Exercise 6.
Electrostatic potentials and their role in protein-protein interactions

1. Load structure 1GHQ of the CR2-C3d complex (CR2: complement receptor 2; C3d: fragment d of complement component C3)
   This file contains 2 Chains for CR2 (Chains B and C) and one for C3d (Chain A)
   CR2 consists off 2 V-shaped all beta-sheet components - each component consists of 2 sushi domains (or short concensus repeats, SCRs, or complement control domains, CCPs) connected with a flexible linker (extended structure)
   C3d consists of an alpha barrel all helical structural motif
2. Goals
   Our first goal is to calculate and compare the electrostatic potentials of the complex CR2-C3d and of the individual components CR2 and C3d
   Our final goal is to assess if electrostatics play a role in recognition and binding
3. Complex CR2-C3d
   in Tool Bar Tools Compute electrostatic potentials
   Use simple Coulomp's law and only charged residues to make the calculation faster
   Center the molecule
   What do you observe?
   Answer: a predominantly positively charged complex - positive charge is more pronounced at the CR2 side - C3d side has negative character
   In Tool Bar Discard electrostatic potential
   You can also save the potential using Tool Bar Save electrostatic potential for later use
4. CR2 alone
   Reload 1GHQ and rename it to 1GHQ_CR2 (remember: use Edit to rename current layer)
   Remove Chain A repeat calculation
   What do you observe?
   Answer: a predominantly positively charged CR2
   Discard the potential
5. C3d alone
   Reload 1GHQ and rename it to 1GHQ_C3d
   Remove Chains B and C repeat calculation
   What do you observe?
   Answer: a predominantly negatively charged C3d
   Discard the potential
6. Mutate a specific residue that affects binding
   Load 1GHQ, remove Chains B and C
   Locate Asp163 (use Control Panel side chain checkmark, color, and zoom in)
   Center the structure on Asp163 by clicking on the 10th button of Tool Bar - re-adjust as needed
   Click on the mutate button (12th) of Toll Bar
   Click on Asp163
   mutate to Ala from the Pop up Window
   Click again on the mutate button to accept the mutation - visulay check the replacement
   Re-calculate potential
   What do you observe?
   Answer: a predominantly negatively charged C3d but of reduced electrostatic field compared to parent structure - this denotes that this mutation is important for binding - indeed experimental data have shown so
   Note that this mutation is not at the dimer interface, which suggests that all charged residues contribute to binding and not only charged residues at the dimer interface - the recognition is owed to long range electrostatic interaction of the molecules involved as whole, however association occurs locally and is predominantly hydrophobic in nature
7. Mapping electrostatic potentials on molecular surfaces
   In Tools Compute surface
   Discard electrostatic potential
   Use "OpenGL rendering" and "Render in solid 3D"
   This is a popular representation for publications