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Particles
Learning Objectives:
Understand the reasons why viruses encode the proteins to make particles Identify the structural types of virus particle Explain how the virus capsid interacts with the host cell and virus genome during replication
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Virus Particles
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Virus Particles
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Virus Particles
One the function of a virus particle is to protect the nucleic acid genome from physical, chemical, or enzymatic damage. On leaving the host cell, the virus enters a hostile environment. The environment is heavily laden with nucleases.
The protein subunits in a virus capsid are redundant, i.e. many copies per particle.
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Virus Particles
The outer surface of the virus is responsible for recognition of and interaction with the host cell. This takes the form of binding of a specific virus-attachment protein to a cellular receptor molecule. The capsid also initiates infection by delivering the genome in a form in which it can interact with the host cell.
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Some viruses are very fragile, but many are able to persist in the environment for long periods.
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Helical capsids
Tobacco mosaic virus (TMV) represents one of the two major structural classes seen in viruses: helical symmetry The simplest way to arrange multiple, identical protein subunits is to use rotational symmetry. Multiple disks can then be stacked on top of one another to form a cylinder.
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Helical capsids
The TMV capsid actually consists of a helix. A helix can be defined mathematically by two parameters:
amplitude (diameter) pitch (the distance covered by each complete turn of the helix)
Helices are simple structures formed by stacking repeated components with a constant relationship (amplitude and pitch) to one another.
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Helical capsids
Helices are described by the number of subunits per turn of the helix, , and the axial rise per subunit, p. The pitch of the helix, P, is therefore
equal to:
P=xp
For TMV, = 16.3, i.e. 16.3 coat protein molecules per helix turn, and p = 0.14 nm. Therefore, the pitch of the TMV helix is 16.3 x 0.14 = 2.28 nm.
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Helical capsids
Helical capsids include those of bacteriophages of the family Inoviridae, such as M13 and fd. These phages are about 900 nm long and 9 nm diameter and the particles contain five proteins. The major coat protein is the product of phage gene 8 (g8p) and there are 2700-3000 copies of this protein per particle, together with approximately five copies each of four minor capsid proteins, g3p, g6p, g7p and g9p, located at the ends of the particle.
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Bacteriophage M13
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Bacteriophage M13
The length of the particle is dependent on
cloning vector.
Unlike most viruses, there is no sharp cut-
Bacteriophage M13
Inovirus phages are 'male-specific', i.e. require the F pilus for infection. On infection, an interaction between g3p located at one end of the filament together with g6p, and the end of the F pilus. This interaction causes a conformational change in g8p, causing the filament to shorten. The end of the particle attached to the F pilus opens, exposing the phage DNA. A second conformational change in g8p causing the phage particle to expel the phage DNA, initiating infection of the host cell.
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Many plant viruses show helical symmetry. These particles vary from approximately
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Rhabdovirus particle
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Icosahedron - a solid shape consisting of 20 triangular faces arranged around the surface of a sphere.
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Icosahedral Symmetry
Icosahedral symmetry is based on the rotation, known as 2-3-5 symmetry: An axis of twofold rotational symmetry through
Icosahedral Symmetry
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Icosahedral Symmetry
Protein molecules are irregularly shaped, not regular equilateral triangles, so the simplest icosahedral capsids are built up by using three identical subunits
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Icosahedral Symmetry
Most icosahedral capsids contain more than 60
subunits.
Icosahedra are stable because of equivalent bonding. With more than 60 subunits it is impossible for all the subunits to be arranged completely. 1962: Caspar and Klug proposed the idea of quasiequivalence.
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Icosahedral Symmetry
In higher order icosahedra, symmetry is defined by the triangulation number of the icosahedron. The triangulation number, T, is defined by:
T = f2xP
where f is the number of subdivisions of each side of the triangular face, f 2 is the number of subtriangles on each face and P = h2 + hk + k2, where h and k are distinct, non-negative integers.
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Triangulation Numbers
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Picornavirus capsids
These viruses have icosahedral capsids, ~30 nm
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Picornavirus capsids
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Picornavirus capsids
Picornavirus capsids contain four structural proteins, three major proteins VP1-3, plus VP4. VP4 is located on the inside of the capsid and not
Picornavirus Assembly
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Enveloped Viruses
'Naked' virus particles, i.e. those in which the capsid proteins are exposed to the external environment, are released by lysis. 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. Viruses leaving the cell must, therefore, allow this membrane to remain intact. This is achieved by extrusion (budding) of the particle through the membrane.
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Budding
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Envelope proteins
An unbroken lipid bilayer coating is effectively inert, and would not permit recognition of receptor molecules on the host cell. Viruses modify their lipid envelopes by the synthesis of several classes of proteins which are associated in one of three ways with the envelope.
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Envelope proteins
Matrix proteins: internal virion proteins whose function is effectively to link the internal nucleocapsid assembly to the envelope. Glycoproteins: transmembrane proteins anchored to the membrane by a hydrophobic domain: External glycoproteins, anchored in the envelope by a single transmembrane domain. Transport channel proteins contain multiple hydrophobic transmembrane domains, forming a protein-lined channel through the envelope.
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Envelope proteins
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Poxviruses
One example of complex virus structures are found in the Poxviridae. Oval or 'brick-shaped' particles 200-400 nm long. These particles are so large that they were first observed in using optical microscopes in 1886, and thought 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 and have been shown to contain more than 100 different proteins.
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Poxviruses
The outer surface of the virion is composed of lipid and protein. The core is biconcave (dumbbell-shaped) and contains two 'lateral bodies' whose function is unknown. The core is composed of a tightly compressed nucleoprotein and double-stranded DNA. Antigenically, poxviruses are very complex. There are at least 10 enzymes present in poxvirus particles, mostly involved in nucleic acid metabolism/genome replication.
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Poxvirus Particle
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Poxviruses
During replication, two forms of poxvirus particle are observed: extracellular forms which contain two membranes intracellular particles which only have an inner membrane Rather than budding at the cell surface or into an intracellular compartment, acquiring a single membrane, these viruses are wrapped by the endoplasmic reticulum, acquiring two layers of membrane.
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Caudovirales:
Myoviridae, Siphoviridae and Podoviridae The tailed phages of enterobacteria have been extensively studied. 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 and also in penetration of the bacterial cell wall using lysozymelike enzymes. Thin protein fibres attached to the plate and the tail plate itself are involved in binding to the receptor molecules in the wall of the host cell.
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The Caudovirales
There are separate assembly pathways for the head and tail sections of the particle, which come together to make up the virion. These viruses illustrate how complex particles can be built up from the simple principles outlined before.
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Geminiviridae
Another example is provided by the structure of geminivirus particles, which consist of two twinned T = 1 icosahedra. Each icosahedron has one morphological subunit missing and the icosahedra are joined so the mature particle contains 110 protein monomers arranged in 22 morphological subunits.
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Reoviridae
Reoviruses have non-enveloped, icosahedral T = 13 capsids composed of double protein shell with a complex structure. The structure of the bluetongue virus core is the largest structure yet determined to atomic resolution (3.5 ). The outer shell of this virus is approximately 80 nm in diameter and the inner shell (core) about 60 nm. The double-stranded RNA genome of the virus is packed tightly inside the core surrounding transcription complexes in the particle.
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Bluetongue virus
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Baculoviridae
Baculoviruses contain 12-30 structural proteins, and consist of a rod-like (hence baculo) nucleocapsid 30-60 nm diameter and 250-300 nm long containing the 88-160 kbp double-stranded DNA genome. The nucleocapsid is surrounded by an envelope, outside which there may or may not be a crystalline protein matrix, referred to as an 'occlusion body'. The function of the occlusion bodies is to confer resistance to adverse environmental conditions.
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Baculoviridae
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Genome packaging
Another problem viruses must overcome is how to encapsidate the virus genome from the background of cellular nucleic acids. In most cases, by the late stages of virus infection, transcription of cellular genes has been reduced and a large pool of virus genomes have accumulated. A specific virus-encoded capsid or nucleocapsid protein is required to achieve this objective.
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Genome packaging
During replication, viruses make mistakes. These can be measured by particle:infectivity ratios, i.e. the ratio of the total number of particles in a virus preparation (counted by electron microscopy) to the number of infectious particles (measured by plaque or limiting dilution assays). This value is in some cases found to be several thousand particles to each infectious virion and only rarely approaches 1:1.
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Genome packaging
Specific nucleotide sequences in the genome (the packaging signal) permit the virus to select genomic nucleic acids from the cellular background. The packaging signal from a number of virus genomes has been identified. Accurate and efficient genome packaging requires information not only from the linear nucleotide sequence of the genome, but also from regions of secondary structure. In many cases, attempts to find a unique, linear packaging signal in virus genomes have failed. The probable reason is that the key to the specific genome packaging lies in secondary structure of the genome.
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The discs have 17 subunits per ring, close to the 16.34 subunits per turn found in mature virus particle.
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Genome Packaging
T = 3 icosahedral RNA virus capsid subunits consist largely of the '8-strand anti-parallel b-barrel' structural motif. In these viruses, positively-charged inward-projecting arms of the capsid proteins interact with the RNA in the centre of the particle. In BPMV, a T = 3 Comovirus with a bipartite genome, the RNA is folded so that it assumes icosahedral symmetry, corresponding to that of the capsid. The regions which contact the capsid proteins are single-stranded and interact by electrostatic forces rather than covalent bonds.
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Summary
The most obvious division of virus structures is into
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