[FW] = Prof. Forest White

[EF] = Prof. Ernest Fraenkel

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), FÓ§rster 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