1. HBC 1019 Biochemistry 1 Trimester 1, 2012/2013
Faculty of Information Science & Technology
LAB REPORT
HBC 1019 - Biochemistry I
Practical 9
Protein Structure and Function
Name : Osama Barayan
ID : 1091105869
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2. HBC 1019 Biochemistry 1 Trimester 1, 2012/2013
Practical 9: Protein Structure and Function
Introduction
In this practical you will learn about protein structure prediction tool. You will used PDB
website to get the information about the protein structure, and used Rasmol to expore the 3D
structure of the protein.
1. Protein 3D structure visualization
There are number of useful free visualization tools available on the Internet. For this
exercise you will use a tool called Rasmol.
Install Rasmol on your computer according to the instructions on the Rasmol site:
(http://www.bernstein-plus-sons.com/software/rasmol/INSTALL.html).
a. Find other molecular visualization tools that are available from the internet.
Give two examples of the visualization tools.
VMD and MOLMOL
Obtaining Structural Information
Many programs have been written to predict secondary structures based only on the primary
structure (amino acid sequence) of a protein. Here is a list of such programs that are available
online:
 PredictProtein (http://www.predictprotein.org). You can request this site to predict
secondary structure online
 JPred (http://www.compbio.dundee.ac.uk/~www-jpred/). If you use the JPred server,
be certain to check the box under #4 to avoid comparison to known PDB structure
files.
b. For this exercise, you will use the sequence of rabbit muscle triose phosphate
isomerase that is given here and submit to two servers that provided above. Compare
the results you receive from different servers.
Can you identify segment where the predictions are not consistent between
servers?
The result are consistent between the servers.
>1R2R: A TRIOSEPHOSPHATE ISOMERASE from rabbit muscle
APSRKFFVGGNWKMNGRKKNLGELITTLNAAKVPADTEVVCAPPTA
YIDFARQKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLG
HSERRHVFGESDELIGQKVAHALSEGLGVIACIGEKLDEREAGITEKVV
FEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRG
WLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLK
PEFVDIINAKQ
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3. HBC 1019 Biochemistry 1 Trimester 1, 2012/2013
c. The structure of rabbit muscle triose phosphate isomerase has been determined by X-
ray crystallography.
Go to the Protein Data Bank web server (http://www.rcsb.org/pdb) and search for
1R2R (the PDB ID for this protein). Once you reach the Structure Explorer page for
1R2R, click on the link for Sequence Details. Scroll down the page to the section
entitled “Sequence and Secondary Structure.” The results shown here for the
secondary structure are based on an analysis of the actual (not predicted) three-
dimensional structure, using the principles developed by Kabsh and Sander [see
http://www.rcsb.org/pdb/help-results.html#sequence_details and Biopolymers 22,
2577–2637 (1983)].
The secondary structure assignments are H = helix; B = residue in isolated beta
bridge; E = extended beta strand; G = 310 helix; I = pi helix; T = hydrogen bonded
turn; S = bend.
Compare your predicted secondary structure results from Part (b) with the
results presented on the PDB site.
Result in part b said helix is 41.9% but in PDB site said 44%.
2. Using Rasmol
Rasmol enable you to explore protein’s 3-D structure.
a. Go back to PDB site for 1R2R and search for the icon download PDB file. Save the
PDB file. Open the Rasmol program, and use the drop-down menu File. .Open to
open 1R2R.pdb. You will initially see a wireframe model that simply displays all the
bonds in the structure as lines. Perform the following steps to get a more informative
view:
Select Display. .Cartoons from the drop-down menu.
Select Colours. .Structure
Now you should be able to see the alpha helix and beta sheet structures in rabbit
muscle triose phosphate isomerase. How many chains are shown in the structure?
What is the dominant structural feature of this protein? Take time to experiment
with the other drop-down menu options on Rasmol.
Chain =4. Dominant structural =alpha helix.
b. All the bonds in the PDB structure file are shown as thin wires, colored according to
Corey-Pauling-Kultun (CPK) coloring rules (oxygen is red, nitrogen is blue, hydrogen
is white, and carbon is gray).
There is seven drop-down menus in Rasmol: File, Edit, Display, Colors, Options,
Export, and Help. Spend a few minutes trying each command in each of the menus.
Perform the following operations:
i. Display. .Backbone. This shows the protein backbone; the bonds actually
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4. HBC 1019 Biochemistry 1 Trimester 1, 2012/2013
connect alpha carbons.
iii. Display. .Cartoon. This shows an image of the protein that clearly displays
helices and sheets. Leave your image in cartoon format and move to the Colours
menu.
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5. HBC 1019 Biochemistry 1 Trimester 1, 2012/2013
iv. Colours. .Structure. This shows alpha helices in magenta, beta sheets in yellow,
and turns in pale blue.
v. Options. .Labels. This command labels all selected atoms.
vi. Export. .GIF. This function enables you to export a still image of the structural
view you just created.
vii. HELP. .User Manual. This is really a critical tool for using Rasmol. In order for
this to work, the help file (Rasmol.hlp in Windows) must be stored in the same
directory as the Rasmol program.
c. Each line in a PDB file is called a “record,” and the first six characters on that line tell
what kind of “record” it is. In your browser, search for SEQRES. As explained in the
PDB Format Description, SEQRES records contain the amino acid or nucleic acid
sequence of residues in each chain of the macromolecule. Hence you can see the
sequence of your protein there. For example, the first few lines of the SEQRES
section are given in Table I (below). Each line contains 13 amino acid residues listed
by their three-letter abbreviations. So residue #27 in chain A is PHE (phenylalanine).
The 12th
character (counting spaces) in each record is a chain identifier. If a protein
contains more than one polypeptide chain, the chains are identified with a letter.
Table I
SEQRES 1
A
248 MET ALA ARG LYS TYR PHE VAL ALA ALA ASN TRP LYS CYS
SEQRES 2
A
248 ASN GLY THR LEU GLU SER ILE LYS SER LEU THR ASN SER
SEQRES 3 248 PHE ASN ASN LEU ASP PHE ASP PRO SER LYS LEU ASP VAL
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6. HBC 1019 Biochemistry 1 Trimester 1, 2012/2013
A
SEQRES 4
A
248 VAL VAL PHE PRO VAL SER VAL HIS TYR ASP HIS THR ARG
SEQRES 5
A
248 LYS LEU LEU GLN SER LYS PHE SER THR GLY ILE GLN ASN
Anything in a PDB file that is not either protein or nucleic acid is considered a
heterogen atom and is referred to with the prefix “het.” So HETNAM is the label for a
record that contains the name of a nonprotein, non-nucleic acid group. Search the
HTML version of the 1R2R file for “HETNAM.”
What are the heterogen groups in this structure?
DIMETHYL SULFOXIDE, MAGNESIUM ION, and 2-AMINO-2-
HYDROXYMETHYL-PROPANE-1,3-DIOL
d. In addition to drop-down menus, Rasmol also has a “command line” window that
enables you to select specific atoms or parts of a structure (amino acid residues, for
example) and change the way they appear. Bring up the command line window and
note the effects of entering the following commands:
i. select hetero and not water (selects nonprotein parts of the structure excluding
water)
ii. spacefill (a van der Waals radius representation)
iii. color cpk (standard chemistry color scheme)
What heteroatoms do you see in this structure?
DMS 235, MG 256, and TRS258
Are any substrates or inhibitors represented in this structure?
No substrate or inhibitor represented in this structure.
Now try more commands:
iv. select protein
v. cartoon off
vi. select sheet
vii. wireframe 30
viii. spacefill 100 (these combined commands yield a ball-and-stick structure)
Can you see the sheet structure now? If not, type the command “cartoon.”
What do you see?
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7. HBC 1019 Biochemistry 1 Trimester 1, 2012/2013
3. Now you have been familiarizing with Rasmol, you need to do the same procedure using
PDB ID: 1o5x to explore its structure, focusing on identifying secondary structures and
looking at the active sites.
a. Download the PDB structure file from PDB site.
What is the title of this record?
1O5X
b. Repeat the steps in 2d. Identify heterogens group for this protein. List down all of the
heterogens or ligands.
2-PHOSPHOGLYCERIC ACID, 3-HYDROXYPYRUVIC ACID and PHOSPHITE
ION
c. Display the active site residues, there are three residues that interact with the 2-
phosphoglycerate: glutamate 165, lysine 12, and histidine 95. Select these residues by
entering the command “select lys12, his95, glu165” in the Rasmol command line
window. Then use the drop-down menu in the structure window to show the residues
in a ball-and-stick format (Display. .Ball & Stick). Finally, enter the command “color
CPK” so that you can distinguish the atoms of the structure.
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8. HBC 1019 Biochemistry 1 Trimester 1, 2012/2013
4. What does CATH and SCOP stands for? What are their functions?
CATH stand for Class, Architecture, Topology, Homologous superfamily. SCOP stand
for Structural Classification Of Protein. Both is used to classified protein.
CONCLUSION
The protein structure can be study by using the PDB and Rasmol. By studying the structure
person can get understand how that protein functions.
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