List of proteins and references
List of proteins and references
Overview of Project
Each student will select a protein to study using the program RasMol.
Using RasMol and the primary literature on the protein, the students will
write a 5 page paper describing the molecule in detail. An appendix of
at least 3-5 RasMol images of the protein will be handed in with the paper.
A copy of the primary literature paper used as the reference is also to
be turned in with your written paper. The images are to be handed in on
a zip disk (this will be returned to you) or they may sent as an attachment
in an e-mail to Dr. Lee. This project is due in class on Friday, November
10.
Background information on the protein. What is the function of the protein, why is it of interest, where is it synthesized or active?RasmolStructural information on the protein. How many subunits are present, what are the secondary structural elements of the protein?
Specific descriptions of molecular interactions of the protein. You need to describe three to four molecular interactions that are important for the protein's function. These descriptions need to be accompanied with Rasmol generated images. You need to clearly articulate the importance of the interactions for the proteins's activity and/or function. These interactions should include hydrogen bonds, electrostatic bonds, and hydrophobic interactions.
Protein Data Bank
The Protein Data Bank site allows
you to search for any protein structure by name or coordinate ID.
You may do this if you want to use a protein not on Dr. Lee's list.
Use the open box to type in the name of the protein you are interested
in working on this semester and hit the return key. If the structure
for the protein is in the database, then you will be linked to a web page
with all the structural information that has been submitted for that protein.
Click on one of the links and you will be directed to a new page containing
the relevant information for that specific structure. Included in
this is the reference(s) for this structure, you should obtain this
reference from the library as soon as possible.
Downloading Protein Files
When you have decided which protein you wish to use for the project
select it through the Protein Data Bank
(preferred) or Molecules
R Us sites. You will be linked to a page showing the results
of your query. Select the Download/Display link from the options
on the left panel. You can then download the coordinates from this
page by selecting TEXT option for the PDB file complete with coordinates.
Wait until the entire page has been downloaded.
Saving the File
Once the page has been downloaded, save the data as a text file.
You should be able to open this in a text editor and see the data that
was downloaded. If you can see this, you should be able to open the
file in RasMol. Open RasMol first and then open the file from within
RasMol. At this point you should see your protein in the RasMol window.
If you have any problems, try the Protein Data Bank site for downloading as the Molecules R Us site may be more problematic. Be certain to select the text format for downloading the corrdinates file and to save the file as a text file.
Problems
RasMol will not open the file I have downloaded.
Open the file in a text editor and make sure the
file was properly downloaded. If you used Netscape Communicator on
a Mac computer you may need to edit the saved file. Delete the first
line of the file (the title) and save the file (make sure you save file
as a text file, not as a word processor document). Try to open the
new file in RasMol now.
Netscape does not save the file to the hard drive.
If the file is not too large you may copy and paste
the file into a text editor and save it from the text editor. Be
sure not to save the file as a word processor document, it must be saved
as a text file.
Another solution is to use Internet Explorer or
a more recent version of Netscape (4.61) to download the file. For
some reason there seems to be a much higher success rate using this browser
instead of Netscape when downloading the pdb files.
Students taking Biochemistry at Fredonia may e-mail Dr. Lee with other problems they have downloading and viewing their molecules.
Hemoglobin Tutorial
This tutorial provides examples of acceptable images for the protein
project using hemoglobin. Some of the interactions discussed in class
are shown and instructions for highlighting specific amino acids and molecular
interactions are given.
Working With Your Protein in RasMol
Once you have downloaded the protein and opened it successfully in
RasMol, you are ready to look at the molecular interactions of the protein.
You may rotate the molecule by moving your mouse, if you ever want to go
back to the original position, simply type "reset". The select command
will allow you to look at specific residues or molecules. If you
downloaded a protein and DNA complex, by typing "select protein" you will
be able to make subsequent commands for the protein molecule (such as "color
red" or "spacefill"). If you want to select a specific amino acid
(for example amino acid residue 117 in your protein), simply type "select
117" and all subsequent commands will act on that residue.
Joanna Tober, who previously took this course has written a very useful
document "Everything you always wanted to know
about Rasmol but were afraid to ask." Check it out for
some additional help.
Saving Your Work in RasMol
When you have selected residues of interest and have a RasMol image
you wish to save (for yourself or to hand in with your project) you need
to write a script in RasMol. Do not save the work, the save-as
command in RasMol will not save the images you have created!
Instead when the molecule is as you would like it, at the prompt type "write
imagename" (for Macs) or "write imagename.gif" for PCs. For example,
if working with the DnaK protein, you would type "write dnak1" for your
first image and "write dnak2" for your second image and so on. Be
careful not to save 2 files to the same name as RasMol will NOT ask you
if you want to overwrite the first file, you will lose it. It
is useful to view your initial saved images in Netscape (or other program
for viewing images) to ensure everything is working properly.
The Manual
The RasMol
Manual contains everything you need to know about the program and a
whole lot more. TL will provide specific instructions and help for
students working on their projects. The Manual is also downloaded
when you get the program off of the internet.
Other Programs and Sites of Interest
Another program one may want to obtain the Chime,
a product of MDL
Information Systems, Inc. Chime is a plug-in that allows Rasmol
commands to be executed on a web browser. This feature allows for
the generation of interactive web pages where specific properties of molecules
can be featured. An example of this is the Online
Macromolecular Museum which was set up by Dr. David Marcey at Kenyon
College. The museum (and David) is now at California Lutheran University.
Check out the tutorials within the museum, to visualize the tutorials one
must have Chime installed on their computer.
This web page is designed for the students taking BI333 (Biochemistry)
at SUNY-Fredonia.
T. Lee
Department of Biology
SUNY- Fredonia
Fredonia, NY 14063