chapter 8: Filamentous Structure of Hard ?-Keratins in the Epidermal Appendages of Birds and Reptiles 235
8.1 Introduction 236
8.2 Sequence Similarities and Differences 239
8.2.1 Filament-Forming Central Domain 239
8.2.2 N-Terminal Domain 243
8.2.3 C-Terminal Domain 244
8.3 Information on the Molecular Structure Derived from X-Ray Diffraction Studies 245
8.4 Further Modelling of the Structure of the Filament 246
8.5 Packing of Filaments in Sheets in Feather Keratin 249
8.6 Physical Properties of ?-Keratins and Their Relationship to Sequence Characteristics 250
8.6.1 Highly Charged Cysteine-Rich Segments 251
8.6.2 Glycine-Tyrosine-Rich Segments 251
8.6.3 Glycine-Rich Segments 252
8.7 Summary 252
References 254
Chapter 9: Tropomyosin Structure, Function, and Interactions: A Dynamic Regulator 257
9.1 Introduction 258
9.2 The Structure of Tropomyosin 260
9.2.1 Alanine Clusters 262
9.2.2 Bends and Holes in Core Packing 264
9.2.3 The Overlap Complex 264
9.2.4 Tropomyosin Dynamics and Transmission of Structural Information 265
9.3 How Does Tropomyosin Bind to Actin? A Design for Weak and Dynamic Binding to the Actin Filament 267
9.3.1 What Constitutes an Actin Binding Site on Tropomyosin? 269
9.3.2 How Does Tropomyosin Assemble on the Actin Filament? 271
9.4 Regulation of the Actin-Myosin Interaction 272
9.4.1 Common Features of Regulation 275
9.4.2 Specific Regulation 275
9.5 Four Tropomyosin Genes, Many Isoforms and Diverse Binding Partners 276
9.5.1 Exon 9 Encodes Isoform-Specific Function 278
9.5.2 Complexes Between Tropomyosin and Tropomodulin 279
9.6 Conclusions 280
References 281
Chapter 10: Titin and Nebulin in Thick and Thin Filament Length Regulation 289
10.1 Introduction 290
10.2 Titin and Nebulin – The ‘‘Molecular Ruler’’ Hypotheses 292
10.2.1 Titin 293
10.2.2 Nebulin 293
10.2.3 The Ruler Hypotheses 295
10.3 Titin/Nebulin in Thick/Thin Filament Assembly During Sarcomerogenesis 295
10.3.1 Electron Microscopy 296
10.3.2 Immunofluorescent Microscopy 296
10.3.3 Relevance to the Titin/Nebulin Ruler-Template Hypotheses 297
10.4 Thick Filament Assembly with Absent/Truncated Titin/Nebulin 298
10.4.1 Titin Truncations 298
10.4.2 Nebulin Truncations 299
10.5 Thick and Thin Filament Length Control – Possible Involved Factors 300
10.5.1 Tropomodulin 300
10.5.2 N-RAP 300
10.5.3 Chaperones 301
10.5.4 Contractile Activity 302
10.6 Thick and Thin Filaments Length Control in Striated Muscles of Invertebrates (Indirect Flight Muscles of Drosophila) 304
10.7 Size Regulation in Non-muscle Biological Structures 306
10.8 Conclusion 308
References 309
Chapter 11: Myosin and Actin Filaments in Muscle: Structures and Interactions 323
11.1 Introduction and Overview of the Sarcomere 324
11.2 Actin Filament Structure 330
11.2.1 3D Reconstruction of Actin Filaments 330
11.2.2 Checking the Steric Blocking Model 330
11.2.3 X-Ray Crystallography of Actin and Myosin 331
11.2.4 Recent High Resolution Thin Filament Helical Reconstructions 333
11.2.5 Finding Troponin – Single Particle Analysis 335
11.2.6 The Thin Filament Regulation Mechanism 340
11.2.7 Nebulin 340
11.3 Myosin Filament Structure 343
11.3.1 Myosin Filament Symmetries 343
11.3.2 Myosin Head Organisation 345
11.3.3 Myosin Filaments in Vertebrate Striated Muscles: MyBP-C and Titin 351
11.3.4 Myosin Filaments in Vertebrate Striated Muscles: The Myosin Head Array 353
11.3.5 Myosin Filaments in Insect Flight Muscle 355
11.3.6 The Myosin Filament Backbone 358
11.3.7 The Vertebrate Myosin Filament Bare Zone 361
11.3.8 Paramyosin Filaments 362
11.3.9 Myosin Filaments in Vertebrate Smooth Muscles 364
11.3.10 Nematode and Limulus Muscles 366
11.4 Future Prospects 367
11.5 Late Breaking Results 368
References 368
Chapter 12: Dystrophin and Spectrin, Two Highly Dissimilar Sisters of the Same Family 376
12.1 Introduction 377
12.2 Dystrophin, Utrophin and Spectrin Structural Domains 378
12.2.1 Common Features of Dystrophin and Spectrin 381
12.2.1.1 Classical ABD Domains at the N-terminal End of Dystrophin, Utrophin and ?-spectrin 381
12.2.1.2 Central Domains are Composed of Repeats with Similar Folds in Triple Helical Coiled-Coils 383
12.2.1.3 EF Domains at the C-Terminal End of Dystrophin, Utrophin and ?-spectrin 384
12.2.2 Dystrophin and Spectrin Structural Dissimilarities 385
12.3 The Scaffolding Function of Dystrophin and Spectrins: Binding to Phospholipids and Organizing Protein-­Protein Assemblies 387
12.3.1 Dystrophin and Spectrin: Two Coiled-Coil Filaments Interacting with Membrane Lipids 387
12.3.2 Examples of Protein Partners of Dystrophin and Spectrin 390
12.4 Dystrophin and Spectrin Mutations Related to Pathologies 393
12.5 Conclusion 397
References 398
Chapter 13: Fibrin Formation, Structure and Properties 407
13.1 Introduction 409
13.2 Biochemistry of Fibrinogen, the Precursor to Fibrin 410
13.2.1 Biosynthesis of Fibrinogen in Hepatocytes 410
13.2.2 Fibrinogen Metabolism 411
13.2.3 Polypeptide Chain Composition of Fibrin(ogen) 412
13.2.4 Overall Structure of Fibrinogen Molecules 414
13.2.5 Domain Structure of Fibrinogen 414
13.2.6 ?-Helical Coiled-Coils of Fibrinogen 415
13.2.7 Ca2+-Binding Sites in Fibrinogen 416
13.2.8 Carbohydrate Moieties of Fibrinogen 417
13.3 Molecular Mechanisms of the Conversion of Fibrinogen to Fibrin 417
13.3.1 General Remarks 417
13.3.2 Enzymatic Release of Fibrinopeptides from Fibrinogen 419
13.3.3 ‘A-a’ Knob-Hole Interactions in Fibrin 419
13.3.4 Fibrin Oligomers and Protofibrils 421
13.3.5 Lateral Aggregation of Protofibrils 422
13.3.6 Role of ‘B-b’ Knob-Hole Interactions 423
13.3.7 The Role of the ?C Regions in Fibrin Formation 424
13.3.8 Fibrin Branching and Network Architecture 425
13.3.9 Fibrin Structure and the Gelation Point 425
13.3.10 Factor XIIIa-Catalyzed Covalent Crosslinking of Fibrin 426
13.4 Variations and Modulation of Fibrin(ogen) Structure and Properties 427
13.4.1 Genetic Polymorphisms of Fibrinogen 427
13.4.2 Post-translational Modifications and Heterogeneity of Fibrinogen 428
13.4.3 Hereditary Fibrinogen Defects (Dysfibrinogenemias, Afibrinogenemia, and Hypofibrinogenemia) 429
13.4.4 Environmental Conditions of Fibrin Formation 430
13.4.5 Fibrin Formation Under Hydrodynamic Flow 433
13.5 Fibrin Mechanical Properties and Their Structural Origins 433
13.5.1 General Remarks 433
13.5.2 Viscoelastic Properties of Fibrin 434
13.5.3 Non-linear Elasticity and High Extensibility of Fibrin 434
13.5.4 Multiscale Structural Mechanics of Fibrin Clots 436
13.5.5 Molecular Structural Origins of Fibrin Mechanical Properties 437
13.5.6 Fibrin as a Biomaterial 439
13.6 Lytic Stability of Fibrin 440
13.6.1 Molecular Mechanisms of Fibrinolysis 440
13.6.2 Modulators of Fibrinolysis 442
13.6.3 Internal and External Fibrinolysis 443
13.7 Conclusions 443
References 444
Chapter 14: Fibrillar Collagens 459
14.1 Introduction 460
14.2 Fibrillar and Non-fibrillar Collagens 461
14.3 Fibrillar Collagen Genes and Polypeptide Chains 461
14.4 Domain Structures of Fibrillar Collagen Chains 465
14.5 Molecular Structure and Stability of the Collagen Triple Helix 467
14.5.1 Overall Chain Conformation and Hydrogen Bonding 468
14.5.2 4-Hydroxyproline and Collagen Stability 469
14.5.3 Additional Mechanisms of Collagen Stabilization 471
14.5.4 Helical Twist of the Collagen Triple Helix 471
14.6 Chain Register in the Collagen Triple Helix 472
14.7 Fibrillar Collagen Biosynthesis 473
14.7.1 Role of 3-Hydroxyproline in Fibrillar Collagens 473
14.7.2 Collagen Chaperones 475
14.7.3 Fibrillar Procollagen C-Propeptide Trimer 476
14.7.4 Proteolytic Processing of Procollagen 477
14.8 Fibril Assembly 479
14.9 Fibril Structure 479
14.10 Fibril Cross-Linking and Degradation 481
14.11 Interactions of Fibrillar Collagens: Nucleators, Regulators and Organizers 482
14.11.1 Collagen Types V/XI Nucleate Heterotypic D-Period Collagen Fibrils 482
14.11.2 Collagen Fibril Regulators on the Fibril Surface 483
14.11.3 Collagen Cell-Surface Receptors 484
14.12 Concluding Remarks 485
References 485
Chapter 15: Recombinant Structural Proteins and Their Use in Future Materials 493
15.1 Introduction 494
15.2 Natural Protein Polymeric Materials: Lessons from Biology 495
15.2.1 Information in Structural Proteins 495
15.2.2 Elastin and Resilin 496
15.2.3 Spider Dragline, Silkworm Cocoon and Some Insect Silks 497
15.2.4 Collagen 497
15.2.5 Hair, Wool, and Some Insect Silks 498
15.3 Addition of Information into Structural Proteins 499
15.3.1 Examples of Designed Information-Containing Recombinant Proteins 502
15.3.2 Constraints Limiting Rational Design of Recombinant Structural Proteins 504
15.3.2.1 Tolerance to Addition of Information 504
15.3.2.2 Absence of a Precise Amino Acid Sequence-Structure Relationship 505
15.3.2.3 Our Understanding of Amino Acid Sequence-Structure-Function Relationship 505
15.4 Commercial Scale Production of Protein Polymers 506
15.4.1 Protein Production Platforms for High Level Expression 507
15.4.2 Downstream Processing Considerations 509
15.5 Formation of Proteins into Materials 509
15.5.1 Processing 510
15.5.1.1 Wet Spinning 510
15.5.1.2 Electrospinning 512
15.5.1.3 Casting of Films, Gels and Sponges 513
15.5.1.4 Spraying and Phase Separation 514
15.5.2 Cross-Linking 515
15.5.2.1 Reaction of Chemical Groups 515
15.5.2.2 Self-Assembly 516
15.6 Silk Proteins Studied in Our Laboratory 516
15.7 Conclusions 519
References 520
Chapter 16: Properties of Engineered and Fabricated Silks 529
16.1 Introduction 530
16.2 Biotechnological Production of Silk 533
16.2.1 Examples of Biotechnologically Produced Silk Proteins: Honey Bee Silk 536
16.2.1.1 Natural Honey Bee Silk 536
16.2.1.2 Recombinant Honey Bee Silk Production 538
16.2.2 Examples of Biotechnologically Produced Silk Proteins: Lacewing Silk 539
16.2.2.1 Natural Lacewing Silk 539
16.2.2.2 Recombinant Lacewing Silk 540
16.2.3 Examples of Biotechnologically Produced Silk Proteins: Caddisfly Silk 541
16.2.3.1 Natural Caddisfly Silk 541
16.2.3.2 Recombinant Caddisfly Silk 543
16.2.4 Examples of Biotechnologically Produced Silk Proteins: Silkworm Silk 544
16.2.4.1 Natural Silkworm Silk 544
16.2.4.2 Recombinant Silkworm Silk 545
16.2.5 Examples of Biotechnologically Produced Silk Proteins: Spider Silk 546
16.2.5.1 Natural Spider Silk 546
16.2.5.2 Recombinant Spider Silk 548
16.3 Processing and Properties of Silk Proteins 551
16.3.1 Fibers and Nonwoven Mats 552
16.3.2 Particles and Capsules 557
16.3.3 Hydrogels, Foams and Sponges 559
16.3.4 Films and Coatings 562
16.4 Conclusion and Outlook 564
References 565
Chapter 17: Biomaterials Made from Coiled-Coil Peptides 576
17.1 Introduction: The Emerging Role of Biomaterials 577
17.2 Coiled-Coil Therapeutics 579
17.3 Coiled-Coil Hydrogels 581
17.4 Immunogenic Coiled-Coil Assemblies 587
17.5 Coiled-Coil Based Nanotubes, Fibrils, and Fibres 588
17.6 Coiled-Coil Composites 595
17.7 Conclusion 597
References 597
Chapter 18: Bioengineered Collagens 602
18.1 Introduction 603
18.2 Background: Collagens 604
18.3 Recombinant Collagens and Expression Systems 606
18.4 Recombinant Collagens with Repeating Triple-Helix Segments 610
18.5 Recombinant Collagens: Binding to Cell Receptors and ECM Proteins 612
18.6 Recombinant Collagens: MMPs and Collagen Degradation 615
18.7 Recombinant Collagen Fusion Proteins 616
18.8 Applications for Designed Recombinant Collagens 617
18.8.1 Applications of Recombinant Animal Collagens 619
18.8.2 Applications of Bacterial Collagens 621
18.9 Summary and Future Directions 623
References 623