Lecture 3 Flashcards
(32 cards)
1
Q
What are the main functions of structural proteins?
A
- Protection of the genome: assembly of a stable, protein shell, specific recognition for the viral genome and packaging of the specific nucleic acid genome, interaction with host cell membranes to form envelope s’il y a lieu
- Delivery of the genome: bind to host cell receptors, uncoating of the genome, fusion with cell membranes, transport of the genome to the appropriate site in the cell (ex: DNA viruses must send their genome to nucleus to be able to replicate)
2
Q
What is a capsid?
A
Protein shell surrounding the genome
3
Q
What is the nucleocapsid?
A
Nucleic acid:protein assembly within the virion
4
Q
What is the envelope?
A
Host cell-derived lipid bilayer
5
Q
What is a virion?
A
Infectious viral particle
6
Q
What does it mean when we say that viral particles are metastable?
A
- They must exist in two states: stable enough to protect the genome and unstable enough to come apart upon infection to deliver the genome
- Energy is put into the virus particle during assembly
- Potential energy used for disassembly if the cell provides the proper signal
- Virus particles themselves have not attained minimum free energy conformation, this is why we say they are spring-loaded
7
Q
How is meltability achieved?
A
- Stable structure is created by symmetrical arrangement of many identical proteins to provide maximal contact
- Unstable structure is possible since the structure is usually not permanently bonded together and can be taken apart or loosened on infection to release or expose the genome
8
Q
How can we learn about viral structure?
A
- EM
- X-ray crystallography
- cryoEM and tomography
- NMR
9
Q
Some facts about EM
A
- Biological materials need to be stained since low inherent contrast
- Can be negatively stained with electron-dense material like uranyl acetate and phosphotungstate, scatter electrons and observe scatter patterns
- Have a resolution of 50-75 angstrinbvd 1A = 0.1 nm
- Detailed structural interpretation is impossible however
10
Q
Facts about cryoEM
A
- Freeze viral particles in water
- Take a bunch of images
- 3D reconstruction of viruses
- even better resolution, almost individual polypeptide chains visible on envelope (dengue)
11
Q
Facts about X-Ray crystallography
A
- Resolution of 2-3 andnhs for viruses
- Viruses must be crystallized which can be difficult
- Bombard with X-Rays
- Collect the diffraction pattern and estimate/calculate the 3D structure
12
Q
Watson and Crick discoveries about symmetry in viral particles
A
- Identical protein subunits are distributed with helical symmetry for rod-shaped viruses and platonic polyhedra symmetry for round viruses
13
Q
What is a subunit?
A
A single folded polypeptide chain
14
Q
What is a structural unit?
A
- Protomer, asymmetric unit
- Unit from which capsids or nucleocapsids are built, can be one or more subunits
15
Q
What are the rules for self-assembly?
A
- Rule 1: Each subunit has identical bonding contacts with its neighbours, repeated interaction of chemically complementary surfaces at the subunit interfaces naturally leads to a symmetric arrangement
- Rule 2: bonding contacts are usually non-covalent (contributing to metastability), reversible, allows for error-free assembly
- Virus particles self-assemble at ideal temperatures in the cell
16
Q
What do we call an “empty” viral particle?
A
It is a virus like particle (VLP) that happens when assembly with no genome. HBV and HPV viruses are made with VLPs (not infectious)
17
Q
Helical symmetry
A
- Coat protein molecules engage in identical, equivalent interactions with one another and the viral genome
- Construction of a large, stable structure from a single protein subunit
- Example: TMV
18
Q
How do you make a round virus?
A
- All round capsid have a precise number of proteins (multiples of 60 starting 60 being smallest)
- Spherical viruses come in many sizes, but capsid proteins are about 20-60 kDa in size
19
Q
What were Caspar and Klug discoveries? What year?
A
- 1962
- They knew from W and C that round capsids are icosahedrons (20 faced Platonic solids, each face an equilateral triangle), no other Platonic solids are used by viruses (that we know of)
- Capsid subunits tend to be arranged as pentamers and hexameters
20
Q
What are the axis of symmetry in an icosahedron?
A
- Fivefold axis
- Threefold axis
- Two fold axis
21
Q
Most simple icosahedral capsid? Example?
A
- 60 identical protein subunits
- The protein subunit is also the structural unit (T=1)
- Interactions of all molecules with their neighbours are identical (head to head, tail to tail)
- Example: Adeno-associated virus 2 (Parvovirus) 25 nm diameter, T=1, 60 copies of a single capsid protein
22
Q
How are larger virus particles built?
A
- By adding more subunits
- Multiple modes of subunits
- Pentamers and hexamers are there
- Bonding interactions are now quasi equivalent (so still head to head or tail to tail but maybe not the exact same subunits each time) (similar but not identical)
23
Q
Example of a larger round virus?
A
- SV40 (polyomavirus)
- 50 nm diameter (2x parvovirus)
- T = 6
- 72 pentamers of VP1 = 360 subunits
- Not identical bonding since some have five around them others have 6 around them
24
Q
What is the triangulation number, T?
A
- The number of facets per triangular face of an icosahedron
- Combining of several triangular facets allows assembly of larger face from same structural unit
- Capsids with T > 1 have a six-fold axis of symmetry as well
25
Mimivirus Cryo-EM
- 400 nm diameter
- T = 1200
- Starfish structure is likely involved in the release of the genome in some way
26
What are some complexities with larger capsids? Example?
- We can have distinct components with different symmetries
- Presence of proteins devoted too specialized roles
- Example: Adenovirus (150 nm, T = 25, 720 copies of viral protein II + 60 copies of protein III, fibres that interact with host cell receptors at the 12 vertices)
- Example 2: tailed bacteriophages, head is icosahedral, contractile tail (attached to one of the fivefold axis of the capsid and built with helical symmetry), has a nice baseplate for attachment
27
What is an envelope and how does a virion acquire one?
- Lipid bilayer derived from host cell by budding of nucleocapsid through a cellular membrane (can be any membrane, Dif virus => Dif membrane, virus-specific), the nucleocapsids in the envelope can be helical or icosahedral
28
Acquisition of an envelope?
Nucleocapsid goes to membrane with viral glycoproteins, cross section of host membrane and budding of the virus
29
What are viral glycoproteins?
- Integral membrane glycoproteins (usually oligomeric)
- Ectodomain: attachment, antigenic sites, fusion of envelope with host cell for entry
- Internal domain: assembly recognizes capsid proteins and genome
30
True or false, envelopes are always structured.
- False they can be structured or unstructured
- Unstructured: can vary in size and shape (pleomorphic)
- Structured: sometimes the capsid can impart structure on the envelope (with 1 to 1 interactions for very structured)
31
What are some exceptions in viral structures?
- Poxvirus: oval virus with dumbbell
- Pandoravirus and Pithovirus: elongated structure with apical pore probably for the release of the genome
- Icosahedral and helical do not account for all viruses but yes for lots of them
32
What are some other virion components?
- tegument: space between nucleocapsid and envelope (allows to carry stuff, can be random or selective) (example: carry RdRp)
- Herpes has tegument whereas togs virus has 1 to 1 interactions => little to no tegument
- Enzymes: polymerases, integrases, associated proteins, proteases, reverse transcriptase, etc.
- Activators of transcription required for efficient infection
- Cellular components: histones, tRNAs, lipids, host proteins, and many more
- Some can even carry ribosomes in their tegument
