I'm looking for both simple and complex assays or technologies than can be used to determine if two competing molecules are competitive or noncompetitive. I figure xray crystallography is a clear one, but say I can't get crystals to form. What other techs or assays could I use to determine this?

It's a protein-protein interaction with a small molecule competing with one of the proteins. This particular set has not been done before. All interactants are purified.

  • $\begingroup$ Can you please describe your setup in a little more detail? Are your ligands small molecules, proteins, or something else? Do you have the purified target protein? Is it a receptor or some other kind of enzyme? Has anyone worked with it in the literature before? $\endgroup$ – MattDMo Jan 19 '16 at 0:14
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    $\begingroup$ If you've got an enzyme and a good activity assay and you want to test if the molecule is an inhibitor, try building Lineweaver-Burke Plots. It can take a lot of work though, because each plotted point is a reaction rate, and determining each reaction rate can take significant effort. Because the plots are reciprocal measures, small errors are easily magnified, so you have to be very very careful to minimize any error whatsoever. But if done well you can determine competitive, non-competitive, or mixed inhibition. $\endgroup$ – user137 Jan 19 '16 at 1:10
  • $\begingroup$ ncbi.nlm.nih.gov/books/NBK92001 has some good guidelines for mechanism of action studies. $\endgroup$ – CKM Jan 19 '16 at 14:44
  • $\begingroup$ Now that I see you are looking at protein-protein interaction, would fluorescence anisotrpy help? If you labeled one protein with a fluorophore, you should be able to observe a change in tumble rate as the other protein binds or falls off. $\endgroup$ – user137 Jan 20 '16 at 1:56
  • $\begingroup$ I'll have to edit the question, I'm looking for label free methods. Sorry about that! $\endgroup$ – Nathan Jan 22 '16 at 18:08

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