Team:Edinburgh/Cellulases (C model)

How does this whole synergy thing even work? It can seem almost magical that having enzymes closer together can increase their usefulness, but consider the following statements about cellulose degradation, all of which are true:

1. Exoglucanase chews away at the end of a cellulase chain, producing cellobiose sugars.
2. Endoglucanase cuts cellulose chains in the middle, essentially turning one chain into two.
3. Cellobiose inhibits the action of the above enzymes.
4. β-glucosidase cuts cellobiose in half, producing two glucose molecules.

Facts 1 and 2 mean that exoglucanase works best with endoglucanase nearby, since every time endoglucanase acts, it produces new chain-ends for exoglucanase to attack. Meanwhile, facts 1, 3, and 4 mean that β-glucosidase helps nearby copies of the other enzymes by preventing the cellobiose from inhibiting them.

Syn: a simple demonstration of synergy

We can demonstrate that there is (potentially) a huge difference between the synergistic and non-synergistic systems with Edinburgh's Syn C program. This is a 2D simulation that works in the following way:

• The world is a 2D grid.
  • Each spot in the grid can contain a sugar, a bond between sugars, or nothing.
• Cellulose is modelled as alternating sugars and bonds: s-b-s-b-s-b-s-b-s-b-s etc etc.
• There are three enzyme types: endoglucanase, exoglucanase, and β-glucosidase.
  • The enzymes move about randomly, in a "brownian motion" manner.
  • If an enzyme is on the same space as a bond, it can cut it:
    • Endoglucanase can only cut bonds away from the ends of a chain.
    • Exoglucanase can only cut bonds if it results in a cellobiose molecule forming.
    • β-glucosidase can only cut cellobiose bonds.
• There is inhibition of exoglucanase by cellobiose; it does not cut bonds if there is a nearby cellobiose molecule.

[[Image:Edinburgh-All-Actions.png|thumb|center|620px|The actions of endoglucanase, exoglucanase, and β-glucosidase.