Spring 2004 Schedule

	Lecture Topic	Lab	Reading
1  (1/19)	Introduction to Structural Biology	Protein Fold Visualization	Class Handout : Summary and Introduction Branden and Tooze : Ch 1-5. Nucleic Acids Res. 28, 235-42 (2000). Nucleic Acids Res. 29, 221-2 (2001).
2 (1/26)	Structural Biology and Protein Motifs	Protein Fold Visualization	Branden and Tooze : Ch 1-5. Struct. 7, 1099-1112 (1999). TIBS 24, 364-7 (1999). Bioinf. 18, 934-8 (2002). Class Notes
3 (2/2)	Protein Homology and  Structural Validation Tools	Homology in Gene Sequences Course : 5% Due : Week 5	Branden and Tooze : Ch 1-5. Nucleic Acids Res. 25, 3389-402 (1997). Struct. 10, 435-40 (2002). Methods Enzymol. 266, 460-80 (1996). BLAST course Optional J Mol Biol 147, 195-7 (1981). J Mol Biol 276, 417-36 (1998). Struct. 3,  535-40 (1995) Chem. Rev. 97, 1251-68 (1997) Creighton, T. E. Proteins.
4 (2/9)	Protein Thermodynamic and Kinetic Aspects	Cambridge Structural Database Course: 5% Due : Week 6	J Mol Biol 311, 325-40 (2001) J Phys Chem B 106, 521-33 (2002). Curr Open Struct Biol 9, 620-6 (1999). Optional Annu Rev Phys Chem 50, 485-516 (1999).
5 (2/16)	Protein Structural Analysis Tools	Maestro and Macromodel Course : 5% Due : Week 8
6 (2/23)	Molecular Mechanics: Force Fields and Solvation		JACS 117, 5179 (1995). J Phys Chem B 102, 3586 (1998). JACS 118 : 11225 (1996). J Comp Chem 19 : 535 (1998).
7 (3/1)	Molecular Dynamics and Sampling Methods	Molecular Dynamics of BPTI Course : 5% Due : Week 10	Curr Opin Struct Biol 7, 181-9 (1997) Nat Struct Biol 9, 646-52 (2002). Optional Biopolymers 60, 96-123 (2001). J Mol Model 7, 306-17 (2001). Nature 420, 102-6 (2002).
8 (3/9)	MIDTERM EXAM
8 (3/12)	Introduction on NMR Method	NMR of Macromolecules Course : 5% Due : Week 12
9 (3/15)	SPRING BREAK
10 (3/22)	NMR - Chemical shifts and proteins	Special Projects NMR  Mathematica simulation of NMR spectra  Assignment of solution NMR spectra of Proteins   Monte Carlo study of the beta turn  Constrained MD using NMR distance constraints  MD study of protein dynamics  Calculation of amino-acid partial charges  QM study of the hydrolysis of an amide  Protein Electrostatics	Biophys textbook online, NMR, chapter 1. (1998). Life 52, 291-302 (2001).
11 (3/29)	NMR - the INEPT sequence		NMR handout Optional Annu Rev Biophys Biomol Struct 29, 213-38 (2000).
12 (4/5)	NMR- Relaxation and the NOE		Optional Relaxation and Dynamic Processes. Protein NMR spectroscopy principles and practice. Academic Press, San Diego (1996). Angew. Chem. Int. Ed. 42, 864-890 (2003). Progress in NMR Spectroscopy 41, 187-231.
13 (4/12)	HIV Protease and Drug Design		Biochim Biophys Acta 1477, 16-34 (2000). Annu. Rev. Biophys. Biomol. Struct. 27, 249-289 (1998). Eur. J. Biochem 219, 707-712 (1994). JACS 116, 10791-2 (1994). Protein Science 5, 495-506 (1996). Optional Biochemistry 35, 9945-50 (1996).
14 (4/19)	DNA Binding Proteins		Quarterly Rev. of Biophys 32, 57-98 (1999). J Mol Biol 285, 2133-46 (1999). J Mol Biol 319, 567-83 (2002). J Mol Biol 314, 619-32 (2001). Protein Science 11, 221-32 (2002). J Comp Chem 23, 1-14 (2001). Optional Biochemistry 35, 14984-91 (1996). Biochemistry 40, 8109-17 (2001). Biochemistry 41, 3286-93 (2002).
15 (4/26)	Examples: Protein
16 (5/3)	Special Projects	---	---
17 (5/10)	FINAL EXAM




Extra readings

1. Nat Struct Biol 7, 740-3 (2000).
2. Proteins 38, 123-33 (2000).
3. J Mol Biol 263, 369-82 (1996).








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