MadSci Network: Biochemistry

Re: How can I determine the amino acid sequence for caspase proteolysis?

Date: Wed Feb 14 14:16:33 2007
Posted By: Karin Crowhurst, Post-doc/Fellow, Biochemistry
Area of science: Biochemistry
ID: 1171215587.Bc

Hi Amy,

I am sorry, I am not totally sure from your question what you want to do, but I will try answering in a couple of ways and hopefully it will be useful to you:

1. if all you need is the amino acid sequence of the protein and you just want to translate from the known DNA sequence of the gene for YCA1, a simple tool can be found at

2. If you want to try to determine or guess at the location of the active site of this putative caspase, then you will likely want to use BLAST. You can align the amino acid sequence of your protein with known caspases (whose active sites have already been mapped) and postulate the location of the cleavage site in your protein by comparison. Unless you already know a bunch of caspases, however, you will have to find those and their sequences. You might start off at the Protein Data Bank for that (

3. If you want to determine the location of the cleavage experimentally, you could have someone run for you a mass spectrometry experiment on the cleaved fragments; knowing the sequence of the protein, you can then calculate where the cleavage site is located, based on the size of the fragments.

As I said at the start, I am a little unclear exactly what you want to do, so hopefully this starts your out. Otherwise, I guess you'll have to post another question and hope you have more luck!

Good luck,


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