ADVANCES I NPROTEIN CHEMISTRY

FREDERIC M . RICHARDS

DAVID S . EISENBER G

JOHN KURIYA N

VOLUME 64

Virus Structure

WAH CHI U

JOHN E . JOHNSON

PREFACE xi

Viral Assembly Using Heterologous ExpressionSystems and Cell Extracts

ANETTE SCHNEEMANN AND MARK J. YOUNG

I. Introduction 1II. The Driving Force behind the Development of

Heterologous Expression Systems for the Study ofViral Assembly and Structure 2

III. Diversity of Heterologous Expression Systems 4W. Guidelines for Choosing a Heterologou s

Expression System 1 6V. Representative Examples of Viral Assembly in

Heterologous Expression Systems 20VI. Conclusions 3 2

References 3 2

Hybrid Vigor : Hybrid Methods in Viral Structure Determinatio n

ROBERT J . C . GILBERT, JONATHAN M . GRIMES, AND DAVID I . STUAR T

I. Introduction 3 7II. Techniques 3 8

III. Hybrids 5 6IV. Conclusion 8 3

References 83

Determination of Icosahedral Virus Structures by Electro nCryomicroscopy at Subnanometer Resolution

Z . HONG ZHOU AND WALE CHIU

I. Introduction 93II. Electron Cryomicroscopy 94

III. Overview of Methods for Subnanometer-resolutio nReconstructions 10 1

IV. Example of Data Collection, Evaluation, and Processing 10 5V. Visualization and Structure Interpretation 11 7

VI. Conclusion 12 2

Structural Folds of Viral Protein s

MICHAEL S . CHAPMAN AND LARS LILJAS

I. Introduction 12 5II. Terminology 12 6

III. Virus Families 12 6IV. Determination of Structural Fold 12 6V. Prototypical Viral Folds 12 8

VI. Survey Through the Virus Families 13 2VII. Common Themes 18 4

VIII. Phylogenetic Relationships 18 5References 18 7

Virus Particle Dynamics

JOHN E . JOHNSON

I. Introduction 19 7II. Particle Fluctuations and Infectivity 19 9

III. Large-Scale Reversible Quaternary Structur eChanges in Viruses 20 3

IV. Large-Scale Irreversible Quaternary Structure Change sin Double-Stranded DNA Bacteriophage 20 9

V. Conclusions 21 6References 216

Viral Genome Organizatio n

B. V. VENKATARAM PRASAD AND PETER E . PREVELIGE, JR .

I. Introduction 219

II. Single-Stranded RNA Viruses 22 1

III. Double-Stranded RNA Viruses 229

IV. Single-Stranded DNA Viruses 235

V. Double-Stranded DNA Viruses 240

VI. Conclusions 246

References 24 8

Mechanism of Scaffolding-Assisted Viral Assembl y

BENTLEY A . FANE AND PETER E . PREVELIGE, JR.

I. Introduction 25 9

II. 4X174 Morphogenesis 26 1

III. Prescaffolding Stages : Coat Proteins and Chaperones 26 1

IV. The OX174 Internal Scaffolding Protein 26 3

V. Genetic Data for Scaffolding Protein Flexibility :

OX174 and Herpesviridae 264

VI. Structural Data for Scaffolding Protein Flexibility :

OX174, P22, and Herpesviridae 266

VII. So What's All This Fuss over These C Termini? 267

VIII. Internal Scaffolding Protein Function in One an d

Two Scaffolding Protein Systems : OX174 versus P2 2

and Herpesviruses 269

IX. The Assembly Pathway of Bacteriophage P22 270

X. The Role of the P22 Scaffolding Protein 272

XI. Functional Domains of the P22 Scaffolding Protein 274

XII. Physical Chemistry of the P22 Scaffolding Protein 280

XIII. The Mechanism of Scaffolding-Assisted Assembly 28 1

XIV. External Scaffolding Proteins 283

XV. The OX174 External Scaffolding Protein 284

XVI. P4 Sid Protein 290

XVII. Herpesvirus Triplex Proteins 292

XVIII. Scaffolding-Like Functions 293

References 295

Molecular Mechanisms in Bacteriophage T7 Procapsid Assembly ,Maturation, and DNA Containmen t

MARIO E . CERRITELLI, JAMES F. CONWAY, NAIQIAN CHENG ,

BENES L . TAUS, AND ALASDAIR C . STEVE N

I. Introduction 30 1

II. Overexpressed T7 and T3 Connectors have 12- and13-Fold Symmetry 303

III. The Procapsid Core has 8-Fold Symmetry : Another

Symmetry Mismatch 303

IV. Procapsid Structure 305

V. Procapsid Maturation : Expansion is Initiated inthe Connector 308

VI. Packaging and Parting of DNA 309

VII. The Mature Capsid Structure : Filled and Empty Shells 310

VIII. Structure of Packaged DNA 315

IX. Summary 319

References 320

Conformational Changes in Enveloped Virus Surfac eProteins During Cell Entr y

DEBORAH FASS

I. Introduction: Multiple Stops on the Protein-Foldin gLandscape 32 5

II. Influenza Hemagglutinin 326III. Retroviruses 33 8IV. Paramyxoviruses Turn Paradigms Upside Down? 350V. Oligomerization State Switches in Flaviviruse s

and Alphaviruses 35 3VI. Concluding Remarks 356

References 357

Enveloped Viruse s

RICHARD J . KUHN AND JAMES H . STRAUSS

I. Introduction 363II. General Structural Features of Enveloped Viruses 364

III. Alphavirus Structure 365

IV. Flavivirus Structure 367

V. Virus Assembly 369

VI. Virus-Cell Fusion 372

VII. Concluding Remarks 373

References 374

Studying Large Viruse s

FRAZER J. RIXON AND WAH CHIU

I. What is a Large Virus? 379

II. Why Large Viruses? 38 1

III. Why Study Large Viruses? 384

IV. Methods of Structural Analysis 385V. Complexity of Organization 386

VI. Structural Folds 393VII. Assembly Mechanisms 394

VIII. Maturation 399IX. Accessory Proteins 400X. Packaging 401

XI. Future Prospects 402XII. Summary 403

References 404

Structural Studies on Antibody-Virus Complexes

THOMAS J . SMITH

I. Introduction 409

II. Background 410III. Structural Studies on Virus-Antibody Complexes 41 2

IV. Conclusions 439

References 443

Structural Basis of Nonenveloped Virus Cell Entr y

PHOEBE L . STEWART, TERENCE S. DERMODY, AND GLEN R. NEMERO W

I. Introduction 455II. Reovirus Cell Entry, Tissue Tropism, and Pathogenesis 456

III. Reovirus Structure 458IV. Proteolysis of the al Protein Regulates Viral Growth

in the Intestine and Systemic Spread 460V. The al Tail Binds Cell Surface Sialic Acid 462

VI. The 61 Head Binds Junctional Adhesion Molecule 463VII. Reovirus-Receptor Interactions Promote Cel l

Death by Apoptosis 464VIII. Picornavirus-Receptor Complexes 465

IX. Poliovirus Cell Entry Mechanisms 466X. Identification of the Poliovirus Attachment Receptor 468

XI. Poliovirus-Associated Lipid Molecules 469XII. Receptors for Rhinoviruses 470

XIII. Receptors for Other Picornaviruses 473XIV. Human Adenoviruses 475XV. Adenovirus Attachment Receptors 476

XVI. Cell Integrins Promote Adenovirus Internalization 478XVII. Signaling Events Associated with Adenovirus

Internalization 48 1XVIII. oc Integrins Regulate Adenovirus-Mediate d

Endosome Disruption 482XIX. Conclusions 482

References 484

AUTHOR INDEX 493SUBJECT INDEX 531