[FW] = Prof. Forest White
[EF] = Prof. Ernest Fraenkel
| SES # | TOPICS | INSTRUCTORS | KEY DATES |
|---|---|---|---|
| 1 | Introduction, goals and rationale for the course, protein-ligand interactions | FW | |
| 2 | Experimental techniques: Titration analysis, fractional saturation, the “pseudo-first order approximation” (PFOA), isothermal titration calorimetry (ITC), mass spectrometry (MS) | FW | |
| 3 | Co-immunoprecipitation (Co-IP) and mass spectrometry (MS), Fӧrster resonance energy transfer (FRET), primary ligation assay (PLA), surface plasmon resonance (SPR) | FW | |
| 4 | Enzyme kinetics, Michaelis-Menten kinetics | FW | |
| 5 | Kinase engineering, competitive inhibition, non-competitive inhibition, epidermal growth factor receptor (EGFR) in cancer, regulation of kinase activity | FW | |
| 6 | Constitutive kinases, modeling kinases, how to shut down kinases, multiple substrates, modeling abstraction, mitogen-activated protein kinase (MAPK) cascade | FW | |
| 7 | Ultrasensitivity / amplification in the MAPK cascade | FW | Protein Networks Project Part 1 Due |
| 8 | Signal shut-down | FW | |
| E1 | Exam 1 | ||
| 9 | Ligand depletion | FW | Protein Networks Project Part 2 Due |
| 10 | Transcription factor (TF) phosphorylation | FW | |
| 11 | Transcriptional regulation: Simple regulation, negative autoregulation, positive autoregulation | FW | Protein Networks Project Parts 3-5 Due |
| 12 | Predictive models of biology, genome editing, sensors, light-activated proteins, new enzymes, electrostatics | EF | |
| 13 | Hydrogen bonding, the hydrophobic effect, how we represent proteins | EF | |
| 14 | Paralogues and orthologues, protein therapeutics | EF | |
| 15 | Specificity | EF | Protein Design Project Part 1 Due |
| 16 | The metropolis algorithm | EF | |
| 17 | Gradient descent, molecular dynamics, ΔΔG for small molecules, pharma priorities | EF | Protein Design Project Part 2 Due |
| E2 | Exam 2 | ||
| 18 | Drug development case study: Imatinib | EF | |
| 20 | Guest lecture by Rebecca L. Carrier. Impact of drug delivery of effectiveness | EF | Protein Design Project Part 3 Due |
| 21 | Protein folding: Thermodynamics | EF | |
| 22 | Kinetics of folding, predicting protein structure | EF | |
| 23 | Structure from sequence | EF | Protein Design Project Part 4 Due |
| 24 | Kinases, graph theory, experimental and computational techniques | EF | |
| E3 | Final Exam | ||
