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Introduction to Virus Structure
Jonathan King, Peter Weigele, Greg Pintilie, David Gossard
v.November, 2008
Virus Structure
Basic shape
17 nm – 3000 nm diameter
Protective Shell - Capsid
– Made of many identical protein
– Symmetrically organized
– 50% of weight
– Enveloped or non-enveloped
Genomic material
– DNA or RNA
– Single- or double-stranded
Virus Structure
• Virus capsids function in:
– Packaging and protecting nucleic acid
– Host cell recognition
• Protein on coat or envelope “feels” or “recognizes”
host cell receptors
– Genomic material delivery
• Enveloped: cell fusion event
• Non-enveloped: more complex strategies &
specialized structures
Electron Microscopy
Mitra, K. & Frank, J., 2006. Ribosome dynamics: insights from atomic structure modeling into cryo-electron
microscopy maps. Annual review of biophysics and biomolecular structure, 35, 299-317.
• In 1953, Crick & Watson proposed …
principles of virus structure
– Key insight:
• Limited volume of virion capsid => nucleic acid
sufficient to code for only a few sorts of proteins of
limited size
– Conclusion:
• Identical subunits in identical environments
• Icosahedral, dodecahedral symmetry
X-ray Crystallography of Viruses
• Symmetry of protein shells makes them uniquely
well-suited to crystallographic methods
• Viruses are the largest assemblies of biological
macromolecules whose structures have been
determined at high resolution
History con’t
• In 50’s & 60’s Klug and others confirmed that
several (unrelated) “spherical” viruses had
icosahedral symmetry
– (Used negative staining & electron microscopy)
• Conclusion:
– Icosahedral symmetry is preferred in virus structure
Similarity to Buckminster Fuller’s
Geodesic Domes
Icosahedral Symmetry
• 12 vertices
• 20 faces
(equilateral triangles)
• 5-3-2 symmetry axes
• 60 identical* subunits
in identical environments
can form icosahedral shell
* asymmetric
Caspar and Klug’s Icosahedral
But …
• Clear evolutionary pressure to make larger capsid
– Using larger subunits helps very little
– Using more subunits helps a lot
• Not possible to form icosahedral shell (of identical units in
identical environments) with more than 60 subunits
• Viruses with more than 60 subunits were observed
• Question:
– How can >60 subunits form an icosahedral shell?
– Will any number of subunits work?
– If so, how would they be organized?
• In 1962, Caspar & Klug proposed the
theory of “quasi-equivalence”
– Not all protein subunits are equivalent
• “Identical” subunits in slightly different
– Only certain numbers of subunits will can be
packed into closed regular lattice.
Caspar & Klug, Cold Spring Harbor, 1962
• Subunits are in “minimally”
different environments
– Pentamers at vertices
– Hexamers elsewhere
• Predicts packing arrangements
of larger capsids
– Shift from T1 to T4 packing
=> 8-fold increase in volume
Spherical viruses have icosahedral symmetry
HK97 Asymmetric Unit
Herpes Simplex Virus at 8.5 Г… resolution
from Wah Chiu and Frazer Rixon in Virus Research (2002)
• Infection depends on spike proteins projecting from capsid
membrane called “Hemagglutinin (HA)”
• These bind sugar molecules on cell surface
• Much of the difference between Hong Kong flu, Swine flu,
Bird flu, and other strains, is in the amino acid sequence
and conformation of the HA protein.
• These differences control what host cell types the virus can
• Immunization against flu involves your immune system
synthesizing antibody proteins that bind the HA protein.
Influenza virus
composition of virus
entry of influenza
into cell
Influenza hemagglutinin:
a pH induced, conformationally controlled trigger
for membrane fusion
100 Г… displacement
of fusion peptide
disordered loop
backbone is
low pH
fusion peptide
Qiao et al. Membrane Fusion Activity of Influenza Hemagglutinin. The Journal of Cell Biology, Volume 141, 19
Influenza Hemagglutinin
• The HA spikes extend like a spring during infection
Trimer Structure
• Long alpha helices form
coiled coil structure
• In mature trimers of HA0,
each monomer is cleaved
into HA1 and HA2.
Evolution of dsDNA viruses
• All known viruses, whether infecting
bacteria or humans, may have evolved from
a single common ancestor, relatively early
in the evolution of organisms.
Common steps in the assembly of all dsDNA
Unique portal ring at one Vertex
Scaffolding proteins
Procapsid assembled empty of DNA
DNA pumped into procapsid through portal
• DNA moves back through portal to enter
P22 Pathway
Herpes viruses also have a portal protein
Herpes portal (UL6) tagged with gold-bead labeled antibodies
visualized by negative stain electron microscopy
Bill Newcomb and Jay Brown, University of Virgin
Cryo-EM structure of purified Herpes portal protein
Trus BL, Cheng N, Newcomb WW, Homa FL, Brown JC, Steven AC.
Structure and polymorphism of the UL6 portal protein of herpes simplex
virus type 1. J Virol. 2004 Nov;78(22):12668-71.
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