n., plural: capsids
Definition: The protein coat of a virus
A capsid is a three-dimensional proteinaceous capsular shell around a virus that encloses the viral genetic material. The capsid is made of several repeating finite number of protein subunits known as capsomeres or protomers. The capsomeres of the protein coat can be associated with or may be closely related to the viral genetic material or nucleic acid. The viral capsid is in the nanometer (nm) size range and possesses a complex and unique mechanical properties.
The capsid serves multiple functions namely, encapsulating and protecting viral genetic material, and transfer of genetic material to the required place in the new host. For serving all these functions, the capsid needs highly specific mechanistic and functional flexibility as well as strength.
The capsid enclosed viral nucleic acid along with the associated protein forms the nucleocapsid. In simple words, the nucleocapsid is composed of the viral nucleic acid and associated protein and is enclosed in a protein coat. However, some complex viruses have capsids with non-protein components like lipids, or in certain viruses, the capsid is further enclosed in a glycoprotein layer, such capsids are known as enveloped capsids.
For example, the herpes simplex virus is an enveloped capsid virus. Interestingly, the herpes simplex virus-infected cells also acquire an enveloping membrane over the nuclear membrane. Thus, giving the infected cell an envelope, which is often referred to as the capsid of a cell. This example helps to clarify, “What is the capsid of a cell?”.
But what is a capsid in a virus? The protein shell of a virus or the virus capsule that encloses the genetic material of the virus is the capsid of a virus.
A capsid is defined as the protein coat surrounding the nucleic acid of a virus. It encloses the genetic material of the virus. (NOTE: aside from virology, the term ‘capsid’ is also used in entomology where a capsid refers to a leaf bug from the insect family Miridae, mirid bug.) Word origin: Latin “capsa”, meaning “box”.
Types of Viral Capsids
Capsid structure or the viral capsule also forms one of the bases of the different virus shapes and the classification of viruses. The types of capsids in viruses can be helical or icosahedral.
The helical capsid, wherein the viral nucleic acid has two free ends and is either in extended condition or is helically coiled or bound. The capsid herein acquires a cylindrical or tubular structure having central space for the genetic nucleic acid. The tubular structure of the helical nucleocapsid can accommodate a large amount of nucleic acid. Thus, the virus acquires a rod-like extended long structure in such a case (Figure 1). For example, the tobacco mosaic virus is a helical virus.
Icosahedral and prolate capsid
The icosahedral capsid and a prolate capsid, wherein the viral nucleic acid may or may not be in a covalently bound circular shape, however, the nucleic acid is in a highly condensed state like a ball of yarn. Thus, the virus acquires a symmetrical, polygonal structure in such a case (Figure 2). Icosahedral and prolate capsid examples, bacteriophage, poliovirus, adenovirus, rhinovirus, etc. HIV capsid is also an example of an icosahedral capsid.
In fact, bacteriophage falls under the category of the prolate capsid. The prolate capsid is an elongated icosahedral capsid (Figure 2)
Origin and Evolution
Although the virus is the most ubiquitously available biological entity. Still, the origin and evolution of the viral structure are not completely known, especially the evolution of capsid is not fully understood. Multiple theories have been proposed for the evolution of capsid.
Some of the hypotheses for the evolution of capsid are ‘virus-first’, ‘reduction hypothesis’, ‘escape hypothesis’. However, none of these hypotheses explains the evolution of viral capsid satisfactorily.
The hybrid ‘chimeric’ model (proposed by Krupovic and coworkers) and the ‘symbiogenic’ model (proposed by Nasir and Caetano-Anollés) explain the evolution of current-day viruses. (Figure 3)
Let’s further look into the shapes of capsids.
Interestingly, these viruses may appear spherical in shape however a closer look reveals an icosahedral shape wherein multiple equilateral triangles fuse together to form an apparently spherical looking icosahedral structure.
The icosahedral capsid has a highly symmetrical geometry. Five (pentons) or six (hexons) capsid protein subunits form the capsomeres in the icosahedral viral geometry. The complexity and size of icosahedral capsid geometry can be described with the help of the triangulation number (T).
The basis of the T number is the Caspar-Klug (CK) theory. According to CK theory, the faces of an icosahedron are created by the 60 identical subunits that are organized into 20 triangles.
The characteristic of the icosahedron geometry includes:
- Rotational symmetry
- Vertices have a 5-fold symmetry
- Edges have 2-fold symmetry
- The center of each triangle has a 3-fold symmetry
From the 3-fold symmetrical axis, each facet of the triangle can be divided into three symmetrical parts that are known as icosahedral asymmetric units (IAU). (Figure 4)
As per the CK theory, icosahedral geometry has all subunits in hexagonal shape except at the triangulation point of each vertex, where the subunit is pentagon in shape. The presence of the pentagon in the icosahedral geometry is responsible for the sphere-like appearance of the icosahedral structure. (Figure 5)
Capsid herein is made up of 60T protein subunits, that result in 12 hexon assembly along with a variable number of hexons [10X(T-1)].
The capsid triangulation number (T) can be calculated using the formula mentioned below:
T= h2 + h. k + k2, where h≥1 and k≥0
Herein, h & k can be visualized as the number of steps taken from the edge of the pentamer followed by a 60º counterclockwise turn followed by k number of steps to reach to next pentamer (Figure 6).
Accordingly, a higher triangulation number is indicative of the larger number of hexagons and therefore a bigger capsid, while a smaller triangulation number indicates a smaller capsid.
Hepatitis B virus, Human papillomavirus, Rhinovirus, and Herpes viruses are some of the examples of viruses that have icosahedral capsids.
In order to increase the capacity to hold the amount of nucleic acid, the icosahedral geometry can be prolonged to form a prolate capsid. A prolate capsid consists of a cylinder with two icosahedral caps at the two ends of the cylinder. This arrangement results in a higher holding capacity of the capsid structure. Bacteriophage is an example of the prolate virus.
A single type of protein subunits a coil around a central axis to form a helical structured capsid. This helical structure may be hollow from the center like a hollow cylindrical tube. The protein subunits or the capsomeres are arranged in a circular disc-shaped pattern and these discs are further connected to each other forming a helical structure with a hollow space in the center, which creates the required room for the encapsulation of the nucleic acid.
This kind of protein subunit arrangement results in filamentous or rod-shaped viruses. These rod-shaped viruses can vary from short and rigid viruses to long and flexible viruses. These viruses may vary from 300nm to 500nm in length and 15-19 nm in width. Tobacco mosaic virus (TMV) is the most studied virus having a helical structured capsid. (Figure 7)
The helical capsid structure offers unique advantages that include:
- Need of single type of protein subunit only. Since the helical structure of the capsid is made up of a single type of protein subunits, the structure is simple that requires less energy, and can be produced from a single gene only.
- An unlimited amount of nucleic acid can be accommodated in the helical capsid. As the length of the helical stricture can be infinite, it can accommodate a huge amount of nucleic acid in it.
Rabies virus, Influenza virus, Mumps virus, Measles virus, and Ebola virus are some examples of the helical capsid viruses.
The primary function of a capsid includes encapsulating the viral genetic material, protecting the genetic material, transporting the genetic material, and release of the genetic material into a new host. The exceptional stability and rigidity of the viruses in extreme environmental conditions are imparted by their capsid structure. This is because the capsid structure functions to protect the genetic material of the virus from harsh environmental conditions. At the same time, this capsid is uniquely flexible which results in transferring the genetic viral material into another host. Thus, infectivity or the capability of a virus to infect depends not only on the intact genetic material but also on the capsid integrity and flexibility. Thus, the capsid is an essential viral structure for the normal functioning of a virus.
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