Proteolytic cleavage detection

Given a protein sequence, CLC Genomics Workbench detects proteolytic cleavage sites in accordance with detection parameters and shows the detected sites as annotations on the sequence as well as in a table below the sequence view.

Detection of proteolytic cleavage sites is initiated by:

        Toolbox | Classical Sequence Analysis (Image gene_and_protein_analysis) | Protein Analysis (Image proteinanalyses)| Proteolytic Cleavage (Image proteolytic_cleavage)

This opens the dialog shown in figure 15.17. You can select one or several sequences.

Image proteolytic_step1
Figure 15.17: Choosing a protein sequence for proteolytic cleavage.

In the second dialog, you can select proteolytic cleavage enzymes. Presently, the list contains the enzymes shown in figure 15.18. The full list of enzymes and their cleavage patterns can be seen in Appendix.

Image proteolytic_step2
Figure 15.18: Setting parameters for proteolytic cleavage detection.

You can then set parameters for the detection. This limits the number of detected cleavages (figure 15.19).

Image proteolytic_step3
Figure 15.19: Setting parameters for proteolytic cleavage detection.

For example, if you have one protein sequence but you only want to show which enzymes cut between two and four times. Then you should select "The enzymes has more cleavage sites than 2" and select "The enzyme has less cleavage sites than 4". In the next step you should simply select all enzymes. This will result in a view where only enzymes which cut 2,3 or 4 times are presented.

Click Finish to start the tool. The result of the detection is displayed in figure 15.20.

Image proteolyticresult
Figure 15.20: The result of the proteolytic cleavage detection.

Depending on the settings in the program, the output of the proteolytic cleavage site detection will display two views on the screen. The top view shows the actual protein sequence with the predicted cleavage sites indicated by small arrows. If no labels are found on the arrows they can be enabled by setting the labels in the "annotation layout" in the preference panel. The bottom view shows a text output of the detection, listing the individual fragments and information on these.