Question: (Closed) Which techniques for finding protein complexes are biased towards stable complexes? Which aren't?
0
gravatar for Qroid
2.7 years ago by
Qroid40
Qroid40 wrote:

My question is about techniques for finding protein complexes (e.g. AP-MS, yeast two-hybrid), and it's in response to a recent answer. From that answer (emphasis mine):

... detection is biased towards stable complexes in AP-MS experiments but that may not be the case if you derive complexes from some other type of experiments like yeast two-hybrid. Note also that it is usually assumed that complexes found in AP-MS experiments are stable.

If AP-MS is usually assumed to find stable protein complexes, are there similar assumptions for other methods? e.g. Does yeast two-hybrid find more or less stable complexes? Also, is there any citable, systematic study that covers this?

edit: I'm specifically wondering about the techniques listed in CORUM e.g. "MI:0007". But any insight will be helpful.

ADD COMMENTlink modified 2.7 years ago by Jean-Karim Heriche21k • written 2.7 years ago by Qroid40

Hello Qroid!

We believe that this post does not fit the main topic of this site.

I'm afraid it's not related to bioinformatics. You should try: http://biology.stackexchange.com/

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 2.7 years ago by Pierre Lindenbaum124k

The question can be construed as trying to understand the experimental details underlying bioinformatics data.

ADD REPLYlink written 2.7 years ago by Jean-Karim Heriche21k

I can edit the question to make it more bioinformatics-y. And yes, it is about understanding the details of bioinformatics data.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by Qroid40
1
gravatar for Jean-Karim Heriche
2.7 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

I don't think there is a definite answer because a lot is down to experimental details like the ionic strength of buffers and the sensitivity of the detection method. Also there is no clear definition of what a stable complex is. However, you can generally assume that methods that involve breaking up the cell and subjecting the lysate to some purification steps can only recover stronger interactions than in vivo methods unless some steps (e.g. cross-linking) are taken to stabilize interactions. In yeast two-hybrid experiments, an interaction leads to a transcriptional response which may be strong enough to be detected even when the interaction is transient/weak. The code MI:0007 refers to "anti tag coimmunoprecipitation". This only tells that one protein was tagged and purified using an antibody against the tag. This doesn't tell anything else, unless a precise definition is somewhere on the web site, like whether the tagged protein was over-expressed or what detection method was used (e.g. mass spectrometry, Western blot...).

ADD COMMENTlink written 2.7 years ago by Jean-Karim Heriche21k
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