(V) 23: Viral Structure

Question 1

Capsid

Answer 1

viral container or shell

Question 2

Virion

Answer 2

a complete infectious particle

Question 3

Nucleocapsid

Answer 3

situation where the capsid also contains the genome

• closely intertwined w/ viral genome

Question 4

Envelope

Answer 4

lipid bilayer membranes enclosing nucleocapsids
- HOST-DERIVED

acquired by budding nucleocapsid

MOST (not all) viruses have an envelope

Question 5

Stability of virions

Answer 5

The virion must be BOTH stable and unstable

Unstable IN the cell
Stable when OUTSIDE the cell

Question 6

When is the virion stable in the infectious cycle? Unstable?

Answer 6

Stable when OUTSIDE the cell
Unstable when INSIDE the cell

Question 7

Protein functions

Answer 7

Protection of the genome
- assembly of protective shell
- recognition and packaging of nucleic acid genome
- forms envelope

Delivery of the genome
- binding external receptors of host cell
- uncoating of genome
- fusion w/ host cell memb (envelopes)
- transport of genome

Other interactions
- w/ host immune system
- to ensure efficient infectious cycle

Question 8

Viral Structural Biology Techniques

Answer 8

• electron microscopy
• cryo-electron microscopy
• X-ray crystallography
• nuclear magnetic resonance spectroscopy (NMR)

Question 9

Electron Microscopy

Answer 9

• negative staining allows to see the shape of virus and envelope

Downside: potential to DESTROY ultrastructural features/structure

Question 10

Negative staining

Answer 10

stain sample w/ ELECTRON-DENSE materials (to absorb electrons)
- allows to see the virus

Question 11

Cryo-electron microscopy

Answer 11

• NO stain = structure preservation
• FLASH FREEZE samples and image at very cold temps (freezing is contrast)
• aims to preserve structure
• uses computers to reconstruct images

Question 12

X-ray crystallography

Answer 12

Key: ability of viral protein/virion to crystallize

• bombard virion w/ X-ray

Ex. “CANYONS” in structure = indentations on cell surface (cell surface receptors to latch onto host receptors)

Question 13

NMR

Answer 13

Nuclear Magnetic Resonance Spectroscopy

• if your protein does not crystallize
• radiation emitted from nucleus in a magnetic field is measured by spectra
• certain nuclei can have a magnetic moment

Question 14

Resolution of Viral Structural Biology Techniques

Answer 14

(Most detailed) X-Ray + NMR > Cry-Electron EM > Electron Microscopy

Cry-Electron, EM and X-ray give FULL virion structures whole NMR only gives viral proteins

EM destroys structure w/ stain

Question 15

What type of viral structural techniques look at the full virion?

Answer 15

Cry-Electron, EM and X-ray give FULL virion structures whole NMR only gives viral proteins

Question 16

Principles of viral genetic economy

Answer 16

Virions are made from MANY copies of a FEW proteins
- viral genome’s coding capacity is limited

Key is SYMMETRY
- if protein subunits on the surface are identical, then contacts will generate a symmetrical object

Question 17

Types of symmetry

Answer 17

Helical symmetry
- for ROD-shaped viruses
- ex. tobacco mosaic virus (TMV)

Polyhedral symmetry
- for ROUND viruses
- ex. simian virus 40

Question 18

Rules of viral symmetry

Answer 18

1. Each subunits had identical bonding contacts w/ neighbouring subunits
   - one set of protein A + B will interact in a similar way to another protein A + B
2. Bonds btwn subunits are mostly via NON-COVALENT interactions
   - so they can be opened up to expose the genome

Question 19

HPV Vaccine

Answer 19

Gardasil is the outer shell of HPV
- NOT the genome

Question 20

Notions on helical symmetry

Answer 20

• a protein subunit interacts w/ an identical protein subunit in an identical manner
• also interacts w/ viral genome
• there are nucleocapsids
• can be composed of one or more types of protein
• nucleoprotein associates w/ viral genome (goal = protect genome)

Ex. measles virus, vesicular stomatitis virus, ebola virus

Question 21

Nucleoprotein

Answer 21

a part of nucleocapsid

Question 22

Ebola virus nucleocapsid

Answer 22

VP30, VP24, VP35 are Ebola viral proteins forming the nucleocapsid

Question 23

Polyhedral capsids

Answer 23

round capsids have a DEFINED number of proteins in multiples of 60
- number of subunits MUST be a multiple of 60

They have ICOSAHEDRAL symmetry

Question 24

Icosahedron

Answer 24

solid w/ 20 faces
- each face is an EQUILATERAL triangle

allows formation of a closed shell w/ 60 identical subunits (3 x20 = 20 identical trimers)

Question 25

Axes of symmetry of icosahedral symmetry

Answer 25

Vertice: 5 fold
Face: 3 fold
Edge: 2 fold

Question 26

Norwalk virus

Answer 26

larger virus
- quasi-equivalent (almost perfect)

Question 27

Quasiequivalent

Answer 27

ALMOST perfectly symmetrical w/ BIGGER viruses

• LOSE 5 fold symmetry = can lose multiple of 60
• can have more than 5 on some vertices

Question 28

Poliovirus Capsid Assembly

Answer 28

• P1 precursor peptide is cleaved to generate the protamer (5S)
• 5 protamers = pentamer

Capsids are formed by assembly of 12 pentamers

5S unit can be snipped to make a more compact icosahedral triangle OR P1 peptide can generate 5S

Question 29

How are envelopes derived from host membranes?

Answer 29

Envelope is acquired by budding nucleocapsid

• viral envelope lipoproteins get placed on cell membrane when ENTERING
• picks up host membrane and viral envelope lipoprotein when they LEAVE

also contain viral envelope glycoproteins

Question 30

Viral envelope glycoproteins

Answer 30

Envelope viral proteins

key elements that interact w/ host cell receptors