We are trying to isolate alpha amylase inhibitor from some bacteria but we are confused whether the inhibitor secreted by the bacteria in the media is carbohydrate or protein.
How about digesting your secretion product with some protease; next destroy the protease (by autoclaving or something) and then do your inhibition test? If you see reduced or no activity compared to undigested control, you can conclude it is a protein I think. You could try a number of things like this; comparing to the control each time? My first thought was infrared spectroscopy, but bacteria produce a lot of things, of course ;-)
Try digesting with Proteinase K which is a broad spectrum serine protease. Digest at 37 degrees and then heat inactivate the Proteinase K at 95 degrees for about 10 minutes. Then run your assay. That should tell you if proteins are involved or not.
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