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The Mexil Engine (In honour of Mathew Exil)

Simuliating a virus shell assembly

  • 95% of human, plant and animal viruses have icosahedral shaped shells. Even Polio, herpes, and AIDS have icosahedral shells. These shells come in a variety of sizes depending upon the virus and are generally made up of pentagons and hexagons.
  • A virus' shell should generally be big enough to contain the genomic information, which is the RNA or DNA of the virus, should be robust enough to withstand the immune system's offences and fragile enough to break down and let the genetic material sneak in the cell.

Note

  • An icosahedral is a geometric shape with 20 sides(or faces), each composed of an equilateral triangle. An icosahedron has what is referred to as 2–3–5 symmetry, which is used to describe the possible ways that an icosahedron can rotate around an axis.

  • "Nearly all previous research on interfering with the infection process has focused on how to prevent a fully-formed shell from binding to a cell. Our work aims at modeling how these shells build in the hopes of eventually suggesting ways of interfering with their growth and causing deformity. If this can be achieved, the genomic information won't fit inside the shell, and the virus won't be viable."

  • "We have developed a hypothesis as to how virus shells form based solely on simple local rules for how proteins interact. We model virus shells as an interconnection network of proteins (i.e. nodes) and their essential binding interactions (i.e. edges). Chemically speaking, the nodes or proteins are usually all identical: however, they can be thought to behave differently because proteins can take on different shapes. We have shown that by utilizing only local communication, each node in the network can be given enough information to uniquely form any size shell. This information consists of the type of a node and its neighbors, bond angles, bond lengths, and torsional angles."

["Local rule-based theory of virus shell assembly." Proc. Natl. Acad. Sci. USA Vol. 91, pp. 7732-7736, Aug. 1994] (http://people.csail.mit.edu/bab/virus/virus.html)

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