Identify domains (tertiary structure)

• compare to closed conformation

  • load adk_closed.pdb

  • select protein

  • new cartoon, color differently from the open structure

  • superimpose: Extensions -> Analysis -> RMSD tool: protein

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

    What is the RMSD after superposition?

  • Investigate how the conformation of the molecule changes.

    • 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?