This tutorial shows how to visualize protein surfaces and their electrostatic potentials using the SPDBV (Swiss PDB Viewer) program.
SPDBV
is multi-platform protein structure visualization program.
As well as having structure modeling capabilities,
the program permits computation and visualization of the electrostatic potentials
of proteins, which is the focus of this tutorial.
The
SPDBV program was written by Nicolas Guex, Alexandre Diemand, Torsten Schwede
Manuel C. Peitsch from the Glaxo Wellcome Experimental Research group.
This is one of the 5 groups that have founded the Swiss Institute of Bioinformatics.
The program is available from http://www.expasy.ch.
The tutorial example: The barnase:barstar complex
In this tutorial, you will explore the surface and electrostatic properties
of two proteins (barnase and barstar) that form a binary complex whose
structure has been determined by x-ray crystallography.
Barnase is an
extracellular ribonuclease. Barstar is an intracellular inhibitor of barnase.
To stop barnase working inside the cell, barstar binds to barnase very
tightly (high affinity) and very quickly (high association rate).
Using SPDBV, you will compute the electrostatic Coulomb potentials of each
protein in vacuo. You will then be able to see that the electrostatic
potentials of the two proteins are complementary. The attractive electrostatic
interactions between the two proteins are important for the speed of
their association, and for the sensitivity of association rates to ionic
strength and to mutation of charged amino acid residues.
Instructions:
To explore the electrostatic and surface properties of barnase and barstar using the SPDBV program:
0. Make a new local directory and go there (e.g. type "mkdir tutorial2 ; cd tutorial2").
Download 2 files 1.pdb and 2.pdb to this directory
(Shift+left_mouse on the links, and save under the same names.)
Or copy them by command "cp /home/client1/data/?.pdb ./".
1.pdb contains the coordinates of barnase and 2.pdb contains the
coordinates of barstar.
1. To start SPDBV, type
> /home/client1/SPDBV/bin/spdbv.sh
2. Now in SPDBV program read in the coordinates of barnase,
Go to menu File, and select submenu Open_PDB_File...
Navigate in the File_Selection window to the directory where 1.pdb is saved,
select the filename and click on the Open button.
3. To manipulate the molecule,
Rotate it by moving the mouse and simultaneously
holding down the left mouse button.
Translate it with the middle mouse button held down.
Rescale/zoom with the right mouse button held down.
4. To display a ribbon representation of the molecule,
- Go to menu Wind -> Control Panel to open a window named Control_Panel.
- Go to the Swiss-PdbViewer window and choose menu Prefs->Ribbons...
In the window that appears, select options "Render
as Solid Ribbon" and "Also in Real Time", click on the OK button.
- Go to the Swiss-PdbViewer window and choose menu Select->All
- Go to the Control Panel window and click on the table header "ribn"
on the Control Panel. You will see the ribbon representation of the molecule overlaid on
the atomic structure.
-You can deselect atoms-bonds from the display
by clicking in the column "show" of the Control_Panel.
To deselect all atoms, press Shift+left_mouse in the "show"
column of any residue.
5. To display the molecular surface colored by electrostatic potential,
- Go to the Swiss-PdbViewer window and choose menu Prefs->Surfaces...
Select Filled_Triangles for General_Appearance,
3 for Quality[0..6], Electrostatic_Potential for Default_Surface_Color,
then click on the OK button.
- Go to the Swiss-PdbViewer window and choose menu Prefs->Electrostatic_Potential...
Select use_partial_Charges for parameters, Coulomb
for Computation_Method, then click on the OK button.
- Go to the Swiss-PdbViewer window and choose menu Tools->Compute_Molecular_Surface. The computation will run interactively and 2 windows will appear
to show you progress of the computation. When it is completed, the surface
of the molecule, colored according to electrostatic potential, will appear.
6. To locate the binding site of barstar,
- Rotate barnase to try to identify the concave positive (blue) part
of the molecular surface. This is the binding site for the barstar inhibitor.
To see this, read in the coordinates of barstar:
- Go to menu File -> Open_PDB_File...
Navigate in the File_Selection window to the
directory where 2.pdb is saved, select the filename and click on the Open button.
- Go to the Swiss-PdbViewer window menu Wind->Layer_Infos
Unselect-select the display of barstar (layer 2) by
clicking on the table cell (2,vis). By rotating the molecules, you
can get an idea of how the barnase electrostatic potential and the position
of barstar are related.
7. To display the surface of barstar coloured with its own electrostatic
potential:
-Select Layer 2 in the window Layer_Infos by
clicking on the table cell (2,Layer), 2 should turn red (explain why).
- Go to the Swiss-PdbViewer window menu Tools->Compute_Molecular_Surface.
When the molecular surface of barstar appears, take a look at it. Do
you think the net charge of barstar is positive or negative?
8. Similarly to pt. 6 above, you can switch on/off the surfaces of barnase/barstar via the table column "vis" in the window Layer_Infos and rotate/translate/scale to observe the surface and electrostatic complementarity of the two proteins.
More things to try (optional) are:
* Alter parameters via Prefs->Surfaces... menu,
E.g. Transparency of surface, General_Appearance (Real_Time)
* Undisplay the surface of molecule 2: unselect Display->Show_Dots_Surface
Try to figure out why the surface of the molecule 1 remains
and how to undisplay it.
Razif Gabdoulline, 2001-2, adaptation from the GRASP tutorial developed
for EMBO predoc courses and the EMBO course in 2000 on Molecular Simulation
by R. Wade and L. Ehrlich. 26-06-2002
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