DeepView/Mutating Amino Acids

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DeepView is a free molecular modeling program available for both Windows and OS X. Here are instructions for using DeepView to mutate an amino acid.

Caution: DeepView cannot predict changes in overall protein conformation after mutating amino acids, and it is unlikely that any existing program can do this reliably. Therefore, mutating one or more amino acids in an existing protein model will allow you to visualize the mutated sidechains in the context of the wild-type protein structure, but the resultating mutated model may not reflect changes that such mutations may induce in protein structure.

The following instructions were written for DeepView 4.1, current in May, 2015 (released October, 2012).

  1. Use DeepView's File menu item "Open PDB File" to load your molecule.
  2. If you can find the residue you want to mutate by inspecting the structure, you can skip this step. If the Control Panel window is not showing, use the Window menu to open it. This allows you to see the sequences of the protein chains. Find the residue of interest in the list in the Control Panel. Click the checkmark in the "show" column while watching the model. You should see the residue of interest disappearing and reappearing. Rotate the molecule to position the residue of interest for a clear view.

    Surface residues are easiest to see. If the residue of interest is buried, you may use the Display menu to turn on Slab. Move the slab plane by holding down the shift key while dragging the mouse up and down.
  3. To confirm that you have the correct residue, click the identification button (top row of large square buttons, near the middle of the row, with a large question mark in it), then click the residue in the 3D image. An identifying label should appear next to the residue you clicked.

  4. Click the Mutate button (in the top row of large square buttons).

  5. Click on the residue you want to mutate, and a menu of the 20 amino acids will open. Release the mouse button and slide the mouse away from the menu, and the current amino acid will be highlighted (highlight not seen in OS X). Click on the target amino acid for the mutation of this residue -- the new sidechain appears immediately!

  6. Notice the rotamer message in red that appears just below the top row of large square buttons.

    • There are a number of possible conformations of the mutated sidechain, called "rotamers". Automatically, a rotamer has been selected with the lowest energy (fewest collisions and most favorable hydrogen bonds, if any). Following "R" are numbers such as 2/7, meaning that there are 7 possible rotamers for this amino acid, and the second has been selected automatically.
    • There may be several rotamer positions with equally low energy. Notice the score following "s:". Negative scores are favorable and positive scores are unfavorable. Click on one of the small triangles near the red rotamer message to step through the possible rotamers, noting the energy score for each one. As you do this, notice the green and pink dotted lines, which represent favorable hydrogen bonds or unfavorable steric collisions, respectively. Choose any one of the lowest energy rotamers that you prefer.

      If you have Slab on, some of the green or pink lines may be hidden because they are outside the slab. Hold down Shift while dragging the mouse up and down to move the slab plane.
    • You may also wish to take into account the probability (value following "p:") of each rotamer for the secondary structure in which the mutated residue occurs.

  7. Click the "Mutate" button again, and either accept or discard the mutation.

  8. If you used the identification button to label the residue, the label does not change to reflect a mutation. Open the "Display" menu, select "Labels" and click on "Clear User Labels".

  9. Use the File menu to Save Current Layer (the one Layer you have loaded). This saves a PDB file that you can use in FirstGlance in Jmol or other software packages.

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Eric Martz

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