The Cleavage sites (Proteases) track predicts cleavage sites for proteases (also termed peptidases or proteinases) and chemicals in a protein sequence using known proteolytic signatures. When you apply Cleavage sites (Proteases) to the Analysis view, Protean 3D searches the protein sequence against the protease library. and displays matches to protease and chemical cleavage sites as markers with different shapes and colors. For a table showing which proteases and chemicals are included in this method, see List of proteases.
The following video demonstrates the use of the Cleavage sites (Proteases) track:
To apply this track to the sequence:
In the Tracks panel, expand Databases and check the box next to Cleavage Sites (Proteases). The track will now be visible in the Analysis view, with a legend matching the marker symbol to a specific protease.
In addition, a list of cleavage sites will appear in the Tracks panel under "Cleavage Sites (Proteases).
To edit track options:
Select the track in the Tracks panel. Open the Track Options section, which appears as follows:
- The drop-down menu lets you select from the following filters based on the protease type or the number of cleavage sites:
| Filter type | Filter description |
|---|---|
| All | All enzymes and chemicals |
| Chemicals | Only chemicals |
| Cuts infrequently | Cleaves a sequence at least once but no more than five times |
| Cuts once | Cleaves a sequence once |
| Enzymes | Only enzymes |
| Fusion tag cleavage | Enterokinase, Factor Xa, HRV3C protease, TEV protease, Thrombin |
| Mass spectrometry | Arg-C, Asp-N, Chymotrypsin, Glu-C, Lys-C, Pepsin, Pancreatic elastase, Thermolysin, Trypsin |
| Nonspecific | Arg-C, Asp-N, Asp-N (N-terminal Glu), BNPS or NCS/urea, Chymotrypsin, Chymotrypsin (low specificity), Clostripain, CNBr, CNBr (methyl-Cys), CNBr (with acids), Formic acid, Glu-C (AmAc buffer), Glu-C (Phos buffer), Hydroxylamine, Iodosobenzoic acid, Lys-C, Lys-N, Lys-N (Cys modified), Mild acid hydrolysis, NBS (long exposure), NBS (short exposure), NTCB, Pancreatic elastase, Pepsin A, Pepsin A (low specificity), Prolyl endopeptidase, Proteinase K, Thermolysin, Trypsin, Trypsin (Arg blocked), Trypsin (Cys modified), Trypsin (Lys blocked) |
| Specific | Caspase-1, Caspase-2, Caspase-3, Caspase-4, Caspase-5, Caspase-6, Caspase-7, Caspase-8, Caspase-9, Caspase-10, Enterokinase, Factor Xa, Granzyme B, HRV3C protease, TEV protease, Thrombin |
| Custom | Allows you to manually define the number of cleavage sites per sequence by using the text boxes below the drop-down menu. |
- In the Number of Sites per Protein area, check one or both boxes, if desired, then enter a number in the corresponding text box.
Click 
if you wish to return to the default value.
Working with proteases in the Analysis view:
| Task | How To… |
|---|---|
| To select an individual cleavage site | Click on its marker above the sequence ruler. |
| To select all visible cleavage sites for a protease or chemical | Click on its name in the legend. |
| To view the protease or chemical name and cleavage site | Hover over the marker above the sequence ruler. |
| To view the full name of the protease or chemical and the number of times it cuts the sequence | Hover over its name in the legend. |
| To view detailed information about a protease | Select its name from the list. The Details panel will then display in-depth information about the protease, including its classification. |
| To create a tab-delimited text file with information about the cleavage frequency of all compounds | Click the "Export Proteases" link in the Actions section of the Details panel. |
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