Molecular Electrostatic Potential Surfaces: Assignments (2012)
- Generate electrostatic potential maps for the chorismate mono-anion in the near-attack conformation, and transition state geometry using the HF/3-21G basis. You can use the geometry of the near-attack conformation that was provided earlier, and the PM3 optimized transition state geometry. Generate also the electrostatic potential map for the oxa, (protonated)aza, and methylene analogs of endo-bicyclic inhibitors using the PM3 optimized geometries from the cm_inhib.tar.bz2 file. Propose your own inhibitor for chorismate mutase, minimize this structure at PM3 level, and generate the electrostatic potential map for this inhibitor using Gaussian. Discuss which of the molecules is most similar to the transition state with respect to electrostatic potentials.
- Generate the electrostatic potential maps for monomers in the two base pairs that we discussed in the lecture as an example of the importance of secondary interactions. Predict which base pair is more stable. Justify your answer.
For each answer, provide images that illustrate your arguments.
Homework: Macromolecular Visualization
Chorismate Mutase
Several transition state analogs have been developed as possible inhibitors for the chorismate mutase. One of the highest affinity inhibitors developed to date is an endo-oxabicyclic transition state analog first synthesized in the Paul A. Bartlett's laboratory at UC Berkeley. This inhibitor has been co-crystallized with chorismate mutases from yeast (3CSM), E. coli (1ECM), B. subtilis (2CHT), M. tuberculosis (2FP2), and with a catalytic antibody that enhances the rate of chorismate isomerization over thousand-fold (1FIG). Your goal is to analyze the binding pockets of some of these proteins, and discuss the similarities and differences in binding of the transition state analog.
As your homework, perform the following tasks and provide the following answers:
- Study the PDB entries 3CSM, 1ECM, and 2CHT. Analyze the active site of each of these three structures and note possible electrostatic / hydrogen bonding interactions between the bound analog and the protein. For each structure, create an image showing a close-up of the active site with residues that are within 3.8 Å from any atom of the bound transition state analog shown as sticks. Orient the structure such that the important interactions are well visible, and a meaningful comparison of three structures is possible (LigAlign plugin may be helpful here). In particular pay attention to:
- Interactions between negatively charged carboxylates in the inhibitor and positively charged side chains
- Interactions between the hydroxyl group in the inhibitor and polar moieties in the protein
- Interactions between the ether oxygen and positively charged residues in the protein
- Create the electrostatic surface potential for the catalytic antibody that catalyzes the Claisen rearrangement (1FIG). A suitable scale for this highly charged protein is from -10 to + 10. Create an image that illustrates the bound transition state analog in the binding pocket of the antibody. Discuss the differences between the active site of the catalytic antibody and the natural enzymes.
- Extract the endo oxabicarboxylic inhibitor from the X-ray structure of the yeast chorismate mutase (create a ligand object, and save it as a PDB file). Overlay the PM3-minimized endo-oxabicyclic inhibitor with the experimental structure using MOLDEN (open the PM3 structure, read the ligand structure, align first manually using ESC to rotate either one of the structures or both, then automatically after hitting TAB and selecting three pairs of matching atoms) or PyMOL. Comment on the the similarity between the PM3-minimized structure and the bound ligand.