Analyzing protein structure and topology

We will use VMD (“Visual Molecular Dynamics”) to learn more about a protein. We use the enzyme adenylate kinase (“AdK”) as an example throughout.

For background on using VMD, look at [Hsin2008] and the VMD tutorial.

Topology and secondary structure

In order to deduce the topology of the protein we will need to load the experimental coordinates into VMD (stored in “structure” file in the PDB format) and then use different representations to more clearly see the underlying secondary and tertiary structural elements.

Load the protein structure

Load AdK in its open conformation (PDB 4AKE) and visualize its topology and secondary structure:

  • get adk_open.pdb from https://becksteinlab.physics.asu.edu/pages/courses/2016/PHY542/practicals/vmd/files/ or from the Protein Databank under accession code (PDB ID) 4AKE.

    Remember in which directory you saved it or better, put it into a dedicated folder for this tutorial.

  • load the coordinate file (“structure”): File ‣ New Molecule

    • Load files for: New Molecule
    • Filename (browse for your file)
    • Determine file type: Automatically

  • settings in VMD (use these settings for all further exercises):

    • Display ‣ Orthographic

    • Graphics ‣ Color: Display: Background: White

    • optional: Try if Display ‣ Rendermode ‣ GLSL works for you.

      This should work with most modern graphics cards that are OpenGL capable. Once VMD uses OpenGL, it will render everything much faster and the results will look much smoother than with the standard (not accelerated) setting. However, if you cannot display certain representations (e.g., VDW) then unset this setting again.

Visualize a protein in cartoon representation

We now want to look at the protein structure in more detail by using different representations and color.

  • Graphics ‣ Representations
    • Selected Atoms: protein (if you downloaded 4AKE from the PDB, use protein and chain A)
    • Drawing Method: New Cartoon representation,
    • Coloring Method: Secondary Structure
  • you can add more representations and switch between them by clicking the representations in the list

Interacting with the visualization

  • moving and rotating with the mouse (when in the rotate view mode)
    • left button: rotate X/Y
    • right button (or left + Command key on Mac): rotate Z
  • keys to switch between different view modes (or use the Mouse menu)
    • r: rotate
    • t: translate
    • s: scale
    • =: reset view (not a mode but very useful), also Display ‣ Reset View =