Homework Set 4 - Secondary Structure Analysis (20 pts)

SEE COMMENTS ON YOUR COMPLETED ASSIGNMENTS

Due Monday, October 9, 11:00 am, at the first of lecture class

There are three kinemage files that came with your CD which pertain to chapter six. I strongly encourage you to view all three and carefully read the text associated with the images. There are also other similar kinemages on the class website for your viewing pleasure. The one I am assigning for graded homework is E03_ScSt.kin, the one concerned with secondary structure. There are several kinemages associated with this file. I want you to focus on kinemage two (the alpha helix) and kinemage three (parallel and antiparallel beta sheets).

The homework assignment consists of three parts.

PART I

The first part requires you to make a table of all the amino acids which contain dihedral angles in these kinemages. This table should include columns for the three letter code of the amino acid, the amino acid number, the phi and psi angles around the alpha carbon of that amino acid, the dihedral of the peptide bond connecting the amino acids, and (except for the carboxyl terminal amino acid) the distance from one alpha carbon the the next alpha carbon in the chain. Remember to include both the parallel and antiparallel sheets in kinemage 3. Clearly indicate what type of secondary structure the amino acids are taken from by using a header over each section as

EXAMPLE OF PART ONE (Taken from a strand of the antiparallel sheet in kinemage 3 of the same file)

ANTIPARALLEL SHEET

Etc.

To measure a dihedral angle in MAGE, just turn on measures (Tools menu) and click four atoms in a row. Simply measuring distances does not require the measures tool. Clicking on two atoms will automatically show the distance between them in the bottom left hand corner.

PART II

The second part of the graded homework is to generate a Ramachandran diagram similar to the one in figure 6-6 of your textbook. On either a piece of graph paper or a computer spreadsheet plot the phi and psi angles you have measured. Use the same X and Y axes as the textbook figure. Plot dihedrals from the helix as circles, dihedrals from the antiparallel sheet as triangles and dihedrals from the parallel sheet as squares. Make your plot large so I can see all the points.

PART III

This is the thinking part where you get to analyze the data and draw conclusions. Look carefully at the table and the figure you have generated. What do they tell you? Do you notice any trends? Do they correspond with what you have heard in lecture and in the textbook about secondary structure? How does your Ramachandran diagram compare to the one in the textbook? Give at least a half page of analysis.