Structure and Physics of Viruses

<p>Foreword</p><p>Preface</p><p>Contributors</p><p><p>Part I. The viral machine</p><p>1. Introduction: the structural basis of virus function<br>1.1 The structure and physics of viruses<br>1.2 Virions and their structural components<br>1.3 Techniques used to study the structure and physics of viruses<br>1.4 The roles of virus particles and their components along the virus life cycle<br>1.5 Experimental and theoretical developments in physical virology <br>1.6 Applied structural and physical virology<br>1.7. Concluding remarks<br>Acknowledgements<br>References and further reading</p><p>2. The basic architecture of viruses<br>2.1 Introduction<br>2.2 How virus structures are studied<br>2.3 Viral capsid symmetry<br>2.4 Quasi-equivalence theory and icosahedral capsid architecture<br>2.5 Variations on the icosahedral capsid theme: multiple layers and prolate icosahedra<br>2.6 Helical capsids<br>2.7 The viral nucleic acid inside<br>2.8 Basic architecture of enveloped viruses<br>Acknowledgements<br>References and further reading</p><p>Part II. Determination of the structure and physical properties of viruses</p><p>3. Conventional electron microscopy, cryo-electron microscopy and cryo-electron tomography of viruses<br>3.1 Introduction<br>3.2 Transmission electron microscopy of viruses<br>3.3 Cryo-electron microscopy of viruses<br>3.4 Cryo-EM image processing and three-dimensional reconstruction<br>3.5 Near-atomic resolution of virus structures by cryo-EM3.6 Reconstructing viruses without imposing symmetry<br>3.7 Reconstructing viruses with helical symmetry<br>3.8 Cryo-electron tomography of viruses<br>3.9 Understanding viruses: some major contributions of electron microscopy and tomography<br>3.10 Perspectives<br>Acknowledgements<br>References and further reading</p><p>4. X-ray crystallography of viruses<br>4.1 Introduction<br>4.2 Basic concepts and general experimental design<br/>4.3 Production and purification of viral particles and proteins for structural studies<br>4.4 Crystallization<br>4.5 Data collection and processing<br>4.6 Phase determination<br>4.7 Map interpretation<br>4.8 Understanding viruses: some major contributions of X-ray crystallography<br>4.9 Perspectives<br>Acknowledgements<br>References and further reading</p><p>5. Nuclear magnetic resonance spectroscopy to study virus structure<br>5.1 Introduction<br>5.2 Physical principles of NMR spectroscopy<br>5.3 Determination of biomolecular structures by NMR spectroscopy<br>5.4 NMR structures of viral macromolecules<br>5.5 Understanding viruses: some major contributions of NMR spectroscopy<br>5.6 Perspectives <br>Acknowledgements<br>References and further reading</p><p>6. Fluorescence, circular dichroism and mass spectrometry as tools to study virus structure<br>6.1 Introduction<br>6.2 Physical principles of fluorescence and circular dichroism (CD) spectroscopies<br>6.3 Fluorescence and CD spectroscopies to study virus structure <br>6.4 Mass spectrometry (MS) as an analytical tool<br>6.5 MS to study virus structure<br>6.6 Perspectives<br>Acknowledgements<br>References and further reading</p><p><p>7. Combined approaches to study virus structure<br>7.1 Introduction: the ‘multi-disciplinary approach’ concept in structural virology <br>7.2 Some classical methods in structural virology: a brief overview<br>7.3 Combining X-ray crystallography and electron microscopy<br>7.4 Dissecting virus structures by combining biochemical, genetic and biophysical tools<br>7.5 Combining electron microscopy and electron tomography <br>7.6 From virus in solution to virus in cells <br>7.7 Emerging hybrid methods <br>7.8 The biology behind the combined methods <br>Acknowledgements<br>References and further reading</p><p>8. Atomic force microscopy of viruses <br>8.1 Introduction <br>8.2 Basic concepts <br/>8.3 AFM implementation<br>8.4 Imaging viruses and other biological objects<br>8.5 Understanding viruses: some major contributions of AFM<br>8.6 Perspectives<br>Acknowledgements<br>References and further reading</p><p>9. Optical tweezers to study viruses<br>9.1 Introduction:  life machinery at the nanoscale<br>9.2 Basic concepts and general experimental design<br>9.3 Optical tweezers<br>9.4 Operation<br>9.5 Understanding viruses:  some major contributions of optical tweezers<br>9.6 Perspectives <br>Acknowledgements<br>References and further reading</p><p>Part III. Structural foundations of virus properties and functions</p><p>10. Assembly of simple icosahedral viruses<br>10.1 Introduction<br>10.2 Icosahedral capsids: symmetry and genetic regulation<br>10.3 Capsid building blocks and assembly intermediates<br>10.4 Forming the capsid<br>10.5 Genome encapsidation and virus maturation<br>10.6 Perspectives and conclusions<br>Acknowledgements<br>References and further reading</p>11. Structure and assembly of complex viruses<br>11.1 Introduction<br>11.2 Molecular composition of complex viruses<br>11.3 Departures from symmetry in quasi-icosahedral capsids<br>11.4 Asymmetric virus particles<br>11.5 Sophisticated regulation of assembly & maturation<br>11.6 Perspectives and conclusions<br>Acknowledgements<br>References and further reading<p><p>12. Nucleic acid packaging in viruses<br>12.1 Introduction.<br>12.2 Structural features of the packaged nucleic acids<br>12.3 Reorganization of the viral capsid during nucleic acid packaging<br>12.4 Components of the packaging machinery<br>12.5 Models for nucleic acid packaging<br>12.6 Perspectives and conclusions <br>Acknowledgements<br>References and further reading</p><p>13. Virus maturation<br>13.1 Introduction<br>13.2 Immature virus particles and maturation strategies <br>13.3 Tetravirus capsid maturation<br/>13.4 Herpesvirus nucleocapsid maturation<br>13.5 Maturation of the human immunodeficiency virus capsid<br>13.6 The role of glycosylation in virus maturation<br>13.7 Virus polyhedra: virus-derived assemblages for long-term survival<br>13.8 Perspectives and conclusions <br>Acknowledgements<br>References and further reading</p><p>14. Virus morphogenesis in the cell: methods and observations<br>14.1 Introduction: cell biology of virus morphogenesis and the concept of the virus factory<br>14.2 Methods for the study of virus-cell interactions during morphogenesis<br>14.3 Molecular mapping of viral morphogenesis<br>14.4 The search for signalling pathways <br>14.5 Perspectives and conclusions<br>Acknowledgements<br>References and further reading</p><p>15. Virus-receptor interactions and receptor-mediated virus entry into host cells<br>15.1 Introduction: virus entry into host cells, the recognition of cell surface molecules<br>15.2 Virus-receptor interactions and receptor specificity switch<br>15.3 Non-enveloped virus entry into host cells: the uncoating process<br>15.4 Perspectives and conclusions<br>Acknowledgements<br>References and further reading</p><p>16. Entry of enveloped viruses into host cells: membrane fusion<br>16.1 Introduction<br>16.2 General principles of membrane fusion<br>16.3 Viral fusion proteins<br>16.4 Early post-entry events<br>16.5 Perspectives and conclusions<br>Acknowledgements<br>References and further reading</p><p>17. Bacteriophage receptor recognition and nucleic acid transfer<br>17.1 Introduction<br>17.2 Proteins used in receptor recognition and nucleic acid transfer<br>17.3 Perspectives and conclusions<br>Acknowledgements<br>References and further reading</p><p>18. Mechanical properties of viruses<br>18.1 Introduction<br>18.2 Mechanical stiffness of virus particles determined by AFM in indentation assays <br>18.3 Intrinsic elasticity of virus capsids: Young´s modulus<br/>18.4 Brittleness and material fatigue of virus capsids<br>18.5 A case study: mechanics of bacteriophage f29<br>18.6 Differences and variations in virus mechanical properties<br>18.7 Structural determinants of the mechanical properties of viruses<br>18.8 Mechanical properties and virus biology<br>18.9 Engineering mechanical properties of virus particles<br>18.10 Perspectives and conclusions<br>Acknowledgements<br>References and further reading</p><p>19. Theoretical studies on assembly, physical stability and dynamics of viruses<br>19.1 Introduction<br>19.2 Architecture of viral shells<br>19.3 Assembly of viruses<br>19.4 Mechanical stability of capsids<br>19.5 Genome delivery and virus egress<br>19.6 Perspectives and conclusions<br>Acknowledgements<br>References and further reading</p><p>Part IV. Applied structural and physical virology</p><p>20. Antiviral agents: Structural basis of action and rational design<br>20.1 Introduction<br>20.2 Drug discovery and potential targets of antiviral<br>intervention<br>20.3 Antiviral drugs and mechanisms of action<br>20.4 Strategies in the development of antiviral drugs: from random screening to structure-based design<br>20.5 Case studies in structure-based antiviral drug development<br>20.6 Viral capsids as targets of antiviral intervention<br>20.7 Perspectives and conclusions<br>Acknowledgements<br>References and further reading</p><p>21. Design of novel vaccines based on virus-like particles or chimeric virions<br>21.1 Introduction <br>21.2 Immunology of vaccines, an overview<br>21.3 The role of size, geometry and molecular patterns in vaccine design<br>21.4 Virus-like particles (VLPs) as antiviral vaccines<br>21.5 VLPs as platforms for foreign antigen display.  Structure-based engineering of VLPs for vaccine development<br>21.6 Use of plant and insect-derived chimeric virions for foreign antigen display<br>21.7 Perspectives and conclusions<br>Acknowledgements<br/>References and further reading</p><p>22. Nanoscale science and technology with plant viruses and bacteriophages<br>22.1 Introduction: viral vs. artificial (synthetic) nanostructures <br>22.2 The control of surface chemistry by genetic engineering and by chemical reactions<br>22.3 Modification of viruses with functional material <br>22.4 Hierarchical assembly into complex structures <br>22.5 Nanoscale analysis and manipulation<br>22.6 Viruses as templates <br>22.7 Electronic devices <br>22.8 Biochemical detection arrays and targeted drug delivery <br>22.9 Other systems <br>22.10 Perspectives and conclusions <br>Acknowledgements<br>References and further reading </p>