Introduction to Bioinformatics, Practical #4:

Exploration of molecular 3D-structures with

RasMol
April 14, 2008
Assignment deadline is the 21.04.08. You can reach 100 points plus 10 bonus
points. Please send your solutions to hettling@few.vu.nl . Please include Assignment 4 and your name in the subject of the email.

1
a) Go to the Protein Data Bank (PDB) website at http://www.rcsb.org/
pdb/home/home.do. You will work with a Zinc-finger DNA-binding complex
throughout this assignment. Enter the PDB identifier 1ZAA into the search
field at the top of the page and press on the site search button. Download
the corresponding .pdb-file 1ZAA.pdb to your computer by clicking on the
download icon next to the identifier. (0P)
b) Start the RasMol program on your computer. On university computers, it
is accessible via the start menu (Windows), on Linux, just type rasmol in
a command shell. If you are working on another computer than a university
workstation, you can download RasMol at http://www.bernstein-plus-sons.
com/software/RasMol_2.7.3. Windows users can click on the link Latest
Windows Installer, Linux users please download the 32-bit binary of RasMol
version 2.7.3.(0P)
c) Open the RasMol manual page at http://www.openrasmol.org/doc/rasmol.
html. (0P)
d) Load the file 1ZAA.pdb that you downloaded in 1a into RasMol (Menu
File Open). You can rotate the molecule around by clicking on it
and dragging with the mouse. You can also zoom in and out by pressing
shift, then click on the molecule and drag the mouse up or down. RasMol
provides both, a user menu and a command-line interface for interaction. As
just a subset of all possible options is accessible via the menu, you will have
to use the command line for some tasks (see documentation or type help
commands in the RasMol command line). (0P)
e) Which experimental method was used to derive this structure? What is the
resolution of the structure? (5P)

f) Describe in a few sentences the function of Zinc-finger proteins in the cell.

(5P)

2
In Menu Display, you can chose several representations to display the
structure. Try all of them.
a) What is the best representation to distinguish between different secondary
structure patterns? (5P)
b) How many alpha helices and how many beta strands are there in the protein?
(10P)
c) Are the beta-strands aligned parallel or antiparallel? Hint: Beta strands are
displayed as arrows in a certain representation. (10P)

3
Select Menu Display Sticks and Menu Colours Chain.
a) Looking closely, you can point out two distinct types of molecules. Which
molecules could that be? (10P)
b) Compare the Sticks representation with the Backbone representation. What
is the difference? (10P)

4
The next task is to display restricted parts of the structure of 1ZAA. You will
have to use the RasMol command-line interface for that. With the commands
restrict and select, certain regions of the structure can be selected. These
regions can be either user-defined residues or atoms, but there are also predefined
sets such as nucleic, hetero, protein or all. Try typing help restrict, help
select and help sets into the command line for more information.
a) Display only the protein part of the structure in the Sticks representation.
Save an image of the structure to a postscript file in Menu Export
PostScript. (By the way, sometimes the images look nicer with a different
background color. Try, for example background white. But the choice is
up to you...) (10P)
Next, go to the space-fill representation of the whole structure by typing select
all and then spacefill on into the command-line. Now, display just the
heterogeneous atoms with restrict hetero By clicking on an atom, its type
is displayed in the command line.
b) How many non-oxygen atoms do you find and what type of atoms are they?
(5P)

c) How many Zn-Atoms does a Zinc-finger domain contain? (Look into a biochemistry book or search in the web!) (5P)
d) How many Zinc-finger domains are there thus in the structure 1ZAA? (5P)
e) (Bonus) Each oxygen atom of the heterogeneous atoms belongs to a HOH
(Water) heterogroup. Why dont you see any hydrogen atoms? (5P*)

5
Now, look into the file 1ZAA.pdb, from which RasMol creates the 3D-view of
the structure. You can open the file with any text editor, such as Notepad on
Windows or Emacs on Linux. If you scroll down in the file, you see an ATOM
section where all atoms of the structure are listed together with their coordinates
in space. Heterogeneous atoms are labeled with HETATM.
a) How many atoms which do not belong to the fraction of heterogeneous atoms
are in the structure? (Watch out, a TER record in the file does not represent
an atom, it stands for the end of a domain!) (10P)
b) How many heterogeneous atoms are there in the structure? (10P)
c) (Bonus) Turn one of the Zinc-finger domains into a Gold-finger domain and
give a short description how you did it. Load the new structure into RasMol
and restrict the displayed atoms to all heterogeneous atoms in the Spacefill
representation. Export a postscript image. (5P*)