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I was wondering what is the protein concentration in an E. coli cell. When studying enzyme kinetics and activity in vitro, I would argue that the substrate and enzyme concentrations resemble those in vivo. As a result, conclusions made by such assays do not apply 100% to the naturally occurring reactions. Are there any examples in literature that address this issue?

Along those lines, what is the concentration of fatty acids/nucleic acids in the cell?

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3 Answers 3

The macromolecule concentration within E Coli is estimated to be around 0.3-0.4 g/ml [1]

The concentrations of your substrate in respect to your enzyme are generally fairly analogous to in vitro studies compared to in vivo studies. However, this is heavily based on the assumption that the diffusion constants for both molecules stay consistent. In many cases that is true and errors can be corrected for using PEG to imitate the crowding effect. And yes, people have begun to look at the question [2]

However, for larger macromolecules like DNA and chromosomes that do see effects from subdiffusive transport, the molecules don't obey diffusive random-wal behavior [3]. The classic model system is the lac repressor which exhibits non-diffusive kinetics due to its interactions with DNA.

  1. http://www.ncbi.nlm.nih.gov/pubmed/1748995
  2. http://www.ncbi.nlm.nih.gov/pubmed/21237136
  3. http://prl.aps.org/abstract/PRL/v104/i23/e238102
  4. http://www.ncbi.nlm.nih.gov/pubmed/7317363
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For a great visualization of the macromolecules inside the cell, check out David Goodsell's illustrations. He tries to reproduce the protein and DNA density within the cell to show how things might be in vivo. Really great stuff.

The answer is - its very concentrated. Compare the density of the cell to that of a typical crystallized protein, which is I believe 0.8 g/ml of protein.

http://mgl.scripps.edu/people/goodsell/

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Composition of E. coli (dry weight): 55% protein, 20% RNA, 10% lipid, 15% other

Protein concentration is about 100 mg/ml or 3 mM. From the size of an E. coli cell, 1 nM is about 1 molecule/cell. This is ~1000 molecules/cell for HeLa cells.

Diffusion coefficient for an "average" protein: D ~ 5-15 microns^2/s, or ~10 ms to traverse an E. coli. For reference, a small metabolite in water diffuses about 30-100x faster.

Reference: Cell 141:1262, Key Numbers in Biology

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