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Computer Exercise 2: Molecular Models of
Proteins
Discussion Section 1:9/14
Discussion Section 2: 9/16
Objectives:
1. Become familiar with the basics of protein
structure.
- See relationship of primary, secondary, tertiary, and
quaternary structure of proteins.
- Recognize structural motifs and their relationship to
overall structure and to function.
- Recognize a domain and its relationship to overall
structure and function.
2. Become familiar with on-line resources for protein
structure and learn to use a molecular viewer.
- Know how to find a particular protein of
interest.
- Know how to gather information on a particular
protein.
- Know how to use a molecular viewer to gain
information.
Introduction:
This exercise can be done on either Mac or PC. It can
work with Netscape and Explorer, if appropriately set up,
although the 3D-viewer works best in Netscape. In the
computer labs, use only Netscape because the 3D-viewer is
installed for Netscape, not Explorer. If you want to try
this on your computer, you'll need to download plug-ins as
directed, and a 3D-viewer, such as Chime or RasMol. These
are available directly through the Web. If you have AOL or
MSN, check first with them. Their proprietary software and
built-in protections have been known to interfere with these
on-line applications. When all else fails, use a school
computer. Ask a computer tech if you're having trouble using
the application software or come to a drop-in computer
tutorial [Fridays 9-11].
Grand Central Station for molecular databases and
modeling is at the National Center of Biotechnology
Information [NCBI]. Their URL:
http://www.ncbi.nlm.nih.gov
From here you can access databases containing information
on protein structure, size, weight, and amino acid sequence.
You can compare proteins from the same and different
species. For those proteins with sufficient information in
the database, you can even get 3D pictures! Which is what
this exercise is all about.
The following directions are for finding a three
dimensional protein on the Web. Remember to use a log as you
go. You can record accession numbers and other link sites.
The log will be useful to return to earlier sites as well as
help in preparing your summary answers.
There are summary questions at the end of this
section. Read them through before you start browsing. You
can answer these as you go, or answer them after browsing
the following sites. Points = 10. Due in 2 weeks
[9/24 & 9/26].
The last thing to do is to Interactive site on
WebCT and make a contribution in the fora.
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Exercise:
As a warm-up activity to molecular modeling, open
Netscape and go to the Kuby text site, click on "molecular
visualizations", and select a chapter. Chapter 4 is a good
choice, since we'll be there shortly. As you go through the
guided explanation, you'll see different types of displays
of the proteins. This will give you an idea of what you can
do during this exercise, and after, with proteins of your
choice.
http://www.whfreeman.com/kuby
You can also try an on-line tutorial on viewing protein
structures:
http://www.rickhershberger.com/darwin2000/
A. Finding and displaying a protein.
1. Go to NCBI:
http://www.ncbi.nlm.nih.gov/Structure/
2. Type the protein you wish to find in the search
bar. Try one of the following if you are looking for some
place to start:
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# Amino acids
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lysozyme- a lytic enzyme found in tears
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129
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ferredoxin- involved in electron
transport
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97
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IP3- signal transduction protein, opens
Ca++ channels
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106
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ARF- involved in assembling coated
vesicles
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175
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- Try to start with smaller proteins, such as those
listed here. When you are comfortable in navigating, try
more complex proteins, such as "Fab" "TCR", "C1q", or
"CD4". [These are immuno-related proteins of
importance, which you'll be hearing about soon.]
3. A structure query page will come up with all
documents in the NCBI database that have protein structures
related to your inquiry. Click on "retrieve documents".
4. A page of summaries will appear giving a short
description of the proteins found. Browse the list, then
select one by checking the box. Then click on "view
structure summary".
5. A structure summary page will come up listing
the compound, taxonomy, etc. Scroll down until you see
Options, Viewer, and Complexity at the
bottom of the page.
6. Under "View" accent the "RasMol" dart. Then
click on the "View/Save Structure".
7. Once the protein model comes up, click on the
MDL prompt in the bottom right corner of the
screen.
a. Drag down to "color" and highlight
"groups". This allows you to easily view a polypeptide
from its amino end to its carboxyl terminus through the
change of rainbow hues.
b. Drag down to "display" and click on
"ribbon". How many different ribbons does your protein
have? What does each ribbon represent? Try some of the
other display types.
c. Look for different structural motifs, such
as a-helix, b-sheet,
and hairpin turn. Which ones, and how many of each, did
you find on your selected protein?
d. Place the arrow on the protein, click and
hold down the mouse. As you move the mouse, you can move
the protein. As you move the protein around, do you see
anything that you couldn't see before? Try also stereo
display and rotation.
e. Try marking individual amino acids. For
example, select cysteine to locate disulfide bond sites.
Or try to mark amino acids which you would predict as
being found on hairpin loops. [See "Shorthand
symbols for amino acids" for abbreviations. See a
biochem or molecular biology reference for amino acid
structures. Or go to "www.whfreeman.com/lodish"
for an on-line reference (scroll down to "macromolecular
tutorials).]
8. Pull up another protein and compare the two.
Write a brief summary of the comparison. [See summary
questions below.]
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B. If you want to find out more about your
protein, or any other protein, you need to go to another
database or use a different application. This is easy to do!
For your protein, many of these databases and applications
can be accessed from your "Structure Summary" page.
1. From the "Structure Summary" page, click on the
colored number that is listed after the "PDB Id".
2. You should see a table with information
regarding who studied the protein and methods used for
studying the protein. If you scroll down, you will see
headings on the left that read "Structural Neighbors",
"Geometry", "Other Sources", etc. This is the spot. As you
browse, do check out "Other Sources"- there is much to be
found here. Have fun finding literature and more information
about your protein.
3. Another good one to try is "PDB Sum". You can
get there through "Other Sources" or by using the URL below:
[Save your PDB Id code to enter at the site.]
http://www.biochem.ucl.ac.uk/bsm/pdbsum
At PDB Sum, you can view secondary structure motifs, and
other details of your sequence.
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Summary Questions:
Try to limit your answers to two typed pages [12 pt
font]. You need not retype the questions.
1. Which protein did you first pick? How many
different peptides did it have? Did it have any beta-sheets?
If so, how many? Did it have any alpha-helices? If so, how
many? Did it have any hairpin loops? If so, how many? Where
there any other features worth noting? If so, what?
2. What was the second protein you picked? Review
its structural characteristics, as you did for the first
one. In what ways was it similar to your first protein? In
what ways was it different?
3. What other related sites did you visit in
connection to one of your two selected proteins? Briefly
summarize the available information at two of these sites.
What new understanding did you gain from visiting these
sites?
4. Go to NCBI's Structure page and enter "1QLF",
then view the structure. Describe the structural
characteristics of chains A and B. What is a domain? How
many domains does each of these two chains have? Identify
what each chain is. How did you find this information?
["Someone told me." doesn't quite cut it.] What is
the function of each of these chains? [In simple terms,
only. We'll get to the deeper issues in a while.]
Interactive
discussion:
Make one original posting to either "Computer problems"
or "Cool sites", or respond to an existing posting. Check
back and read new postings. They may contain information or
sites which you'll find useful.
Further
exploration:
If you want to learn more about exploring protein
structure, making illustrations of protein models, and
seeing how these methods can be applied try the following
tutorials:
http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dtut.shtml
The new CN3D has some nice advantages and features. It is
pretty easy to learn, and you'll learn more about proteins
in the process. Some students have preferred this viewer to
Chime/RasMol when viewing primary and tertiary structure
together.
http://molvis.sdsc.edu/protexpl/
By exploring the tutorials for Chime, you'll discover
additional features which can be quite useful. Several
students have used images they generated using Protein
Explorer in formal presentations and in other classes.
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