Methods for Protein Structure DeterminationBCHM 669B: Special Topics, Fall 2004 |
| Course meets in CBSO 2118, TuTh 9:30-10:45 am |
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Professor: David Fushman |
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This is a graduate level course designed as an introduction to modern methods for biomolecular structure determination at atomic level resolution. The course will cover the theory and basic principles underlying of the two major high-resolution experimental methods: X-ray crystallography and nuclear magnetic resonance (NMR), and some theoretical methods for protein structure prediction and protein molecular dynamics simulations. The course will start with a review of physico-chemical properties of biomacromolecules, their composition, and principles of their three-dimensional architecture. While all the above-mentioned methods will be covered, the in-depth emphasis will be on the determination of protein structure and dynamics in solution using NMR. The students will learn NMR pulse sequence design (including product operator formalism), principles of multidimensional NMR, methods for protein signal assignment and structure calculation, studies of protein-ligand interactions, and "model-free" analysis of protein dynamics. In addition to theoretical studies the students will get hands-on experience in NMR data analysis and in simulation of the outcome of NMR experiments on a computer.
Prerequisites: calculus, undergrad. biochemistry and physical chemistry. |
Syllabus | |
Textbooks | |
| Required: | Cantor & Schimmel, Biophysical Chemistry, W.H.Freeman |
| Van de Ven, Multidimensional NMR in Liquids, Wiley-VCH. | |
| Recommended: | Cavanagh et al., Protein NMR Spectroscopy, Acad. Press |
| M.Levitt, Spin Dynamics: basics of nuclear magnetic resonance, Wiley | |
| Tinoco et al.,Physical Chemistry. 3rd Ed., Prentice Hall, 1995 | |
| Branden & Tooze, Introduction to Protein Structure, 2nd Ed., Garland Publ | |
| Web Site for Protein Data Base: http://www.rcsb.org/pdb/ | |
| Web site for Virtual NMR Spectrometer: http://www.vsnmr.org | |