Identify domains (tertiary structure)¶

• load the open conformation of AdK (4AKE) as in the Analyzing protein structure and topology example

• compare to the closed conformation

  • load adk_closed.pdb (either download from https://becksteinlab.physics.asu.edu/pages/courses/2016/PHY542/practicals/vmd/files/ or from the PDB 1AKE ... or use VMD’s PDB autoloader and type “1AKE” in the File ‣ New Molecule dialog)

  • select protein (or protein and chain A if you see two AdK molecules)

  • represent as new cartoon, color differently from the open structure

  • superimpose: use Extensions ‣ Analysis ‣ RMSD tool: and select protein and backbone to superimpose structures in such a way to minimize the RMSD between all backbone atoms,

    \[\mathrm{RMSD} = \sqrt{\frac{1}{N} \sum_{i=1}^N (x_{a,i} - x_{b,i})^2}\]

    What is the RMSD after superposition?

  • Investigate how the conformation of the molecule changes between the open and the closed conformation.

    • Which regions (domains) “move”?
    • Identify two moving domains (called “NMP” and “LID”) and one constant region (“CORE”):
      • give residue ranges (tip: use Extensions ‣ Analysis ‣ Sequence Viewer)
      • color regions differently and also mark them in your topology diagram

  • align on CORE domain only

    • What is the final RMSD when aligned on CORE only, i.e. how similar are the CORE regions in the two structures?
    • What is the overall protein RMSD, assuming that the two structures are superimposed on CORE?