Chemistry 323
Principles of Protein Structure

In this assignment we will use the program MAGE to visualize different principles of protein structure. Each MAGE file consists of one or more kinemages which is an interactive graphic window where you can rotate the molecule being displayed, measure distances, zoom in and out, etc. The author of a MAGE file can define several views to highlight points of emphasis. Each kinemage has a caption window and a text window. As you work with MAGE you should think as if you are reading a textbook with dynamic and interactive figures.

The computers in the Chemistry Department Computer Laboratory all have MAGE on the hard drive and the World Wide Web (WWW) browser, Netscape, is configured so that MAGE automatically launches as a helper program whenever you click on a link whose file name has the extension .kin. Netscape will download the file to the hard drive of the computer that you are working on and open it with MAGE.

If you know how to configure your computer, you can download for yourself the Macintosh version or the Microsoft Windows version of MAGE as well as the Kinemage (.kin) files and work on your own computer without being attached to the network.

You are to examine the five kinemage files as listed below. Read the text windows and examine the structures in detail noticing the things in the structures that the text window discusses. Jot down a brief outline (phrases and key words) of the salient features of each kinemage to turn in. In some cases I may ask some additional questions.

Here are the 5 kinemage files for this assignment. Click on each one to download the file and work through the assignment.

• Conformational analysis of a polypeptide

  Additional questions

  • Set the phi-psi angles of the peptide in this kinemage to the values set below and examine the resultant structure. For this part of the exercise turn off the sidechain so that only the beta carbon remains. Indicate whether the phi-psi angles are in a forbidden or allowed region of the Ramachandran diagram. If they are in the forbidden region, give which interactions which are sterically unfavorable. If they are in the allowed region, tell which major secondary structure class they correspond to and make sure you can pick out that structure visually.

                     phi = 0     psi = 0 
                     phi = -57   psi = -47 
                     phi = 120   psi = 90 
                     phi = -119  psi = 113 
                     phi = 120   psi = -120 
                     phi = -90   psi = -120 
                     phi = 57    psi = 47 

• Basic motifs of protein structure: the alpha helix and the beta sheet
• All alpha proteins
• Alpha/beta proteins
• Anti-parallel beta proteins