Cours RMN Master 2 Chimie et physico-chimie: des molécules aux bio-systèmes

Transcription

1 Monique CHAN-HUOT Cours RMN Master 2 Chimie et physico-chimie: des molécules aux bio-systèmes Séance 4 et 5: 21/11/2011 et 28/11/2011 RMN et biologie structurale (stratégies de marquage isotopique et excpérience RMN) Produits d opérateurs Littérature: NMR: the toolkit, P. J. Hore, J. A. Jones, S. Wimperis, Oxford University Press, New york, 2000 Cours de J. Mispelter Références citées dans les diapos

2 13 Protein Data Base C (pdb) NMR SPECTRA recordsat 77 DIFFERENT 243 protein ph structures X-Ray 87 % solution NMR 12 % electron microscopy hybrid solid-state NMR 0.1 % fiber diffraction electron crystallography neutron diffraction

3 chemical shifts region for ptoteins

4 13 influence of C NMR the strength SPECTRA AT ofdifferent the magnetic ph field

5 13 C NMR SPECTRA AT DIFFERENT ph determination of the structure of a big biomolecule by solution NMR Quantitative dynamics and binding studies of the 20S proteasome by NMR RemcoSprangers& Lewis E. Kay Nature 445,

6 13 limits of C NMR liquid-state SPECTRA NMR AT DIFFERENT of proteins ph

7 13 example C NMR SPECTRA of a solid-state AT DIFFERENT NMRpH Atomic-Resolution Three-Dimensional Structure of HET-s( ) Amyloid Fibrils by Solid- State NMR Spectroscopy Hélène Van Melckebeke, Christian Wasmer, Adam Lange, Eiso AB, Antoine Loquet, Anja Böckmann, and Beat H. Meier*, J. AM. CHEM. SOC. 2010, 132,

8 13 limitations C NMR SPECTRA of solid-state AT DIFFERENT NMRpH microcristalline lyophilized Preparation of protein nanocrystals and their characterization by solid state NMR Rachel W. Martin and Kurt W. Zilm Journal of Magnetic Resonance 165 (2003)

9 13 C CP MAS of microcrystals of C-ter centrine + XPC P17 21 T, 1.3 mm, 40 khz CO C aromatic CHα CH 3 Ala + Ile spherulites and plates 9 T 2.5 mm, 10 khz CHβ Ser+Thr mostly plates 9 T, 2.5 mm, 10 khz mostly spherulites δ 13 C / ppm

10 13 limitations C NMR SPECTRA of solid-state AT DIFFERENT NMRpH

11 gene cloning into a plasmid vector vector interested gene clone + insertion molecular recombination cleavage with restriction endonuclease ligase enzyme A A T TC G A A T TC G staggered cuts with cohesive ends G C T T AA G C T T AA A A T TC G G C T T AA + A A T TC G G C T T AA

12 purification of alanine racemase transformation multiplication with ampicillin 2 days 1 day Expression with IPTG sonication with lyzozyme ½ day

13 purification of alanine racemase heat 70 C streptomycin treatment 1 day Lys 2 days OH column purification, concentration, hydroxylamine treatment P O H N OH NH 2 OH P O H N H OH N N 3-5 days Total time purification = days without cloning part 3.3 mg cost 154 euros (Sigma Aldrich)

14 highlight pictures

15 production of 13 C, 15 N and 2 H protein STEP 1 STEP 2 STEP 3 5 l bacteria culture in M9 (H 2 O, 6 h) washing (3 x centrifugation g, 25 C) 5 l M9 (D 2 O) + 13 C-( 2 H)-Uglucose + 15 NH 4 Cl + IPTG 200 um expression (14 h) purification yield: 100 mg

16 production 13 C- 15 N and 13 C- 15 N-D 2 O 12 x M9 medium composition 1 l D 2 O filtered (235 ) 2 mm MgSO 4 3 um vit. B1 100 um CaCl 2 3 um Fe.SO 4 30 ug.l -1 Cm 75 ug.l -1 Km 3 g 13 C, 2 H-U-D-glucose (255 ) 1 g 15 NH 4 Cl (11 ) 5 l ~ euros 1 l culture in M9 medium (Km, Cm) for 1h diluted in 4 l of M9 (6 h) 3 x centrifugation 5 min g, 25 C 4 l culture in M9 medium (Km, Cm) in D 2 O containing 13 C-( 2 H)-U-glucose and 15 NH 4 Cl DO = 0.25 DO = IPTG 200 um after 1 h culture stopped after 14 h DO = 2.0

17 purification of the human centrine 2 C terminal lysis French press heating T bath = 62 C for 10 min. DEAE 10 mm EDTA! Sephalex 1.5 % ammonium bicarbonate concentration Ph-TSK 10 mm EDTA! 13 C, 15 N, 2 H m UV-vis = 110 mg m lyoph.= 180 mg + 13 C, 15 N m lyoph.= 75 mg

18 13 how toc read NMR SPECTRA a 3D NMR AT DIFFERENT experiment ph?

19 HSQC: hetero single quantum coherence

20 HSQC: C-ter Human centrine + XPC P17

21 NOESY

22 TOCSY

23 HNCO

24 HNCACB HNCACB

25 Strip plot C-ter Human centrine + XPC P17

26 IVL : Isoleucine Valine Leucine

27 Labelling scheme Blue: 1,3-glycerol Red: 2-13C glycerol isotopomers

28 protein segmental labelling

29 protein trans-splicing

30 assignement method

31 Calcul d un ensemble de structures

32 ensemble de structures calculées

33 cryo probe

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36 13 vector presentation C NMR of SPECTRA I AT DIFFERENT ph x, I y and I z for a single spin 1/2

37 13 transformation C NMR SPECTRA of the prodcut AT DIFFERENT operators ph

38 13 representation C NMR of the SPECTRA spectra AT and DIFFERENT energy phdiagrams

39 13 schematic NMR C spectrum SPECTRA AT of DIFFERENT a pair ofph spin 1/2

40 13 C NMR SPECTRA AT DIFFERENT ph vector representation of some product operator for a 2 spin system IS

41 13 C NMR SPECTRA AT DIFFERENT ph representation of some of the product operators for a two spin IS system

42 13 transformation C NMR SPECTRA of the AT product DIFFERENT operators ph

43 13 C NMR SPECTRA 2D NMR AT DIFFERENT ph 2D Fourier transform

44 13 C NMR SPECTRA AT DIFFERENT ph evolution of the magnetization vector during the pulse