Viral protein

Viral structural proteins

Most viral structural proteins are components for the capsid and the envelope of the virus.

Capsid

The genetic material of a virus is stored within a viral protein structure called the capsid. The capsid is a "shield" that protects the viral nucleic acids from getting degraded by host enzymes or other types of pesticides or pestilences. It also functions to attach the virion to its host, and enable the virion to penetrate the host cell membrane. Many copies of a single viral protein or a number of different viral proteins make up the capsid, and each of these viral proteins are coded for by one gene from the viral genome. The structure of the capsid allows the virus to use a small number of viral genes to make a large capsid.

Several protomers, oligomeric (viral) protein subunits, combine to form capsomeres, and capsomeres come together to form the capsid. Capsomeres can arrange into an icosahedral, helical, or complex capsid, but in many viruses, such as the herpes simplex virus, an icosahedral capsid is assembled. Three asymmetric and nonidentical viral protein units make up each of the twenty identical triangular faces in the icosahedral capsid.

Viral envelope

The capsid of some viruses are enclosed in a membrane called the viral envelope. In most cases, the viral envelope is obtained by the capsid from the host cell's plasma membrane when a virus leaves its host cell through a process called budding. The viral envelope is made up of a lipid bilayer embedded with viral proteins, including viral glycoproteins. These viral glycoproteins bind to specific receptors and coreceptors on the membrane of host cells, and they allow viruses to attach onto their target host cells. Some of these glycoproteins include:

• Hemagglutinin, neuraminidase, and M2 protein in the influenza virus
• gp160, composed of subunits gp120 and gp41, in the human immunodeficiency virus (HIV).

Viral glycoproteins play a critical role in virus-to-cell fusion. Virus-to-cell fusion is initiated when viral glycoproteins bind to cellular receptors.

Viral membrane fusion proteins

The fusion of the viral envelope with the cellular membrane requires high energy to occur. Viral membrane fusion proteins act as catalysts to overcome this high energy barrier. Following viral glycoprotein binding to cellular receptors, viral membrane fusion proteins undergo a change in structure conformation. This change in conformation then facilitates the destabilization and fusion of the viral envelope with the cellular membrane by allowing fusion loops (FLs) or hydrophobic fusion peptides (FPs) on the viral envelope to interact with the cell membrane. Most viral membrane fusion proteins would end up in a hairpin-like conformation after fusion, in which FLs/FPs and the transmembrane domain are all on the same side of the protein.

Viral glycoproteins and their three-dimensional structures, before and after fusion, have allowed a wide range of structural conformations to be discovered. Viral membrane fusion proteins have been grouped into four different classes, and each class is identified by characteristic structural conformations:

• Class I: Post-fusion conformation has a distinct central coiled-coil structure composed of signature trimer of α-helical hairpins. An example of a Class I viral fusion protein is the HIV glycoprotein, gp41.
• Class II: Protein lacks the central coiled-coil structure. Contains a characteristic elongated β- sheet ectodomain structure that refolds to give a trimer of hairpins. Examples of class II viral fusion proteins include the dengue virus E protein, and the west nile virus E protein.
• Class III: Structural conformation is a combination of features from Class I and Class II viral membrane fusion proteins. An example of a Class III viral fusion protein is the rabies virus glycoprotein, G.
• Class IV: Class IV viral fusion proteins are fusion-associated small transmembrane (FAST) proteins. They do not form trimers of hairpins or hairpin structures themselves, and they are the smallest known viral fusion proteins. FAST proteins are coded for by members of the nonenveloped reoviridae family of viruses.