Biochemistry 765 Syllabus, Spring 2003

Tu,Th 1:30-2:48 PM, BioSci 676, 3 credits

Weeks 6-10: Biomolecular NMR spectroscopy

http://www.biosci.ohio-state.edu/~mfoster/biochem765

downloads: 765_downloads

Mark P. Foster

Foster.281@osu.edu

Office: 734 Riffe Bldg.

Ph: 2-1377, LAB: 688-8146

Recommended Texts:

Cavanagh, et al., Protein NMR, Academic Press, 1996

Evans, Biomolecular NMR Spectroscopy, Oxford University Press, 1995 (revised 1996)

Levitt,  Spin Dynamics,  Wiley, 2001

Other Texts:

Jardetsky and Roberts, NMR in Molecular Biology, Academic Press, 1981

Derome, Modern NMR Techniques for Chemistry Research, Pergamon Press, 1987

Grant and Harris, Eds., Encyclopedia of Nuclear Magnetic Resonance, Wiley, 1996

Wütrich, NMR of Proteins and Nucleic Acids, Wiley, 1986

Ernst, Bodenahusen & Wokaun, Principles of Nuclear Magnetic Resonance in One and Two Dimensions, OUP, 1987

 

Journals:

Journal of Magnetic Resonance (J. Magn. Reson.)

Journal of Biomolecular NMR (J. Biomol. NMR)

Progress in NMR Spectrocopy

Journal of the American Chemical Society (J. Am. Chem. Soc.)

 

On-line:

http://www.nmr.de/ (NMR Knowledge Base, Germany) *

http://www.cis.rit.edu/htbooks/nmr/bnmr.htm (Joseph P. Hornak, RIT)

http://www.bmrb.wisc.edu/ (BioMag Res Bank)

http://www.spincore.com/nmrinfo/nmr_s.html (U. Florida NMR Server)

Grading:

Problem sets: 20%

Midterm exam: 80%

Biochem 765 Course Outline

The NMR phenomenon

Jardetsky & Roberts, Ch. II, IV; Evans, Ch. 1; Cavanagh, Ch 1, 5; Keeler, Intro to Q. Mech.; Keeler, Product Operators.

1.     Nuclear spin, precession, spin states, equilibrium magnetization, vector model, rotating frame, radio frequency pulses, Fourier transform, chemical shift

2.     Spin echoes, scalar coupling, product operators, magnetization/polarization transfer

3.     Dynamics: the NMR timescale, relaxation, NOE, dynamics (fast, intermediate and slow exchange).

Beyond 1D 1H NMR

            Evans, Ch. 2, Cavanagh, Ch. 4

4.     2D NMR: COSY, NOESY, TOCSY; Heteronuclear NMR; INEPT, HSQC

5.     3D NMR: NOESY-HSQC, TOCSY-HSQC triple resonance.

NMR properties of biomolecules

            Evans, Ch. 4, 9

6.     Proteins: amino acids, chemical shifts, spin systems, secondary structures, NOEs, coupling constants

7.     Nucleic acids: nucleotides, chemical shifts, spin systems, structures, base pairing

Structure determination

            Evans, Ch. 3

8.     Distance geometry, restrained molecular dynamics (annealing) simulations

Specific examples

9.     Molecular recognition, chemical shift mapping, filtered experiments, SAR by NMR, transfer NOE, drug design, complexes

10.  Dynamics from heteronuclear relaxation: HIV protease, DHFR, SH2 domains

Exam