Viruses
Viruses are small intracellular parasites that invade the cells of virtually all known organisms. They reproduce by utilizing the cell's machinery to replicate viral proteins and genomic material, generally damaging or killing the host cell in the process; subsequentelly, a large number of newly generated viruses go on to infect other cells. Viruses are responsible for a wide variety of human diseases, ranging from the common (influenza and colds) to the exotic (AIDS, West Nile virus and Zika). Some viruses which are not dangerous to humans can also be exploited in technological applications, in addition, viruses find use in genetic engineering applications and increasingly in the design of new nanomaterials. At the very least, all viruses contain two components: the capsid (a protein shell), and a genome, consisting of either DNA or RNA. Some viruses also include accessory proteins to aid in infection, and in some cases a lipid bilayer to further protect their contents from the environment. The viral life cycle itself is deceivingly simple: viruses enter the cell, typically (but not always) through the interaction of their capsid with a receptor on the cell surface; the virus must then somehow disassemble its capsid to release its genetic material and any necessary helper proteins. The viral genome is then replicated and the proteins it codes for are synthesized to produce the raw material for the production of new viral particles; these new viruses then assemble and bud from the cell either through the membrane or upon cell death.
Spotlight: Squeezing a Virus (Oct 2009)
Viruses are the simplest life forms known. In fact, one can question if they are life forms at all, as they cannot exist without infecting a host cell and using its machinery for replication. The virus is indeed just a package material surrounding a genetic message that instructs the host cell to replicate the virus. It looks like a soccer ball, but is a million times smaller (see also the March 2006 and January 2007 highlights). The infection, a well known example being infection of human cells by a flu virus, involves the virus to approach a human cell and dock onto it, become internalized by the cell, bursting then its package, called the capsid, and release the genetic message. The virus capsid needs to be sturdy and impermeable up to the approach to the cell, but then become brittle and porous to release the genetic material. Obviously, the virus capsid must have very distinct mechanical properties to function. To investigate these properties experimental and computational biophysicists teamed up. The experimentalists placed empty capsids of the hepatitis B virus onto a small chip and mechanically squeezed the capsid then with an extremely small tip, measuring how much force is needed to squeeze the spherical capsid down repeatedly. Computational researchers using NAMD repeated the experiment in simulation. As they reported recently, simulation gave the same forces as the experiment, but yielded also a detailed picture of the capsid mechanics. More on our "Molecular dynamics of viruses" web site.
