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Large-Scale
Protein Movements
BACKGROUND: Normal mode analysis (NMA) investigates the slowest motions
in macromolecular systems. NMA calculates vibrational normal modes that have
the lowest frequencies, which describe the largest movements in a protein and
are the ones that are functionally relevant in terms of bioactivity. This
procedure provides several of the most vibrational modes and their animation.
These vibrational modes can be computed for the whole protein as well as
for its active site. If you explore the total conformational changes of a
protein you should compute modes for the whole protein. If you need to know
which movements happen in the active site, you should calculate modes for the
active site.
Note: In order to calculate modes for
the whole protein it is very important that it has no missing amino acid inside
of the residue sequence. If a protein does not meet this requirement, calculate
modes only for the active site.
Selecting
Protein
Choose the Tools->Large-scale protein movements item
from the Main Menu.
Choose the chains that form the protein. When selected, the chains are
zoomed in on and shown in sticks.
Choose whether modes will be computed for the whole protein or for the
active site. In the first case, choose Off (Figure 38) in the Wizard and in the
second case On.
Figure 38 - Active Site Selection
If this option is off, then press the Compute button to start the
mode's calculations.
If you chose the active site, then you should proceed with building a
box for the active site.
Building a Box
The box is necessary to indicate the active site. It is characterized by
three orthogonal directions and their sizes.
In order to construct a box, the following requirements should be met:
·
All active site atoms should be
covered by the box and by other words, and all important chemical groups of the
active site should lie inside of it.
·
The sequences of residues which are
inside of the box must not have missing residues.
Select the center of the box and select any atom that is approximately
in the middle of the active site. After clicking on the atom, a cube with dimensions
20x20x20 will appear (Figure 39).
Figure 39 - Box
Now you have to adjust the box position and size.
·
The box has axes OX, OY and OZ,
which are displayed on the screen.
·
If you decide to change a size of
one of the axes, you should use the Wizard, which will automatically appear
(Figure 40).
Figure 40 - Wizard
·
Just click on the Size button
and choose the size. The box will automatically be changed.
Note: The default size is 20A. The
following options are available: 5A, 10A, 15A, 20A and 25A.
Results of the Procedure
After completing the calculations, the program provides you with a few
of the most important vibrational modes, their animation (Figure 41) and
convenient tools for working with modes.
Figure 41 - Several
Frames of a Protein's Movement
Animation:
·
Download a mode as a molecule.
·
Use the Movie controls (Figure 42)
to manage the animation.
Figure 42 - Movie Controls
Modeling:
·
Select ON in the Protein
Flexibility Option when calculating the IC50 (Figure 43), docking a
molecule, screening the library etc.
Figure 43 - Wizard
Note: If the Protein Flexibility
Option is OFF, then the protein is treated as a rigid structure. If it is
ON, then full protein flexibility will be taken into account in modeling.