Sorry if my question is very basic for biology majors because I am not. I am trying to build a mathematical model of a particular pathway using systems of differential equations and in order to reduce the number of parameters, I need to know the total concentration of multiple enzymes. How are enzyme concentrations usually reported in the literature so I can google it? Also, this does not seem to me to be a straightforward measurement for professional biologists, so how are enzyme concentrations actually measured or approximated? Thanks in advance!
Hi again TheLast Cipher,
Enzymes in a cell are usually semi-quantified by the: Western Blot technique.
But there are lesser known techniques.
E.g. For a Western Blot the unit of measurement is the color intensity of the enzyme band on the blot membrane.
If I were you I would look for journal articles covering your pathway of interest.
Covers the electron transport chain (Co-enzyme Q10)
If you can get through the pay-wall & read their results and you will find:
"Western blot analysis of membrane protein isolated from keratinocytes derived from one young and old donor. A representative picture out of five experiments is displayed."
Also they used and I quote:
Maybe you could comment on which pathway and I can find some assisting material.
The BioNumbers site (https://bionumbers.hms.harvard.edu/search.aspx) is often useful for these types of questions, if you're interested in an order of magnitude. However, if you want precise concentration ratios (i.e. something like "is there twice as much Ras as ERK, or more like half as much"), you are unlikely to get a definitive answer.
These may be cell type-dependent and even vary from cell to cell due to noise. You probably want to simulate your network with a variety of absolute concentration, and then the most interesting behaviors are those that are reasonably robust to the exact numbers used (results that depend on, e.g., having almost exactly the same number of molecules of Ras as ERK are likely irrelevant as they would be too "brittle" inside a living cell). Once you find out what the necessary limits are for a given behavior that you find interesting, you could think about checking whether values reported by the literature indeed tend to fall within those bounds.