There are several programs that allow the inspection and manipulation of 3-D structural protein data. In this course we use the swiss protein data bank viewer, and to a lesser extend chime, an add-on to Netscape, that allows viewing 3-D structures.

SPDBV is an excellet choice, because it also provides an interface to the Swiss Protein databank modeling software.

These are several excellent on-line tutorials available to learn the use spdbv:

The basic tutorial at

http://www.usm.maine.edu/~rhodes/SPVTut/index.html

And a course on structure, spdbv, and modeling

http://www.expasy.ch/swissmod/course/course-index.htm

The exercise in this section is taken with slight modifications from Gale Rhode's the basic tutorial, many of the exercises in the following sections parallel exercises in the basic tutorial.

You can retrieve pdb files from the NCBI, or from the protein structure data bank at Rutgers University. (To do so search for the file, click the explore link and right click on the link that indicated download uncompressed pdb file.) (The ones used in the course are also available here).

Do the following:

Start SPDBV

load 1HEW.pdb (hit return)

click the right mouse buttom

click on the three cursor control buttoms and rotate/move/enlarge lysozyme picture

click on the page icon and go through the pdb file

open the control window (DISPLAY-menu).

open the align window (DISPLAY-menu)

select all

display Ramachandran plot

in the control window select different residues

select all

Explore different coloring (CPK, secondary structure, accessibilty) and display options (show CA trace only, show oxygen, …)

REMARK: If you do serious work save your work periodically, sometimes it is impossible to recover from inadvertent mouse clicks)

Select (left mouse bottom at the buttom of the control panel) the NAG inhibitor.

Color CPK

Invert selection

Color secondary structure

Invert selection

Tools calculate H-Bonds

right click side column to turn off sidechain display

select Neighbors of selected aa

hit return

click right mouse bottom on side header in control panel (acts only on selected residues)

select group properties Non-polar aa

click on Header COL in display panel select blue color to color hydrophobic residues blue

Are there “blue” residues interacting with the N-Acetyl glucosamines? How come?

Play around, if in doubt use the ? buttom. 

The worst that can happen is that you'll have to restart your computer.

Open the alignment window and display the complete lysozyme molecule. Observe the color change in the structure that happens when you move the mouse over the sequence in the alignment window.

The resulting display after some beautifications might look like this:

yellow: the NAG inhibitor;
blue: residues in the binding pocket that are non-polar, depicted as space filling balls;
red: other amino acids in the binding pocket;
gray: the rest of the Lysozyme molecule, but only the backbone.

Other things to try:
  3D rendition (in the display menu),
  slab view (shift and mouse move the slab),
  explore the make up of the pdp file (text icon below the cursor control),
  have a look at the opening control window (upper left icon below the cursor control).

If you right click on a residue in either the alignment window or the control window, the display centers on this residue.

Control and mouse click adds residues to the list of selected residues (works in either window)

Can you obtain a figure similar to the one below?
Go to the control panel click on the little black triangle to the right of the col column and select color ribbon, then secondary structure in the color menu. Display ribbon in the control panel, remove the other displays .....