BCMB / CHEM 8190 Biomolecular NMR GRADUATE COURSE OFFERING IN NUCLEAR MAGNETIC RESONANCE

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1 BCMB / CHEM 8190 Biomolecular NMR GRADUATE COURSE OFFERING IN NUCLEAR MAGNETIC RESONANCE "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 and functional 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.

2 Syllabus I. Introduction A. M 1/11 Prestegard Magnetic properties of nuclei and electrons precession 5-32 L B. W 1/13 Prestegard RF pulses and spin relaxation - Bloch equations L, L II. Instrumentation A. M 1/18 MLK Jr. Holiday (no class) B. W 1/20 Prestegard - a look at probes Instrumental considerations L C. M 1/25 Prestegard Processing Fourier transform methods and data L * Friday Labs are scheduled separately intro to computer systems 1/08, 1/15

3 Biomolecular NMR 2010 Biomolecular NMR - short history ~ 1985 first protein structure Compared to X-ray ~ 1953 first protein structure Today ~ 13 % of structures in the PDB come via NMR higher for nucleic acids Unique applications weak associations, membrane associations, in-cell observation New challenges need new methods NMR is still an evolving science

4 Can NMR Make a Unique Contribution? Membrane Proteins, Protein-Protein Interactions, Ligand Binding

5 NMR and Biology: Recognition Bloch and Purcell Nobel Prize in Physics 1991 Richard Ernst Nobel Prize in Chemistry 2002 Kurt Wuthrich Nobel Prize in Chemistry 2003 Lauterbur and Mansfield Nobel Prize in Physiology and Medicine

6 Computers Were Primitive in 1966

7 Varian HR 220 Early Superconducting Magnets Required a Lot of Care And Feeding

8 High Field (220 MHz), but Still 1D CW NMR

9 80 s Approach: 2D 1 H- 1 H NMR: 9 kda Protein assign resonances, collect NOE s, calculate structure

10 Extension to 3D: Through-bond Correlations in Peptides Isotope Labeling is Key

11 Today Very Large Systems Can Be Studied: Proteasome Subunit Sprangers, R., and Kay, L.E Probing supramolecular structure from measurement of methyl H-1-C-13 residual dipolar couplings. Journal of the American Chemical Society 129:

12 NMR is widely applicable to structure and function of biomolecules 1. Baldus, M Biological solid-state NMR, methods and applications. Journal of Biomolecular Nmr 39: Boehr, D.D., Dyson, H.J., and Wright, P.E An NMR perspective on enzyme dynamics. Chemical Reviews 106: Flinders, J., and Dieckmann, T NMR spectroscopy of ribonucleic acids. Progress in NMR Spectroscopy 48: Lindon, J.C., Holmes, E., and Nicholson, J.K Metabonomics in pharmaceutical R & D. Febs Journal 274: Mittermaier, A., and Kay, L.E New tools provide new insights in NMR studies of protein dynamics. Science 312: Tamm, L.K., and Liang, B.Y NMR of membrane proteins in solution. Progress in NMR Spectroscopy 48: Tzakos, A.G., Grace, C.R.R., Lukavsky, P.J., and Riek, R NMR techniques for very large proteins and RNAs in solution. Annual Review of Biophysics and Biomolecular Structure 35: Yee, A., Gutmanas, A., and Arrowsmith, C.H Solution NMR in structural genomics. Current Opinion in Structural Biology 16: Zartler, E.R., and Shapiro, M.J Protein NMR-based screening in drug discovery. Current Pharmaceutical Design 12:

13 Spin Properties B0 µ = γ I Iz = hm E = -µ B0 for I = 1/2 m = -1/2 p = exp(-ei/kt)/z E ν = γb0/2π Mz = γhσipimin0 B0 m = 1/2 2 2 = N0γ h B0 I(I+1) 3kT

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15 Spin ½ Nuclei are Most Useful in Biomolecular NMR

16 Polypeptides are Rich in NMR Active Nuclei Amide 15 N Amide 1 H Cβ 13 C Cα 1 H C 13 C Me 1 H Cα 13 C

17 Nuclear Properties Reference: Cottingham & Greenwood (1986) Not all nuclei have magnetic moments, Why? Not all nuclei are equally abundant, Why? Spins vary, Why? Magnetogyric ratios vary, Why?

18 Fundamental Particle Properties e - N S Beam in field gradient Stern Gerlach experiment: Na atom - 1 unpaired electron Two spots implies quantized moments: +/- 1/2 protons and neutrons are also spin 1/2 particles

19 Current Loop Model for Magnetic Moments M r Area, S i M = i S i in Coulomb s -1 S in m 2 M in JT -1 (Tesla) Estimates: i = -ev/(2πr), S = πr 2, M (or µ) = -erv/2 µ = -e(r x v)/2, L = m e r x v, µ = -e/(2m e ) L = γ L = γh/(2π)l γ = -g (e/(2m e )), g = Lande g factor

20 Values of Particle Magnetogyric Ratios Electron: g 2, γ e = x T -1 s -1 Proton: expect 1/m p dependence, 1/2000 and positive 2.7 x 10 8 T -1 s -1 Neutron: similar mass to proton -1.8 x 10 8 T -1 s -1

21 Shell Model of the Nucleus V(r) Simple Rules: r 0 0 r 0 a) spherical particle in a box potential ψ = R nl (r) Y lm (θ,φ), E(n,l) ladder of energy levels like H atom, but all ls allowed b) strong coupling of spin and orbit angular momentum quantized total: j = l +/- 1/2 for spin 1/2 particle larger j, lower energy (usually)

22 Shell Model Rules Continued c) Treat protons and neutrons separately and fill from bottom up assuming 2j + 1 degeneracy d) Assume particle pair strongly within levels: only unpaired spins count - total spin angular momentum given by j of level for unpaired spin e) sign of moment depends on sign of moment for fundamental particle but changes sign when moment subtracts instead of adds to l in giving j

23 Energy Level Diagram n+1 j degeneracy total 2s 1/ d 1p 3/2 4 5/2 6 1/ /2 4 1s 1/2 2 2

24 Examples of Nuclear Properties 16 8 O - most abundant in Earth s crust. 8 protons, 8 neutrons - 2 magic #s. All particles paired - no moment C - 6 protons, 7 neutrons. All protons paired. One neutron unpaired in 1p 1/2. j = l - 1/2. Therefore, negative moment subtracts from l. Positive γ spin 1/2 particle