Structure Flashcards
What is a subunit (protein subunit)?
Single folded polypeptide chain
What is a structural unit?
Unit from which capsids or nucleocapsids are built
May compromise one protein subunit or multiple different protein subunits
What is a capsid?
The protein shell surrounding the nucleic acid genome
What is a nucleocapsid?
The nucleic acid-protein assembly packed within the virion
Used when this assembly is a discrete substructure of a particle
What is an evelope?
The host cell-derived lipid bilayer carrying viral glycoproteins
What is a virion?
The infectious virus particle
What is a metastable structure?
A structure has not attained the lowest free energy state
What is resolution?
The minimal size of an object that can be distinguished by microscopy or other methods of structural analysis
What is helical symmetry?
The symmetry of regular wound structures defined by the relationship P = u x p
P = pitch of the helix u = the number of structural units per turn p = the axil rise per unit
What is icosahedral symmetry?
The symmetry of an icosahedron the solid with 20 faces and 12 vertices related by axes of two three and five fold rotational symmetry
What is a glycoprotein?
a protein carrying covalently linked sugar chains (oligosaccharides)
What is an integral membrane protein?
Proteins that are embedded in a lipid bilayer with external and internal domains connected by one or more membrane-spanning domains
What are membrane-spanning domains?
A segment of an integral membrane protein that spans the lipid bilayer
Often alpha-helical
What are the two main functions of virion proteins of the viral genome?
Protection
Delivery
Why are virus particles considered “metastable”?
Because they need to be strong enough to protect the viral genome and labile enough to be released or uncoated inside the host cell
Has to be stable AND unstable
- stable = protects viral genome
- unstable = delivery/uncoating
Self-assembly —>
Uncoating
As individual proteins assemble to form a large capsid, their surface charge and polarity is ____ while their contact region is ____. This leads to a __ in the energy of the capsid system and provides the driving force for capsid ___
Minimized
Maximized
Decrease
Self-assembly
What is the smallest thing scientists can see when using X-ray crystallography?
Atoms
What structure(s) was determined by X-ray crystallography?
DNA, Penicillin, Vitamin B-12, Insulin, Hemoglobin
What limitations does X-ray crystallography have?
Requires proteins to be packed together in a stable organized structure
Some proteins are too flippy to line up in a crystal
Requires the formation and creation of crystals
What does Cryo-electron microscopy (Cryo-EM) use as a energy source?
Uses electrons rather than light as energy source
How does Cryo-EM assemble pictures?
Computer algorithms assemble multiple pictures of sample into one composite 3D image
How are proteins in Cryo-EM orientated?
proteins in sample can be in multiple orientations
Where are proteins kept in Cryo-EM?
Thin layer of liquid and frozen
An icosahedron comprises _ equilateral triangular faces related by _, __, and __ axis of rotational symmetry.
20; 5; 3; 2
What do h and k represent in the Triangulation equation?
0 and/or any positive integer
What does a virus need to be alive?
Genetic material and a capsid
What is the difference between capsid and nucleocapsid?
Nucleocapsid is the same structure as a capsid, but an envelope is present
What are the bonding interactions in the virus capsid?
Non-covalent
If it was covalent, it will be stronger
What are the steps in X-ray crystallography workflow?
Step 1: crystal
x-rays
Step 2: Diffraction pattern
phrases
Step 3: Electron density map and atomic model
fitting in between
Atomic model back to diffraction pattern is called refinement
What is a chimera?
composed of more than one organism/species
How has Cryo-EM improved resolution over time?
Lower resolution = better
X-ray crystallography had a higher resolution than Cryo-EM
What is the Cryo-EM structure of Zika virus?
Frozen, hydrated ZIKV
- Black boxes: smooth, mature virus particles
Icosahedral symmetry
- Black triangle: 5-fold, 3-fold, 2-fold
How do viruses build protective coats (capsids)?
Helical symmetry
Icosahedral symmetry
Complex symmetry
Which viruses have helical symmetry?
Tobacco Mosaic Virus (TMV)
Vesicular stomatitis virus (VSV, Cryo-EM)
Nucleocapsid (N) protein bound to RNA (decamer; x-ray crystl.
How to know whether it is helical or icosahedral symmetry?
Helical symmetry as it is wrapping around the genomes
How to know whether capsid or nucleocapsid?
Nucleocapsids are substructures found within
Capsids are substructures of a whole particle
What are simple icosahedral capsids?
60 identical protein subunits
Identical interactions between subunits
How do we build larger virus particles with icosahedral symmetry?
Add more subunits
Bonding interactions:
Quasiequivalent
What is Quasiequivalent?
Similar but not identical
Capsid > 60 subunits
Noncovalent binding properties of subunits
What is a triangulation number (T)?
Number of facets per triangular face of an icosahedron
Determines size of capsid
- capsids with T>1 have a 6-fold axis of symmetry
How to find amount of viral capsids?
60 * T (T determines size)
units = proteins
What are enveloped viruses?
Host derived lipid bilayer
How are the envelope in viruses acquired?
Through budding of nucleocapsid through cell membrane
What kind of symmetry do nucleocapsids have?
May have icosahedral or helical symmetry
What is the external domain of the integral membrane glycoprotein for?
Binding to cell receptors, sugars
What is the internal domain of the integral membrane glycoprotein for?
Essential for virus assembly
Where are viral envelope glycoproteins located?
Perpendicular or parallel to lipid membrane
What makes complex virus particles complex?
Head is icosahedral and tail is helical
Describe Bacteriophage T4.
Complex virus -------------------------------- Head: Icosahedral symmetry - dsDNA genome - T= 13 (End) - T = 20 (Midsection)
Tail: Helical symmetry
- injection of viral genome into host cells
Describe Mimivirus.
Icosahedral symmetry
Dense coat of long fibers
Unique “starfish”-shaped structure
Describe Pithovirus/Pandoravirus.
Pithovirus siberium
- isolated from permafrost soil sample in Siberia
Amphora (vase-like) shape
Protruding “cork”
What are some nonstructural components in virus particles?
Enzymes
- polymerases, integrases
- capping enzymes
- topoisomerases
- proteases
Other viral proteins
- non-enzymatic
- important for viral replication
Cellular components
- tRNAs, lipids, histones, glycoproteins, antiviral proteins
