Description
Answer the following questions (1 page per question minimum). Use external resources (all sources needed have been provided) as the data needed to write this paper.
1. Secondary/tertiary/quaternary structure if known, otherwise any efforts to obtain the structure and/or why is doing so a problem?
2. Important amino acid residues for binding (if receptor/enzyme) and for catalysis (if enzyme)
3. Types of interactions important in binding (hydrogen bonds, electrostatics, van der Waals, etc.)
4. Enzyme catalysis: Necessary cofactors, proposed catalytic mechanism, important catalytic principles (metals, general acid/base, nucleophilic or electrophilic chemistry)
5. Function/reaction, kinetics and/or binding affinity as applicable. (For non-enzyme proteins, kinetics will almost certainly NOT apply…but binding of ligand should be discussed in some way.) Kinetics include: Michaelis-Menten/steady-state parameters (kcat, Km), are there multiple substrates? Is sequential vs. ping-pong and/or random vs. ordered known? For binding affinity for a non-enzyme protein, is Kd (dissociation constant) known? Do multiple compounds bind, presumably with different binding affinities? What is/are the “best” substrates/ligands for binding?
6. Inhibitors: Are competitive/uncompetitive/noncompetitive/mixed inhibitors known? Are these inhibitors reversible or irreversible? Are any clinically used/applicable/sold as drugs?
7. pH dependence: Is anything known about the pH dependence of your protein/enzyme of interest? This part of your paper should focus on pH changing the activity and/or binding of your enzyme/protein and should NOT focus on “stability” or denaturation. If you chose a non-enzyme protein, it is much less likely you will have much to say about this. You may be able to make some general conclusions/hypotheses, though. For instance, if it turns out that an aspartate residue is critical for ligand binding, a significant change in pH would be likely to disrupt that interaction. If the binding interactions are mostly hydrophobic/van der Waals, pH is much less likely to have an effect.
