Download the file for cytochrome c (oxidized form)
There are 4 icons under the PDB identifier
Click on the ico that looks like text
This is a preview of the data file
Rasmol is installed on the computers in 360 Scitech or you can install it on your own computer if you have one.
Assignment
You must answer all questions in red and
complete
all tasks with red headers. Hand in the assignment as
the week following on the day you have lab.
2. Find PDB identifier 2C2C
Download the file for cytochrome c (oxidized form)
There are 4 icons under the PDB identifier
Click on the ico that looks like text
This is a preview of the data file
The information should look like this: (click
here)
It is of value to do this to make sure it is the file that you
want to
down load.
3. Now download the entire PDB file for
viewing.
Click on the Icon with an arrow. The file can Either be
saved to
disk or opened directly
*You may also choose to look at the molecule using a PDB viewer
(such
as CHIME) by selecting [PDB viewer] or RasMol by selecting
[Motifs-RasMol].
You will open a saved PDB file manually in RasMol.
6. Open the molecule by clicking
File: Open and selecting
the PDB file saved in your network account.
A wireframe molecule will appear in the viewing window.
You will need to view the molecule and command line for this
exercise.
Expand the viewing window so that it fills the opper ¾ of
the
screen.
Expand the command window so that it fills the remaining ¼
of
the screen.
Sometimes when Rasmol opens the command line is minimized on the lower task bar. If you can't find the command line window look along the bottom of your screen and click on the Rasmol type there.
7. Manipulate the molecule using the mouse:
Translation - Right mouse button
Rotation - Left mouse button
Rotation in a plane - Shift - Right mouse button
Zoom Shift - left mouse button
8. Locate residues (amino acids) and particular atoms by using the mouse to pick or select atoms (i.e., click on an atom and the result is shown in the command window). The command window tells you which atoms are being selected and to what amino acid they belong. If you can't see the amino acid selected zoom in using the mouse. If you don't have the primary sequence in front of you type show sequence in the command line to see the sequence in the command line.
Note: many of the following tasks can be accomplished by typing the correct command into the command line or accessing the task descriptor from the pull down menus. You may do either to accomplish the task. Many commands, however, are only available through the command line. The command line allows greater flexibility and detail control.
9. Change the viewing type by selecting
Display from the
viewing window menu bar.
If only certain residues are changing, then type select all
(or
use pull down menu).
Practice changing display types for the protein this can be
accomplished
using the pull down menu.
10. Display particular amino acids:
Type
select all and choose Display - wireframe
Type
select ala to look at all of the alanines in the protein
(75 atoms should be selected)
Type
color red (all alalines should be red)
To view alaline as ball and stick select Display - Ball
and
Stick.
You can select any amino acid (again, type show sequence if you
need
to know what amino acids are present in the molecule). Practice
looking
for the loctions of various amino acids by selecting them one at a
time
and changing their color and Display style.
Typical colors: Red, orange, yellow, green, blue,
violet,
purple, brown, gold, cyan, black, white, grey, greentint,
greenblue,hotpink,
magenta, pink, pinktint, redorange, skyblue, bluetint,
yellowtint.
Other colors are generated by specifying the RedGreenBlue
triplet
values as in color[255,0,0] for red; color
[0,255,0]
for
green; and color [0,0,255] for blue and all values
in
between.
Change the molecule's color to purple by typing select all
and
then color [255,0,255]. When you are finished, type select
all,
and reset the display to
wireframe
and color cpk.
11. Display particular atoms:
Type select all and then wireframe (this is an
alternative
way Of changing the display)
Cytochrome c contains an iron metal center - Type select iron to
identify
the iron in the protein.
Type
color orange (iron should be orange).
View it as a ball and stick model.
The iron is in a porphyrin ring. Identify the porphyrin ring
by typing
select ligand.
Change its color to red and display it as a ball and stick .
Type
select iron and change its color to
yellow.
Type
select backbone to select the protein backbone.
Change the display to ribbon by typing ribbon.
Change the backbone color to grey.
Select the sidechains by typing select sidechain.
Change the color to greentint.
Change the background color to white by typing
background white.
Practice changing styles and colors and
rotate
and move the molecule to make this molecule resemble the
picture shown
below
Copy and paste your final picture into Word or Wordperfect to be included in your report. If possible print in color; if no indicate what colors were present on the screen in pencil on your printout.
12. You can select individual amino acids by typing
select
# (i.e.,
select 12 will select amino acid number 12; select
1-12 will select residues 1-12).
This is useful for identifying domains (structurally independent
units
in a protein) or to highlight regions of interest in a protein
sequence
(i.e., beta sheets, helices, turns).
Is the metal and ligand part of the domain you selected?
Again adjust colors, etc to make the protein resemble the structure below.
Include the rasmol file name and number for HEW and the other proteins selected.(for example the cytocrome c utilized in the above exercises was:
HEADER ELECTRON TRANSPORT PROTEIN (CYTOCHROME)
03-NOV-83
2C2C 2C2C 3
COMPND CYTOCHROME $C=2= (OXIDIZED)
(information copied from the downloaded pdb
file)
If the protein contains a ligand,
emphasize
it by color and display type. If it is an enzyme and you
know the
amino acids in the active site then highlight them in some
fashion site
(i.e. the active site of HEW lysozyme is described in Voit and
Voit
Biochemsitry 3 ed on pp. 508-515
figures 15.10-15.14)
Write a short (1 paragraph) synopisi for each protein you have selected stating its classification, significance, and function and properly reference it. Use your textbook to get some ideas on types/classes of proteins to display.