Exercise 4.
Analyze the dimerization interface

1. Load structure 1GAR of enzyme GART (GlycinAmide Ribonucleotide Transformulase)
   Note that some residues are missing and may be automatically reconstructed (drawn in magenta)
   You can enable/disable the automatic reconstruction in loading Preferences
   We will address how to build a loop in Exercise 5.
   Note that this is the structure of a homodimer
2. Rotate the molecule to visualy identify the dimer interface
   Use coloring to identify the dimer interface: click on Color By chain
   Personally, I prefer to use colors other than red, green, blue to color the Chains
   Remember the standard colors: red for acidic, blue for basic, green for hydrophobic, grey for polar, and yellow for sulfur containing
   Use coloring to identify the type of side chains while keeping the backbone color as is: click on Color Act on side chains , click Color again By type
3. Identify specific residues that form the dimer interface
   Click Select Groups close to another chain -- in the "Display options" use "Display only groups that are within 3.3 Å "
   Why I chose 3.3 Å?
   Which side chains form inter-monomer H-bonds?
4. Inter-monomer electrostatic interactions
   Which side chains form inter-monomer salt bridges?
   Click Select Groups close to another chain -- in the "Display options" use "Display only groups that are within 6.0 Å "
   Hint: you can artificially alter the H-bond maximum distances in Preferences to get the characteristic dotted lines, BUT DON'T FORGET TO SET IT BACK TO ITS PROPER VALUE!
5. Inter-monomer hydrophobic interactions
   Which side chains form inter-monomer hydrophobic contacts
   Re-display the whole molecule
   Identify contacting inter-monomer side chains colored in green
6. Inter-monomer surface complementarity
   Is there geometric surface complementarity?
   Remove Chain A
   Hint: In Control Panel select all residues of Chain A - click on Build Remove selected residues
   Click on Tools Compute molecular surface
   Color Act on surface - change color as needed
   Load again file 1GAR
   Select the second 1GAR structure
   Remove Chain B
   Compute molecular surface
   Color Act on surface - change to a different color from Chain A
7. Another way to check the interface of the two monomers is by using solvent surface accessibility
   Act on the whole protein (Chains A + B)
   Use Select Accessible a.a. select greater or eaqual than 30%
   Selected residues will be colored in red in Control Panel
   Repeat on one Chain alone (Chain A or B)
   Check which residues are newly selected, these are the residue previously burried under the dimer interface and now are solvent exposed