Download Problem 2

Problem 2. I was curious about the neighborhood of the helix, so I made a
picture of the whole protein.
Clearly this helix is likely to be involved in binding the heme.
Next I went to the helical wheel web site and made a picture; I also made a
picture of just that helix with Rasmol, selecting the hydrophobic residues and
coloring them:
Noticing that His 93 is in between two hydrophobic residues that should face the
interior of the protein, I decided to see if that His was bound to the heme iron:
Bingo.
Problem 3. The first thing I did was to go to the PDBSum server and enter the
code for the protein I picked, human serum transferring, 1d3k. PDB Sum gives a
complete analysis of the protein structure, including domains and motifs.
I found the protein to consist of two domains:
Reading from the graphics I found domain A to consist of residues 93-248 and
domain B is residues 4-78 plus 250-305. Looking at the graphic of the overall
structure, I found residues 79-92 to form several turns connecting the domains.
I then made a picture to display the domains:
To locate motifs, I consulted PDBSum again. It pointed out two  motifs, one
of which proved to be a :
The web site also located a single -hairpin and several -bulges. I had no idea
what a -bulge is, so I picked one and made a picture.
Finally, a -loop was indicated, and I had no idea what one of those was either.
So here it is:
It looks like just a twisted -strand.
Finally, to see how this all fit together, I made a picture of the protein with all the
motifs picked out. The  motifs are red, the -hairpin is green, the -bulge is
cyan, and the -loop is purple:
Problem 10. We can use either Rasmol or SwissPDB to examine the structure.
I used Swiss PDB first, displaying the heme in spacefilling model, and then using
the mode that allows me to pick an atom and display all residues with XX
distance of it. This is the ninth button from the left, with an eye, a circle, and 1 Å
displayed. I chose an atom on the heme (aiming for the iron, but missing) and a
distance of 6.0 A:
Rice (1ccr)
Tuna (5cyt)
Using Rasmol, we need the “select within” and “restrict selected” commands I
typed “select within (5.0, iron)” and then “restrict selected”, so the display
contained only the residues within 5 A of the iron. Then I selected and displayed
the heme. The results:
Rice (1ccr)
Tuna (5cyt)
Clearly, the ligands on the iron are strongly conserved, as is the Tyr, which is
probably hydrogen bonding to one of the heme nitrogens.
Finally, I did a sequence alignment using BioEdit:
The two proteins have 55% sequence identity and 69% similarity. The red lines
mark the conserved His and Met, which are both within strongly conserved
regions of the protein. Most of the variation appears to be at the N-terminal ends
of the proteins, well away from the functional part.