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Principle of molcular virology > Lecture 2 - Symmetry, DNA/RNA viruses, Casper-Klug theory > Flashcards

Lecture 2 - Symmetry, DNA/RNA viruses, Casper-Klug theory Flashcards

1
Q

What type of virus is the Rhinovirus?

A
  • (+)ssRNA
  • Order: Picornavirales
  • Group IV
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2
Q

What classification is the enterovirus?

A
  • (+) ssRNA
  • Group IV
  • E.g. Entero Coxsackie, ECHO viruses
  • Cause hand foot mouth disease
  • Picornaviridae (Family)
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3
Q

What virus causes Hand, Foot and Mouth disease?

A
  • Aphthovirus (a picornavirus)
  • Group IV
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4
Q

What classification is Norovirus and what does it cause?

A
  • (+) ssRNA
  • Group IV
  • Winter vomiting
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5
Q

What classification is Rotavirus and what does it cause?

A
  • dsRNA virus
  • Group III
  • causes severe diarrhea in infants
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6
Q

What is the genomic structure of Hepatitus B and what classification is the virus?

A
  • Four genes, 1 is structural (capsid)
  • Class VII (DNA-RT)
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7
Q

What classification is the Herpes simplex virus?

A
  • dsDNA
  • Class I
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8
Q

What are the structures of a dsDNA phage?

A
  • Icosohedral head containing DNA
  • Neck
  • Helical sheath
  • Tail fibre
  • Baseplate
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9
Q

What does MS2 stand for?

A

Male specific 2 virus

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10
Q

What are the features of MS2?

A
  • ‘sexually transmitted’ E.coli pathogen
  • infect male Escherichia coli by the F-pilus
  • only has 4 genes, only 1 of which is structural
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11
Q

What (generally) do viruses have in common?

A
  • Icosohedral symmetry,
    • consisting of 20 trangles
    • 5 meet at each of the 12 vertices
    • hexagon cluster between each triplet of pentagons
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12
Q

What are the differences between DNA and RNA? (Important)

A

DNA

  • helical symmetry
  • very stable (when double stranded)
  • stiff, long persistance length (helical symmetry)
  • cells/viruses need to use mechanisms to condense it (takes a lot of energy to get into capsid)

RNA

  • mostly single stranded
  • flexible backbone, can fold back to form stem loops, important for enzymatic and catalytic properties.
  • changes conformation a lot due to brownian motion
  • can form complex secondary structures with catalyctic activity (e.g. ribozymes)
  • a branched polymer (important for assembly)
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13
Q

How did Watson and Crick contribute to understanding the structure of viruses?

A
  • Looked at images of viruses, idetified as spherical.
  • Cannot have been perfectly spherical as biological structures must be made up of lots of indiviual builiding blocks
  • Easiest way to attain this is through symmetry
  • Most effective is to use on building block over and over again
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14
Q

Why do viruses use symmetry? (Important)

A
  • Genetic economy (minimalism)
  • Assembly (building blocks are interchangable)
  • Minimum energy (most stable)
  • Size of the container v. coding length (nucleic acid is heavier than the information it encodes, reuse genes)
  • Many viral components have multiple functions (RNA for coassembly, immunosupressive envelope CKS-17 in HIV, overlapping ORFs, polyproteins)
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15
Q

What type of symmetry does Ebola have?

A
  • Helical symmetry
  • String like
  • Filovirus
  • Has foldable structure
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16
Q

How has virus structure been visualised?

A
  • Cryo-EM or X-ray
  • By icosohedral averaging
  • Showed centres of 5, 3 and 2 fold symmetry
  • But little info on structure of genome
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17
Q

What is the dominating factor in viral structure?

A

The geometry

  • Number of geometrically possible symmetrical structures is mathematically limited
  • There are conserved folds
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18
Q

Why are the conserved folds in viral structure important?

A

Potential for novel antiviral strategies to inhibit assembly

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19
Q

What is the structure of viruses?

A
  • Protein shell (viral capsid) is made up of protein clusters (capsomers)
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20
Q

What are the features of an icosahedral virus head?

A
  • 12 pentameric vertices
  • in between pentamers have doughnut shaped capsomers (hexagons)
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21
Q

What does an icosahedral net consist of?

A
  • 20 triangles
  • 12 vertices

An icosohedron is a 20-faced polyhedron

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22
Q

Why did Casper and Klug introduce quasi-equivilence? (1962)

A
  • Icosahedral symmetry can only account for 60 identical subunits at most in the capsid
  • viruses exists with many more subunits (Herpes virus)
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23
Q

What is Casper-Klug’s theory of quasi-equivilence?

A
  • Accounts for the arrangement of proteins on the surface of icosahedral virus particles
  • Orginial theory based on electron microscope studies
  • constitute large trangles for multiple small triangles to expand the number of possible subunits (60 subunits becomes 240 subunits)
  • can have larger and larger structures with more hexagons on each face -
  • 5 fold symmetry at corners, 2 fold symmetry at boundary of each face, 3 fold symmetry of small triangles within each face
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24
Q

Why does Casper Klug theory decide that the planar representation of viral structure must be by a hexagonal lattice not triangular?

A
  • Triangular lattice misses triangles that are broken up on the edge of the large triangles
  • All options represented by beginning at the midpoint of a hexagon and moving to midpoint of another hexagon.
  • Depending on how far you go can build larger and larger icosohedrons
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25
Q

What smallest structure can be denoted by C-K theory?

A

T=1 virus

  • 12 pentameric clusters
  • 60 protein subunits
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26
Q

What is handedness?

A
  • When there are two different ways to construct a capsid which are mirror symmetrical images of each other.
  • Forms two enantiomorphs of each other.
  • One will be left handed and one will be right handed - meaning the triangles will wrap around the edges differently
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27
Q

When does handedness not occur?

A

h = 0 or h = k or k = 0

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28
Q

What is dextro and laevo?

A

The two enantiomorphs of handed capsids

  • Dextro (K>H): right
  • Laevo (K<h></h>

</h>

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29
Q

What angle is between H and K lines?

A

60 degrees

30
Q

List the T numbers from 1 to 36

A

1, 3, 4, 7, 9, 12, 13, 16 19, 21, 25, 27, 28, 31, 36

31
Q

In C-K theory, what structure of the capsid is invarient?

A
  • Capsomeres are invarient (not capsid)
  • Introduces local (6-fold) symmetry
32
Q

Why was C-K theory predictive?

A
  • Predicted structure of viruses purely based on theoretical considerations
  • Viruses following the predicted surface lattices have been discovered experimentally
33
Q

Why is the pentamer in the icosohedral shape important?

A

Pure hexagons have a planar structure but if introduce a pentamer by cutting out a corner it forces curvature

34
Q

What is a T-number?

A
  • The t-number is the number of subdivisions of an icosohedral face
  • Classify the different ways in which surface lattices can be constructed
  • Given in terms of the h and k steps
35
Q

What are the formula for viral structures of the capsid?

A

T = h2 + hk + k2

60T protein subunits in a capsid with T number = T

(20T triangular faces with 3 proteins each)

12 pentamers

10(T-1) hexamers

36
Q

How come the T number equation is related to pythagorus?

A

h component = x direction

k component = y direction and some x direction

K not orthological but at 60 degrees (hexagonal lattice)

37
Q

What does ‘triangulation’ refer to?

A

The number of small triangles fits into large triangles

38
Q

What is the T number structure of the Chikungunya virus?

A
  • h = 2
  • k = 0
  • T = 4
  • 4 triangles
  • 240 subunits
  • 12 pentamers
  • 30 hexamers
39
Q

How does CK improve limit of subunits?

A

From 60 to 60T

40
Q

What is the capsid structure of the Mimivirus?

A
  • Capsid has a diameter of 400nm
  • Protein filaments measuring 100nm project from the surface of the capsid
  • Total length of the virus up to 600nm
  • T number of 900-1200
41
Q

What symmetry do bacteriophages have?

A
  • Isocohedral symmetry (head)
  • Helical symmetry (tail)
42
Q

What is the capsid structure of HSV?

A
  • h = 4
  • K = 0
  • T = 16
  • 16 triangles, 960 subunits, 150 hexamers, 12 pentamers
43
Q

What is the capsid structure of the rotavirus?

A
  • h=3
  • k=1
  • t=13
  • 13 triangles
  • 780 subunits
  • 12 pentamers
  • 120 hexamers
44
Q

What virus does not fit with CK theory?

A

Human papilloma virus

Rayment et al (1982) and Liddington et al (1991) observe virus with only 72 pentamers neccessitating the use of ideas from penrose tilings and quasicrystals

45
Q

What is the viral tiling theory?

A

A more general version of the CK theory that describes how surfaces can be tesselated in terms of tiles. Protein subunits are located in the corners of the tiles that meet at the global and local symmetry axis.

Advantages:

  • Describes the structure of parpoviridae wilst reporducing the tiling of viruses in casper-klug
  • has the ability to locate bonds between subunits

CK theory was quasiequivilent and triangular

Alternatives are:

  • Quasiequivilent but not triangular (but only one tile e.g. kite or rhombus or pentamer)
  • More than one type of tile (Penrose tilings e.g. combination of kite and rhombus)
46
Q

What are the capsid features of the Pariacotovirus?

A
  • T=3 capsid
  • One prototile
    • triangle with three decorated vertices (blue, red and green)
  • Rules: blue vertices must meet blue vertices, red must have green on both sides and vice versa
    • Vertex atlas: Two vertex stars (b,b,b,b,b) and (r,g,r,g,r,g)
47
Q

What are the capsid features of the bacteriophage MS2?

A
  • T=3 capsid
  • Two rhombus prototiles (one tile with red and blue the other with green marks at both ends)
  • Matching rules: blue meets blue, red meets green
  • Vertex atlas: 3 stars (b,b,b,b,b), (r,g,r,g,r,g) and (b,b,r,g,g,r)
48
Q

What are the capsid features of the poliovirus?

A
  • t=3 virus
  • one prototile (kite with blue decoration where two long edges meet and red and green at the other vertices)
  • Matching rules: blue meets blue, red meets green
  • Vertex atlas: Three stars (b,b,b,b,b), (r,g,r,g,r,g) (r,g,r,g)
49
Q

What information does the type of tiling (in viral tiling theory) provide about viral structure?

A
  • information on the relative orientations of the capsid proteins
  • information on internal bonding structure
    • e.g. in a triangular tile, all three proteins are bound together in a trimer interaction and in a rhombus shaped tile, two proteins are bound as a dimer
50
Q

Under the viral tiling theory, what differs and what remains the same about different viruses with a T=3 triangulation number?

A
  • Numbers and locations of the pentamers and hexamers are the same
  • Relative orientations are different (internal bonding)
51
Q

Why has a non-quasiequivelent theory of viral capsid structure been developed and what does it explain?

A

Explains the 72 pentameric structure of human papilloma viruses and SV40 (Paporviridae)

These are isocohedral but not quasi-equivelent

Have more than one tile (Penrose tilings)

Same layout as a t=7 virus but pentamers instad of hexamers

52
Q

What is the capsid structure of SV40?

A

4 vertex stars

53
Q

what is the capsid structure of RNA viruses?

A

Cross section through shows capsid forms a polyhedral cage with RNA

54
Q

Give examples of viruses that vary from icosahedral symmetry

A
  • Geminivirus
  • Caudovirus
55
Q

How do Geminiviruses vary on typical icosohedral symmetry?

A
  • consist of twinned T=1 icosohedra
  • fused at one of the pentameric vertices
  • particles consist of 110 capside protein subunits and one molecule of dsDNA of around 2.8 k.b
56
Q

What are three caudoviruses and what are their T numbers

A

Myoviridae (T=13) (e.g. Entero-phage T4)

Podoviridae (T=7) (e.g. bacteria phage T7)

Siphoviridae (T=7 e.g. Entero-bacteria phage lambda)

Three families with slightly different tail

57
Q

What is the purpose of the bacteriophage tail?

A

To inject genomic information through the injectosome complex in the tail, forces DNA into the bacterium

Tail has 12 fold symmetry

58
Q

What are the largest viruses?

A

Pandoravirus

  • has sac like shape
  • has a pore
  • 1micron long
  • 2500 genes
  • encodes own tRNA

Pithovirus

  • 2.5 microns
  • 500 genes
  • no symmetry needed as dsDNA v stable, can have lots
  • larger than many bacteria
59
Q

What is the structure of Poxvirus?

A
  • dsDNA
  • Has: outer envelope, lateral body, core envelope, core fibrils, pallisade layer, surface tubules
  • Has large number of genes and can reuse builiding blocks without having to use symmtery
60
Q

What are the features of Bacculoviruses and their particules?

A

Bacculoviruses

  • dsDNA
  • v complex insect virus
  • useful for recombinant DNA techniques for expressing recombinant DNA e.g. vaccine expression

Bacculovirus particles

  • Injested by insect host
  • Have budded virus particle
    • involved in replication and cell-cell spread within insect
  • Occluded virus particle
    • virus particles in association with capsid proteind and DNA proteins to form virion which is surrounded by polyhedrin
    • produced late in infection
    • released into environment when the insect dies
61
Q

What viruses are examples of complex structures? (important)

A

HIV - conical

Mimivirus - giant, hair like structures

Pandora virus - sac like shape with pore

Pithovirus - No symmetry

Poxvirus - core, pallisade layer and surface tubules

Bacculo viruses

62
Q

What is the structure of the HIV core structure?

A
  • made up of pentamers and hexamers but has lost symmetry
  • follows same kind of layout as an icosohedron
  • T3 capsid surrounds
63
Q

What envelope proteins does HIV have?

A

Between lipid envelope and nucleocapsid have matrix proteins, the internal tails of external glycoproteins interact with the matrix proteins to form a trimer (spike)

Transport channels on lipid envelope

64
Q

What experimental techniques can/have be used to elucidate the structure of viruses?

A
  • X-ray (early work by watson and crick and KC)
  • NMR (complicated for whole virus but used for individual protein subunits)
  • Cryo-electronmicroscopy: single particle analysis and tomography (- as viruses often as small as a wave of light so optical light microscope cannot be used, need EM)
65
Q

How can radiation damage be minimised when doing a cryo-EM?

A

Transmission electron microscopy electron beam causes radiation damage in the sample, rapid freezing minimises this and fixes the particle in its natural environment (in vitreous ice without orming disruptive ice crystals)

66
Q

What problems are encountered with cryo-EM?

A

TEM images are 2D projections of the object showing the distribution of density through the object. A 3D construct is generated by combining many images of the object taken from a range of viewing angles. In vitreous ice the distribution of orientations is fairly random leading to icosohedral averaging.

Therefore anything that is icoshedral is washed out.

Can’t see if RNA/DNA is disordered in the capsid because of averaging.

67
Q

Why do viruses have an icosahedral shape?

A

Largest (discrete) symmetrical structure that could be found in 3D [has order 60]

Highest ratio of inside space to outside - maximize container volume while minimizing the portion of the genomic sequence needed to code for the container

68
Q

What virus shows helical symmetry? What is the formula?

A
  1. Tobacco mosiac virus (Helical capsid)
  2. Bacteriophage M13
  3. Ebola
  4. P= μ x p
  • P: pitch of helix
  • μ: subunits per turn of the helix
  • p: axial rise per subunit
69
Q

What are the features of icosahedral symmetry?

A
  • 6 axes of 5-fold symmetry
  • 10 axes of 3-fold symmetry
  • 15 axes of 2-fold symmetry
70
Q
A

Principle of molcular virology (7 decks)

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