1 Protein Databank

Form and function follow each other closely in biochemistry, particularly regarding the study of proteins. As a result, much research is dedicated to determining the 3-dimensional structure of proteins and other biological macromolecules. So that others may benefit from the research, these structures are commonly deposited in a publicly accessible database, to be retrieved by anyone who wishes to examine the structure. This database is called the Protein Data Bank (PDB), and is accessible online at www.rcsb.org. We will use the database to access different protein structures, and examine them using software which is also freely available online.

In a web browser, visit www.rcsb.org. The page includes a field for searching the database archive. While it is possible to search the database using a keyword search (the name of your protein, etc.) it is much more convenient to search by pdb id. Start your exploration of the PDB by searching for hen egg white lysozyme, pdb id 1HEW. Your search will be more specific if you search by pdb id rather than by keyword. You should be able to bring up a page with information about the structure for the protein, including the authors of the article publishing the structure, the type of protein, and the date on which the structure was published.

The page youve opened includes links to several different ways of looking at this information. We are interested in downloading a copy of the file to the local computer. Click the Download/Display File link, and click the link to download the pdb file without compression. In order to download to a file rather than viewing the file in your browser, you may have to right-click on the link and select Save Target As Save the file as 1HEW.pdb in a convenient location.

Open the downloaded file in a text editor and answer the following questions:

• How many protein atoms (not heteroatoms) are in the structure of the protein?
• How many atoms are associated with the NAG group?
• What type of atom is conspicuously absent in the protein structure?
• What do the numbers next to each atom represent? What significant information is not provided by each atom entry?

While there is much information to be gained by looking at the pdb file itself, it is more helpful to view the structure in a program. The program we will use is called PyMol, and is available at http://www.pymol.org if it is not already installed on your computer. Pymol will help us address further questions about the protein. Open 1HEW.pdb in PyMol, either by double-clicking the 1HEW icon, or by starting PyMol and opening the 1HEW.pdb molecule.

Probably the best way to learn about this program is to explore it for yourself. A couple of helpful hints are in order, though.

• Most of the methods for displaying the molecule will be familiar to you (CPK, ball-and-stick, etc.). The new methods will be the ribbon display and the cartoon display. These capture the geometry of the polypeptide that makes up the majority of the protein. In particular, the cartoon depiction shows helices in the protein as cylinders, and strands as arrows.
• One of the most helpful aspects of software like this is the ability to select subsets of the atoms for an alternate display. This is done in PyMol using the select command. More information about this command can be found by typing HELP SELECT and/or HELP SELECTIONS at the command prompt.
• When you are ready to generate a picture for export, type RAY at the command prompt. This will generate a much nicer picture that will be immediately lost as soon as you try to manipulate the molecule in any way.

Your lab report should also include the following:

• An image of lysozyme in cartoon format (no sticks or lines), with the NAG group in space-fill.
• An image of lysozyme in stick format, showing the distance between an atom in the protein and and atom in the NAG group.
• An image of the protein you were assigned for the molecular modeling project in cartoon format, with its hetero group in space-fill.
• The citation of the article in which your protein structure was published.
• The experimental method used to determine the structure of your protein.
• The organism from which your protein was derived.
• The number of helices in your assigned protein.

2 PubMed Database

It is important in medical and biochemical research, among other disciplines, that a comprehensive store of information be available to the researcher. In order to facilitate research in these fields, the United States government has established an online database collecting literature information from the past 40 years. This database is called PubMed, and can be found as a link in the website of the National Center for Biotechnology Information: http://www.ncbi.nlm.nih.gov. Use this online database to find the citations listed below. Save these citations to the PubMed clipboard, and save the clipboard to a file or send it as an email.

1. In the PDB file for lysozyme, find the last author listed. Use PubMed to find a citation for another article by this author.
2. Find the citation for an article that discusses the specificity of hen egg white lysozyme.
3. Find a citation for a review article about lysozyme structures.
4. List the citation for the article in which the structure of your protein was published.
5. List two additional citations for articles about the protein you were assigned.