5.2 Proteins

1. Purpose

In nature proteins are the tireless workers that keep the machinery of life in the cells up and running. The same is true in this simulator system. It is the proteins that actually do things. Currently there are several different types of proteins defined in this system, and each one has a specific function. As more and more features are added then more protein types will be added to carry out the functions necessary to perform those features.

2. Basic Protein Properties

Protein Properties
Protein Type: This is used to determine the type of protein to load.
Binding ID: This is a generic ID that is used to bind this protein to its partner. This will be used differently based on the type of protein.
Degrade Rate: This determines the rate at which this protein is degraded in the cell.
Table 1. These are the basic properties common to all proteins.

All proteins have the basic properties shown in table 1. Each different type of protein usually has more properties defined that are specific to it. When the proteins are being loaded from the gene the first part that is loaded is the type of protein. The different protein types are discussed more in following pages. The binding ID is a tag that is used differently by each of the different types of proteins. One of the key concepts in this system is that each protein has to match up with something else in order to be able to do anything. For example, A receptor must bind a ligand in order to be active. A transcription factor must bind an enhancer in order to perform its function, and so on. The binding ID of each protein is what is used to match up a protein with its counterpart. Finally, every protein is degraded. Nothing lasts forever, and that includes the proteins in our bodies and in this simulation. At each time step a certain percentage of all of the proteins are destroyed. The degrade rate is what determines how much protein is destroyed each step.

3. Protein Types

Transcription Factor: These proteins regulate the rate of transcription of genes. They can speed it up or slow it down to a stop.
Gene Controllers: These proteins actually turn the genes on and off. Unlike transcription factors, the effects of GC's are long term. Once turned off the gene stays off until turned back on again.
Receptors/Ligands: These proteins allow cells to communicate with each other. Membrane to membrane receptor/ligands are used for local communication. And cell receptor/diffusible ligand is used for long range communication.
Protein Regulators: Transcription factors and gene controllers give us the ability to regulate genes. This type of protein gives us the ability to regulate the activity of proteins. There are two versions of protein regulators. Allosteric regulation can activate or inhibit proteins when the regulator is present. Kinase regulators act like a switch to turn the protein on or off.
Table 2. These are the different types of proteins that are currently defined.

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