Nuclear Magnetic Resonance
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1 Nuclear Magnetic Resonance Lectures for CCB 538 James Aramini, PhD. CABM 014A J.A.! 04/21/14!
2 April 21!!!!April 23!! April 28! Outline 1. Introduction / Spectroscopy Overview! 2. NMR Spectroscopy Theory and Practice! 3. Protein NMR & Resonance Assignment! 4. Structure Determination &!!Biological NMR Applications!
3 ! Introduction The Tree of Knowledge of Science!!!!Richard Ernst!!(Nobel Prize in Chemistry 1991)! Medicine! Biology! Chemistry! Richard Ernst! Father of modern NMR! Nobel Prize 1991!! Physics!
4 Biological Spectroscopy! Spectroscopy is the study of matter and its properties by investigating light, sound, or particles that are emitted, absorbed or scattered by the matter under investigation.!!!!! E = hν
5 Biological Spectroscopy NMR Spectroscopy! Infrared! (for 2o structure)! X-ray Crystallography! UV Spectroscopy! Circular! Dichroism! Mass! Spectrometry! ! Actual:! ! + H/D exchange! λ = 280nm proteins! λ = 260nm nucleic acids!
6 NMR: Historical Timeline 1946: Bloch, Purcell: first 1 H NMR spectrum 1913: First X-ray Structure (Bragg; Diamond) 1950: Proctor, Yu: 14 N NMR spectrum of NH 4 NO 3 Dickinson: 19 F NMR of fluorinated compounds -> concept of chemical shift 1953: Overhauser effect -> NOE -> internuclear distance information 1966: Ernst: Fourier Transform ( FT ) NMR 1971: Jeener: 2D FT NMR 1985: Wüthrich: first protein NMR solution structure BPTI (6.5 kda; 58 a.a.); homonuclear ( 1 H) 1990: Bax, Kay, Wagner, others: 3D NMR + 13 C, 15 N isotopic labeling protein NMR assignment/structure To date: Explosion of technical and experimental advances 1958: First X-ray crystal structure of protein (Kendrew et al) Myoglobin (17 kda; 153 a.a.)
7 NMR: Historical Timeline 1950: Frequency shift (chemical shift) Dickinson: 19 F NMR in Tesla = 10,000 Gauss -> 0.7 Tesla field -> 30 MHz instrument δ = 117 ppm Literature ( 19 F vs. CFCl 3 ): SbF 3 : 85 ppm BeF 2 : -20 ppm ΔField Consider: 600 MHz spectrometer -> 14.1 Tesla
8 NMR: Historical Timeline 1966: Continuous Wave (CW) vs. Fourier Transform (FT) CW! FT! CW: field/frequency sweep ( OLD ) FT: simultaneous excitation ( modern NMR ) - signal averaging (S/N) - higher resolution - PW excitation SW - pulse sequence programming - line shape distortions (vs. CW)
9 John Kendrew! Nobel Prize 1962! Protein Structure Determination: Xray vs. NMR X-ray NMR diffracting crystals observe heavy atoms 1920s 1 st structure of protein: 1950s Practical Aspects Producing enough protein for trials; SeMet labeling Crystallization time and effort Crystal quality / stability Synchotron beam lines Kurt Wüthrich Nobel Prize 2002! solution or solid state observe distances between H s 1940s 1 st structure of protein: 1985 Practical Aspects Producing enough ( 2 H) 13 C/ 15 N labeled protein for collection Sample conditioning Size of protein Spectral analysis is slow and error prone
10 NMR Spectroscopy: A Short Course
11 NMR Spectroscopy: A Short Course Typical Applications of NMR: 1) Structural (chemical) elucidation - Natural product chemistry - Synthetic organic chemistry - analytical tool of choice of synthetic chemists - used in conjunction with MS and IR 2) Study of dynamic processes - reaction kinetics - study of equilibrium (chemical or structural) 3) Structural (three-dimensional) studies - Proteins, Protein-ligand complexes - DNA, RNA, Protein/DNA complexes - Polysaccharides 4) Drug Design - Structure Activity Relationships by NMR 5) Solid State NMR 6) Medicine - MRI - Metabolomics O NH OH Taxol O O HO O NMR Structure of MMP-13 complexed to a ligand O O O O O O O OH MRI images of the Human Brain
12 Nuclear Spin B o B o = 0 B o > 0 Randomly oriented Highly oriented B o > 0 β ΔE = h ν N like bar magnets B o = 0 α S
13 Nuclear spin µ = γ I h µ - magnetic moment γ - gyromagnetic ratio I - spin quantum number h - Planck s constant m I magnetic quantum number µ Nuclear Spin I is a property of the nucleus! Mass # Atomic # I!! Odd Even or odd 1/2, 3/2, 5/2!! Even Even 0!! Even Odd 1, 2, 3..! NMR INACTIVE! I = 0! NMR ACTIVE I = ½! I > ½!! quadrupolar!
14 Every element has at least 1 NMR active isotope
15 Nuclear Spin Energy Levels 2I + 1 nuclear energy levels => 2I transitions!!! I = ½ I > ½ ΔE = γhb o = hν L I = 1! I = 3 / 2!
16 NMR Sensitivity and Magnet Technology ΔE = h ν α B 0 Increase in magnet strength is a major means of increasing Sensitivity S/N α (B 0 ) 3/2 $0.8M! $1.5M! $4.0M! 14.1 T 18.8 T 21.2 T!! 1 Tesla = 10,000 G! Earth s magnetic field: 0.6G!
17 NMR Radio 15 N! 13 C! 31 P! 1 H! MHz! MHz! ! ΔE = h ν o ΔE = γ h B o / 2π Isotope Net Spin γ / MHz T -1 Abundance / % 1 H 1/ H H 1/ P 1/ Na 3/ N gyromagnetic ratio! 15 N 1/ C 1/ F 1/
18 NMR Spectroscopy: A Short Course Let s do a simple! experiment:! B o z 90 o pulse B o z M o x B 1 on x B 1 M xy y ω ω 1 = γb 1 y 1 ω 1 Free Induction Decay (FID) t1 sec [Time (s)] FT Spectrum [Frequency (Hz)]
19 NMR Spectroscopy: A Short Course NMR Vocabulary Observable Name Quantitative Information Peak position Chemical shift (δ) δ(ppm) = [ν obs ν ref / ν ref ] x 10 6 chemical (electronic) (ppm) environment of nucleus Peak Splitting Coupling Constant (J) peak separation neighboring nuclei (Hz) (intensity ratios) (torsion angles) Peak Intensity Integral unitless (ratio) nuclear count (ratio) relative height of integral curve T 1 dependent Peak Shape Line width Δυ = 1/πT 2 molecular motion (Hz) peak half-height chemical exchange dynamics δ
20 NMR Spectroscopy: A Short Course Chemical Shift ΔE = hν L = h (1 σ) γb o / 2π shielding constant! (local fields at nucleus)! electrons electrons in B 0 => current => tiny field opposing B 0! e- withdrawing! inductive effect!e- donating!!!
21 NMR Spectroscopy: A Short Course Chemical Shift!!! ring current effect!! Deshielding! δ! Shielding! δ! Definition: 1 H ν ref (= 0 ppm) organic: TMS!!!!!!aqueous: DSS
22 NMR Spectroscopy: A Short Course Chemical Shift Dispersion: 1 H < 13 C (!) 1 H! 13 C!
23 NMR Spectroscopy: A Short Course Spin-Spin Coupling (a.k.a. Scalar Coupling; J-Coupling): - Through-bond interaction between nuclei via electrons - Multiplet = 2nI + 1 (n = # equivalent neighboring nuclei) 2-4 bonds! CH 3 CHCl 2!
24 NMR Spectroscopy: A Short Course Spin-Spin Coupling in Biological NMR: I. Information on torsional angles => structural information H! H! θ H! C! C! H! J related to torsional angle between coupled nuclei - Karplus J(φ) = Acos 2 φ + Bcosφ + C Phi in Proteins:! H N H α 3 J HNHα Sugar Puckering:! S N H2ʼ H1ʼ H2ʼ H1ʼ 3 J H1ʼH2ʼ 7-8 Hz 1 Hz
25 NMR Spectroscopy: A Short Course Spin-Spin Coupling in biological NMR: II. 1 H-X coupling (X = 13 C, 15 N, 31 P) 1 J( 1 H- 13 C) Hz 1 J( 1 H- 15 N) Hz i. Extremely important in ii. Residual Dipolar Couplings multi-dimensional NMR => experimental set-up 15 N isotropic aligned INEPT 1 H
26 NMR Spectroscopy: A Short Course Nuclear Relaxation: The Core of NMR Relaxation: magnetization returning to equilibrium state after rf pulse described by 2 time constants! T 2!!!! T 1 T 2 spin-lattice spin-spin longitudinal transverse α sampling rate α 1/Δν 1/2! inversion recovery T 2 T 1 spin-echo / CPMG
27 NMR Spectroscopy: A Short Course T 1 and T 2 are intimately related to molecular motion/dynamics Many Nuclear Relaxation Mechanisms: I = ½ Dipole-Dipole:!!α r -6 Chemical Shift Anisotropy (CSA): α B 2! 0 Scalar Coupling: X-Y (Y = I > ½)! Others.!!I > ½ Quadrupolar: extremely efficient! Principle relaxation mechanism for: 1 H, 13 C- 1 H, 15 N- 1 H
28 NMR Spectroscopy: A Short Course T 1 and T 2 are intimately related to molecular motion/dynamics Dipole-Dipole Relaxation and Molecular Motion (τ c ): narrow signals broad signals
29 An NMR Spectrometer magnet transmitter Pulse generator Pr obe Fr equency synthesizer switch ADC Computer SPH 020 sample amplifier AF amplifier detector RF am plifier
30 NMR Probes and Samples NMR Probes NMR Samples RT vs. CRP! 270 μl! 40 μl! 400 μl! NMR Robotics
31 NMR Spectroscopy: A Short Course Sample Preparation: Biological Solution NMR I. Concentration: ca. 0.1 to 1 mm range (ALOT!) II. Volume: 1.7-mm tube: 40 μl (sample limited) 5-mm tube: μl (Shigemi) III. ph: typically < 7 (avoid NH exchange) IV. Buffer: i. 1 H NMR: try to avoid big buffer peaks; deuteration ii. isotope edited: not a big issue V. Salt: increases pulse lengths and bad for CRP; < 500 mm VI. T, η: anything that τ c is generally good ( Δν 1/2 ) => η and T (if your protein can withstand it) VII. D 2 O: 5-10% D 2 O for a lock ; 100% also used VIII. Labeling: 15 N, 13 C/ 15 N, 2 H/ 13 C/ 15 N.. Peptide NH exchange vs. ph
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