Proteolytic cleavage detection

1. Select the protein sequence or sequences that you would like to analyze
2. Set the parameters for detection
3. Select proteolytic cleavage enzymes
4. View results

In step 2, you have the option of choosing among these parameters:

• Exclude enzymes based on number of matches.
  Certain proteolytic enzymes cleave at many positions in the amino acid sequence. For instance proteinase K cleaves at nine different amino acids, regardless of the surrounding residues. Thus, it can be very useful to limit the number of actual cleavage sites before running the analysis.
• Exclude fragments based on length.
  Likewise, it is possible to limit the output to only display sequence fragments with a length within a chosen range. Both upper and lower limits can be chosen.
• Exclude fragments based on mass.
  The molecular weight is not necessarily correlated to the fragment length as amino acids have different molecular masses. For that reason it is also possible to limit the search for proteolytic cleavage sites to be within a certain mass range.

In step 3, you can select proteolytic cleavage enzymes (see figure above)

The output options of the proteolytic cleavage site detection are several. One option is to display two views on the screen:

• The top view shows the actual protein sequence with the predicted cleavage sites indicated by small arrows.
• The bottom view show a text output of the detection, listing the individual fragments and information on these.

Click here to read more about Proteolytic cleavage in our “Bioinformatics explained” section