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Acapsid is the protein shell of avirus, enclosing itsgenetic material. It consists of severaloligomeric (repeating) structural subunits made ofprotein calledprotomers. The observable 3-dimensional morphological subunits, which may or may not correspond to individual proteins, are calledcapsomeres. The proteins making up the capsid are calledcapsid proteins orviral coat proteins (VCP). The virus genomic component inside the capsid, along with occasionally presentvirus core protein, is called thevirus core. The capsid and core together are referred to as anucleocapsid (cf. alsovirion).
Capsids are broadly classified according to their structure. The majority of the viruses have capsids with eitherhelical oricosahedral[2][3] structure. Some viruses, such asbacteriophages, have developed more complicated structures due to constraints of elasticity and electrostatics.[4] The icosahedral shape, which has 20 equilateral triangular faces, approximates asphere, while the helical shape resembles the shape of aspring, taking the space of a cylinder but not being a cylinder itself.[5] The capsid faces may consist of one or more proteins. For example, thefoot-and-mouth disease virus capsid has faces consisting of three proteins named VP1–3.[6]
Some viruses areenveloped, meaning that the capsid is coated with a lipid membrane known as theviral envelope. The envelope is acquired by the capsid from an intracellular membrane in the virus' host; examples include the inner nuclear membrane, theGolgi membrane, and the cell's outermembrane.[7]
Once the virus has infected a cell and begins replicating itself, new capsid subunits are synthesized using theprotein biosynthesis mechanism of the cell. In some viruses, including those with helical capsids and especially those with RNA genomes, the capsid proteins co-assemble with their genomes. In other viruses, especially more complex viruses with double-stranded DNA genomes, the capsid proteins assemble into empty precursorprocapsids that include a specialized portal structure at one vertex. Through this portal, viralDNA is translocated into the capsid.[8]
Structural analyses of major capsid protein (MCP) architectures have been used to categorise viruses into lineages. For example, the bacteriophage PRD1, the algal virusParamecium bursaria Chlorella virus-1 (PBCV-1),mimivirus and the mammalianadenovirus have been placed in the same lineage, whereas tailed, double-stranded DNA bacteriophages (Caudovirales) and herpesvirus belong to a second lineage.[9][10][11][12]
The icosahedral structure is extremely common among viruses. Theicosahedron consists of 20 triangular faces delimited by 12 fivefold vertexes and consists of 60 asymmetric units. Thus, an icosahedral virus is made of 60N protein subunits. The number and arrangement ofcapsomeres in an icosahedral capsid can be classified using the "quasi-equivalence principle" proposed byDonald Caspar andAaron Klug.[13] Like theGoldberg polyhedra, an icosahedral structure can be regarded as being constructed from pentamers and hexamers. The structures can be indexed by two integersh andk, with and; the structure can be thought of as takingh steps from the edge of a pentamer, turning 60 degrees counterclockwise, then takingk steps to get to the next pentamer. The triangulation numberT for the capsid is defined as:
In this scheme, icosahedral capsids contain 12 pentamers plus 10(T − 1) hexamers.[14][15] TheT-number is representative of the size and complexity of the capsids.[16] Geometric examples for many values ofh,k, andT can be found atList of geodesic polyhedra and Goldberg polyhedra.
Many exceptions to this rule exist: For example, thepolyomaviruses andpapillomaviruses have pentamers instead of hexamers in hexavalent positions on a quasi T = 7 lattice. Members of the double-stranded RNA virus lineage, includingreovirus,rotavirus and bacteriophage φ6 have capsids built of 120 copies of capsid protein, corresponding to a T = 2 capsid, or arguably a T = 1 capsid with a dimer in the asymmetric unit. Similarly, many small viruses have a pseudo T = 3 (or P = 3) capsid, which is organized according to a T = 3 lattice, but with distinct polypeptides occupying the three quasi-equivalent positions[17]
An elongated icosahedron is a common shape for the heads of bacteriophages. Such a structure is composed of a cylinder with a cap at either end. The cylinder is composed of 10 elongated triangular faces. The Q number (or Tmid), which can be any positive integer,[18] specifies the number of triangles, composed of asymmetric subunits, that make up the 10 triangles of the cylinder. The caps are classified by the T (or Tend) number.[19]
The bacteriumE. coli is the host forbacteriophage T4 that has a prolate head structure. The bacteriophage encoded gp31 protein appears to be functionally homologous toE. coli chaperone protein GroES and able to substitute for it in the assembly of bacteriophage T4 virions during infection.[20] Like GroES, gp31 forms a stable complex withGroELchaperonin that is absolutely necessary for the folding and assemblyin vivo of the bacteriophage T4 major capsid protein gp23.[20]
Many rod-shaped and filamentous plant viruses have capsids withhelical symmetry.[21] The helical structure can be described as a set ofn 1-D molecular helices related by ann-fold axial symmetry.[22] The helical transformation are classified into two categories: one-dimensional and two-dimensional helical systems.[22] Creating an entire helical structure relies on a set of translational and rotational matrices which are coded in the protein data bank.[22] Helical symmetry is given by the formulaP = μ x ρ, whereμ is the number of structural units per turn of the helix,ρ is the axial rise per unit andP is the pitch of the helix. The structure is said to be open due to the characteristic that any volume can be enclosed by varying the length of the helix.[23] The most understood helical virus is the tobacco mosaic virus.[21] The virus is a single molecule of (+) strand RNA. Each coat protein on the interior of the helix bind three nucleotides of the RNA genome. Influenza A viruses differ by comprising multiple ribonucleoproteins, the viral NP protein organizes the RNA into a helical structure. The size is also different; the tobacco mosaic virus has a 16.33 protein subunits per helical turn,[21] while the influenza A virus has a 28 amino acid tail loop.[24]
The functions of the capsid are to:
The virus must assemble a stable, protective protein shell to protect the genome from lethal chemical and physical agents. These include extremes ofpH or temperature and proteolytic and nucleolyticenzymes. For non-enveloped viruses, the capsid itself may be involved in interaction with receptors on the host cell, leading to penetration of the host cell membrane and internalization of the capsid. Delivery of the genome occurs by subsequent uncoating or disassembly of the capsid and release of the genome into the cytoplasm, or by ejection of the genome through a specialized portal structure directly into the host cell nucleus.
It has been suggested that many viral capsid proteins have evolved on multiple occasions from functionally diverse cellular proteins.[25] The recruitment of cellular proteins appears to have occurred at different stages of evolution so that some cellular proteins were captured and refunctionalized prior to the divergence of cellular organisms into the three contemporary domains of life, whereas others were hijacked relatively recently. As a result, some capsid proteins are widespread in viruses infecting distantly related organisms (e.g., capsid proteins with thejelly-roll fold), whereas others are restricted to a particular group of viruses (e.g., capsid proteins of alphaviruses).[25][26]
A computational model (2015) has shown that capsids may have originated before viruses and that they served as a means ofhorizontal transfer between replicator communities since these communities could not survive if the number of gene parasites increased, with certain genes being responsible for the formation of these structures and those that favored the survival of self-replicating communities.[27] The displacement of these ancestral genes between cellular organisms could favor the appearance of new viruses during evolution.[26]
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