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I know that protein synthesis is governed by a lot of factors (I'm mostly studying the mTOR pathway), but I'm looking for some kind of marker that will indicate the global protein synthesis rates.

I know there are tissue-specific markers (like actin/myosin in muscle) but I'd like something more that is ubiquitous and is proportional to global protein production (maybe a muscle can make more or less myosin depending on whether there are some factors).

I assume protein synthesis factors (like mTOR, S6K1 etc.) are quickly regulated, so they cannot be used as markers.

So, what would serve as the best molecular marker?

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    $\begingroup$ Witness is a wrong term. "Marker" is a right term for what you mean. I edited the question. See if this matches with what you intend to ask. $\endgroup$ – WYSIWYG Feb 16 '16 at 10:18
  • $\begingroup$ You could measure the fractional synthesis rate in vivo in humans if that's what you're after, e.g. ajpendo.physiology.org/content/273/1/E99.short describes it extensively. $\endgroup$ – pbond Aug 16 '16 at 23:59
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The answer will not satisfy you. The truth is no protein marker will do.

On one hand you seem to be looking at some individual, representative protein, which you could measure by immunoblot. But most proteins are in scant concentrations, just as many as required for their job, and go up and down depending on their specific roles, rather than on general metabolic trends. Even if some general control mechanism increases protein synthesis across the board, in a cell proteins are 20% actin, 20% tubulin, 0.0001% 4E-BP and 0.0001% p70-S6K (made-up numbers for the sake of example), any 1% total protein increase you'd like to measure would be 200,000 easier to detect in tubulin than in p70-R6K. In order to be a marker of general control of protein synthesis, the marker protein you'd want to measure should be a plentiful protein, with little to no specific control.

On the other hand, those are the characteristics of a house-keeping gene. So you won't be able to normalize such a "representative" blot! Normalizing house-keeping by house-keeping, you will have pretty much no change.

Embrace labeling experiments. Even there, the right normalization is debatable. If anything, the fact that everyone does those, rather than looking at protein X, should be an indication of how much you will struggle to prove points about protein synthesis rate using anything else.

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  • $\begingroup$ That's a really interesting answer, and you make points. You are right about labeling experiments, but I cannot do that in my current project. $\endgroup$ – Dan Chaltiel Mar 28 '16 at 21:24

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