- You have previously seen the primary amino acid
sequence and should have identified
the cysteine (sulphur containing) amino acids of
carboxypeptidase-A. Now, let's identify the
position of the sulphur containing amino acids relative to each
other. To do this type in the
following commands. Pressing
the 'enter' or 'return' key executes the
command.
Commands :
select sulphur (enter)
This command selects all sulphur atoms in the molecule
colour yellow (enter)
All selected atoms are now yellow.
cpk (enter)
CPK is the space that an atom occupies, so all sulphur
residues are now 'spacefilled' yellow. The 'spacefill' command does the same thing.
Point the cursor at each of the sulphur atoms and
click with the mouse button (you may need to enlarge the image using the mouse plus the 'Shift' key).
Look in the message box
and record the number and identity of the amino acids.
Test your knowledge!
Carboxypeptidase should now look similar to the image above! Click on the image to see a larger version.
Step Three - Hydrophobic vs Polar Residues
Now compare the distribution of the hydrophobic and
polar amino acid residues in carboxypeptidase A.
Rotate and resize the molecule at any stage to observe the
effects of your commands.
Commands :
cpk off (enter)
reset (enter)
select all (enter)
This command selects all atoms in the molecule
colour white (enter)
All selected atoms are now white.
select hydrophobic (enter)
All hydrophobic side chains are selected.
cpk (enter)
select polar (enter)
All polar side chains are selected.
colour red (enter)
cpk (enter)
Observe the distribution of polar and nonpolar amino acid
residues
Next we can use the slab command to 'slice'
through the molecule at various
positions from front to back. We first reset the zoom position
to normal. With the slab commands
we will work our way from the front to the back of the molecule.
What do you expect to observe
as you move your way through the molecule?
Commands :
reset (enter)
resets the zoom to normal position
slab 20 (enter)
shows a slice one fifth (20%) of the way through the
molecule
slab 30 (enter)
slab 40 (enter)
slab 50 (enter)
slab 60 (enter)
slab 70 (enter)
slab 80 (enter)
slab 90 (enter)
slab 100 (enter)
Test your knowldege!
Step Three - Chemical Properties
RasMol (and Chime) defines 'Sets' of amino (and nucleic)
acids based on their structural and/or
chemical properties. Predefined Sets are available. For a
complete listing of Predefined Sets, refer to the
RasMol Manual.
Let's have a look at a graphic view of some of these
sets.
Commands :
select all (enter)
cpk off (enter)
colour yellow (enter)
select acidic (enter)
Acidic amino acids selected
colour red (enter)
Acidic amino acids are now red. Zoom in and click on a few atoms to identify the which residues are acidic!
select basic (enter)
colour blue (enter)
select hydrophobic (enter)
colour magenta (enter)
You can also define your own sets :
define newset ser,thr,gln,asn (enter)
select newset (enter)
colour green (enter)
Finally, let's look at the CPK model for the sets we've
chosen :
select acidic, basic, hydrophobic, newset (enter)
cpk (enter)
What is in common between the acidic, basic and
newset of amino acids?
Single click on the icon above if you wish to check your
work.
Test your knowldege!
Step Four - Structural Properties
Rasmol defines sets for the major structural characteristics
of proteins. You can readily isolate the secondary structures
in the enzyme using the select command.
In the following exercise, you should OBSERVE the alpha-helical,
beta-sheet and beta-turn content of carboxypeptidase A
Let's first look at the alpha-helices present in
carboxypeptidase A.
Commands:
select all (enter)
cpk off (enter)
colour yellow (enter)
select helix (enter)
colour magenta (enter)
ribbon (enter)
A ribbon is woven through the backbone of the
helices.
How many alpha helices can you see?
Let's now have a look at the beta-pleated sheets:
select all (enter)
ribbon off (enter)
colour yellow (enter)
select sheet (enter)
colour redorange (enter)
ribbon (enter)
Now find the turns in the molecular structure :
select all (enter)
ribbon off (enter)
colour yellow (enter)
select turns (enter)
colour cyan (enter)
ribbon (enter)
Now put all the structures together :
select all (enter)
colour yellow (enter)
select turns (enter)
colour cyan (enter)
select helix (enter)
colour magenta (enter)
select sheet (enter)
colour redorange (enter)
select all (enter)
ribbon (enter)
The secondary structure may be clearer if you turn the wireframe bits off
wireframe off (enter)
Test your knowldege!
Now let's isolate an alpha helix and examine it more
closely.
Commands :
select all (enter)
wireframe on (enter)
ribbon off (enter)
colour yellow (enter)
restrict 13-32 (enter)
centre 22 (enter)
Viewing is now restricted to amino acids 13 to 32 comprising
one of the alpha helices. Molecule is centred (for rotation) on one of the residues within the alpha helix.
hbonds (enter)
hydrogen bonds between atoms appear as dotted lines.
select oxygen (enter)
colour red (enter)
select nitrogen (enter)
colour blue (enter)
Resize and reposition the helix on your screen if
necessary.
select 13-32 (enter)
ribbon (enter)
Test your knowldege!
Finally, let's isolate the pleated sheet structure and
examine it more closely.
Commands :
select all (enter)
reset (enter)
ribbon off (enter)
hbonds off (enter)
wireframe (enter)
restrict sheet (enter)
hbonds (enter)
ribbon (enter)
Resize and reposition the sheet on your screen as necessary.
Test your knowldege!
End of Tutorial Exercise
