B Examples


Example 1: Building B-form DNA.

Example 2: Building a short polypeptide, bovine oxytocin.

Example 3: Sketching free-form molecules.


Example 1: Building B-form DNA.

The first example shows how to make a simple model of b-form DNA, with a

sense sequence of (gcgatta). From the Build/Add option of the Menu Bar, select

Polynucleotide ( Figure 1 ).

Figure 1a. Selecting Polynucleotide from the Menu Bar.

The polynucleotide dialog box appears. The dialog allows many options to be specified

but for the purpose of this example, we will use the default options which result in b-form

DNA. In the Add Base (Pair) section of the dialog, select in the following order:

  1. G - (C)
  • C - (G)
  • G - (C)
  • A - (T)
  • T - (A)
  • T - (A)
  • A - (T)
  • 5'-CAP
  • 3'-CAP
  • You will see the sequence as it is being built in the box above the Help button. The above sequence of

    button clicks results in b(gcgatta). The 5'-CAP and 3'-CAP buttons serve to replace the sense and anti

    5' terminal phosphates with hydrogens and adds hydrogens to both the sense and anti 3' terminal oxygens.

    Figure 1b: Adding base-pairs to the polynucleotide.

    After the sequence has been entered, click on Done. Then click on the rotate button from

    the Tool Bar (Figure 1c). Drag the mouse (while holding down the left mouse button) in the

    screen area to rotate the DNA into a satisfactory view.

    Figure 1c: Using the rotate button to orient the DNA.


    Example 2: Building a short polypeptide, bovine oxytocin.

    Bovine oxytocin is a short polypeptide hormone which contains a disulfide bridge. This

    nonapeptide has the sequence Cyx-Tyr-Ile-Gln-Asn-Cyx-Pro-Leu-Gly, where the Cyx

    cysteine residues at positions 1 and 6 are bonded via the S-S linkage. In this example, we

    model bovine oxytocin using the polypeptide model builder and geometry optimization.

    From the Build/Add option of the Menu Bar, select Polypeptide ( Figure 2a ).

    Figure 2a: Invoking the Polypeptide model builder.

    Enter the sequence of the polypeptide by clicking on the residue buttons in the following order:

    1. Cyx
  • Tyr
  • Ile
  • Gln
  • Asn
  • Cyx
  • Pro
  • Leu
  • Gly
  • The peptide will be build in an Extended conformation with all torsion angles set to 180 degrees (Figure 2b).

    Figure 2b: Polypeptide dialog and construction of small peptide.

    After the sequence has been entered, click on Done and use the rotate tool to position

    the polypeptide as shown in Figure 2c. After the peptide has been properly oriented,

    select the Build Tool (Figure 2c) to create the disulfide bridge. Using the left mouse

    button, click on the sulfur of the Cyx residue at position 6. While holding the mouse

    button down, drag over to the sulfur of the Cyx at position 1 and release the mouse button.

    A S-S bond should have been created as shown in Figure 2c.

    Figure 2c: Creating the disulfide bridge.

    The S-S bond measures over 19 Angstroms long and so clearly this is not an equilibrium

    geometry. To minimize the energy of the structure, select Minimize from the Molecular

    Mechanics option of the Tool Bar. This will run 100 steps of steepest descent energy minimization.

    Figure 2d: Minimizing the energy of the molecule.

    From the Molecular Mechanics option of the Menu Bar, select Minimization Options.

    For the Conjugate Gradient Algorithm (Figure 2e), select Fletcher-Reeves. Set the Maximum

    Iterations to 500 and click on Done. From the Molecular Mechanics option, select Minimize.

    Figure 2e: Minimization Options dialog.

    To allow the system to overcome any potential energy barriers, we will conduct a short

    simulated annealing run. From the Molecular Dynamics option of the Menu Bar, select

    Options. Change the Cool Time to be 5 picoseconds (ps) and click on Done. Now click on

    Start Trajectory under Molecular Dynamics.

    Figure 2f: Molecular Dynamics Options dialog.

    After the simulated annealing run is complete, minimize the energy once again by clicking

    on Minimize under Molecular Mechanics. The resulting structure, shown in Figure 2g, shows

    a more plausible cyclic peptide, with an S-S bond length of 2.05 Angstroms.

    Figure 2g: Minimized structure of bovine oxytocin.


    Example 3: Sketching free-form molecules.

    This example illustrates how the use the Build Tool to sketch molecules in the B window.

    First, from the Build/Add option of the Menu Bar, select Show Periodic Table. A periodic table

    should appear (Figure 3a). The default drawing element is carbon.

    Figure 3a: The Periodic Table dialog.

    Select the Atom Labels and Build Tool buttons on the Tool Bar (Figure 3b).

    Figure 3b: The Build Tool and Atom Labels tools.

    Position the mouse on the screen and while pressing the left mouse button down, drag the

    mouse to the lower right to create a bond as shown in Figure 3c.

    Figure 3c: Creating a bond.

    After releasing the mouse button, hold it down again and drag the mouse up to the upper right

    to create a third atom. Repeat the process and drag to the lower right so you have the same

    molecule as shown in Figure 3d.

    Figure 3d: Using the Build tool.

    Now, change the alkane to an ester by changing the default drawing element to oxygen.

    The default drawing element will be red. Click on the Oxygen atom in the periodic table.

    Now click on atom C2 (Figure 3e) to change it from a carbon to an oxygen.

    Figure 3e: Changing the element type of an atom.

    Now add a ring to this structure. Close the Periodic Table dialog and from the Build/Add

    option of the Menu Bar, select Add Ring and Cyclohexane. After the message

    Click to place Cyclohexane appears, click on atom C0 to add a bond from this atom to

    a cyclohexane ring (Figures 3f,3g).

    Figure 3f: Adding cyclohexane to the sketched molecule.

    Now add hydrogens by selecting Add Hydrogens from the Build/Add pulldown menu option (Figure 3g).

    Figure 3g: Adding hydrogens to the molecule.

    Now select Minimize from the Molecular Mechanics option to optimize the geometry

    of the structure (Figure 3h) using the steepest descent algorithm.

    Figure 3h: Minimizing the structure of the molecule.

    After the geometry optimization, the molecule should look similar to the one shown in

    Figure 3i.

    Figure 3i: Minimized structure of the molecule.

    To change the rendering from wireframe to a spacefilling CPK model, from the Display

    option of the Menu Bar, select Render and Spacefill (Figure 3j).

    Figure 3j: Changing the rendering to a spacefilling CPK model.

    The model should look similar to the one shown in Figure 3k.

    Figure 3k: Spacefilling CPK model.

    Now, save the molecule as a PDB file. From the File option, click on Save (Figure 3l).

    Figure 3l: Saving the molecule as a PDB file.

    If you are using a Netscape browser and you have imported the B Object Signing

    Certificate, you will get a warning message similar to the one shown in Figure 3m. If you

    are using a different browser, such as Microsoft Internet Explorer, you will need to import

    the Authenticode Object Signing Certificate. If you are using the stand-alone (application,

    non-applet) version, you will not receive these warning messages and will be able to open

    and save files without any trouble.

    Figure 3m: Netscape Java Security warning message.

    Click on Grant to allow the applet to write the PDB file to your hard drive. A dialog will

    appear, as in Figure 3n, which enables you to specify the name and location of the file.

    Figure 3n: File dialog.