Capsid Protein

Viruses are small obligate intracellular parasites with a RNA or DNA genome encased in a virus-coded protein sheath. Viruses can be thought of as mobile genetic components that are most likely of cellular origin and have a lengthy history of co-evolution with their hosts. Viruses need specialised host cells to propagate because they lack the extensive metabolic and biosynthetic machinery found in eukaryotic and prokaryotic cells. A virion is a fully formed virus particle.

The virion's primary role is to deliver its DNA or RNA genome into the host cell, where it can be expressed (transcribed and translated) by the cell. A symmetric protein capsid contains the viral DNA, as well as any associated basic proteins. The nucleocapsid is made up of the nucleic acid-associated protein nucleoprotein and the genome. The nucleocapsid of enveloped viruses is encased in a lipid bilayer produced from the modified host cell membrane and studded with virus envelope glycoproteins on the outside.

This article will study protein capsid in viruses and classification of viruses in detail.

Properties of Virus 

1. They are non-cellular organisms with a protective cocoon around them.

2. The existence of spikes aids in the virus's attachment to the host cell.

3. These viruses do not proliferate, do not grow, do not respire, and do not metabolise.

4. They have a nucleic acid core made up of DNA or RNA and are enveloped by a protein shell called a capsid.

5. They are classified as both living and nonliving organisms. When these viruses are present outside of host cells, they are dormant, but when they enter host cells, they become active. These viruses invade the host cell and reproduce within it using enzymes and raw materials.

The diagram below shows the protein capsid in viruses.

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Classification of Viruses

Morphology: Viruses are classified according to their size and form, chemical makeup and genome structure, and mechanism of replication. Many filamentous and pleomorphic viruses have helical morphology in the protein capsid. A helical array of protein capsid in viruses (protomers) wraps around a helical filament of nucleic acid to form helical nucleocapsids. The nucleocapsids of many "spherical" viruses have an icosahedral shape. Identification and classification are aided by the number and arrangement of capsomeres (morphologic subunits of the icosahedron). An outer envelope is found on many viruses.

Chemical Composition and Mode of Replication:A virus's genome can be made up of single-stranded (ss) or double-stranded (ds), linear or circular DNA or RNA. The entire genome can fit into one nucleic acid molecule (monopartite genome) or many nucleic acid segments (multipartite genome) (multipartite genome). Different replication techniques are required for different types of genomes.

Structure of Virus 

The components of virus include:

1. Protein Capsid in Virus: The capsid is the protein shell that encases the nucleic acid; it is also known as the nucleocapsid because of the nucleic acid it contains. The protein capsid shell  is made up of capsomers, which are protein subunits grouped into a shell. They are intimately linked to nucleic acids and mirror their structure, which is either a rod-shaped helix or a polygon-shaped sphere. The capsid has three purposes: 1) it protects the infectious nucleic acid from enzyme digestion, 2) it has special sites on its surface that allow the virion to attach to a host cell, and 3) it contains proteins that allow the virion to penetrate the host cell membrane and, in some cases, inject the infectious nucleic acid into the cytoplasm.

2. Envelope: The protein capsid in viruses  is surrounded by a glycoprotein envelope. The envelope is made up of two lipid layers (lipoprotein bilayer) that are interspersed with protein molecules and can contain both host cell and viral membrane material. During the viral budding process, the virus acquires lipid molecules from the cell membrane. The virus, on the other hand, replaces the proteins in the cell membrane with its own proteins, resulting in a hybrid structure made up of lipids from the cell and proteins from the virus. Many viruses have glycoprotein spikes on their envelopes that aid in attachment to specific cell surfaces.

3. Nucleic Acid: The genetic information for the production of all proteins is encoded in the nucleic acid of each virus, just as it is in cells. In prokaryotic and eukaryotic cells, double-stranded DNA is responsible for this, although only a few viruses employ DNA. The single-stranded RNA is used by most viruses to store all of their genetic material. RNA-based viruses are divided into two categories. Because it works as messenger RNA for direct synthesis (translation) of viral protein, genomic RNA is referred to as a plus strand in most cases. However, a handful have RNA with negative strands. The virion possesses an enzyme termed RNA-dependent RNA polymerase in these circumstances (transcriptase).

Classification of Viruses Based on Morphology

1. Identical protein subunits (protomers) self-assemble into a helical array enclosing the nucleic acid in the replication of viruses with helical symmetry, which follows a similar spiral pattern. Nucleocapsids can take the form of hard, very elongated rods or flexible filaments, and electron microscopy may often reveal details of the capsid structure in both cases. Helical nucleocapsids are classified by length, width, helix pitch, and the number of protomers per helical turn, in addition to being flexible or stiff and naked or wrapped.

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2. Icosahedral Symmetry

A polyhedron with 20 equilateral triangular faces and 12 vertices is known as an icosahedron. Axes of five fold rotational symmetry are defined by lines passing through opposite vertices: all structural characteristics of the polyhedron repeat five times for every 360° of rotation about any of the fivefold axes. Threefold rotational symmetry axes are formed by lines through the centres of opposite triangular faces; twofold rotational symmetry axes are formed by lines through the midpoints of opposed edges. 532 symmetry is defined as a polyhedral or spherical icosahedron with fivefold, threefold, and twofold axes of rotational symmetry.

The protomers, or structural polypeptide chains, of most icosahedral viruses are grouped in oligomeric clusters called capsomeres, which can be easily distinguished by negative staining electron microscopy and create the closed capsid shell. The arrangement of capsomeres into an icosahedral shell facilitates the classification of such viruses by capsomere number and pattern. The distribution of capsomeres between the nearest pair of vertex capsomeres (called penton: those through which the fivefold symmetry axes pass) is required for this.

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3. Virus Core Structure 

Little is known about the packing or arrangement of the viral genome within the core, with the exception of helical nucleocapsids. Simple nucleocapsids with 1 to 2 protein species make up small virions. The nucleic acid genome is complexed with basic protein(s) in the core of larger viruses, which is protected by a single- or double-layered capsid (comprising more than one species of protein) or an envelope.

Classification of Viruses Based on the Presence of Nucleic Acid

1. DNA

The virus that has DNA as its genetic material is known as a DNA virus. DNA viruses are divided into two categories.

Picornaviruses, Parvoviruses, and other single-stranded DNA viruses are examples.

Adenovirus, Herpes virus, and other double-stranded DNA viruses

2. RNA

The virus that has RNA as its genetic material is known as an RNA virus. The RNA virus is divided into two categories.

Reovirus, for example, is a double-stranded (ds) RNA virus.

RNA virus with a single strand (ss). Positive sense RNA (+RNA) and negative sense RNA (-RNA) are the two types of RNA (-RNA). Single-stranded RNA viruses include the poliovirus, hepatitis A, rabies virus, and influenza virus.

Classification of Viruses Based on the Replication Properties and Site of Replication

1. Viruses enter the host cell here, where they reproduce and assemble within the cell organelles. Replication within the host cell's cytoplasm.

For example, all RNA viruses, with the exception of the Influenza virus.

2. Replication within the host cell's nucleus and cytoplasm.

Influenza virus, poxvirus, and other viruses are examples.

3. Within the nucleus of the host cell, replication takes place.

All DNA viruses, with the exception of the pox virus.

4. The virus replicates via a double-stranded DNA intermediate.

All DNA viruses, Retroviruses, and several tumor-causing RNA viruses are examples.

5. The virus replicates via a single-stranded RNA intermediate.

All RNA viruses, with the exception of Reovirus and tumor-causing RNA viruses, for example.

Classification of Viruses Based on the Host Range

There are four main types of viruses based on the type of host:

Animal Viruses 

These viruses infect animals, including humans, by infiltrating their cells. The influenza virus, mumps virus, rabies virus, poliovirus, Herpes virus, and others are all examples of animal viruses.

Plant Viruses 

Invasion of plant cells is how these viruses infect plants. Potato virus, tobacco mosaic virus, beet yellow virus, turnip yellow virus, cauliflower mosaic virus, and other plant viruses are well-known examples.

Bacteriophage :Bacteriophage is a type of virus that infects bacterial cells. Bacteriophages come in a variety of shapes and sizes, including DNA virus, MV-11, RNA virus, page, and others.

Virus Infecting Insects

Insect virus, commonly known as the viral pathogen of insects, is a virus that infects insects. In the present agricultural landscape, these viruses are thought to be a strong biocontrol agent. Insect virus examples include Ascovirus virions and Entomopox virus.

Classification of Viruses Based on the Mode of Transmission

• Infections that spread through the air and into the respiratory tract are known as airborne infections. Swine flu and rhinovirus, for example.

• The virus is transmitted through contaminated water or food via the faecal oral route.

Hepatitis A virus, Poliovirus, and Rotavirus, for example.

• Sexually transmitted diseases (STDs) - Virus transmission via sexual contact with an infected person. Retroviruses, human papillomaviruses, and other viruses are examples.

• Transfusion-transmitted illnesses occur when a virus is delivered during a blood transfusion.mHepatitis B virus, Human Immunodeficiency Virus, and other viruses are examples.

• Zoonoses – Virus transmission to humans via the bites of infected animals, birds, and insects. Viruses such as Rabies.

Did You Know?

Robert Gallo of the United States and Luc Montagnier of France were the first to isolate the HIV virus in 1983. Since then, there has been a significant amount of study focused on the AIDS causal agent, and much has been discovered about the virus's structure and typical course of action. The human immunodeficiency virus (HIV) is a virus that attacks the immune system of the body.  It can lead to disease called AIDS  if HIV is not treated (acquired immunodeficiency syndrome).

There is currently no viable treatment available. People who contract HIV are infected for the rest of their lives.

HIV can be managed with the right medical care. HIV-positive people who get proper treatment can live long, healthy lives while also protecting their relationships.

HIV belongs to the retroviruses, a group of atypical viruses that store their genetic information in the form of ribonucleic acid (RNA). HIV and other retroviruses can produce deoxyribonucleic acid (DNA) from RNA with the help of an enzyme called reverse transcriptase, whereas most cells do the opposite, transcribing the genetic information of DNA into RNA. The enzyme's action allows HIV's genetic information to be permanently integrated into a host cell's genome (chromosomes).