Chapter 3 - Genomes

Use chapter as reference.

Chapter 4 - Virus Structure

Chapter 4 - Virus Structure

How are genomes protected?

1)2)3)

Chapter 4 - Virus Structure

• Why look at structure of viruses??

– Models for protein-protein & protein-NA complexes

– Receptor binding sites might be drug targets (rhinovirus)

– Antigenic sites on virion

– Neutralizing vs non-neutralizing Abs

– Escape mutants

– ?? why few serotypes of poliovirus, but many for rhinovirus

– Uncoating and assembly could be targets for therapeutics

– Often final assembly includes proteolytic processing

– ?? why poliovirus is acid stable, but rhinovirus is not

Assume basic knowledge of protein structure

Box 4.1

Chapter 4 - Virus Structure

• Basically: nucleic acid + protein capsid for protection (+ extras)

– Self assembling structures (often)– Built out of repeating units - economy and assembly

• Coding triplet = 1000 Daltons; 1 amino acid = 100 Daltons MW• Therefore DNA or RNA cannot encode single protein to act as protein coat.

– Advantages of subunits:

– minimal genetic info,– less wastage in building a functional particle

• smaller units discarded if faults in translation or folding of protein

– stable virus stucture• Repeated patterns of subunits leads to maximum stability• Self-assembly because of minimum free energy in system

Chapter 4 - Virus Structure

• But:

– Use of subunits leads to limited virus architecture

– Proteins may have some regular structure - helix; sheet

• But tertiary structure of proteins is not symmetrical

– Since the subunits not symmetrical, need to:

• arrange subunits symmetrically with maximum bonding

Chapter 4 - Virus Structure

Most viruses use 1 of 2 structural principles

- rod-like - thread like appearance, helical structure

- isometric - roughly spherical

NB helical nucleocapsid can be surrounded by spherical outer shell

Rod-like viruses

• Arrange protein subunits in circle to form a “cylinder” with space for genome

• Actually, it’s helical• Why not cylinder rather than helical??

Rod 18 x 300 nm 17.5 kDa subunit

Units per turn (u ) for TMV = 16 1/3 Axial rise per unit (p ) for TMV = 0.14 nm

Pitch of the helix ( P = u x p ) 2.3 nm

Can build TMV virion in the absence of RNA TF protein specifies structure

How is this assembled?

How is this assembled?

TMV

Assembly of subunits around RNA must be orderly

Subunits must have more affinity for each other that for RNA- pre-assemble small sections

Unique origin of assembly ~ 800 nucleotides from 3' end - growth towards 5' end rapid + double disks- growth towards 5' end rapid + monomers or sm. aggregates

RNA passes through axial channel, each subunit has 3 basic amino acids, binds 3 nucleotide phosphates

TMV

Disassembly:

For TMV, is co-translational

As RNA translated from 5' end, protein coat subunits removed

Mass of coat protein = 14.5 kDaMass of ribosome = > 1000 kDa

ICOSAHEDRAL VIRUSES

Originally discovered by comparing EM shadowed viruses with various models.

For self assembly need to have simple rules. How to divide surface of sphere into regular units…. Caspar and Klug.

Simplest and most common shape for virions shows icosahedral symmetry- must have 2, 3 and 5 fold symmetries

- most efficient biological container is a geodesic dome design

link to ICOSAHEDRON structure

link to Principles of Virus Architecture

Icosahedron = 20 equilateral triangular facets, 12 vertices (pentamers)

Flat hexagon

Remove one triangle

Connect 2 free edges

‘ 3 dimensions

= pentamer

Icosahedron

In simplest form:- each facet has 3 identical protein subunits b/c needs 3-fold symmetry

Icosahedron

Larger viruses use more subunits rather than larger proteins.

If use multiples of 60 subunits, but not all positions are the same…

b/c this introduces hexamers between pentamer vertices

Get: quasi-equivalence if single type of protein used

Get: PseudoT3 if multiple proteins used

PSEUDO-T3 symmetry (a, b and c are different)

Triangulation number = square of the distance between pentamer vertices

- reflects number of triangles mapped onto sphere

For: T = 1 x 20 triangular facets x 3 subunits = 60

T = 3 .......................................... = 180

T = 4 .......................................... = 240

Only for T=1, with 60 identical subunits, is

each subunit in equivalent position

1

MO

T = 1 + 0 + 0 = 1

Triangulation number

= OM

2

H + HK +K

22

=

OM = distance between

2 pentamer vertices

1

HK

O

M

Triangulation number

H + HK +K

22

=

T = 1 + 1 + 1 = 3

Loops and tails…

Assembly - from pre-assembled units

"Genes" for protomer subunits are contiguous in genome- translation, cleavage, assembly of basic unit = 1 process

To assemble into pentamers and hexamers - requires different bonding preferences- non-covalent bonding, easier to reject mistakes

Pentamers / hexamers + RNA seeds assemble of complete capsids

Final cleavage of VP0 gives VP2 + VP4 as assembled- ?? locks in place for stability- ?? primes for release of RNA

These are WRONG!!!!!

Bonus Q.

Some bigger viruses:

Some variability:

Link to: virology.wisc.edu/virusworld/