IGEM:Stanford/2009/Notebook/Marys iGEM Notebook/2009/08/05

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2 The IPP-->B-carotene-->RA Model Fig 2.1 A quick sketch of the IPP-->RA process

The process above can be devided into two procedures:
 * IPP*8-->B-carotene
 * B-carotene(+Blh)-->Retinal(+RalDH)-->Retinoic Acid

2.1 Modeling on the production of B-carotene
The process of IPP producing B-carotene is quite complex, as shown in the Fig 2.2. In this process, we basically care about two main issues:
 * 1) Yield output of B-carotene ([B-carotene]/[All Caronoids]).
 * 2) Velocity of the whole process

2.1.1 Yield output of B-carotene We found the B-carotene distribution in yeast in [1]. Below is an important form as to the issue. Form 2.1 B-carotene distribution [1] Basically, using the cluster of "YB/I/E I", in the final product of caronoids, we get 68% of B-carotene, highest percentage in the paper. (Also 29% Phytoene, and 3% Neurosporene.) "YB/I/E tHMG1 I", producing 52% of B-carotene, might be another choice.

2.1.2 Production rate of B-carotene As this is a really long process....Basically, the velocity is mainly dependent on the most time-consuming reaction in the whole chain. Thus, Leon and I looked for the kcat values of different enzymes in the procedure, as shown in the cart below: Form 2.2 Paremeters in the IPP-->B-carotene model. (Source: mostly from Brenda) Apparently, cyclization of Lycopene is the slowest reaction, as the concentration of enzymes are approximately in the same level.

2.2 Modeling on the B-carotene-->RA process
The production of RA is mainly based on a chain of two catalyzed reactions, as shown in the graph below: Fig 2.3 The production of RA Neither Retinal nor RA has any other degrading process in E.coli. Degrading rate of B-carotene is 9.769e-9 s^-1. Other paremeters we use in this model are shown in the form below: Form 2.3 Parameters used in the B-carotene-->RA model

2.3 Simulation and Analysis

 * Equations for the IPP-->RA process:

Daily Work
Goals
 * Find out the missing kcat values for the IPP-->B-carotene model. Calculate the approximate producation rate of B-carotene.
 * If the velocity of NO activating SoxR is found, finish the NO-->SoxS-SoxR model.

Project
 * Device I: Anti Inflammatory Device

Accomplishments
 * At last found all the paremeters needed for the IPP-->B-carotene model....(12:15p) Now trying to build up the model.

Problems
 * The rate/velocity of NO activating SoxR?

Alternative Solutions

Weekly Goals

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