Protein Ligand Binding
Equations for protein-ligand equilibria and fractional occupancy; binding
curve (Y vs [L])
Types of interactions important in protein-ligand binding
Entropic and enthalpic contributions to free energy of binding
Specificity/selectivity and affinity
Examples of Protein- Ligand Interactions
Estrogen receptor/androgen receptor
Immunoglobulins
Lectins
Protein-DNA complexes
1
Myoglobin and Hemoglobin
Reversible binding of O2 to heme
Structure, properties, binding curve of myoglobin
Structure, properties, binding curve of hemoglobin
Cooperativity
Allosteric regulation (positive/negative, homotropic/heterotropic)
Differences between the R-state and the T-state
2
The Bohr Effect
2,3-BPG
Hemoglobin variants (fetal hemoblogin, HbS)
Enzymes
Classification of reactions into six enzyme classes
Ways that enzymes catalyze reactions
Proximity/orienttion
Acid-base catalysis
Nucleophilic catalysis
Transition state stabilization
Metal ion catalysis
3
Enzyme Kinetics
Progress curves ([P] vs t for a particular [E] and [S]
General equation for a single substrate reaction
Saturation kinetics and the steady-state condition
Michaelis-Menten equation and plot
Lineweaver-Burk plots
Meaning/interpretation of Vmax, KM, kcat, kcat/KM
4
Types of two-substrate kinetic mechanisms (ternary complex vs. ping
pong) and how to distinguish them by kinetics
Ternary Complex
Ping Pong
Mechanisms
Chymotrypsin and other serine proteases/esterases
5
Cysteine Proteases, metalloproteases, aspartyl proteases
6
Lysozyme (and other retaining glycosides
7
Alcohol dehydrogenase
Enolase
Kinases
8
Triosephosphate Isomerase
Glutamine Synthetase
Enzyme Regulation
Positive and negative allosteric regulation in ATCase
9
Reversible covalent modification – phosphorylation (glycogen
phosphorylase)
Irreversible covalent modification – zymogens (digestive protease activation,
blood clotting)
Inhibitors as Drug and Toxins
What enzymes do they inhibit?
What type of inhibitor (covalent, competitive) are they?
What is the physiological effect of inhibiting that enzyme( why are they used?)
Organophosphate compounds
b-lactam antibiotics
Statins
10
HIV protease inhibitors
Non-steroidal anti- inflammatory agents
Gleevec
11
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