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	=== Enzyme Targets ===		=== Enzyme Targets ===
		+	*Sadly there was no crystal structure of either enzyme we could use to locate the sites to introduce mutations
		+	**However, we used the literature available to locate spots where we would want to introduce mutations
-		+	==== Propionate CoA-transferase ====
-		+	*According to Selmer et al. 2002, there is a catalytic glutamate found in all CoA-transferases
		+	**Using alignment tools along with the crystal structure of YdiF CoA transferase (That shares 45% sequence identity with the Propionate CoA-transferase) we were able to locate the catalytic glutamate in our enzyme
		+	**Also, we were able to locate the oxyanion hole of the enzyme
		+	**These two regions along with those mentioned in the Lee paper's were the targets for our MAGE oligos (4 in total)
		+	[[File:PCTmagetargets.jpg]]
	=== Pathway Engineering ===		=== Pathway Engineering ===

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Revision as of 18:51, 31 August 2013

	Project Overview	Validate PLA synthesis	Develop bioassay	Apply MAGE	Introduce export system	Make a bioplastic

Contents 1 Aims for the Project 2 MAGE Targets 2.1 Enzyme Targets 2.1.1 Propionate CoA-transferase 2.2 Pathway Engineering

Aims for the Project

1. Engineer strains of E. coli to validate PLA synthesis
   
2. Develop bioassay to screen PLA production
   
3. Apply MAGE to optimize PLA production, guided by FBA
   
4. Introduce type 1 secretion system to export and extract PLA
   
5. Make a bioplastic

MAGE Targets

• The first step in applying MAGE is finding MAGE targets. This involved reading numerous scientific papers learning as much as possible about the heterologous enzymes, and the pathway that was being used to create the PLA

Enzyme Targets

• Sadly there was no crystal structure of either enzyme we could use to locate the sites to introduce mutations
  • However, we used the literature available to locate spots where we would want to introduce mutations

Propionate CoA-transferase

• According to Selmer et al. 2002, there is a catalytic glutamate found in all CoA-transferases
  • Using alignment tools along with the crystal structure of YdiF CoA transferase (That shares 45% sequence identity with the Propionate CoA-transferase) we were able to locate the catalytic glutamate in our enzyme
  • Also, we were able to locate the oxyanion hole of the enzyme
  • These two regions along with those mentioned in the Lee paper's were the targets for our MAGE oligos (4 in total)

Pathway Engineering

Figure 6: This figure shows how to design a oligo depending on which strand and which replichore the gene is located.

List of Papers:
Jacob et al. 1997
Matsuzaki et al. 1998
Sawers et al. 1998
Park et al. 2002
Selmer et al. 2002
Takase et al. 2002
Fong et al. 2005
Matsumoto et al. 2005
Rangarajan ES et al. 2005
Matsumoto et al. 2006
Jung et al. 2009
Matsumoto et al. 2009
Juang et al. 2010
Orth et al. 2010
Yang et al. 2011
Kandasamy et al. 2012
Yang et al. 2013