BCMB / CHEM 8190 Biomolecular NMR
GRADUATE COURSE OFFERING IN NUCLEAR MAGNETIC RESONANCE (Fall 2002)
"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_02.
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 Journalism building on Hooper Street (JRL-303). The rooms at Georgia Tech and Georgia State will be posted as soon as they are available (see Dr. Gelbaum (Tech), Dr. Lynn (Emory) or Drs. Yang or Germann (GaSt). On Fridays students will be introduced to software tools in an interactive workstation session at their local sites (MGL in Chemistry for UGA students).
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UGA
Instructors: Prestegard (JP), Legault (PL), Omichinski (JO)
Georgia State Instructors: Yang (JY), Germann (MG) Emory Instructors: Lynn (DL) Inquiries to Professor Prestegard - jpresteg@ccrc.uga.edu |
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Text: "Protein
NMR Spectroscopy, Principles & Practice" |
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Supplementary Text: "2D
NMR: Density Matrix and Product Operator Treatment" |
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Supplementary Text: "Nuclear
Magnetic Resonance Spectroscopy" |
Course Syllabus
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Interactive Workstation Sessions (Friday Labs) |
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Holidays |
class
notes
web notes
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Date |
Instructor |
Topic |
Text pages |
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I. Introduction |
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M 8/19 |
JP |
B.
Magnetic nuclei and biological applications (first class to match GaTech and GSU schedules) |
1-24 |
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W 8/21 |
JP |
C.
Rf pulses and spin relaxation - Bloch equations |
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F 8/23 |
PL |
Introduction to UNIX |
131-145 |
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II. Instrumentation |
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M 8/26 |
JP |
A.
Instrumental considerations - a look at probes |
95-105 |
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W 8/28 |
JP? |
B. Fourier transform methods and data Processing
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105-111 |
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F 8/30 |
JP? |
Classical Simulations – with PENCIL |
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M 9/02 |
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Labor Day - no class |
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III. Quantum Mechanical Description - Density Matrices |
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W 9/04 |
JP |
A.
Spin operators and their time dependence |
25-33 |
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F 9/06 |
PL |
Intro to data processing, weighting functions |
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M 9/09 |
JP |
C.
Density matrix - evolution and interpretation |
33-37 |
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W 9/11 |
JP |
D.
Second order spectra |
37-40 |
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F 9/13 |
PL |
Felix - Intro to Macros and Felix |
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IV. Product Operator Formalism |
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M 9/16 |
JP |
A.
Density matrix in Product Operator Form |
73-79 |
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W 9/18 |
JP |
B.
RF pulses and Evolution
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79-93 |
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F 9/20 |
JP |
Simulation
of second order spectra (GAMMA) |
79-93 |
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M 9/23 |
JP |
C.
Product operators for two spins |
185-203 |
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V. Complex Pulse Sequences |
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W 9/25 |
JP |
A.
Basic homo- and hetero- nuclear experiments, COSY and HSQC |
411-446 |
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F 9/27 |
JP |
Product Operators and Maple |
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M 9/30 |
PL |
B.
TOCSY and NOESY |
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W 10/02 |
PL |
C.
Extension to 3D |
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F 10/04 |
PL/JO |
multidimensional processing NMR PIPE |
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VI. NMR Spectral Parameters |
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M 10/07 |
DL |
A. Dipolar Coupling in Solids |
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W 10/09 |
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-----
Midterm ----- |
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F 10/11 |
JP |
Lab |
518-528 |
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M 10/14 |
JP |
B. Scalar Coupling |
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W 10/16 |
JP |
C. Chemical shifts & Spin relaxation
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H188-216, 270-286 |
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F 10/18 |
PL/JO |
Data display using NMR Draw |
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VII. Assignment Strategies: Proteins |
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M 10/21 |
JO |
A.
Protein secondary structure |
447-467 |
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W 10/23 |
JO |
B.
Triple resonance experiments for proteins |
468-517 |
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F 10/25 |
PL |
Assignments using NMR View |
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VIII. NMR Assignments of Nucleic Acids |
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M 10/28 |
PL |
A.
Heteronuclear assignment strategies for RNA and DNA |
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W 10/30 |
PL |
B.
Heteronuclear assignment strategies for RNA and DNA |
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F 11/01 |
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FALL BREAK at UGA - no class |
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M 11/04 |
JO |
C.
Sequential assignment strategies in proteins |
533-543 |
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IX. Applications to Structure and Dynamics |
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W 11/06 |
JO |
A.
Structure determination protocols |
543-554 |
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F 11/08 |
PL |
Assignments using NMR View II |
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M 11/11 |
MG |
B.
Molecular motions in nucleic acids and proteins |
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X. Other Applications |
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W 11/13 |
JP |
A.
Drug discovery, SAR by NMR |
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F 11/15 |
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Structure Calculation with CNS |
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M 11/18 |
JP |
A. Residual
dipolar couplings and pulsed field gradients |
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W 11/20 |
NH |
B.
Ion binding sites in macromolecules |
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F 11/22 |
PL |
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M 11/25 |
NH |
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M 12/02 |
JY |
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W 12/04 |
JY |
E.
Chemical exchange rates |
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F 12/06 |
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TH 12/12 |
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FINAL EXAM |
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