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Course Syllabus

Lecture Schedule
       
Date Instructor TopicSuggested Reading
      L – Levitt    C – Cavanagh
I. Introduction
M 1/10 Prestegard A. Magnetic properties of nuclei and electrons - precession 5 – 32 L
W 1/12 Prestegard B. RF pulses and spin relaxation - Bloch equations 32 – 46 L, 626 – 627 L
       
II. Instrumentation
M 1/17   MLK Jr. Holiday (no class)  
W 1/19 Urbauer A. Instrumental considerations - a look at probes 72 – 87 L
M 1/24 Prestegard B. Fourier transform methods and data Processing 89 – 122 L
       
III. NMR observables – Classical and Quantum Descriptions
W 1/26 Prestegard A. Spin operators and their time dependence 169 – 184 L
M 1/31 Urbauer B. Scalar Couplings 211 – 216 L
W 2/2 Urbauer C. Spin Relaxation and NOEs 226 – 236 L, 588 – 594 L
M 2/7 Prestegard D. Chemical Shifts 192 – 200 L
       
IV. Density Matrices and Product Operator Formalism
W 2/9 Prestegard

A. Density Matrix and Simulation of Second Order Spectra   

344 – 355 L
M 2/14 Prestegard B. Density Matrix Treatment of RF Pulses and Evolution 355 – 356 L
W 2/16 Prestegard C. Density Matrix in Product Operator Form 357 – 384 L
V. Basic Pulse Sequences
M 2/21 Prestegard A. Coherence transfer in COSY 388 – 398 L
W 2/23 Prestegard B. Basic heteronuclear experiments INEPT and HSQC 418 – 434 L, 410 – 447 C
M 2/28 Prestegard C. TOCSY and NOESY 543 – 569 L
W 3/2 Prestegard D. Extension to 3D 447 – 467 C
F 3/4   ----- Midterm -----  
       
VI. Assignment Strategies: proteins and nucleic acids
M 3/7 Urbauer A.Triple resonance experiments for proteins 468 – 530 C
W 3/9 Urbauer B. Sequential assignment strategies in proteins 533 – 543 C
M 3/14   Spring Break (no class)  
W 3/16   Spring Break (no class)  
M 3/21 Germann C. Homonuclear assignment strategies for RNA and DNA  
W 3/23 Germann

D. Heteronuclear assignment strategies for RNA and DNA

NOESY Solution

 
       
VII. Applications to Structure and Dynamics
M 3/28 Prestegard A. Molecular motions in nucleic acids and proteins  
W 3/30 Prestegard B. Dipolar Coupling in Solids 203 – 210 L
M 4/4 Prestegard C. Residual Dipolar Coupling 425 – 432 L
W 4/6 Prestegard D. Structure determination protocols 543 – 554 C
       
VIII. Other Applications
M 4/11 Hud

A. Ion binding sites in macromolecules - Part 1

    Reference

  
W 4/13 Hud

B. Ion binding sites in macromolecules - Part 2

    PDF file of lecture slides

 
M 4/18 Prestegard C. Drug discovery, SAR by NMR, STD, Tr-NOEs  
W 4/20 Prestegard D. TROSY, Paramagnetic Effects  
M 4/25 Yang E. Chemical exchange rates  
       
IX. Advanced Techniques
W 4/27 Yang A. Protein folding, amide exhange rates 488 – 504 L
M 5/2 Prestegard B. Gradients, imaging and diffusion  
F 5/6   FINAL EXAM (8:00 – 11:00) Room 508, Chemistry