Chemistry 333: Protein Structure and Function

 

Problem Set #2: Introduction to the Protein Data Bank and RasMol

Due September 23rd at the beginning of class

 

Following last week’s problem set, you should be able to find a file in the PDB, browse through it to learn a little about the methods and the molecule, save the file onto your desktop, and look at the protein using RasMol.  This week we will practice these skills with a new protein.

 

1.  On the PDB website, find file 1BT9.pdb.  From the summary information and header, answer the following questions:

 

What is the name of this protein?   

 

What kind of protein is it? 

 

What is the resolution of the structure, and by what method was it solved?

 

Does this protein have a quarternary structure in the crystal?  In nature?

 

What heteroatoms are present in this structure?

 

How many alpha helices does it have? How many beta strands? How many beta sheets?

 

 

Now, download the file, open it in RasMol, and take a look at the protein.  How does it differ from myoglobin, and how is it similar?

 

 

 

 

The ColorąGroup command colors the protein from blue to red (N to C terminus), and the cartoons command puts arrowheads on each strand.  Use this representation of the protein to help you to draw a 2-dimensional topology diagram for Ompf porin.

 

 

 

 

 

 


You should guess by now that this protein formes a pore through the outer membrane of E. coli.   Use Displayą spacefill and then turn the protein around until you can see the pore through the middle of it.  “How wide is it?” you say.  Funny you should ask!   In the white command-line window, type “set picking distance” and then back in the black picture window, click on two atoms on the inside face of the pore.  The distance between them will be reported to you in the white command-line window in Ćngstroms.  Try this several times to measure an average pore diameter:

 

 

 

 

Starting from a monochrome, space-filling model, select the hydrophobic, polar, and charged amino acids separately and color each a different color.  (try typing “select hydrophobic” then “color green” then “select polar” then “color red” etc. in the white window…).  Do you seen any pattern to the location of these different kinds of side chains on the outside and the pore?  Why does this make sense, or why not?  Is this pattern uniform?

 

 

 

 

 

 

 

 

 

 

 

 

 

RasMol will also find the hydrogen bonds in the structure. Starting from a non-spacefilling respresentation of the protein, type “hbonds” and then “color hbonds white.”  You should see little white dashed lines wherever there are hydrogen bonds. 

 

How many H-bonds are holding together the last two (most C-terminal) strands of the big beta sheet?  (hint: try using “zoom” and  Options->slab mode to position the strands so you can see them!)

 

 

 

What groups are the hydrogen bond donors and acceptors?  Where are the side chains?
2.  Please go back to the structure of myoglobin that we examined last week, 1DWR.pdb.  The chemistry of the active site centers around the iron atom.  Sketch out a picture of the active site showing the heme and all of the atoms most closely surrounding the iron.

 

 

 

 

 

 

 

 

 

 

 

 

 

Is the heme connected to the protein by hydrogen bonds?  If so, how many, and between which groups?  If not, what other interactions appear to hold the heme group in place inside the protein?

 

 

 

 

 

 

 

 

Look at the N-terminal ends of the helices in myoglobin.  Do you see any of the kinds of helix capping interactions we discussed last week (i.e. bonds between the backbone and side chains holding the end of the helices together)?  If so, name one such bond.  What does your survey tell you about the frequency of such interactions?  Hint: It will help you to select and color hbond, sidechain, and protein separately; if you click on one end of a hydrogen bond, Rasmol will tell you what atom it is.

 

 

 

 

 

 

 

 

3. Now, please use what you learned yesterday at Sandy Ward’s very helpful library resource tour and use the webpage she has kindly made for us to find out more about either myoglobin or porin (your choice) from a review article in the peer-reviewed scientific literature.  Write not more than one and a half typed pages (<400 words) about the basic structure and function of the protein, and include a citation to the reference(s) you used.

 

4. Modeling your picture after figure 2.4 in your text, draw a helical wheel diagram for the following alpha-helical sequence:

KELEELAKKLKDLAKELL

Do you see any pattern?  Where might you find a helix of this composition?