Spring 2003 Schedule

Week	Lecture Topic	Lab	Reading
1  (1/20)	Structural Biology	Protein Fold Visualization	Branden and Tooze : Ch 1-5
2 (1/27)	Introduction to Protein Motifs	Protein Fold Visualization	B&T Ch 1-5
3 (2/3)	Structural Information : the Protein Database (PDB) and Structural Validation Tools	Cambridge Structural Database: Visualization and Ramachandran Plots Continued	Branden and Tooze : Ch 6, 17 Curr Opin Struct Biol 9, 164-9 (1999).  J Mol Biol 311, 325-40 (2001).
4 (2/10)	Protein Homology and Structure Prediction	Homology in Gene Sequences
5 (2/17)	Protein Thermodynamic and Kinetic Aspects
6 (2/24)	Molecular Mechanics : Force Fields and Solvation	Maestro and Macromodel	JACS 117, 5179 (1995). J Phys Chem B 102, 3586 (1998). JACS 118 : 11225 (1996). J Comp Chem 19 : 535 (1998).
7 (3/3)	Molecular Mechanics : Sampling Methods and Molecular Dynamics	Maestro and Macromodel	Curr Opin Struct Biol 7, 181-9 (1997) Nat Struct Biol 9, 646-52 (2002). Optional Biopolymers 60, 96-123 (2001).
8 (3/10)	Molecular Mechanics : Special Topics	Molecular Dynamics of BPTI	J Mol Model 7, 306-17 (2001). Nature 420, 102-6 (2002).
9 (3/17)	SPRING BREAK (All Labs due)
(3/24)	MIDTERM EXAM (March 24 2003)
10 (3/24)	Introduction to NMR for Structural Genomics	Special Projects Monte Carlo study of the beta turn Constrained MD using NMR distance constraints MD and Protein Conformational dynamics Charge fitting QM Calculation of Amide Hydrolysis Protein Electrostatics	Annu Rev Biophys Biomol Struct 29, 213-38 (2000). Principles of magnetic resonance. Springer-Verlag, Berlin, New York (1990).
11 (3/31)	NMR for Protein Structure Determination
12 (4/7)	NMR for Protein Dynamics		Relaxation and Dynamic Processes. Protein NMR spectroscopy principles and practice. Academic Press, San Diego (1996). Nat Struct Biol 7, 740-3 (2000). Proteins 38, 123-33 (2000). J Mol Biol 263, 369-82 (1996).
13 (4/14)	DNA Binding Proteins		Biochemistry 35, 14984-91 (1996). J Mol Biol 285, 2133-46 (1999). Biochemistry 40, 7947-56 (2001). Biochemistry 40, 8109-17 (2001). J Mol Biol 314, 619-32 (2001). Biochemistry 41, 3286-93 (2002).
14 (4/21)	HIV Protease and Drug Design		Biochemistry 35, 9945-50 (1996). Biochim Biophys Acta 1477, 16-34 (2000).
15 (4/28)	ATP Synthase		Curr Opin Struct Biol 11, 393-6 (2001).
16 (5/7)	Special Projects	---	---
17 (5/11)	FINAL EXAM





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