.. -*- coding: utf-8 -*-

.. |->| replace:: →


.. _Tertiary_structure:

=======================================
 Identify domains (tertiary structure)
=======================================

- load the open conformation of AdK (4AKE_) as in the
  :ref:`Secondary_structure` 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 :menuselection:`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 :menuselection:`Extensions --> Analysis -->
    RMSD tool:` and select *protein* and *backbone* to superimpose
    structures in such a way to minimize the RMSD between all
    backbone atoms,

    .. math::

       \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 :menuselection:`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?

.. Solution: domains
.. 
..   * CORE 1-29, 60-121, 160-214
..   * NMP 30-59
..   * LID 122-159
..  Final RMSD when aligned on CORE: 1.97 A, overall 8.0 A

.. _1AKE: http://www.rcsb.org/pdb/explore/explore.do?pdbId=1AKE
.. _1AKE pdb: http://doi.org/10.2210/pdb1ake/pdb

.. _4AKE: http://www.rcsb.org/pdb/explore/explore.do?pdbId=4AKE
.. _4AKE pdb: http://doi.org/10.2210/pdb4ake/pdb