BCMB / CHEM 8190 Biomolecular NMR
GRADUATE COURSE OFFERING IN NUCLEAR MAGNETIC RESONANCE
SPRING 2004
"Biomolecular Nuclear Magnetic Resonance" is a course intended for all graduate students with an interest in applications of nuclear magnetic resonance (NMR) to problems in structural biology. It will begin with a treatment of the fundamentals that underlie magnetic resonance phenomena and develop this into a basis for experimental design, interpretation of data, and critical reading of the literature. The course will assume students have had some introduction to NMR through a basic course in spectroscopy or an introductory NMR course such as CHEM/BCMB 6190. Some previous exposure to elementary quantum mechanics and its applications in spectroscopy would also be useful, but we will attempt to provide sufficient background material to aid those who have not had this exposure.
There will be weekly problem sets; the sets will not be graded, but they will serve as important preparation for the midterm and the final. The sets will be posted on the website near the beginning of each week and answers will appear near the end of the week. Grades will be based on performance on the midterm and the final exam. A complete syllabus and additional information are available through the course website, http://tesla.ccrc.uga.edu/~jhp/nmr_04.
Class Time: M,W,F, 10:10-11:00
Location: This course is being taught with the cooperation of faculty at the University of Georgia, Georgia State University, Emory University, and Georgia Tech. On Monday and Wednesday of each week lectures will be given via a tele-conferencing network. At UGA, the teleconferencing room is in the South OISD Building on Hooper Street (teleconference room). The rooms at Georgia Tech and Georgia State will be posted as soon as they are available (see Dr. Gelbaum (Tech), or Drs. Yang or Germann (Georgia St). On Fridays, students will participate in aninteractive problem-solving session and software demonstrations at their local sites (VMGL in Chemistry for UGA students).
| UGA Instructors: Prestegard (JP), Urbauer (JU) Georgia State Instructors: Yang (JY), Germann (MG) Inquiries to Professor Prestegard - jpresteg@ccrc.uga.edu |
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Text: "Spin Dynamics - Basics of Nuclear Magnetic Resonance" M. H. Levitt. (Levitt) |
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Supplementary Text: "Protein NMR Spectroscopy, Principles & Practice" (Cavanagh) |
Course Syllabus
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Interactive Work Stations (Friday Labs) |
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| Exams | ||
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Holidays |
web notes| Date |
Instructor |
Topic |
Text pages |
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| I. Introduction |
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| M 1/12 |
JP |
A. Magnetic properties of nuclei and electrons - precession
(first class to coincide with GSU schedule) |
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5-32 Levitt |
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| W 1/14 |
JP |
B. Rf pulses and spin relaxation - Bloch equations |
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32-46, 626-627 |
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| F 1/16 |
JP |
Introduction to UNIX |
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| II. Instrumentation | |||||||||
| W 1/21 |
JU |
A. Instrumental considerations - a look at probes |
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72-87 Levitt |
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| F 1/23 |
JG |
Classical Simulations – with PJNMR |
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| M 1/26 |
JP |
B. Fourier transform methods and data processing | |
89-122 Levitt |
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| III. Quantum Mechanical Description - Density Matrices | |||||||||
| W 1/28 |
JP |
A. Spin operators and their time dependence | 169-184 Levitt |
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| F 1/30 |
JU |
Intro to data processing, weighting functions - MestRe-C |
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| M 2/02 |
JP |
C. Density matrix - evolution and interpretation | |
344-355 Levitt |
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| W 2/04 |
JP |
D. Second order spectra | |
226-236, 588-594 Levitt |
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| F 2/06 |
JU |
Intro to NMRPipe and NMRDraw |
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| IV. Product Operator Formalism | |||||||||
| M 2/09 |
JP |
A. Density matrix in Product Operator Form |
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355-356 Levitt |
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| W 2/11 |
JP |
B. RF pulses and evolution |
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357-384 Levitt |
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| F 2/13 |
JP |
Simulation of second order spectra (GAMMA) |
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79-93 Levitt |
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| M 2/16 |
JP |
C. Coherence transfer in COSY |
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388-398 Levitt |
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| V. Complex Pulse Sequences | |||||||||
| W 2/18 |
JP |
A. Basic heteronuclear experiments, INEPT and HSQC |
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418-434 - Levitt 410-447- Cavanagh |
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| F 2/20 |
JP |
Product Operators and Maple |
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| M 2/23 |
JP |
B. TOCSY and NOESY |
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543-569 Levitt |
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| W 2/25 |
JP |
C. Extension to 3D |
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447-467 Cavanagh |
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| F 2/27 |
JU |
Multidimensional processing NMR PIPE |
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| VI. NMR Spectral Parameters | |||||||||
| M 3/01 |
JP |
A. Scalar Coupling |
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211-216 Levitt |
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| W 3/03 |
JP |
B. Dipolar Coupling in Solids | |
209 -210 Levitt |
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| F 3/05 |
JP |
MIDTERM |
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| SPRING BREAK at UGA - no class | |||||||||
| M 3/15 |
JP |
C. Residual Dipolar Coupling |
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425 -432 Levitt |
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| W 3/17 |
JP |
D. Chemical Shifts |
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192-200 Levitt |
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| F 3/19 |
JU |
Data display and analysis using NMRDraw |
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| M 3/22 |
JP |
E. Spin relaxation and NOEs |
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513-549 Levitt |
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| VII. Assignment Strategies: Proteins | |||||||||
| W 3/24 |
JU |
A. Triple resonance experiments for proteins |
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468-530 Cavanagh |
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| F 3/26 |
JU |
Assignments using NMRView |
UPDATE |
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| M 3/29 |
JU |
B. Sequential assignment strategies in proteins | UPDATE |
533-543 Cavanagh |
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| VIII. NMR Assignments: Nucleic Acids | |||||||||
| W 3/31 |
MG |
A. Homonuclear assignment strategies for RNA and DNA |
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| F 4/02 |
JU |
Assignments using NMRView Part II |
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| M 4/05 |
MG |
B. Heteronuclear assignment strategies for RNA and DNA |
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| IX. Applications to Structure and Dynamics | |||||||||
| W 4/07 |
JP |
A. Structure determination protocols |
UPDATE |
543-554 Cavanagh |
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| F 4/09 |
JU |
REVISED Structure Calculation with CNS |
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| M 4/12 |
JP |
REVISED A. Drug discovery, SAR by NMR |
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| X. Other Applications |
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| W 4/14 |
JP |
REVISED B. Molecular motions in nucleic acids and proteins |
UPDATE |
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| F 4/16 |
JP |
Special Demo/Lecture on NMR View by Dr. Bruce Johnson |
Meet in teleconferencing rooms | ||||||
| M 4/19 |
NH |
B. Ion binding sites in macromolecules |
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| W 4/21 |
NH |
C. Bound waters in macromolecules |
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| F 4/23 | JP |
Analysis of structure with RDC's |
NEW |
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| M 4/26 |
JY |
D. Protein folding, amide exchange rates | UPDATE |
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| W 4/28 |
JY |
E. Chemical exchange rates
| UPDATE |
488-504 Levitt |
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| W 4/30 |
JP |
F. Gradients, imaging, and other NMR applications CLASS CANCELLED
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| F 5/07 | FINAL EXAM OISD Teleconferencing Room Friday, May 7 |
This will be an open book, limited time exam designed to take about 2 hours, but you will have about two and one-half hours. You may use notes you have from class and any textbook you find useful, but you must bring materials you plan to use with you to the exam; you cannot leave the room to get other materials. You may also use a calculator. There will be a mix of short questions and longer problems. Emphasis will be about 2/3 to 1/3 on material after and before the midterm respectively. (see Problem Sets page for exam examples and answers) |
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