[3] Basic Virus Structure

• 2 Minimum Requirements:

  1. Nucleic acid
  2. Protein coat
• Other terms for virus structure:

  1. Virion
  2. Capsid
  3. Structural unit
  4. Nucleocapsid
  5. Envelope
• Lipid bilayer covering the virus composed of cell membrane derived from the host cell


  Envelope
• Assembly of nucleocapsid genome and protein

  Nucleocapsid
• May be composed of one or more polypeptides

  Structural unit
• Protective protein shell that envelopes the genome

  Capsid
• Infectious virus particle outside of host cell


  Virion
• T or F: The capsid cannot be composed of only one stable polypeptide structural unit

  False
• Types of virus modifications:

  1. Proteins covalently bound at both ends of dsDNA or ssDNA
  2. Linear DNA with complementary bases with another DNA (capped with protein)
  3. Some RNA with a poly A tail
  4. Repeated sequences
  5. Single or multiple molecules as their genome
• The Poly A Tail is used so that the ribosome can recognize it for translation
• Types of repeated sequences:

  1. Direct terminal repeats
  2. Inverted terminal repeats
• Examples of single or multiple molecules as genome:

  1. Segmented genomes
  2. ) Example: Influenza A with 8 molecules
  3. Multipartite genomes
  4. ) Example: Cowpea mosaic virus
• Segmented and multipartite genomes are advantageous for viruses with very long genomes
• Segmented genomes lead to reassortment, leading to rapid evolution
• Proteins encoded by the genome:

  1. Structural proteins
  2. Nonstructural proteins
• Structural proteins play a role in the viral structure

  • Nucleocapsid protein, membrane proteins, spike proteins
• Nonstructural proteins are important for the replication or expression of the genome
• These proteins facilitate the release of the virus from the host cell, or modulate host cell defenses

  Accessory proteins
• The viral genome generally encodes gene products for:

  1. Replication
  2. Expression
  3. Assembly and Packaging
  4. Regulation of reproduction cycle
  5. Modulation of host
  6. Transmission
• The rabies virus changes the behavior of the host to increase transmission
• Information NOT contained in viral genomes:

  1. Complete protein synthesis machinery
  2. Genes encoding for proteins of energy metabolism and membrane biosynthesis
  3. Telomeres or centromeres
• Protein importance (structure)

  1. Structural or capsid proteins - protection of the genome
  2. Recognition and packaging of nucleic acid envelope
  3. Interaction with host cell membranes to form the envelope
• Protein importance (genome delivery):

  1. Presence of receptors on the envelope
  2. Binding signals disassembly of virions
  3. induction of fusion with host cell membranes so nucleocapsid can be released
  4. Can direct the genome to the appropriate site
• Protein importance (other functions)

  1. Can interact with cellular components for transport to intracellular sites during assembly
  2. Can interact with cellular components to ensure efficient infectious cycle
• Types of nucleocapsid symmetry

  1. Helical
  2. Isometric
  3. Complex/Asymmetrical
• Helical structures are made via identical noncovalent interaction with other subunits
• Due to the open structure of helical symmetry, any volume can be enclosed by varying the length of the helix
• TMV is a classic example of the helical structure, where a single capsid protein is repeated 2130 times
• Helical Structure Advantages:

  1. Easily self-assembles because of 1 polypeptide
  2. Maximal NA-protein interaction

  Disadvantages:

  1. Must be completely broken down for nucleic acid release in host cell
  2. Maximal surface area to volume ratio
• Isometric symmetry is based on the icosahedron shape

  • 20 equilateral triangles
  • 60 identical subunits
• Discrete structure that makes up isometric symmetry


  Capsomeres
• Number of small structural units per triangular phase

  Triangulation
• Higher triangulation value leads to a larger virus
• Isometric symmetry advantages:

  • Minimum surface area to volume ratio
  • Does not need to undo the entire nucleic acid

  Disadvantages:

  • Difficult to assemble
  • Requires other proteins to assemble
• The reovirus or bluetongue virus has 2 protein shells, leading to greater stability
• Metastability:

  1. Stable - genome is protected during extracellular phase
  2. Unstable - when genome enters host so it can disable
• The energy of the assembled virion is not at minimum

  • This leads to an increase of energy when attaching to virus, powering disassembly
• Complex or asymmetrical symmetry can be a:

  1. Combination of other symmetries
  2. Asymmetry
• Examples of complex symmetry:

  1. Tailed bacteriophages
  2. Pox virus with lipid membrane
• Classification of naked viruses:

  1. Influenza - each fragment of genome has helical symmetry
  2. Herpesvirus - matrix proteins and tegument proteins