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MIMM 324 > 3. Structures of Viruses > Flashcards

3. Structures of Viruses Flashcards

1
Q

what are the 2 general functions of structural proteins in a virus?

A
  1. protect the genome
  2. deliver the genome
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2
Q

what are the 3 ways that structural proteins protect the genome?

A
  1. assemble into a stable, protective protein shell
  2. specific recognition and packaging of the nucleic acid genome
  3. interact with host cell membranes to form the envelope
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3
Q

what are the 4 ways that structural proteins deliver the genome?

A
  1. bind to host cell receptors
  2. uncoat the genome
  3. fuse with cell membranes
  4. transport of genome to the appropriate site in the cell
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4
Q

where does the word “capsid” come from?

A

Latin capsa = box

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5
Q

what is the capsid?

A

protein shell surrounding the genome

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6
Q

what is a nucleocapsid?

A

a term mainly used for enveloped viruses –> nucleic acid/protein core within the virion

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7
Q

why is the term nucleocapsid mainly used for enveloped viruses?

A

a non-enveloped virus is essentially the nucleocapsid

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8
Q

what is a viral envelope?

A

lipid bilayer derived from any host membrane (golgi, lysosome, plasma membrane)

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9
Q

what is a virion?

A

infectious viral particle

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10
Q

what does it mean for a virus to be metastable?

A

have an optimal balance of STABLE and UNSTABLE states

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11
Q

describe the stable and unstable states of a virus particle

A

STABLE –> must protect the genome in the environment
UNSTABLE –> must come apart upon infection to release nucleic acid

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12
Q

what are 2 things that could make a virus particle unstable?

A
  1. pH
  2. proteases
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13
Q

describe the energy involved in the stability/instability of virus particle

A

Add energy during assembly
Use up the potential energy for disassembly

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14
Q

Are virus particles at the minimum free energy conformation? Why?

A

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

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15
Q

describe the stable structure of a virus particle

A

SYMMETRICAL arrangement of many identical capsid proteins to allow maximal contact –> weak individual interactions but strong sum of interactions

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16
Q

describe the unstable structure of a virus particle

A

virus particle can be taken apart/loosened to release the genome

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17
Q

describe the interactions between capsid proteins in the stable state

A

NOT permanently bonded (i.e. not covalent), just weak interactions

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18
Q

what are the 4 methods we use to learn about viral structure?

A
  1. electron microscopy
  2. X-ray crystallography
  3. electron cryomicroscopy (cryoEM) and tomography
  4. nuclear magnetic resonance spectroscopy (NMR)
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19
Q

what is NMR used for?

A

less used for the capsid as a whole, more used for small single proteins

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20
Q

describe the use of electron microscopy

A

negative staining with electron-dense material but impossible to get detailed structural interpretation

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21
Q

what is the resolution of electron microscopy?

A

50-75A

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22
Q

what are 2 examples of negative stains for electron microscopy?

A
  1. uranyl acetate
  2. phosphotungstate
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23
Q

describe the use of Cryo-EM

A

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

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24
Q

what is the resolution of cryo-EM?

A

can reach near-atomic resolution (3-5A)

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25
Q

what is the gold standard method for looking at viruses?

A

X-ray crystallography

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26
Q

why is X-ray crystallography the gold standard for looking at viruses? what is the issue with it?

A

highest resolution but laborious –> not always possible for capsids/virus particles to crystallize

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27
Q

what was the first virus structure found by X-ray

A

tomato bushy stunt virus

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28
Q

what 2 things did Watson and Crick find about viral structure

A
  1. capsid proteins distribute with helical symmetry for rod-shaped viruses
  2. capsid proteins distribute with platonic polyhedra symmetry for round viruses
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29
Q

what are the 3 parts of a capsid

A
  1. SUBUNIT
  2. PROTOMER
  3. CAPSOMERE
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30
Q

what is a capsid subunit?

A

single folded capsid protein

31
Q

what is a capsid protomer?

A

asymmetrical, structural unit –> minimal unit from which capsids/nucleocapsids are assembled

32
Q

what is a capsomere?

A

assembled from protomers –> pentamers and hexamers

33
Q

describe the assembly of viruses

A

capsid proteins SELF ASSEMBLE into VIRUS LIKE PARTICLES

34
Q

what are virus like particles used for?

A

vaccines!

35
Q

describe the HPV vaccine

A

L1 capsid proteins are expressed in yeast to make HPV virus like particles which presents to the immune system as the virus

36
Q

what are the 2 rules of viral self-assembly?

A
  1. each subunit makes identical contacts with its neighbours
  2. the binding contacts are NON-COVALENT and WEAK
37
Q

why can viruses self-assemble into a symmetric arrangement?

A

there are repeated interactions of chemically complementary surfaces at the subunit interfaces which naturally lead to symmetry

38
Q

describe the interactions between subunits

A
  • chemically complementary (hydrophobic, +/- charge) but non-covalent and weak
  • reversible and meta-stable
39
Q

why is self-assembly considered to the be error-free assembly?

A

very dynamic assembly of subunits –> less favourable to assemble until subunits become a pentamer, then favourable to grow

40
Q

describe helical symmetry/assembly

A

1 type of coat protein engage in identical, equivalent interactions with each other AND the viral genome

41
Q

what is the term used for a round virus?

A

icosahedral

42
Q

what is the number of proteins in an icosahedral?

A

MULTIPLES OF 60 –> 60, 180, 240, etc.

43
Q

what is the size of capsid proteins?

A

20-60 kDa

44
Q

describe an ICOSAHEDRON
- # and shape of faces
- arrangement of pentamer
- # of vertices to form pentamer

A
  • 20 triangular faces
  • 5 triangles arrange in a pentamer
  • 12 vertices (i.e. center of pentamer)
45
Q

what are the 3 types of axes of symmetry in an icosahedron? and how many of each?

A
  • 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)
46
Q

what is the minimal number of subunits in an icosahedron?

A

60 identical subunits with 3 per triangular face

47
Q

interactions of all subunit molecules with their neighbours are ________ / _______

A

interactions of all subunit molecules with their neighbours are IDENTICAL / QUASIEQUIVALENT (head-to-head, tail-to-tail)

48
Q

what is an example of an icosahedron virus with T=1?

A

adeno-associated virus 2 (parvovirus)

49
Q

how are larger icosahedrons built?

A

add HEXAMERS!!!!

50
Q

how do you calculate the number of pentamers and hexamers in an icosahedron?

A

capsid of 60*T subunits:
- 12 pentamers (always 12)
- 10(T-1) hexamers

51
Q

what does T stand for? what is it a measure of?

A

triangulation number –> a measure of capsid size

52
Q

compare the shape of pentamers and hexamers

A

pentamers are more curved, hexamers are more flat

53
Q

when you add hexamers to an icosahedron, is it still an icosahedron?

A

NO!! but maintains icosahedral symmetry

54
Q

describe the number of subunits, pentamers, and hexamers in a capsid with T = 3

A

60T = 603 = 180 subunits
12 pentamers
10(T-1) = 10(3-1) = 20 hexamers

55
Q

what is quasiequivalence?

A

when a capsid contains more than 60 subunits (T>1), each subunit has a quasiequivalent position

56
Q

if subunits arrange as pentamers and hexamers, how can they be quasiequivalent if diff shapes?

A

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

57
Q

the triangulation number is the number of _________

what does this indicate about T=1 virus? T=4 virus?

A

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

58
Q

describe large complex capsids

A

large complex capsids have distinct components with different symmetries

proteins have specialized roles

59
Q

what does adenovirus have on each of its vertices?

A

adenovirus has fibers at each of its 12 vertices

60
Q

describe the capsid of tailed bacteriophages

A

HEAD = icosahedral capsid
contractile TAIL = helical capsid attached to head

61
Q

what is the function of the baseplate of tailed bacteriophages?

A

for attachment

62
Q

how do enveloped viruses acquire its envelope?

A

budding of nucleocapsid thru cellular membrane

63
Q

what type of symmetry can nucleocapsids have inside the envelope?

A

helical or icosahedral symmetry

64
Q

describe the 2 steps of viral budding

A
  1. viral capsid assemble close to budding site
  2. virus undergoes budding where viral glycoproteins are on the surface
65
Q

what are viral envelope glycoproteins?

A

integral membrane proteins modified with sugars

66
Q

what are the 2 domains of viral envelope glycoproteins? describe their roles

A
  1. ectodomain –> attachment, antigenic sites, fusion
  2. internal domain –> assembly
67
Q

what are spike proteins?

A

oligomeric glycoproteins

68
Q

what are 3 additional virion components in the capsid?

A
  1. enzymes
  2. transcription activators
  3. cellular components
69
Q

what are 4 enzymes found in the virion?

A

polymerases, integrases, associated proteins, proteases

70
Q

why are transcriptional activators required in a virion?

A

for efficient infection

71
Q

what are some examples of cellular components found in a virus?

A

histones, tRNAs, lipids, host proteins

72
Q

why might viruses have histones?

A

viral dsDNA wrapped around cellular histone

73
Q

are all cellular components in a virus helpful?

A

no! virus may just be sloppy and take up things

MIMM 324 (37 decks)

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