Team:CityU HK/collaboration

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CUHK : Computer simulation of the “Nitrogenase System”

This year, the CityU HK iGEM team collaborated with the CUHK iGEM team.


How did we help the CUHK iGEM team?


We met the CUHK iGEM team in early October 2014. At the meeting, each party presented our projects and we were impressed with each other’s project goals. Following our discussion, the CityU team agreed to collaborate with the CUHK iGEM team to perform computer simulation/modelling of the “Nitrogenase System” that the CUHK team was working on. We succeeded in producing a modelling system for their Nitrogenase project.



The Model

The computer simulation works on two enzyme kinetic systems as shown below.


Fig. 1 Two Enzyme Kinetic Systems. (a) System I-a single one. (b) System II-combination of two kinetic systems.


The table below presents the Vmax and Km of both enzyme systems.


Nitrogenase (30 °C)

Hydrogenase (80 °C)

Vmax

0.0175 nmol CH4/ nmol MoFe protein /sec

5.28x10-6 nmol H+/ nmol hydrogenase/ sec

Km

16 mM HCO3

0.037 mM H2


Based on the parameters provided, we compared the two enzyme kinetic systems using Matlab simulation.


Equations



Results

A comparison of the two systems using Matlab simulation is shown in Fig. 2. The difference between the product output of the two systems are provided by the data in Fig.4 and Fig.5.



Fig. 2 Matlab code. Input: V1max, K1m and A10 are the initial parameter settings of the system I. V2max, K2m are those of system II. t represents the time.




Fig. 3 A. Relationship between substrate [A] and product [C]. B. Relationship between substrate [A] and difference between [C3] and [C1] .


Acknowledgement

The modelling was performed by Dr. Zhu Yuan of the Department of Biology and Chemistry, City University of Hong Kong.




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