Analyzing protein dynamics

Analyze a molecular dynamics simulation trajectory of the closed-to-open transition of AdK [Beckstein2009].

Download the topology file adk.psf and the trajectory file adk_dims.dcd from https://becksteinlab.physics.asu.edu/pages/courses/2016/PHY542/practicals/vmd/files/ .

Visualization

  • load adk.psf with adk_dims.dcd (use load all at once, this is faster in general)
  • color domains and show as new cartoon
    • resid 30 to 59: blue (NMP)
    • resid 122 to 159: yellow (LID)
    • not (resid 30 to 59 122 to 159) (or resid 1 to 29 60 to 121 160 to 214): gray (CORE)
  • play (loop: rock) (use the triangle button on the main VMD window)

RMSD change

Measuring distances

Measure distances interactively:

  • ‘2’ (or Mouse → Label → Bonds)
  • click tip of LID and tip of NMP
  • play the trajectory: label changes dynamically
  • Graphics → Labels: Bonds
    • select
    • Graph (preview)
    • Graph...
  • try different distances between residues (use the CA) and plot together: which change, which don’t?
    • What would be good distances to report on conformational changes, e.g. for FRET?
    • Try also [Beckstein2009]
      • I52-K145
      • A55-V169
      • A127-A194