Biological Sciences
Viral Capsid
A viral capsid is a protein shell that encloses the genetic material of a virus. It provides protection for the viral genome and helps in the process of infecting host cells. The capsid plays a crucial role in the virus's ability to survive outside a host and to initiate infection.
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10 Key excerpts on "Viral Capsid"
eBook - PDF- Edward K. Wagner, Martinez J. Hewlett, David C. Bloom, David Camerini(Authors)
- 2009(Publication Date)
- Wiley-Blackwell(Publisher)
Viral Capsids The capsid is a complex structure made up of many identical subunits of viral protein – often termed a capsomer. The capsid functions to provide a protein shell in which the chemically labile viral genome can be maintained in a stable environment. The association of capsids with genomes is a complex process, but it must result in an energetically stable structure. While viruses can assume a range of shapes, some quite complex, given the dimensions of virus struc- ture and the constraints of the capsomer’s structural parameters, a very large number assume one of two regular shapes. The first is the helix, in which the capsomers associate with helical nucleic acid as a nucleoprotein – these can either be stiff or flexible depending upon the properties of the capsid’s proteins themselves. The other highly regular shape is the icosa- hedron, in which the capsomers form a regular solid structure enfolding the viral genome. Despite the frequency of such regular shapes, many viruses have more complex and/or less regular appearances, these include spindle, kidney, lemon, and lozenge shapes. Further, some viruses can assume different shapes depending upon the nature of the cells in which they mature, and some groups of viruses – notably the pox viruses – are distinguished by having a number of different shapes characterizing specific members of the group. Arrangement of the capsid around its viral genetic material is unique for each type of virus. The general properties of this arrangement define the shape of the capsid and its symmetry, and since each type of Table 5.1 Classification of viruses according to the ICTV.
eBook - PDF- Carlos Tello Lacal(Author)
- 2019(Publication Date)
- Delve Publishing(Publisher)
This fact holds despite the fact that they are parasitic and depend on the host cell for reproduction by hijacking the host cellular machinery. Each virus has its own adaptation to the various hosts which they can infect and the various environments in which they survive. This notwithstanding, they have the nucleocapsid structure which basic and common for all viruses. The viral nucleocapsid has a basic composition of the viral genome which has been enclosed in the Viral Capsid. The Viral Capsid is primarily made of the structural proteins. The capsid plays an important role in the survival of the virus. It has a number of functions such as offering the viral genome protection. It is also essential for viral recognition to the host cell Principles of Molecular Virology 44 before it gets attached to the surface of the host. Following successful attachment, the virus can then get incorporated in the host cell internal from which it can initiate viral replication. The conformation of the capsid is also very important in determining the time at which the virus is released. The Viral Capsid usually alters its conformation, and this allows for timely release of the viral nucleic acid even as it maintains its stability to prevent environmental insults to the virus from the outer environment. The viral genome may either be single-stranded or double-stranded DNA or RNA. Viral genomes are of different sizes which consequently makes the diameter sizes variable. The smallest of the viruses are approximated to be 3 kbp which is a length that can be compared to microbial genomes. The number of proteins encoded for by various genomes corresponds to the respective sizes of the genomes. Consequently, the larger viruses bearing large viral genomes will encode for more protein subunits and the reverse is also true. The monomers encoded for by the genomes which are the individual protein subunits tend to present in a symmetrical structure.
eBook - PDF- M.V. Nermut, A.C. Steven(Authors)
- 1987(Publication Date)
- Elsevier Science(Publisher)
The capsid = outermost protein shell enclosing either nucleic acid only, or a nucleoprotein complex, or a core. Capsids have cubic (mostly icosahedral) sym- metry, but cylindrical (usually aberrant) forms are also known. Morphological units forming the capsid are called capsomers; those with six neighbours are six- coordinated or hexavalent; capsomers at vertices of the icosahedron have five neighbours, are therefore five-coordinated or pentavalent. Capsomers consist of polypeptide protomers called structure units. This follows the original definition by Caspar et al. (1962) that ‘structure units are the smallest functionally equivalent building units of a capsid’. The nucleocapsid (NC) = nucleic acid within an icosahedral protein shell (capsid) or within a helical protein complex. More than one virus protein is often associated with NA. Though ‘capsid’ means a closed shell (box) it has been commonly used to designate both icosahedral and linear nucleic acid/protein(s) complexes. Linear nucleocapsids form either flexible helices (nucleohelix) or in a few cases small nucleosome-like bodies (beads on string). Most enveloped viruses (Myxo-, Paramyxoviridae) possess ‘nucleohelices’; the nucleosome-like organization has been best shown in members of Papovaviridae. However, in many families the structure of the NAIprotein complex is not known and many linear nucleocapsids are only assumed to be helical. The envelope or virus membrane = lipid bilayer with glycoprotein projections (spikes, knobs, etc.) called peplomers. Some envelopes contain additional protein apposed to their inner surface or even inserted into the lipid bilayer (e.g. Cor- onaviridae). The core = internal body containing nucIeoprotein complex within a protein shell (core-shell). The core can be icosahedral (e.g. adenovirus, type C oncovirus), spherical or cylindrical (e.g. myxovirus) and enclosed in a capsid or in an envelope. Viruses vary widely in their shapes, sizes and architecture.
eBook - PDFVirology
Principles and Applications
- John Carter, Venetia Saunders(Authors)
- 2014(Publication Date)
- Wiley(Publisher)
A second function of many capsids is to recognize and attach to a host cell in which the virus can be replicated. A third function may be to ensure that the virus genome is transported to the location within the cell where the genome can be transcribed and replicated. Although the capsid must be stable enough to survive in the extracellular environment, it must also be able to alter its conformation so that, at the appropriate location in the host cell, it can release its genome. For many viruses the capsid and the genome that it encloses constitute the virion. For other viruses a lipid envelope (Section 3.5.1), and sometimes another layer of protein, surrounds this structure, which is referred to as a nucleocapsid. Capsids are constructed from many molecules of one or a few species of protein. The individual pro- tein molecules are asymmetrical, but they are organ- ized to form symmetrical structures. Some examples of symmetrical structures are shown in Figure 3.8. A symmetrical object, including a capsid, has the same appearance when it is rotated through one or more angles, or when it is seen as a mirror image. For the vast majority of viruses the capsid symmetry is either helical or icosahedral. 3.4.1 Capsids with helical symmetry The capsids of many ssRNA viruses have helical symmetry; the RNA is coiled in the form of a helix and many copies of the same protein species are arranged around the coil (Figure 3.9(a), (b)). While the RNA is within the coil for many viruses, there is evidence that the RNA of some viruses is on the surface of the coil. The coiled ribonucleoprotein forms an elongated structure, which may be a rigid rod if strong bonds are present between the protein molecules in successive turns of the helix, or a flex- ible rod (Figure 3.9(c)) if these bonds are weak. The length of the capsid is determined by the length of the nucleic acid. helix icosahedron rod cone Figure 3.8 Symmetrical structures.
eBook - PDF- Dongyou Liu(Author)
- 2016(Publication Date)
- CRC Press(Publisher)
1 1.1 PREAMBLE Viruses (singular, virus, meaning toxin or poison in Latin) are noncellular, submicroscopic infectious agents that can only replicate inside the cells of another organism. Measuring from 20 to 400 nm (or 10 –8 –10 –6 mm) in diameter, viruses are 10–100 times smaller than prokaryotes (10 –7 –10 –4 mm), 1000 times smaller than eukaryotes (10 –5 –10 –3 mm). Since the majority of the viruses (including those described in the early reports) are small enough to pass through conventional sterilizing filters (0.2 μ m), viruses were initially described as filterable agents. Morphologically, viral particles (or viri-ons) vary from simple helical and icosahedral forms, to more complex structures with tails or an envelope. The envelope is composed of lipids and proteins, which may display as spikes in some viruses giving distinct appearance. A major role of the envelope is to protect a virus from adverse external con-ditions. Underneath lies at least one protein surrounded by a protein shell (known as capsid). The protein capsid guards the nucleic acid within [either a single- or double-stranded nucleic acid made up of ribonucleic acid (RNA) or deoxyri-bonucleic acid (DNA)] while other proteins (enzymes) enable the virus to enter its appropriate host cells, to reproduce by taking advantage of host cellular machinery, and to evolve within infected cells by natural selection [1]. Virology is a branch of biological sciences that is devoted to the studies of viruses including their identification, biology, ecology, epidemiology, pathogenesis, genetics, immunology, control, and prevention, and so on. Correct identification of the viruses to species and/or subspecies level is a prerequisite for the study of virology. Without knowledge of virus iden-tity, attempts to investigate other aspects of a particular virus may be flawed.
eBook - PDF- Marc H.V. van Regenmortel, Brian W.J. Mahy(Authors)
- 2010(Publication Date)
- Academic Press(Publisher)
VIRIONS This page intentionally left blank Principles of Virion Structure J E Johnson and J A Speir, The Scripps Research Institute, La Jolla, CA, USA ã 2008 Elsevier Ltd. All rights reserved. Introduction The virion is a nucleoprotein particle designed to move the viral genome between susceptible cells of a host and between susceptible hosts. An important limitation on the size of the viral genome is its container, the protein capsid. The virion has a variety of functions during the virus life cycle ( Table 1 ); however, the principles dictating its archi-tecture result from the need to provide a container of maximum size derived from a minimum amount of genetic information. The universal strategy evolved for the pack-aging of viral nucleic acid employs multiple copies of one or more protein subunit types arranged about the genome. In most cases the subunits are arranged with well-defined symmetry, but there are examples where assembly intermediates and sometimes mature particles are not globally symmetric. The assembly of subunits into nucleoprotein particles is, in many cases, a spontaneous process that results in a minimum free energy structure under intracellular conditions. The two broad classes of symmetric virions are helical rods and spherical particles. Helical Symmetry The nucleoprotein helix can, in principle, package a genome of any size. Extensive studies of tobacco mosaic virus (TMV) show that protein subunits will continue to add to the extending rod as long as there is exposed RNA. Protein transitions required to form the TMV helix from various aggregates of subunits are now understood at the atomic level. It is clear that subunits forming the helix display significant polymorphism in the course of assembly; however, excluding the two ends of the rod, all subunits are in identical environments in the mature helical virion. This is the ideal protein context for a mini-mum free energy structure.
eBook - PDFBio-Synthetic Hybrid Materials and Bionanoparticles
A Biological Chemical Approach Towards Material Science
- Alexander Boker, Patrick van Rijn(Authors)
- 2015(Publication Date)
- Royal Society of Chemistry(Publisher)
For instance, micelles or DNA-amphiphiles can be introduced into the capsid. This effectively creates a hydrophobic cavity that is stabilized by the virus shell. 68 9.3.2 Nanoparticle Encapsulation Electrostatic encapsulation is not limited only to organic molecules and poly-mers. The same can be applied to rigid inorganic nanoparticles, allowing the creation of biohybrid structures that combine protein cages with inor-ganic physical properties and states, such as superparamagnetism, plasmon absorption and similar confined electromagnetic states. 60,69 Dragnea et al. first showed the tendency for citrate- or tannic acid-capped gold nanoparticles to be trapped inside the virus capsid of BMV upon reassem-bling a capsid in the presence of these particles. 70 Small particles were shown to be tightly bound inside the capsid and exhibited a change in spectroscopic Figure 9.12 CCMV can be assembled into a variety of architectures based on the template presented: (a) 16 nm T1 capsid using PSS; 59 (b) 22 nm T2 capsid using PSS; 63 (c) 27 nm T3 capsid using PSS; 63 and (d) 17 nm diameter tubes using double-stranded DNA. 67 (e) Scheme showing the encapsulation of nanoemulsion droplets in CCMV; (f) TEM images of nanoemulsion droplets encapsulated by one, two or three protein shells depending on buffer conditions. 66 (b, c) Reprinted from ref. 63, Copyright 2007, with permission from Elsevier. (d) Adapted with permission from ref. 67. Copyright 2006 American Chemical Society. (f) Adapted with permission from ref. 66. Copyright 2008 American Chemical Society. 225 Virus-Based Systems for Functional Materials properties. Although these surface ligands carry negative charge, the role of surface charge is more prominent when DNA linkers are attached to the gold particle prior to encapsulation. 71 By using a small DNA or RNA chain bound to a nanoparticle, it is possible to form a nucleation site for the coat protein shell.
eBook - PDF- Ellen G. Strauss, James H. Strauss(Authors)
- 2002(Publication Date)
- Academic Press(Publisher)
2.14. The nucleocapsid has a diameter of 400 Å, and is a regular icosahedron with T =4 symmetry. It is formed from 240 copies of a single species of capsid protein of size 30 kDa. The structure of the the capsid protein itself has been solved to atomic resolution by conventional X-ray crystallography (Fig. 2.15). It has a structure that is very different from the eightfold sandwich described above (compare Fig. 2.15 with Figs 2.3B and 2.4). Instead, its fold resembles that of chymotrypsin, and it has an active site that consists of a catalytic triad whose geome-try is identical to that of chymotrypsin. The capsid protein is an active protease that cleaves itself from a polyprotein pre-cursor. The interactions between the capsid protein subunits that lead to formation of the T =4 icosahedral lattice have been deduced by fitting the electron density of the capsid protein at 2.5-Å resolution into the electron density of the nucleocapsid found by cryoelectron microscopy (Fig. 2.14B). The combined approaches of X-ray crystallography and cryoelectron microscopy thus define the structure of the shell of the nucleocapsid to atomic resolution. The envelopes of alphaviruses contain 240 copies of each of two virus-encoded glycoproteins. These two glyco-proteins form a heterodimer and both span the lipid bilayer as Type I integral membrane proteins (having a membrane-spanning anchor at or near the C terminus). The C-terminal cytoplasmic extension of one of the glycoproteins interacts in a specific fashion with a nucleocapsid protein, and the 240 glycoprotein heterodimers form a T =4 icosahedral lattice on the surface of the particle. Three glycoprotein het-erodimers associate to form a trimeric structure called a spike, easily seen in Figs. 2.5 and 2.14. The apex of the spike contains the domains that attach to receptors on a sus-ceptible cell.
eBook - PDF- Yury Khudyakov, Paul Pumpens, Yury Khudyakov, Paul Pumpens(Authors)
- 2015(Publication Date)
- CRC Press(Publisher)
However, coat proteins of some helical capsids also form crystallizable disk-like structures, for which high-resolution structures can be solved, as exemplified by rabies virus nucleoprotein– RNA complex [29]. One of the best studied helical viruses is tobacco mosaic virus, for which high-resolution structure has been obtained by fiber diffraction [30]. The capsid of tobacco mosaic virus forms a rigid rod, which is roughly 300 Å long and 180 Å in diameter (Figure 1.10). Axial rise per subunit is 1.2 Å and there are 16 1/3 monomers per turn of helix. 1.10 ENVELOPED VIRUSES Nucleocapsids of both helical and icosahedral viruses can have a lipid envelope of cellular origin, in which viral mem-brane proteins are embedded. In some viruses, like HIV and influenza, membrane forms the outer layer of virion (external membrane), while in some other viruses, for example, flavivi-ruses and alphaviruses, membrane is surrounded by an outer protein layer (internal membrane). Usually, viral proteins in envelope are not arranged symmetrically; however, there are some notable exceptions. In alphaviruses, such as Sindbis virus [31], Chickungunya virus [32], and Venezuelan equine encephalitis virus [33], two concentric T = 4 protein layers enclose the membrane in between them. The inner protein layer is represented by FIGURE 1.9 Geometry of geminiviruses. Two truncated T = 1 icosahedrons, each with a missing pentamer, are joined together. Notice that in contrast to prolate icosahedral particles, geminivi-ruses have a concavity in the middle. 10 Viral Nanotechnology nucleocapsid protein and the outer by envelope proteins E1 and E2. Both protein layers are interconnected by trans-membrane helices (Figure 1.11). Flaviviruses represent another interesting type of sym-metry. Even though the envelope is made of 180 protein monomers, the actual subunit arrangement does not cor-respond to T = 3 quasisymmetry.
eBook - PDF- Mavis Agbandje-McKenna, Robert McKenna(Authors)
- 2010(Publication Date)
- Royal Society of Chemistry(Publisher)
68 Consensus is indicated by greater than 40% sequence identity per column. 173 Evolution of Viral Capsid Structures – the Three Domains of Life The icosahedral capsids ( B 180 MDa) are composed of hexamers and pen-tamers arranged on a T ¼ 16 surface lattice enclosing a linear dsDNA genome. The genome ranges in size, depending on the family member, from 80 000 to 250 000 bp. The hexamers and pentamers are composed of multiple copies of a single gene product. A number of minor capsid proteins or cementing proteins and a portal associate with the major capsid protein to make the capsid shell. The number and positioning of the minor capsid proteins differ slightly between the members of the family. Although the capsid shells also vary in thickness and size, they are close to 160 A ˚ thick and B 1250 A ˚ from opposing vertices. The major capsid protein can be segmented into three sections: the ‘floor’ ( B 50 A ˚ thick), the ‘middle’ ( B 30 A ˚ ) and the ‘upper’ domain ( B 85 A ˚ ). 53 Herpesvirus capsids assemble as spherical procapsids that irreversibly mature into icosahedral-shaped capsids. Time-lapse cryo-EM studies of HSV-1 capsids undergoing this maturation in vitro have revealed the conformational change to involve rotational and translational movement of the ‘floor’ domain that progresses into the ‘triplex’ and ‘upper’ domains. 54 The motions observed in the ‘floor’ domain are akin to the motions observed for the HK97 gp5 protein during capsid expansion. The HSV-1 major capsid protein (VP5) The major capsid protein of herpes simplex virus 1 (HSV-1) is 149 kDa. The crystal structure of the ‘upper’ domain, solved to 2.9 A ˚ resolution, shows a novel fold that is predominantly a -helical. 55 Structural data for the ‘floor’ and ‘middle’ domains are available from an 8 A ˚ cryo-EM map of the HSV-1 capsid.
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