3. Structures of Viruses Flashcards
what are the 2 general functions of structural proteins in a virus?
- protect the genome
- deliver the genome
what are the 3 ways that structural proteins protect the genome?
- assemble into a stable, protective protein shell
- specific recognition and packaging of the nucleic acid genome
- interact with host cell membranes to form the envelope
what are the 4 ways that structural proteins deliver the genome?
- bind to host cell receptors
- uncoat the genome
- fuse with cell membranes
- transport of genome to the appropriate site in the cell
where does the word “capsid” come from?
Latin capsa = box
what is the capsid?
protein shell surrounding the genome
what is a nucleocapsid?
a term mainly used for enveloped viruses –> nucleic acid/protein core within the virion
why is the term nucleocapsid mainly used for enveloped viruses?
a non-enveloped virus is essentially the nucleocapsid
what is a viral envelope?
lipid bilayer derived from any host membrane (golgi, lysosome, plasma membrane)
what is a virion?
infectious viral particle
what does it mean for a virus to be metastable?
have an optimal balance of STABLE and UNSTABLE states
describe the stable and unstable states of a virus particle
STABLE –> must protect the genome in the environment
UNSTABLE –> must come apart upon infection to release nucleic acid
what are 2 things that could make a virus particle unstable?
- pH
- proteases
describe the energy involved in the stability/instability of virus particle
Add energy during assembly
Use up the potential energy for disassembly
Are virus particles at the minimum free energy conformation? Why?
no –> if it was at minimum free energy, virus particle would be too stable and wouldn’t be infectious
therefore, there is some energy in the capsid to allow disassembly
describe the stable structure of a virus particle
SYMMETRICAL arrangement of many identical capsid proteins to allow maximal contact –> weak individual interactions but strong sum of interactions
describe the unstable structure of a virus particle
virus particle can be taken apart/loosened to release the genome
describe the interactions between capsid proteins in the stable state
NOT permanently bonded (i.e. not covalent), just weak interactions
what are the 4 methods we use to learn about viral structure?
- electron microscopy
- X-ray crystallography
- electron cryomicroscopy (cryoEM) and tomography
- nuclear magnetic resonance spectroscopy (NMR)
what is NMR used for?
less used for the capsid as a whole, more used for small single proteins
describe the use of electron microscopy
negative staining with electron-dense material but impossible to get detailed structural interpretation
what is the resolution of electron microscopy?
50-75A
what are 2 examples of negative stains for electron microscopy?
- uranyl acetate
- phosphotungstate
describe the use of Cryo-EM
no staining required –> freeze virus particles in water and take a bunch of images of virus on flat surface, then computer makes 3D reconstruction of virus structure
what is the resolution of cryo-EM?
can reach near-atomic resolution (3-5A)
what is the gold standard method for looking at viruses?
X-ray crystallography
why is X-ray crystallography the gold standard for looking at viruses? what is the issue with it?
highest resolution but laborious –> not always possible for capsids/virus particles to crystallize
what was the first virus structure found by X-ray
tomato bushy stunt virus
what 2 things did Watson and Crick find about viral structure
- capsid proteins distribute with helical symmetry for rod-shaped viruses
- capsid proteins distribute with platonic polyhedra symmetry for round viruses
what are the 3 parts of a capsid
- SUBUNIT
- PROTOMER
- CAPSOMERE
what is a capsid subunit?
single folded capsid protein
what is a capsid protomer?
asymmetrical, structural unit –> minimal unit from which capsids/nucleocapsids are assembled
what is a capsomere?
assembled from protomers –> pentamers and hexamers
describe the assembly of viruses
capsid proteins SELF ASSEMBLE into VIRUS LIKE PARTICLES
what are virus like particles used for?
vaccines!
describe the HPV vaccine
L1 capsid proteins are expressed in yeast to make HPV virus like particles which presents to the immune system as the virus
what are the 2 rules of viral self-assembly?
- each subunit makes identical contacts with its neighbours
- the binding contacts are NON-COVALENT and WEAK
why can viruses self-assemble into a symmetric arrangement?
there are repeated interactions of chemically complementary surfaces at the subunit interfaces which naturally lead to symmetry
describe the interactions between subunits
- chemically complementary (hydrophobic, +/- charge) but non-covalent and weak
- reversible and meta-stable
why is self-assembly considered to the be error-free assembly?
very dynamic assembly of subunits –> less favourable to assemble until subunits become a pentamer, then favourable to grow
describe helical symmetry/assembly
1 type of coat protein engage in identical, equivalent interactions with each other AND the viral genome
what is the term used for a round virus?
icosahedral
what is the number of proteins in an icosahedral?
MULTIPLES OF 60 –> 60, 180, 240, etc.
what is the size of capsid proteins?
20-60 kDa
describe an ICOSAHEDRON
- # and shape of faces
- arrangement of pentamer
- # of vertices to form pentamer
- 20 triangular faces
- 5 triangles arrange in a pentamer
- 12 vertices (i.e. center of pentamer)
what are the 3 types of axes of symmetry in an icosahedron? and how many of each?
- 20 three-fold axes of symmetry (1 for each triangular face)
- 12 five-fold axes of symmetry (1 for each vertex, center of pentamer)
- 30 two-fold axes of symmetry (1 for each edge)
what is the minimal number of subunits in an icosahedron?
60 identical subunits with 3 per triangular face
interactions of all subunit molecules with their neighbours are ________ / _______
interactions of all subunit molecules with their neighbours are IDENTICAL / QUASIEQUIVALENT (head-to-head, tail-to-tail)
what is an example of an icosahedron virus with T=1?
adeno-associated virus 2 (parvovirus)
how are larger icosahedrons built?
add HEXAMERS!!!!
how do you calculate the number of pentamers and hexamers in an icosahedron?
capsid of 60*T subunits:
- 12 pentamers (always 12)
- 10(T-1) hexamers
what does T stand for? what is it a measure of?
triangulation number –> a measure of capsid size
compare the shape of pentamers and hexamers
pentamers are more curved, hexamers are more flat
when you add hexamers to an icosahedron, is it still an icosahedron?
NO!! but maintains icosahedral symmetry
describe the number of subunits, pentamers, and hexamers in a capsid with T = 3
60T = 603 = 180 subunits
12 pentamers
10(T-1) = 10(3-1) = 20 hexamers
what is quasiequivalence?
when a capsid contains more than 60 subunits (T>1), each subunit has a quasiequivalent position
if subunits arrange as pentamers and hexamers, how can they be quasiequivalent if diff shapes?
hexamers are not much different from pentamers, so each subunit experiences a similar environment in each shape and are arranged similarly BUT non-covalent properties are not exactly identical
the triangulation number is the number of _________
what does this indicate about T=1 virus? T=4 virus?
the triangulation number is the number of structural units in each triangular face of an icosahedron
T=1 virus –> each triangular face contains 1 structural unit
T=4 virus –> each triangular face contains 4 structural units
describe large complex capsids
large complex capsids have distinct components with different symmetries
proteins have specialized roles
what does adenovirus have on each of its vertices?
adenovirus has fibers at each of its 12 vertices
describe the capsid of tailed bacteriophages
HEAD = icosahedral capsid
contractile TAIL = helical capsid attached to head
what is the function of the baseplate of tailed bacteriophages?
for attachment
how do enveloped viruses acquire its envelope?
budding of nucleocapsid thru cellular membrane
what type of symmetry can nucleocapsids have inside the envelope?
helical or icosahedral symmetry
describe the 2 steps of viral budding
- viral capsid assemble close to budding site
- virus undergoes budding where viral glycoproteins are on the surface
what are viral envelope glycoproteins?
integral membrane proteins modified with sugars
what are the 2 domains of viral envelope glycoproteins? describe their roles
- ectodomain –> attachment, antigenic sites, fusion
- internal domain –> assembly
what are spike proteins?
oligomeric glycoproteins
what are 3 additional virion components in the capsid?
- enzymes
- transcription activators
- cellular components
what are 4 enzymes found in the virion?
polymerases, integrases, associated proteins, proteases
why are transcriptional activators required in a virion?
for efficient infection
what are some examples of cellular components found in a virus?
histones, tRNAs, lipids, host proteins
why might viruses have histones?
viral dsDNA wrapped around cellular histone
are all cellular components in a virus helpful?
no! virus may just be sloppy and take up things
