viral structures

Question 1

what is a virion?

Answer 1

a complete infectious particle

Question 2

what is a capsid?

Answer 2

viral container/shell

Question 3

what is a nucleocapsid?

Answer 3

when the capsid is intertwined with the genome

i.e. the capsid contains elements of the genome

Question 4

what is the envelope? describe it

Answer 4

when there is a lipid bilayer membrane enclosing the capsid

host-derived from when the virus exits the cell; gives the virus an advantage when infecting hosts

contains viral proteins – this is how the virus will interact with receptors!

the viral envelope glycoproteins are newly synthesized and then embedded into the host membrane where it will wait for virus which will take it as it leaves host cell

Question 5

what other interactions do capsid proteins assist with aside from protecting the genome and delivering it?

Answer 5

with cellular components for transport to intracellular sites of assembly

with cellular components to ensure an efficient infectious cycle

with the host immune system
- in rare cases, capsid proteins are enough to induce immune response

Question 6

how was the viral structure first observed?

Answer 6

was first observed thru electron microscopy

SOME viruses are smaller than ribosomes, some larger… but they’re smaller than other organelles

uses negative staining with electron-dense materials (to absorb electrons), giving a contrasted image
- allows you to see elements of the structure, such as the envelope

the downside of electron and microscopy is that it tends to destroy certain structural elements
- can’t appreciate fine details

Question 7

describe x-ray crystallography in regards to how it’s used to observe viruses

Answer 7

technique depends on the ability of viral proteins/virion to crystallize

even more detailed than cryo-electron microscopy

darker areas are canyons
areas that interact with receptors for attachment

Question 8

describe cryo-electron microscopy in regards to how it’s used to observe viruses

Answer 8

main method used now because it doesn’t damage the virus

no stain, so the structure is preserved

instead, flash freeze samples and image at very cold temperatures – the freezing provides the contrast
- can see more details!

use of computers to reconstruct images

Question 9

describe nuclear magnetic resonance spectroscopy (NMR) in regards to how it’s used to observe viruses

Answer 9

used if your protein does not crystallize

depends on the radiation emitted from a nucleus in a magnetic field - to obtain key info on how the proteins behave

radiation emitted are measured by spectra

inherent property of certain nuclei to have a magnetic moment

we can see how proteins behave in 3D – NOT the whole virion
- a limitation as we are exclusively looking at specific proteins

Question 10

list the different methods of observing viral structures in order from least detailed to most detailed

Answer 10

electron microscopy

cryo-electron microscopy

x-ray and NMR

cryo-electron microscopy’s resolution could surpass x-ray and NMR one day

note that all the other techniques aside from NMR, gives full virion structures!
- NMR only gives viral proteins

Question 11

describe the protein composition of viruses

Answer 11

virions are made from many copies of few proteins

lacks a variety of proteins because they do not have enough power/size to accommodate multiple proteins

Question 12

how is the virus able to fit in so many proteins onto its capsid?

Answer 12

with such a small area, it take thousands of proteins to make the shell

all these proteins are able to compactly form a shell due to symmetry

protein subunits on the surface are identical and the contacts (between subunits) will be identical as well

Question 13

what are the 2 types of symmetry present in viruses?

Answer 13

helical symmetry
- for rod shaped viruses
e.g. tobacco mosaic virus

polyhedral symmetry
- for round viruses
e.g. simian virus 40

Question 14

what are the 2 rules of symmetry (for all types) that provides the basis for assembly

Answer 14

each subunits had identical bonding contacts with neighbouring subunits
- achieves higher level of symmetry

bonds between subunits are mostly via non-covalent
- makes it easy to break apart for when the genome needs to be exposed!

Question 15

how is gardasil a HPV vaccine when it has no elements of the HPV genome?

Answer 15

the shell of HPV is synthesized using synthetic yeast systems and coat proteins for hepatitis B virus and human papilloma virus which self-assembles into shells

this shell is enough to illicit an immune response (immunogenic)

Question 16

describe the structure of helical symmetry

Answer 16

nucleic acid found in the middle and is surrounded by proteins
- like a shawarma stick

the protein subunits interacts with other identical protein subunits in an identical manner

nucleocapsid
- the subunits also interact with the viral genome that’s found in the middle
- they can be composed one type of protein or multiple types

in more complex structures, nucleoproteins will associate with viral genomes… this is the case for ebola

Question 17

what are some viruses that exhibit helical symmetry

Answer 17

measles virus

vesicular stomatitis virus

ebola virus

Question 18

what proteins form the nucleocapsid of the ebola virus?

Answer 18

VP30, VP24, VP35

Question 19

describe the structure of polyhedral symmetry

Answer 19

round or spherical capsids

regardless of the irregularly shaped proteins, viral capsids are able to appear round/spherical due to symmetry

it was observed that round capsids have a defined number of proteins
- proteins are often in multiples of 60
- number of subunits were 60, 180, 240, 960…

this is how viruses are so round and efficient

Question 20

describe the structure of icosahedral symmetry (a type of polyhedral)

Answer 20

polyhedral solid with 20 faces
- each of the faces is an equilateral triangle (it’s symmetrical)

accommodates genomes and efficiently protects them

allows formations of a closed shell with a minimum of 60 identical subunit (3 subunits per face x 20 trimers)

Question 21

what are the rules for the axis of symmetry present in icosahedrons? what are the exceptions?

Answer 21

“5 fold axis of symmetry” found at the vertex
- 5 proteins attached to one vertex

“3 fold axis of symmetry” found at the face
- 3 proteins on a face

“2 fold axis of symmetry” found at the edge
- 2 proteins attached to an edge

rules tend to be less upheld as the virus becomes bigger

this is to accommodate more proteins… rules are still there - just not as strict

referred to as quasi-equivalence
- the extent of similarity between these structurally unique environments occupied by the chemically identical subunits in the virus capsid
- a virus is called quasi-equivalent if it is almost perfectly symmetrical - these are bigger viruses

Question 22

describe capsid assembly using poliovirus as an example

Answer 22

made on a string

proteins will fold with interactions (generally non-covalent)

once joined together, 3CDpro, a protease cuts the string, creating a protamer (5S unit)

5 protamers assemble into a pentamer

12 pentamers form the capsid