Lecture 3 Flashcards
What are the functions of structural proteins?
-Protection of the genome
-delivery of the genome
What do structural proteins have to do?
Structural proteins have to:
-Assembly of a stable, protective shell
-specific recognition and packaging of the nucleic acid genome
-Interaction with hist cell membranes to form the envelope
What do structural proteins participate in: Delivery of the genome explained
in order to deliver the genome, the structural proteins have to
-bind to host cell receptors
-uncoat the genome
-fusion with cell membrane (for enveloped viruses)
-need to transport of the genome to the appropriate site in the cell in the nucleus
What is a capsid?
comes from the latin capsa=box
protein shell surrounding the genome
what is the nucleocapsid?
core
nucleic acid with capsid around it: protein assembly with the virion
what is an envelope?
viral membrane
host cell-derived lipid bilayer that surrounds viral particles
what is a virion?
infectious viral particle
Virus particles are homostable or metastable?
they are metastable
-they must exist in 2 states:
they must protect the genome aka stable
they must come apart upon infection aka unstable
True or false: energy is put into the virus particle during uncoating
false
True or false: energy in put into the virus particle during assembly so that it can release viral particles when they find the right cell
True or false: metastability is the potential energy used for dissasembly of the cell provide the proper signal
true
viral particles themselves have not attainted minimum free energy conformation they are sort of spring loaded
How is metastability acheaved?
Stable structure:
Created by symmetrical arrangement of many identical proteins to provide maximal contact
Unstable structure:
Structure is not usually permanently bonded together
use non-covalent bonds
can be taken apart or loosened on infection to release or expose the genome
How do we learn about viral structure?
-electron microscopy
-x-ray crystallography
-electron cryomicroscopy (cryoEM) and tomography
-Nuclear magnetic resonance spectroscopy aka NMR
Electron microscopy
-Biological materials have little inherent contrast - need to be stained
-Negative staining with electron-dense material (uranyl acetate, phosphotungstate), scatter electrons (1959)
-Resolution 50-75 Å (1 Å = 0.1 nm)
-you look at the scatter pattern
-Detailed structural interpretation is impossible
Cryo-EM
-Freeze viral particles in water
-Take a bunch of images
-3D reconstruction of viruses
you get better resolution and you can almost see the individual polypeptide chains
X-e=ray crystallography
-you make crystals
-bombard the crystal with x ray
-collect the diffraction pattern of those
-calculate the 3d structure of the protein or virion
excellent resolution
What did Watson and Crick discovered other than DNA structure?
symmetry in viruses!!!
- Identical protein subunits are distributed with helical
symmetry for rod-shaped viruses Platonic polyhedra symmetry for round viruses
- Platonic polyhedra symmetry for round viruses
what is a subunit?
single folded polypeptide chain
what is a structural unit?
a protomer aka asymetric uni
unit from which capsids or nucleocapsids are built: one or more subunits
What are the rules for “self assembly?”
Rule 1: Each subunit has ‘identical’ bonding contacts with its neighbors
Repeated interaction of chemically complementary surfaces at the subunit interfaces naturally leads to a symmetric arrangement
Rule 2: These bonding contacts are usually non-covalent
Reversible
Error-free assembly
Meta-stable
they kinda break apart and reassemble up until they get that good stable conformation
True or false:All capsid proteins can self assemble into ‘virus- like particles’ (VLPs)
False: Many capsid proteins (aka they do not have viral genome)can self assemble into ‘virus-like particles’ (VLPs)
HBV and HPV vaccines are VLPs made in yeast
Helical symmetry
-Coat protein molecules engage in identical, equivalent interactions with one another and with the viral genome
-Construction of a large, stable structure from a single protein subunit aka 1 capsid protein on RNA binds with other capsids
How are viruses able to get round capsids?
• All round capsids have a precise number of proteins (multiples of 60 are common - 60, 180, 240, 960, etc)
• Spherical viruses come in may size, but capsid proteins are 20-60 kDa in size
What did Caspar and Klug do?
-they knew from watson and cricks work that round capsids are icosahedrons aka no other platonic solids were used
-Capsid subunits tended to be arranged as hexamers and pentamers
Icosahedral symmetry
icosahedron: solid with 20 faces, each an equilateral triangle
-allows the formation of a closed shell with smallest number (60) of identical subunits
Simple icosahedral capsids
-made of 60 identical protein sub units
-the protein subunit is the structural unit
-interactions of all molecules with their neighbors are identical aka had to head and tail to tail all at the penton
true or false: adeno associated virus 2 aka parvovirus is a helical virus
FALSE it is a simple icosahedral virus
25 nm
t=1
-60 copies of a single capsid protein
How are larger virus particles built?
-by adding more subunits
-3 modes of subunit packing
-pentamers and hexamers
-bonding interactions are quasiequivalent: all engage to tailto tail and head to head
What is quasiequivalence
-When a capsid contains more than 60 subunits, each occupies a quasiequivalent position to one another
-the non-covalent binding properties of subunits in different structural environments are similar but not identical
true or false SV40 aka polyomavirus has 60 sububnits
-falseeeeeee àit is 50 nm
-t=6
-72 pentamers of VP1= 360 subunits
what is triangulation number T?
the number of facets per triangular face of an icosahedron
-combining several triangular facets allows assembly of larger face from same structural unit
true or false: mimivirus has a T of 1200
true
large complex capsids
-distinct components with different symmetries
-presence of proteins devoted to specialized
- e.g. Adenovirus (150 nm, T=25, 720 copies of viral protein II + 60 copies of protein III, fibers at the 12 vertices
What physical components of tailed bacteriophages?
-head: icisahedral capsid
-contractile tail (attached to one fivefold access of the icosahedral capsid)
built with helical symettry
-baseplate
for attachment
true or false: capsids can’t be covered by host membrane
FALSE
Capsids can be covered by host membranes (envelope)
what is an envelope and how is it aquired?
-Envelope is a lipid bilayer derived from host cell
-Envelope acquired by budding of nucleocapsid through a cellular membrane
Can be any cell membrane (virus- specific)
-nucleocapsids inside the envelope may have helical or icosahedral symmetry.
how do u aquire an envelope?
the virus gets replicated inside a cell including viral glycoproteins that’ll gp to the membrane of the cell
when the virus wants to get out it’ll bud off and I’ll become enveloped with that cell’s membrane that has the glycoproteins
viral envelope glycoproteins
-integral membrane glycoproteins
-ectodomain: responsible for attachment, antigenic sites, fusion
-internal domain: responsible for assembly
-oligomeric: spikes like the one on sars cov
true or false: envelopes can be structured or unstructured
true
• Unstructured envelopes
- Can vary in size and shape
(pleomorphic)
• Structured envelopes
- Sometimes the capsid can impart structure on the envelope
true or false: envelopped viruses are all the same aka no exception
falseee there are exceptions like the poxvirus that is not icasehidral
the pandoravirus and the pithovirus have an apical pore probs important for the release of the virus
what are a virions components?
-capsid
-core
-tegument
-enveloppe if envelopped
-enzymes
polymerases, integrases, associated proteins, proteases and etc
-activators of transcription-required for efficient infection
-cellular components-histones trna(HIV), lipids, host proteins and more
what is a tegument?
space between nucleic acid and the enveloppe you can put random stuff in it or like an RT
