Analyzing protein dynamics

Analyze a trajectory of the closed-to-open transition of AdK [Beckstein2009]:

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
  • resid 122 to 159: yellow
  • not (resid 30 to 59 122 to 159) (or resid 1 to 29 60 to 121 160 to 214): gray
• play (loop: rock)

RMSD change

• RMSD change over the trajectory: Extensions/Analysis/RMSD Trajectory Tool
• Is the result consistent with the result of your RMSD analysis of the static structures?

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?