Introduction to Virus Structure Tutorial Jonathan King, Peter Weigele, Greg Pintilie, David Gossard (MIT) v.November, 2008 Virus Structure вЂў Size вЂ“ вЂў Basic shape вЂ“ вЂ“ вЂў 17 nm вЂ“ 3000 nm diameter Rod-like вЂњSphericalвЂќ Protective Shell - Capsid вЂ“ Made of many identical protein subunits вЂ“ Symmetrically organized вЂ“ 50% of weight вЂ“ Enveloped or non-enveloped вЂў Genomic material вЂ“ DNA or RNA вЂ“ Single- or double-stranded Virus Structure вЂў Virus capsids function in: вЂ“ Packaging and protecting nucleic acid вЂ“ Host cell recognition вЂў Protein on coat or envelope вЂњfeelsвЂќ or вЂњrecognizesвЂќ host cell receptors вЂ“ Genomic material delivery вЂў Enveloped: cell fusion event вЂў 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. History вЂў In 1953, Crick & Watson proposed вЂ¦ principles of virus structure вЂ“ Key insight: вЂў Limited volume of virion capsid => nucleic acid sufficient to code for only a few sorts of proteins of limited size вЂ“ Conclusion: вЂў Identical subunits in identical environments вЂў Icosahedral, dodecahedral symmetry X-ray Crystallography of Viruses вЂў Symmetry of protein shells makes them uniquely well-suited to crystallographic methods вЂў Viruses are the largest assemblies of biological macromolecules whose structures have been determined at high resolution History conвЂ™t вЂў In 50вЂ™s & 60вЂ™s Klug and others confirmed that several (unrelated) вЂњsphericalвЂќ viruses had icosahedral symmetry вЂ“ (Used negative staining & electron microscopy) вЂў Conclusion: вЂ“ Icosahedral symmetry is preferred in virus structure Similarity to Buckminster FullerвЂ™s Geodesic Domes Icosahedral Symmetry вЂў 12 vertices вЂў 20 faces (equilateral triangles) вЂў 5-3-2 symmetry axes вЂў 60 identical* subunits in identical environments can form icosahedral shell * asymmetric Caspar and KlugвЂ™s Icosahedral shell But вЂ¦ вЂў Clear evolutionary pressure to make larger capsid вЂ“ Using larger subunits helps very little вЂ“ Using more subunits helps a lot вЂў Not possible to form icosahedral shell (of identical units in identical environments) with more than 60 subunits вЂў Viruses with more than 60 subunits were observed вЂў Question: вЂ“ How can >60 subunits form an icosahedral shell? вЂ“ Will any number of subunits work? вЂ“ If so, how would they be organized? Quasi-equivalence вЂў In 1962, Caspar & Klug proposed the theory of вЂњquasi-equivalenceвЂќ вЂ“ Not all protein subunits are equivalent вЂў вЂњIdenticalвЂќ subunits in slightly different environments вЂ“ Only certain numbers of subunits will can be packed into closed regular lattice. Caspar & Klug, Cold Spring Harbor, 1962 Quasi-equivalence вЂў Subunits are in вЂњminimallyвЂќ different environments вЂ“ Pentamers at vertices вЂ“ Hexamers elsewhere вЂў Predicts packing arrangements of larger capsids вЂ“ Shift from T1 to T4 packing => 8-fold increase in volume Spherical viruses have icosahedral symmetry Homunculattice HK97 Asymmetric Unit Outside Inside Herpes Simplex Virus at 8.5 Г… resolution from Wah Chiu and Frazer Rixon in Virus Research (2002) Influenza вЂў Infection depends on spike proteins projecting from capsid membrane called вЂњHemagglutinin (HA)вЂќ вЂў These bind sugar molecules on cell surface вЂў 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. вЂў These differences control what host cell types the virus can infect. вЂў 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 structured low pH fusion peptide Qiao et al. Membrane Fusion Activity of Influenza Hemagglutinin. The Journal of Cell Biology, Volume 141, 19 Influenza Hemagglutinin вЂў The HA spikes extend like a spring during infection http://www.roche.com/pages/facets/10/viruse.htm http://hsc.virginia.edu/medicine/basic-sci/cellbio/jgruenke.html Trimer Structure вЂў Long alpha helices form coiled coil structure вЂў In mature trimers of HA0, each monomer is cleaved into HA1 and HA2. Evolution of dsDNA viruses вЂў 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 viruses вЂў вЂў вЂў вЂў Unique portal ring at one Vertex Scaffolding proteins Procapsid assembled empty of DNA DNA pumped into procapsid through portal ring вЂў DNA moves back through portal to enter cell P22 Pathway Herpes viruses also have a portal protein portal complex 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.