week 9 - virus structure

Question 1

viruses contain 3 major components

Answer 1

1. Genome (nucleic acid)
2. Viral capsid or core
3. Viral envelope (and in some cases)
   viral genomes do not contribute much to virus structure but can facilitate assembly of capsids

Question 2

main building blocks of viral capsids (cores) and viral envelopes are:

Answer 2

Viral structural proteins

1. To protect the genome by assembling a stable protein shell
2. Specifically recognised and package the viral genome
3. To facilitate the formation of viral enveloped from cellular sources

Question 3

• All viruses no matter how complex or simple contain a…

Answer 3

capsid or core

Question 4

most capsids are…

Answer 4

spherical or tubular

Question 5

capsids and typically built of…

Answer 5

structural units comprised of subunits

 Subunit = structural protein (can be 1 or multiple different proteins)
 Low coding capacity drives simplicity of form and function

Question 6

how to build a virus

Answer 6

protein subunits –> structural units –> structural units (more) —> capsid

Question 7

more virus capsids are:

Answer 7

spherical (3-D spherical objects)

Question 8

capsids
watson and crick propose:

Answer 8

virus cubic symmetry

 There are 5 platonic solids
 Each face is identical
 The number of contacts for each face is equal

Question 9

virus structure
caspar and klug 1950s

Answer 9

using X ray diffraction note that viruses have a 5-, 3-, 2-fold symmetry with 12 spikes

Question 10

virus capsids are…

Answer 10

icosahedrons

only they have 12 vertices

Question 11

ability to determine how many subunits a virus is composed of

Answer 11

• T = triangulation number (Caspar and Klung 1962)
• Assumption that simple capsids are built from many copies of 1 structural protein
• Assuming that each protein has the same type and number of contacts the maximum number of subunits is 60
• Derived by 5-fold symmetry at each of the 122 vertices
• Simple icosahedral virus is defined as T=1
• T=1 viruses are built from 60 subunits
• T number is the standard used to describe the structure of icosahedral virus

Question 12

T1 viruses: roughly the same size?

Answer 12

• They are all roughly the same size: 60 subunits (cant be any bigger) imposes a size constraint

Question 13

to build a bigger virus

Answer 13

• Can have multiple proteins in one structure

e.g.

T=1 x 5 (12 vertices) = 60 subunits

T=3 x5 = 15 (12 vertices) = 180 subunits

T=4 x 5 = 20 (12 vertices) = 240 subunits

Not changing no. of spike proteins but
Increasing no. of subunits

Question 14

odd shaped viruses

Answer 14

• To obtain curvature cannot use these hex
• Pentagon to provide curvature

Question 15

odd shaped viruses
examples:

Answer 15

HIV
influenza
poxviruses
giant viruses

Question 16

odd shaped viruses:
Poxviruses

Answer 16

Don’t know how the core of this is built
* Complex
* Better technology in order to understand
* If know how virus is built can attack

Question 17

3 different kinds of virus particles

Answer 17

helical

icosahedral

complex

Question 18

viral enveloped proteins:
come in 3 flavours

Answer 18

o Structural proteins: Give structure
o Binding proteins: To cell surface, Virus can attach
o Fusion proteins: Forms a pore, Genome/capsid delivered into host cell
 Typically in triomers or hexomoers
 E.g. fusion proteins work better if loads in one place
 Larger hole etc.

Question 19

viral enveloped proteins:
usually…

Answer 19

oligomeric (trimers)

Question 20

viral enveloped proteins:
termed…

Answer 20

“spike” proteins (these are usually the fusion proteins)

Question 21

viral enveloped proteins:
often…

Answer 21

glycosylated (virial glycoproteins)
o Sticky, attach, protection

Question 22

viral enveloped proteins:
integral membrane proteins…

Answer 22

span the viral lipid bilayer membrane

Question 23

viral enveloped proteins:
often connect to…

Answer 23

internal viral structural proteins (assures correct capsid packaging during assembly)

Question 24

Viral particles can have many other proteins components

Answer 24

• Enzymes (polymerases (replicate), integrases, proteases (clip virial proteins so become integrated))
• Cell components (histones, lipids, host modulators)
• Cell structural components (actin and intermediate filaments)

Question 25

viral structure summary:
viral particles come in …

Answer 25

all shapes and sizes

Question 26

viral structure summary:
there are 3 main building blocks…

Answer 26

genome

capsids

sometimes envelopes

Question 27

viral structure summary:
the norm is….

Answer 27

icosahedral symmetry

but there is exceptions to this rule

Question 28

When building a virus one must consider metastability

Answer 28

Two truths
- All virus capsids must be built as stable structures capable of protecting the genome in transit from one host cell or organism to another
- All virus capsids must be readily and efficiently broken down or disassembled to release the viral genome when entering a host cell

Both of these things often occur in the same host cell compartment
THIS IS CALLED THE ASSEMBLY-UNCOATING PARADOX

Question 29

How is metastability achieved?

Answer 29

1. Viruses are built through symmetrical arrangement to assure maximal contact between structural subunits
2. The structure is not permanently bound together (not covalent)
   - Can be loosened or disassembled by cellular cue during entry
   - This allows for release or the genome into host cells