Virus Structure (eBook)

Cover 1
Contents 6
Preface 12
Chapter 1. Viral Assembly Using Heterologous Expression Systems and Cell Extracts 14
I. Introduction 14
II. The Driving Force behind the Development of Heterologous Expression Systems for the Study of Viral Assembly and Structure 15
III. Diversity of Heterologous Expression Systems 17
IV. Guidelines for Choosing a Heterologous Expression System 29
V. Representative Examples of Viral Assembly in Heterologous Expression Systems 33
VI. Conclusions 45
References 45
Chapter 2. Hybrid Vigor: Hybrid Methods in Viral Structure Determination 50
I. Introduction 50
II. Techniques 51
III. Hybrids 69
IV. Conclusion 96
References 96
Chapter 3. Determination of Icosahedral Virus Structures by Electron Cryomicroscopy at Subnanometer Resolution 106
I. Introduction 106
II. Electron Cryomicroscopy 107
III. Overview of Methods for Subnanometer-resolution Reconstructions 114
IV. Example of Data Collection, Evaluation, and Processing 118
V. Visualization and Structure Interpretation 130
VI. Conclusion 135
References 135
Chapter 4. Structural Folds of Viral Proteins 138
I. Introduction 138
II. Terminology 139
III. Virus Families 139
IV. Determination of Structural Fold 139
V. Prototypical Viral Folds 141
VI. Survey Through the Virus Families 145
VII. Common Themes 197
VIII. Phylogenetic Relationships 198
References 200
Chapter 5. Virus Particle Dynamics 210
I. Introduction 210
II. Particle Fluctuations and Infectivity 212
III. Large-Scale Reversible Quaternary Structure Changes in Viruses 216
IV. Large-Scale Irreversible Quaternary Structure Changes in Double-Stranded DNA Bacteriophage 222
V. Conclusions 229
References 229
Chapter 6. Viral Genome Organization 232
I. Introduction 232
II. Single-Stranded RNA Viruses 234
III. Double-Stranded RNA Viruses 242
IV. Single-Stranded DNA Viruses 248
V. Double-Stranded DNA Viruses 253
VI. Conclusions 259
References 261
Chapter 7. Mechanism of Scaffolding-Assisted Viral Assembly 272
I. Introduction 272
II. øX174 Morphogenesis 274
III. Prescaffolding Stages: Coat Proteins and Chaperones 274
IV. The øX174 Internal Scaffolding Protein 276
V. Genetic Data for Scaffolding Protein Flexibility: øX174 and Herpesviridae 277
VI. Structural Data for Scaffolding Protein Flexibility: øX174, P22, and Herpesviridae 279
VII. So What’s All This Fuss over These C Termini? 280
VIII. Internal Scaffolding Protein Function in One and Two Scaffolding Protein Systems: øX174 versus P22 and Herpesviruses 282
IX. The Assembly Pathway of Bacteriophage P22 283
X. The Role of the P22 Scaffolding Protein 285
XI. Functional Domains of the P22 Scaffolding Protein 287
XII. Physical Chemistry of the P22 Scaffolding Protein 293
XIII. The Mechanism of Scaffolding-Assisted Assembly 294
XIV. External Scaffolding Proteins 296
XV. The PX174 External Scaffolding Protein 297
XVI. P4 Sid Protein 303
XVII. Herpesvirus Triplex Proteins 305
XVIII. Scaffolding-Like Functions 306
References 308
Chapter 8. Molecular Mechanisms in Bacteriophage T7 Procapsid Assembly, Maturation, and DNA Containment 314
I. Introduction 314
II. Overexpressed T7 and T3 Connectors have 12- and 13-Fold Symmetry 316
III. The Procapsid Core has 8-Fold Symmetry: Another Symmetry Mismatch 316
IV. Procapsid Structure 318
V. Procapsid Maturation: Expansion is Initiated in the Connector 321
VI. Packaging and Parting of DNA 322
VII. The Mature Capsid Structure: Filled and Empty Shells 323
VIII. Structure of Packaged DNA. 328
IX. Summary 332
References 333
Chapter 9. Conformational Changes in Enveloped Virus Surface Proteins During Cell Entry 338
I. Introduction: Multiple Stops on the Protein-Folding Landscape 338
II. Influenza Hemagglutinin 339
III. Retroviruses 351
IV. Paramyxoviruses Turn Paradigms Upside Down? 363
V. Oligomerization State Switches in Flaviviruses and Alphaviruses 366
VI. Concluding Remarks 369
References 370
Chapter 10. Enveloped Viruses 376
I. Introduction 376
II. General Structural Features of Enveloped Viruses 377
III. Alphavirus Structure 378
IV. Flavivirus Structure 380
V. Virus Assembly 382
VI. Virus–Cell Fusion 385
VII. Concluding Remarks 386
References 387
Chapter 11. Studying Large Viruses 392
I. What is a Large Virus? 392
II. Why Large Viruses? 394
III. Why Study Large Viruses? 397
IV. Methods of Structural Analysis 398
V. Complexity of Organization 399
VI. Structural Folds 406
VII. Assembly Mechanisms 407
VIII. Maturation 412
IX. Accessory Proteins 413
X. Packaging 414
XI. Future Prospects 415
XII. Summary 416
References 417
Chapter 12. Structural Studies on Antibody–Virus Complexes 422
I. Introduction 422
II. Background 423
III. Structural Studies on Virus–Antibody Complexes 425
IV. Conclusions 452
References 456
Chapter 13. Structural Basis of Nonenveloped Virus Cell Entry 468
I. Introduction 468
II. Reovirus Cell Entry, Tissue Tropism, and Pathogenesis 469
III. Reovirus Structure 471
IV. Proteolysis of the 1 Protein Regulates Viral Growth in the Intestine and Systemic Spread 473
V. The a1 Tail Binds Cell Surface Sialic Acid 475
VI. The s1 Head Binds Junctional Adhesion Molecule. 476
VII. Reovirus–Receptor Interactions Promote Cell Death by Apoptosis 477
VIII. Picornavirus–Receptor Complexes 478
IX. Poliovirus Cell Entry Mechanisms 479
X. Identification of the Poliovirus Attachment Receptor 481
XI. Poliovirus-Associated Lipid Molecules 482
XII. Receptors for Rhinoviruses 483
XIII. Receptors for Other Picornaviruses 486
XIV. Human Adenoviruses 488
XV. Adenovirus Attachment Receptors 489
XVI. Cell Integrins Promote Adenovirus Internalization 491
XVII. Signaling Events Associated with Adenovirus Internalization 494
XVIII. av Integrins Regulate Adenovirus-Mediated Endosome Disruption 495
XIX. Conclusions 495
References 497
AUTHOR INDEX 506
SUBJECT INDEX 544
Color Plate Section 557