viral capsid structures Flashcards
What is the function of capsids?
protect against physical, chemical and enzymatic damages
Why are only a few or one protein subunits for the capsid encoded in the genome?
economy rules –> small particle size and thus small genome size since a nucleic acid can never encode for a single capsid protein that is bigh enough to enclose and protect the whole genome
what is the simplest way of capsid formation?
one type of protomer
what shape do capsids have?
rod shaped or roughly spherical
describe the symmetry of tobacco mosaic virus
helical symmetry –> made up by 2,200 protein subunits (jelly roll)
what is the simplest way to arrange multiple, identical protein subunits? by what is the form defined?
rotationnal symmetry (helix) -> definded by amplitude and pitch
How can the pitch be calculated?
P = µ * p
with: µ= number of subunits per turn
and p= axial rise per supunit
describe the capsid form which many bacteriophages have and what the major coat protein is
helical capsids –> rod shape
g8p is major coat protein
which forms do mature and immature viruses have?
mature: icosahedron
immature: dodecahedron
Why must capsid protein subunits recognize each other with precision (specificity)?
because virus particles assemble spontaneously from individual components
Why are icosa- and dodecahadron the optimal form?
allow a maximum numver of identical object to form a closed symmetrical shell
how is an icosahedron built?
is built from 20 identical equilateral triangles–> triangular tiles are arranged side by side to that they can enclose the volume inside the icosahedron
Name the numbers of vertices, faces (tiles) and edges and their rotation axis of an icosahedron
- 12 vertices with 5 fold rotation axis
- 20 tiles each with 3 fold rotation axis
- 30 edges each with a 2 fold rotation axis
–> remember 60
Which symmetry do tiles of icosahedroins have? what is the derived minimal, total number of objects in an icosahedron? Do many viruses have this minimal number?
tiles have 3 fold symmetry (= 3 identical objects are needed to form one tile) –> 20 tiles *3 = 60
thus 60 asymmetric units (proteins)
–> but only few viruses have only 60 subunits (e.g. satellite virus)
Why do asymmetric units need more than one subunits in self sufficient viruses ? How do these subunits look like?
long genomes –> larger volume of capsid required
–> subunits can be identical or differen –> only certain multiples of 60 subunits are likely to occur (1,3,4,7…) –> triangulation number
how can the triangulation number be calculated?
T = h^2+hk+k^2
what do the variables h and k of the triangulation number describe? what do they mean
describe how far away two 5-fold symmetries are in a capsid with a lot of 6 fold symmetries
h = straight steps
k= corner
What are the characteristics of T3 viruses?
- T =3
- 180 subunits
- A subunits interact ariund the 5 fold axes
- B and C subunits interact around the 3 fold axes
- 3 subunits each of B and C arranged in a pseudosymmetric way (3 fold becomes pseude 6 fold)
What are the characteristics of T4 viruses?
- 240 subunits
- 4 different types of subunits: A, B. C, D
- A: 5-fold
- D: 3 fold
- b and C: 2 fold + 2 d subunits
- A, B, C: interact around a pseudo 3 fold axes clsutered around 5 folds
describe the capsid of tomato bushy stun virus
- 3 domains in each protomer: R, S and P with connecting regions: a and h
- 3 possible conformations
- a only ordered in C –> interdigitate
- P domains interact pair wise across 2 fold axes –> protrusions
- 180 P domains form 90 protrusions
describe the capsid of picornaviruses?
- T3 capsid despite 4 protomers (vp4 completely buried inside the particle)
- 60 copies each of 4 polypeptides (VP1- VP4)
- vp1-vp4 translated from viral RNA as single polyppetide (processed post translationally by 3CD)
- VP0, VP1 and VP3 –> assembly of shell beginns –> VP0 cleaved into VP2 and VP4
- virus shell built from 12 pentamers
how do picornaviruses arrange 180 subunits similarly to T=3 plant viurses (one type of polypeptide) despite having 4 different peptides?
plant virus: conformational differences
picorna: 3 chemicaly different polypeptide chains with local structural differences
What is the canyon hypothesis?
Vp1 subunits form a pentamer with a mountain in the middle of the pentamer –> canyon formation at the sides of the 5 subunits –> these are antibody binding sites
how can uncoating of viral capsids be inhibited by drugs?
by inhibiting the canyon
describe the greek key motif
- formed in a eight stranded beta sheet or barrel
- greek key is formed when one of the connection of 4 antiparallel b-strands is not a hairpin connection but strand n is connected to strand n+3 or n-3 instead of n+1 or n-1
describe the 3D structure of proteins called jelly roll
beta strands are arranged into two seperate sheets: strand 1,8,3,6 and 2,7,4,5
spice between the sheets is filled by hydrophobic side chains
polypeptide chain has 8 straight sections interrupted by loop regions
