Structure and Physics of Viruses (eBook)

ForewordPrefaceContributorsPart I. The viral machine1. Introduction: the structural basis of virus function1.1 The structure and physics of viruses1.2 Virions and their structural components1.3 Techniques used to study the structure and physics of viruses1.4 The roles of virus particles and their components along the virus life cycle1.5 Experimental and theoretical developments in physical virology 1.6 Applied structural and physical virology1.7. Concluding remarksAcknowledgementsReferences and further reading2. The basic architecture of viruses2.1 Introduction2.2 How virus structures are studied2.3 Viral capsid symmetry2.4 Quasi-equivalence theory and icosahedral capsid architecture2.5 Variations on the icosahedral capsid theme: multiple layers and prolate icosahedra2.6 Helical capsids2.7 The viral nucleic acid inside2.8 Basic architecture of enveloped virusesAcknowledgementsReferences and further readingPart II. Determination of the structure and physical properties of viruses3. Conventional electron microscopy, cryo-electron microscopy and cryo-electron tomography of viruses3.1 Introduction3.2 Transmission electron microscopy of viruses3.3 Cryo-electron microscopy of viruses3.4 Cryo-EM image processing and three-dimensional reconstruction3.5 Near-atomic resolution of virus structures by cryo-EM3.6 Reconstructing viruses without imposing symmetry3.7 Reconstructing viruses with helical symmetry3.8 Cryo-electron tomography of viruses3.9 Understanding viruses: some major contributions of electron microscopy and tomography3.10 PerspectivesAcknowledgementsReferences and further reading4. X-ray crystallography of viruses4.1 Introduction4.2 Basic concepts and general experimental design4.3 Production and purification of viral particles and proteins for structural studies4.4 Crystallization4.5 Data collection and processing4.6 Phase determination4.7 Map interpretation4.8 Understanding viruses: some major contributions of X-ray crystallography4.9 PerspectivesAcknowledgementsReferences and further reading5. Nuclear magnetic resonance spectroscopy to study virus structure5.1 Introduction5.2 Physical principles of NMR spectroscopy5.3 Determination of biomolecular structures by NMR spectroscopy5.4 NMR structures of viral macromolecules5.5 Understanding viruses: some major contributions of NMR spectroscopy5.6 Perspectives AcknowledgementsReferences and further reading6. Fluorescence, circular dichroism and mass spectrometry as tools to study virus structure6.1 Introduction6.2 Physical principles of fluorescence and circular dichroism (CD) spectroscopies6.3 Fluorescence and CD spectroscopies to study virus structure 6.4 Mass spectrometry (MS) as an analytical tool6.5 MS to study virus structure6.6 PerspectivesAcknowledgementsReferences and further reading7. Combined approaches to study virus structure7.1 Introduction: the ‘multi-disciplinary approach’ concept in structural virology 7.2 Some classical methods in structural virology: a brief overview7.3 Combining X-ray crystallography and electron microscopy7.4 Dissecting virus structures by combining biochemical, genetic and biophysical tools7.5 Combining electron microscopy and electron tomography 7.6 From virus in solution to virus in cells 7.7 Emerging hybrid methods 7.8 The biology behind the combined methods AcknowledgementsReferences and further reading8. Atomic force microscopy of viruses 8.1 Introduction 8.2 Basic concepts 8.3 AFM implementation8.4 Imaging viruses and other biological objects8.5 Understanding viruses: some major contributions of AFM8.6 PerspectivesAcknowledgementsReferences and further reading9. Optical tweezers to study viruses9.1 Introduction:  life machinery at the nanoscale9.2 Basic concepts and general experimental design9.3 Optical tweezers9.4 Operation9.5 Understanding viruses:  some major contributions of optical tweezers9.6 Perspectives AcknowledgementsReferences and further readingPart III. Structural foundations of virus properties and functions10. Assembly of simple icosahedral viruses10.1 Introduction10.2 Icosahedral capsids: symmetry and genetic regulation10.3 Capsid building blocks and assembly intermediates10.4 Forming the capsid10.5 Genome encapsidation and virus maturation10.6 Perspectives and conclusionsAcknowledgementsReferences and further reading11. Structure and assembly of complex viruses11.1 Introduction11.2 Molecular composition of complex viruses11.3 Departures from symmetry in quasi-icosahedral capsids11.4 Asymmetric virus particles11.5 Sophisticated regulation of assembly & maturation11.6 Perspectives and conclusionsAcknowledgementsReferences and further reading12. Nucleic acid packaging in viruses12.1 Introduction.12.2 Structural features of the packaged nucleic acids12.3 Reorganization of the viral capsid during nucleic acid packaging12.4 Components of the packaging machinery12.5 Models for nucleic acid packaging12.6 Perspectives and conclusions AcknowledgementsReferences and further reading13. Virus maturation13.1 Introduction13.2 Immature virus particles and maturation strategies 13.3 Tetravirus capsid maturation13.4 Herpesvirus nucleocapsid maturation13.5 Maturation of the human immunodeficiency virus capsid13.6 The role of glycosylation in virus maturation13.7 Virus polyhedra: virus-derived assemblages for long-term survival13.8 Perspectives and conclusions AcknowledgementsReferences and further reading14. Virus morphogenesis in the cell: methods and observations14.1 Introduction: cell biology of virus morphogenesis and the concept of the virus factory14.2 Methods for the study of virus-cell interactions during morphogenesis14.3 Molecular mapping of viral morphogenesis14.4 The search for signalling pathways 14.5 Perspectives and conclusionsAcknowledgementsReferences and further reading15. Virus-receptor interactions and receptor-mediated virus entry into host cells15.1 Introduction: virus entry into host cells, the recognition of cell surface molecules15.2 Virus-receptor interactions and receptor specificity switch15.3 Non-enveloped virus entry into host cells: the uncoating process15.4 Perspectives and conclusionsAcknowledgementsReferences and further reading16. Entry of enveloped viruses into host cells: membrane fusion16.1 Introduction16.2 General principles of membrane fusion16.3 Viral fusion proteins16.4 Early post-entry events16.5 Perspectives and conclusionsAcknowledgementsReferences and further reading17. Bacteriophage receptor recognition and nucleic acid transfer17.1 Introduction17.2 Proteins used in receptor recognition and nucleic acid transfer17.3 Perspectives and conclusionsAcknowledgementsReferences and further reading18. Mechanical properties of viruses18.1 Introduction18.2 Mechanical stiffness of virus particles determined by AFM in indentation assays 18.3 Intrinsic elasticity of virus capsids: Young´s modulus18.4 Brittleness and material fatigue of virus capsids18.5 A case study: mechanics of bacteriophage f2918.6 Differences and variations in virus mechanical properties18.7 Structural determinants of the mechanical properties of viruses18.8 Mechanical properties and virus biology18.9 Engineering mechanical properties of virus particles18.10 Perspectives and conclusionsAcknowledgementsReferences and further reading19. Theoretical studies on assembly, physical stability and dynamics of viruses19.1 Introduction19.2 Architecture of viral shells19.3 Assembly of viruses19.4 Mechanical stability of capsids19.5 Genome delivery and virus egress19.6 Perspectives and conclusionsAcknowledgementsReferences and further readingPart IV. Applied structural and physical virology20. Antiviral agents: Structural basis of action and rational design20.1 Introduction20.2 Drug discovery and potential targets of antiviralintervention20.3 Antiviral drugs and mechanisms of action20.4 Strategies in the development of antiviral drugs: from random screening to structure-based design20.5 Case studies in structure-based antiviral drug development20.6 Viral capsids as targets of antiviral intervention20.7 Perspectives and conclusionsAcknowledgementsReferences and further reading21. Design of novel vaccines based on virus-like particles or chimeric virions21.1 Introduction 21.2 Immunology of vaccines, an overview21.3 The role of size, geometry and molecular patterns in vaccine design21.4 Virus-like particles (VLPs) as antiviral vaccines21.5 VLPs as platforms for foreign antigen display.  Structure-based engineering of VLPs for vaccine development21.6 Use of plant and insect-derived chimeric virions for foreign antigen display21.7 Perspectives and conclusionsAcknowledgementsReferences and further reading22. Nanoscale science and technology with plant viruses and bacteriophages22.1 Introduction: viral vs. artificial (synthetic) nanostructures 22.2 The control of surface chemistry by genetic engineering and by chemical reactions22.3 Modification of viruses with functional material 22.4 Hierarchical assembly into complex structures 22.5 Nanoscale analysis and manipulation22.6 Viruses as templates 22.7 Electronic devices 22.8 Biochemical detection arrays and targeted drug delivery 22.9 Other systems 22.10 Perspectives and conclusions AcknowledgementsReferences and further reading