CAVER Analyst examples

The following example demonstrates the usage of CAVER Analyst on a case study described in detail by Pavlova et al. More examples and information can be found in the supplementary material for the CAVER Analyst publication in the Bioinformatics journal. The supplement is available here.

Case study – Engineering enzyme activity

Redesigning access tunnels of the haloalkane dehalogenase DhaA resulted in 32-fold increase in activity with toxic environmental pollutant 1,2,3-trichloropropane (TCP). The study demonstrates the power of combining rational design with directed evolution focused to the access tunnels. Additional information can be found in the article by Pavlova et al. published in Nature Chemical Biology.
  1. Loading the structures
  2. The study was performed with wild type and C176Y mutant of the haloalkane dehalogenase DhaA. The users are provided with the structures in PDB format wt_dhaa.pdb and m1_dhaa.pdb. These structures can be obtained by downloading examples.zip and unzipping the 'structures' folder.

  3. Setting the binding site for tunnel computation
  4. The CSA database does not contain any records for these structures thus the user must define the starting point manually, e.g., by defining the surrounding residues. In both structures, the active site is defined by the residues 106, 107, 130, and 272. They can be set using the 'Add Item...' button in the Tunnel Computation window, section Surrounding items. It opens the following window:

    Window for defining the new binding site

  5. Launching tunnel computation
  6. In this case the parameters present in the Tunnel Computation window or the CAVER 3 Computation Settings should have the following values:
    • Maximum distance (Å)= 5
    • Minimal probe radius = 0.7
    The computation is then launched using the 'Compute Tunnels' button. This is performed for both structures and then their structure alignment can be achieved using Structure → Alignment.

  7. Interpretation of results
  8. The active site of wild type DhaA is an occluded cavity with two major access tunnels: (i) the main tunnel and (ii) the slot tunnel (Figure 1). Mutant carrying substitution in the main tunnel (C176Y) limits the access of water molecules to the active site cavity and resulting in higher activity with TCP (see Figure 2).

    The main (in blue) and the slot (yellow) tunnels of the haloalkane dehalogenase DhaA

    Figure 1.The main (in blue) and the slot (yellow) tunnels of the haloalkane dehalogenase DhaA.

    Comparison of the wild type DhaA (left) and the DhaA mutant C176Y (right). The main tunnel is closed by the introduced mutation (in orange).

    Figure 2.Comparison of the wild type DhaA (left) and the DhaA mutant C176Y (right). The main tunnel is closed by the introduced mutation (in orange).

CAVER 3.0 example

Examples of using CAVER can be found in the user guide (starting at page 59).

CAVER 3.0 PyMOL Plugin example

The following steps demonstrate the usage of CAVER PyMOL Plugin.
  • open the molecule 1MJ5 using the PyMOL application
  • launch CAVER plugin: Plugin -> CAVER 2.0...
  • make sure that the location of PyMOL is specified correctly
  • if necessary, change the location of the output directory
  • set the number of tunnels to be calculated to three: type "3" to the "Number of tunnels" field
  • specify the starting point of the calculation:
  • - select residues from the surroundings of the starting point using the PyMOL command promt: "select start, i. 108 or i. 272"; this command will create PyMOL selection "(start)" containing two catalytic residues - Asp 108 and His 272
    - type "start" to the "Specify selection" field
    - click "Convert to x,y,z (will be shown below)" button
  • click "Compute tunnels" button
  • save the current session for the future use: File -> Save Session As...


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