1/28/09 continued- VIRUS STRUCTURESergei Nekhai, Ph.D.Objectives:•Enveloped viruses•Complex viruses•Virus maturation, assembly and release•Packaging of viral RNA or DNAStructure of Viruses(Baker et al.)Characteristic size scale is 30-100 nm.Structures are known at “atomic resolution” - see Viper website.Highly symmetric - think hard about what this implies about assembly!Enveloped Viruses• Enveloped Viruses• Influenzavirus• herpes simplex virusEnveloped Viruses• Many viruses have devised strategies to exit from the infected cell without its total destruction.• All living cells are covered by a membrane composed of a lipid bilayer - the viability of the cell depends on the integrity of this membrane. Viruses leaving the cell must, therefore, allow this membrane to remain intact.• This is achieved by extrusion (buddingbudding) of the particle through the membrane, during which process the particle becomes coated in a lipid envelope derived from the host cell membrane & with a similar composition.Viral BuddingFormation of enveloped virus particles• The structure underlying the envelope may be based on helical or icosahedral symmetry & may be formed before or as the virus leaves the cell.• In the majority of cases, enveloped viruses use cellular membranes as sites allowing them to direct assembly.• The formation of the particle inside the cell, maturation & release are in many cases a continuous process.• The site of assembly varies for different viruses - not all use the cell surface membrane; many use cytoplasmic membranes such as the Golgi apparatus, others, such as herpesviruses, which replicate in the nucleus may utilize the nuclear membrane. In these cases, the virus is usually extruded into some form of vacuole, in which it is transported to the cell surface & subsequently released.Envelope proteins• If the virus particle became covered in a smooth, unbroken lipid bilayer, this would be its undoing.• Such a coating is effectively inert, & although effective in preventing desiccation of or enzymatic damage to the particle, would not permit recognition of receptor molecules on the host cell.• Therefore, viruses modify their lipid envelopes by the synthesis of several classes of proteins which are associated in one of three ways with the envelope.Viral Structure••Matrix proteins:Matrix proteins:are internal virion proteins whose function is effectively to link the internal nucleocapsid assembly to the envelope. Such proteins are not usually glycosylated & are often very abundant, for example, in retroviruses they comprise approximately 30% of the total weight of the virion.••GlycoproteinsGlycoproteins::are transmembrane proteins anchored to the membrane by a hydrophobic domain, & can be subdivided into two types by their function:••External External glycoproteinsglycoproteinsare anchored in the envelope by a single transmembrane domain.••Transport channel proteinsTransport channel proteinscontain multiple hydrophobic transmembrane domains, forming a protein-lined channel through the envelope.Viral Structure: Envelope ProteinsComplex Virus Structures• However, there are many viruses whose structure is more complex than those with helical symmetry or icosahedral symmetry.• In these cases, although the general principles of symmetry are often used to build part of the virus shell, the larger & more complex viruses cannot be simply defined by a mathematical equation as can a simple helix or icosahedron.• Because of the complexity of some of these viruses, they have defied attempts to determine detailed atomic structures.Poxviruses• Example of complex viral structure-Poxviridae.• These viruses have oval or 'brick-shaped' particles 200-400 nm long.• These particles are so large that they were first observed in using high-resolution optical microscopes in 1886, & thought at that time to be 'the spores of micrococci'.• The external surface of the virion is ridged in parallel rows, sometimes arranged helically.• The particles are extremely complex & have been shown to contain more than 100 different proteins.Poxviruses• Under the electron microscope, thin sections of poxviruses reveal that the outer surface of the virion is composed of lipid & protein.• This surrounds the core, which is biconcave (dumbbell-shaped), & two 'lateral bodies' whose function is unknown.• The core is composed of a tightly compressed nucleoprotein & the double-stranded DNA genome is wound around it.• Antigenically, poxviruses are very complex, inducing both specific & cross-reacting antibodies - hence the possibility of vaccinating against one disease with another virus (e.g. the useof Vaccinia virus to immunize against smallpox (variola) virus).• Poxviruses & a number of other complex viruses also emphasize the true complexity of some viruses - there are at least 10 enzymes present in poxvirus particles, mostly involved in nucleic acid metabolism/genome replication.Poxvirus ParticlePoxviruses•During replication, two forms of poxvirus particle are observed:–extracellular forms which contain two membranes–intracellular particles which only have an inner membrane•Poxviruses & other virus with complex structures obtain their membranes in a different way from "simple" enveloped viruses such as retroviruses or influenza.•Rather than budding at the cell surface or into an intracellular compartment, acquiring a single membrane, these complex viruses are wrapped by the endoplasmic reticulum, acquiring two layers of membrane.BacteriophagesFigure 13.5a• Complex virus– Head is polyhedral– Tail is helical– It is surrounded by a protein coat (capsid)Caudovirales:Myoviridae, Siphoviridae & Podoviridae• The tailed phages of enterobacteria have been extensively studied for excellent reasons - easy to propagate in bacterial cells, can be obtained in high titres, & are easily purified, facilitating biochemical & structural studies.• The head of the particles consists of an icosahedral shell with T = 7 symmetry, attached by a collar to a contractile, helical tail. At the end of the tail is a plate which functions in attachment to the bacterial host & also in penetration of the bacterial cell wall using lysozyme-like enzymes associated with the plate.• Thin protein fibres attached to the plate & the tail plate itself are involved in binding to the receptor molecules in the wall of thehost cell.The Caudovirales•