Endy: PTL Logic

I am working to develop a new type of logic, called Post-Translational Logic, or PTL. PTL devices regulate the post-translational modifications of proteins to define system state and control cell function.

Current synthetic biological circuits make use of protein-DNA and RNA-RNA interactions to control gene expression in bacteria-- such circuits are Protein-DNA logic, or PDL. A brief comparison of the two types of logic is as follows:

PDL

• Engineered around gene expression
• Typical parts: transcriptional regulators, translational regulators
• Typical signal: PoPS, resulting in desired cellular concentrations of proteins.
• Easier to engineer than PTL
• Slow response time (hours)
• Uses one subset of cellular functions

PTL

• Engineered around protein modifications
• Typical parts: kinases, phosphorylation sites, docking sites
• Typical signa: rate of modification, resulting in desired state of proteins.
• More difficult to engineer than PDL
• Fast response time (seconds)
• Explores a new set of applications

In designing PTL logic, I am working to answer the following questions:

• What is a PTL part?
• What is a PTL device?
• What signals are passed between devices?
• What are device performance specifications?

Below I will describe some of my ideas.

Tthe most intuitive definition of a PTL device