Team:Edinburgh/Presentation

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Presentation

Contents

Introduction

Edinburgh's 2011 iGEM project is all about synergy - the ability some enzymes have to work better when close together. In 2010, the Slovenian team found a way to arrange enzymes in the cytoplasm so as to achieve synergy. We wondered whether it would be possible to get extracellular enzymes close together.

Edinburgh's project is also about biorefineries, which are special types of refineries in which biomass, such as cellulose, is converted into useful products. Our project is a feasibility study into the creation of a biorefinery using cellulases arranged in a synergistic manner.

Part One: Modelling

The first question we asked is: what is this synergy phenomenon and how does it work?

Cellulose is a long chain of glucose sugars. Consider the following statements about cellulose degradation:

  • One type of cellulase, exoglucanase, attacks the end of a chain, producing disaccharides called cellobiose.
  • Another type, endoglucanase, cuts the chain in the middle.

We can immediately see that these two facts mean the enzymes work best together: the enzyme that cuts chains in the middle also produces new chain ends for the other enzyme to attack.

Now consider the following:

  • Exoglucanase is inhibited by the presence of cellobiose.
  • A third enzyme, β-glucosidase, cuts cellobiose into glucose.

Here then we have another case of enzymes working best together.

We constructed computer models to investigate the above phenomena.

C

[Play animation]

Our first model is an ad hoc model written in C. Here cellulose is placed on a two dimensional grid, and cellulases move over the grid. There are two simulations: in one, the enzymes move about freely. In the other, enzymes travel in triplets, each triplet containing one of each enzyme.

This model is very simplistic but does show that the synergy effect makes sense.

Kappa

A more sophisticated model uses the Kappa modelling language. FIXME

Part Two: Human Practices