#### xaktly | Virology

Structures of viruses

The virology pages are organized like this:

### Structures of viruses

The genome of a virus – its business end, consisting of RNA or DNA – is susceptible to being broken up and rendered useless by host defenses and other environmental factors. It must, therefore, be protected if a virus is to infect a host cell successfully and co-opt the host machinery to make copies of itself.

All viruses enclose their genetic material in a capsid (Latin root = "case") made of protein. Sometimes capsids are coated with a phospholipid membrane derived from host cell, and some viruses surround the genome with an inner capsid, a nucleocapsid.

All viral capsids are composed of many identical copies of just a few small-to-average sized proteins (20-50 KDa, see pro tip below). Those proteins, modules that can sometimes form more than one kind of quaternary structure complex, are the repeating building blocks of the amazing and diverse virus structures we can observe.

Capsid proteins are often named with the prefix "VP," for "viral protein" or "virion protein." The name VP20 would be a viral protein of mass 20 KiloDaltons (KDa), approximately.

Virus structures have to be held together tightly enough so that they can protect the enclosed genetic material, but not so tightly that they won't be able to open up and release that material (or sometimes let host-cell proteins in) when it's time. It's a tricky balance. The resulting protein structures are called metastable, implying that they lie on the cusp of an energetic divide, and could as easily remain together as fall apart.

We can break the structures of viruses down into two main categories, based mostly on the symmetry of their construction from protein subunits, and one catch-all category, the "complex structures."

• Helical
• Icosahedral
• Complex

We'll use those three categories. Viruses are further classified as to whether the genetic material is contained inside a single capsid, inner and outer capsids, and/or whether they receive a membrane envelope (outer coating). Viruses are referred to as being enveloped or non-enveloped.

Here are just a few examples (electron micrographs) of the main types of virus particles

##### Helical

The Ebola virus is a rod-shaped virus that tends to twist a bit at one end. The rod is formed from many copies of a single viral protein that assemble in a helical pattern, forming a hollow tube. Ebola viruses are roughly 80 nm (800 Å) in diameter and they can exceed 1000 nm long.

##### Icosahedral

The Corona virus is an icosahedral (roughly soccer-ball shaped) virus with protein "spikes" located at the vertices. Several copies of one or more distinct viral proteins assemble to form a highly-symmetrical closed form – an icosahedron. Coronavirus capsids are about 50 nm (500 Å) in diameter.

##### Complex

The structure of the Lambda phage (a phage is a virus that infects bacteria) is a complex structure consisting of a rod-like helical section, an icosahedral "head" and several smaller structures like the protein bits that look like legs. The diameter of the icosahedral "head" is about 55 nm and the "tail" is about 150 nm long.

#### Pro tip:

In biology, the atomic mass unit (amu) is called the Dalton (Da). The mass of carbon is 12 amu or 12 Da. The average mass of the 20 amino acids (aa) is 110 Da, so a 10 KDa (10,000 Da) protein consists of about

$$\frac{10,000 \, Da}{110 \, Da/aa} = 91 \, \text{amino acids}$$

Think of it as about 90 amino acids for every 10 KDa of mass.

### Three structural types, ± envelopes

The three classes of virus structure are shown – just schematically – here. Helical packing of many copies of (usually) just one protein forms a cyclindrical capsid that encloses the viral genome, either loosely or by forming close contacts with the DNA or RNA. Spherical particles have icosahedral symmetry, sometimes with the geometry of a soccer ball. Complex viruses can be combinations of icosahedral and helical construction, and sometimes something quite different. We'll go through each of these below.

#### Simple modules → complex structures

Viruses are efficient. The complete capsid structure of a typical virus is composed of no more than just two or three proteins, and often just one, arranged symmetrically so as to build a hollow structure that is strong enough to contain and protect the traveling genome, yet sufficiently weakly-bound that the capsid can open to release the genetic material when needed.

While the primary structure of a protein is completely determined by covalent bonds, the 2˚, 3˚ and 4˚ structures depend on weaker intermolecular attractions, such as hydrogen bonds and charge-charge interactions. These weaker interactions can be quite specific, binding two proteins or parts of one protein in a very specific conformation. Because they are weaker than covalent bonds, they can be relatively easily broken as needed.

A good paradigm for these weak interactions is the base-pairing between the two strands of the DNA double helix: The helices are quite spefically matched to one another through H-bonding interactions, but bound weakly enough that they can be separated for transcription and copying.

The only thing needed for a virus particle capsid to assemble is the presence of its constituent proteins. That is, if all parts of a viral capsid are present in a cell or a solution, viral capsids (virus-like particles or VLPs) will spontaneously self-assemble.

The arrangement of constituent proteins in virus capsids follow simple symmetry rules.

### Helical viruses

Helical virus capsids are composed of hollow cyclinders formed from a repeated protein unit(s) that link to neighboring proteins in a spiraling pattern. The genetic material is usually wound in a helical pattern inside the cylindrical capsid. Here's a schematic depiction of how it looks.

#### Example: Tobacco mosaic virus (TMV)

The tobacco mosaic virus (TMV) is a nice example of a non-enveloped helical virus. TMV was the first virus ever isolated, so we know a lot about it. TMV causes the leaves of tobacco plants to have a mottled appearance, and therefore affects its commercial value.

A leaf on a TMV-infected tobacco plant shows mottled coloring. A healthy leaf is a continuous green color. Image: Clemson University - USDA Cooperative Extension Slide Series

Electron micrographs of TMV show the virus particles to be cylindrical, and of uniform diameter and length. These virus particles are rigid, but helical viruses need not be completely rigid in form, as we shall see.

Image: Public domain

The cylindrical capsid of TMV is composed of 2130 copies of a single coat protein called CP (for "coat protein" – I know, shocking). Here is an artistic representation of that capsid. The proteins are in blue (identical, but alternately shaded so that you can differentiate neighboring molecules), and the ssRNA strand, comprising 6400 bases, is in red. It folds in a helix in close contact with the inner ends of the capsid proteins.

Source: Protein data bank

A ribbon representation of the structure of the 158 amino-acid (so that's about 1.75 KDa) coat protein (CP) of TMV is shown below. Two molecules are shown to give an idea of their packing in the capsid. Each chain is covalently-linked, and consists of a group of four alpha helices with a fifth (on the left) directed toward the inside of the capsid. Three RNA bases form weak attachments to every CP protein. The attractive interactions between any two CP molecules are due to weaker intermolecular forces such as hydrogen bonds (H-bonds).

#### Example: Ebola virus

Ebola virus, which causes a severe hemorrhagic fever in humans, is an enveloped helical virus that forms often-bent tubes containing its RNA genome. Note the similarities between this electron micrograph of ebola viruses and the one above.

Image: Public domain

Here is a schematic view of the structure of Ebola.

The RNA genome is coated with two capsid proteins called N and VP30. These inner capsids are sometimes referred to as nucleocapsids because they (1) coat the nucleic acid polymers directly and (2) are the innermost of two capsid layers. The outer capsid of Ebola is formed from copies of two proteins, VP24 and VP40, the latter being most abundant and mainly responsible for the structure of the capsid. VP24 plays a role in inhibiting several cellular virus defenses. The outer capsid receives a membrane coating from the host, and displays copies of a glycoprotein along its surface. The Ebola capsid also encloses its own RNA polymerase (RNAp) and a multi-purpose helper protein called VP35.

#### Self-assembly

All of these example viruses will spontaneously self assemble in solution if we can arrange for all of the protein and genetic components to come together artificailly in the lab. We can also make empty (of genetic material) virus particles called VLPs, virus-like particles, that contain no genetic material. VLPs have been used in this way as cell-specific delivery systems in living organisms, like humans. VLPs are a target of a lot of research. They have been used to create vaccines and to attempt various gene therapies.

### The icosahedron and icosahedral symmetry

The icosahedron is one of the Platonic solids, objects identified by Plato which are regular, closed polyhedrons with congruent, regular (all sides congruent) polygon faces, with the same number of faces meeting at each vertex. The five platonic solids are

• tetrahedron (four triangular faces)
• cube (six square faces)
• octahedron (eight triangular faces)
• dodecahedron (twelve pentagonal faces)
• icosahedron (twenty triangular faces)

The figures above illustrate the symmetry elements of a simple icosahedron. Icosahedrons have 30 two-fold axes of symmetry (red, one for each edge), 20 three-fold axes of symmetry (green, one for each face), and 12 five-fold axes of symmetry (blue, one for each vertex).

While many virus capsids have icosahedral symmetry, their appearance is nearly spherical. That's not a contradiction. When we refer to icosahedral symmetry, we refer to the symmetry of construction of the capsid, not necessarily its shape.

The soccer ball is an example of a truncated icosahedron, one in which there is one kind of vertex (three sides meet) and two kinds of faces: pentagons and hexagons. In order for an icosahedral solid to be able to close, it must include five pentagons, the black faces of the soccer ball.

The covalent molecule C60, a major component of soot, forms as a truncated icosahedron. This symmetry is ubiquitous in nature.

#### Pro tip

An object need not have an icosahedral shape to have icosahedral symmetry.

#### Arrangement of viral proteins on an icosahedron

Icosahedral packing of three VPs is illustrated schematically here. VP1, VP2 and VP3 form a triangle, and 24 such triangles form the complete icosahedron. In the figures below, the structures of several viruses are shown, some in ribbon diagrams and some as space-filling models. Each was determined from detailed structural measurements. See if you can identify triangular, pentagonal and hexagonal subunits in each.

#### Rotavirus

The rotavirus causes much of the childhood diarrhea around the globe. In countries without the means to sufficiently clean water, or which lack the means to rehydrate sufferers with electrolyte-containing solutions, infected children often die. Two vaccines (as of 2021) are now available. If they can be distributed, many young lives may be saved.

#### Dengue virus

The Dengue virus causes Dengue fever, which can be dangerous upon the first infection. If a human is infected a second time, the chances of survival are currently drastically reduced. Dengue is an arbovirus, one that is transmitted by an arthropod insect, in this case, the mosquito Aedes aegypti. See if you can identify triangular and pentagonal substructures in the image.

#### Hepatitis B

The Hepatitis B virus infects cells of the liver and can lead to cirrhosis (hardening of the organ through scarring), liver cancer and other kinds of liver failure. A small set of proteins forms a fairly complex virus structure.

#### Norwalk virus

The Norwalk virus is a norovirus. It is causes gastroenteritis – generally vomiting, diarrhea and dehydration. The disease is uncomfortable but usually resolves within a couple of days. Norovirus infections are second to colds (caused by rhinovirus or coronavirus) in the US.

#### Make your own virus model

You can make your own icosahedral virus model. Click here to download a .pdf file that you can print, cut out with scissors and tape or glue together. It's a good exercise to get a better feel for the symmetry of icosahedral virus particles.

### Complex structures

Complex structures can consist of helical and icosohedral elements or they can take some other shape. Here is a brief tour of a couple of interesting complex viruses.

#### Lambda phage

A phage is a virus that infects a bacterium. An electron micrograph of the lambda phage, which infects the Escherichia coli (E. coli) bacterium, was shown above. Here is a schematic diagram of the phage. It acts like a sort of syringe to inject its DNA genome into its host.

#### The Rabies virus

The rabies virus is a bullet-shaped virus consisting of nucleocapsid that surrounds a single-stranded -RNA genome. Glycoproteins project through the membrane derived from host cells.

Source: modified from the figure in Abraham, et al., Int. J. Current Microbiology & Appl. Sci., 6(12):2064-2085 (2017).

Rabies affects the central nervous system of humans. As of 2021, there is no cure for an infected person who is showing symptoms of rabies. Caught immediately, there is antibody treatment and a vaccine than can stem the infection during its incubation period. In the US, rabies affects only a handful of people per year.

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### Protein structure

There are four levels of protein structure:

1. 1˚ or primary structure is the ordering of the amino acids along the polypeptide chain.
2. 2˚ or secondary structure is the formation of alpha helices, beta sheets and other structure that depends upon the sequence.
3. 3˚ or tertiary structure is specific interactions between secondary structure elements to form the completed fold of a protein.
4. 4˚ or quaternary structure is specific attractive interaction between one or more protein sub-units (identical or different) to form a stable complex of proteins.
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### Virome

The virome revers to the collection of all viral genomes, or even just viruses, that live within an organism, a set of organisms or a region on Earth. It is used rather loosely in context.

We can refer, for example, to the global virome (all viruses on Earth) or the human virome, the viruses that infect humans.

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