CHEM 451: Data & Analysis

Prepare a plot of the small hydrophobic seed protein crambin from Crambe hispanica (1CRN). Color the ribbon diagram, by secondary structure, using an approximation of primary colors of your favorite National Football League team (Hint: follow the link to your team of choice, identify the color you'd like to use and divide each number of the RGB color value triplet by 255 to produce the MolScript required 0.0 to 1.0 inclusive range for RGB colors.).

Describe the secondary structure you see. How would you classify this protein fold according to the SCOP or CATH database? Explain.

Ribonuclease A (RNase A) is the pancreatic ribonculease from Bos taurus, the cow (9RSA). The active site of RNase A is composed of HIS 12, LYS 41 and HIS 119. Prepare a ribbon diagram of RNase A highlighting the sidechain residues of this active site. Prepare the ribbon diagram in greyscale and plot the sidechains in standard colors. (Hint: this crystal of RNase A forms with two molecules in the asymmetric unit; plot only the B chain. You should rotate the structure in order to get a good view of the active site, no overlapping active site residues, please.).

Prepare a plot of T4 lysozyme (2LZM) in which each atom is colored according to the reported thermal factor. In the color scheme, use blue for low thermal factors and red for high thermal factors (think ice to fire) with intermediate values in shades of purples. Since this is a non–trivial undertaking, use the following code to generate the MolScript input file for your structure (save the text in file, set the execute bit and run the program giving the low and high thermal factors, a pipeline in the shell should help you find those values quickly, and the coordinate file as input. Both the program and the convention for calling it are illustrated below. Note that this program is specific for this PDB input file and will require modification to work generally.).

[user@451]$ cat bythermal
#! /bin/awk -f

BEGIN {
  FS = " "
  min = 0
  max = 50
  print "title \"T4 LYSOZYME\""
  print ""
  print "plot"
  print ""
  print "read mol \"2LZM.pdb\";"
  print ""
  print " transform atom * by centre position atom *;"
  print ""
  print " set segments 20;"
  print ""
}

{
  range = max - min
  if($1 ~ /^ATOM/) {
    blue = (range + min - $11) / range
    red = 1.0 - blue
    printf "%s%s%s%s%s%s%0.3f%s%0.3f%s", " set atomcolour require atom ", $3, " and in residue ", $5, $6, " rgb ", red, " 0.0 ", blue, ";\n"
    print " cpk require atom " $3 " and in residue " $5 $6 ";"
  }
}

END {
   print ""
   print "end_plot"
}
[user@451]$

In order to call this program, find the minimum and maximum values of the thermal factor in the structure and use this calling convention, assuming that your script and the file 2LZM.pdb are in the current working directory (and no, the values of min and max used in this example are not correct).

What did you learn about the thermal factor from this plot?

Prepare of plot of horse heart myoglobin (1YMB). In your plot, use greyscale for the ribbon diagram, and display the organic portions of the bound heme as a ball and stick model with the central iron atom in a spacefilling representation. Be sure to use the most typical variant of the Corey, Pauling, Koltun coloring scheme for the bound heme group. This structure has an associated sulfate anion. Is it likely that this sulfate anion is biologically relevant? Explain.