NMR of large protein systems: Solid state and dynamic nuclear polarization. Sascha Lange, Leibniz-Institut für Molekulare Pharmakologie (FMP)

Transcription

1 NMR of large protein systems: Solid state and dynamic nuclear polarization Sascha Lange, Leibniz-Institut für Molekulare Pharmakologie (FMP)

2 The Aim of the Game solution NMR other methods solid state NMR x-ray crystallography electron microscopy % of structures deposited in protein data base (PDB) solution-state NMR requires rapid reorientation of soluble biomolecules X-ray crystallography requires high-quality single crystal solid-state NMR no need for large well-ordered crystals or highly-purified proteins works for immobilised proteins, no inherent limitation on complex size

3 Anisotropic effects in solid state NMR why is anisotropy difficult? liquids: rapid random tumbling averages anisotropic chemical shifts and couplings small lines, high signal! solids: no tumbling, interactions depend on orientation of the single molecules (anisotropic) very broad lines, low signal! anisotropic interactions lead to massive line broadening! 9/26/2014 3

4 Anisotropic effects in solid state NMR why is anisotropy difficult? anisotropy of heteronuclear dipolar interaction homonuclear dipolar interactions chemical shift anisotropy anisotropic interactions lead to massive line broadening! 9/26/2014 4

5 Anisotropic effects in solid state NMR heteronuclear dipolar interaction θ B 0 +B I B 0 +B S B 0 9/26/2014 5

6 Anisotropic effects in solid state NMR homonuclear dipolar interactions θ B 0 +B I B 0 +B I B 0 flip-flop-term 9/26/2014 6

7 Anisotropic effects in solid state NMR Chemical Shift Anisotropy B 0 +B local B 0 spherical symmetry non-axial symmetry axial symmetry 9/26/2014 7

8 Anisotropic effects in solid state NMR Chemical Shift Anisotropy B 0 +B local B 0 9/26/2014 8

9 Anisotropic effects in solid state NMR how to get rid of it? 3cos = = the magic angle! 9/26/2014 9

10 Anisotropic effects in solid state NMR how to get rid of it? 3cos = = the magic angle! 9/26/

11 Anisotropic effects in solid state NMR how to get rid of it? 54.7 = the magic angle! 9/26/

12 Magic Angle Spinning (MAS) how to get rid of it? but the information is NOT LOST FOEVER! (more information at 5pm by Barth-Jan van Rossum) 9/26/

13 Magic Angle Spinning (MAS) Maximum spinning frequency depends on rotor diameter some typical diameters: 4.0 mm 15 khz (1,400,000 x g) 3.2 mm 25 khz (2,700,000 x g) 2.5 mm 35 khz (3,500,000 x g) ( x g) Solid-state NMR is brute force

14 Magic Angle Spinning (MAS) no inherent limitation on complex size : What does it mean? SH3 domain 62 residues (~7 kda) OmpG 281 residues (~34 kda) type III secretion system 80 residues)

15 Dynamic Nuclear Polarization (DNP) low sensitivity is one of the biggest bottlenecks in solid state NMR E hυ0 N β kt kt N α = e = e E = γhb 0 2π sensitivity depends on: gyromagnetic ratio γ of the nuclei the higher the better (e.g. 1 H vs. 13 C) energy difference (i.e. magnetic field strength B 0 ) the stronger the better sample temperature the cooler the better

16 Dynamic Nuclear Polarization (DNP) Why is (solid state) NMR so insensitive Small net magnetic moment (polarization) aligned with B z N 0 N β α = e E kt = e hυ kt ΔE = hv = 5.6 x J 1H T h = Js k b T = 4.1 x J k b = JK -1 E hυ0 N β kt kt 10,000 1 H spins up (I z is aligned with B z ) N α = e = e 9,999 1 H spins down (I z is aligned against B z )

17 Dynamic Nuclear Polarization (DNP) DNP = transfer of the high electron polarization to nearby nuclei CP-Spectrum of SH3 with DNP without DNP 13 C-chemical shift K E hυ0 N β kt kt N α = e = e theoretical enhancement = γ e γ n e.g. for Protons: γ e γ 1H 660 9/26/

18 Dynamic Nuclear Polarization (DNP) The DNP-Spectrometer needed amount 5 nmol / 25 µl (0.2 mm)

19 Dynamic Nuclear Polarization (DNP) The DNP-Spectrometer Gyrotron produces 250 GHz microwaves Standard 400 MHz NMR magnet Cooling Cabinet controls sample temperature ~95K 3 pressurized exchangers within one dewar Gyrotron controller liquid N2 reservoir

20 DNP-Mechanism: 1. The Solid Effect δ < ω n Tritylradical 2ω n δ norm. 1 H-enhancemet DNP (-) microwave frequency

21 DNP-Mechanism: 1. The Solid Effect δ < ω n Tritylradical 2ω n δ norm. 1 H-enhancemet DNP (+) microwave frequency

22 DNP-Mechanism: 2. The Cross Effect ω e1 - ω e2 = ω n

23 DNP-Mechanism: 2. The Cross Effect ω n > ω n > δ δ norm. 1 H-enhancemet DNP (-) microwave frequency Irradiation with ω e1 leads to at the same time:

24 DNP-Mechanism: 2. The Cross Effect ω n > ω n > δ δ DNP (+) norm. 1 H-enhancemet microwave frequency Irradiation with ω e2 leads to at the same time:

25 DNP as a Tool for Structural Biology two main drawbacks of DNP inhomogeneous broadening due to cooling homogeneous broadening due to addition of radicals fast motion cooling

26 DNP as a Tool for Structural Biology Ala55 at low temperatures we can detect different conformers! Pro45 Ala55 Pro K 95 K 293 K 95 K Modell system: SH3 26

27 DNP as a Tool for Structural Biology and we can determine coalescence temperatures! Modell system: SH

28 DNP as a Tool for Structural Biology two main drawbacks of DNP inhomogeneous broadening due to cooling homogeneous broadening due to addition of radicals

29 DNP as a Tool for Structural Biology NP the radical is causing homogeneous line broadening TOTAPOL increases T 2 -Relaxation and therefore (homogeneous) line broadening TOTAPOL increases T 1 -Relaxation line width [ppm] TOTAPOL-conzentration [mm] TOTAPOL-conzentration [mm] e.g. broader lines, causing lower S/N e.g. shorter repetition times are possible (higher S/N per time unit)

30 DNP as a Tool for Structural Biology the radical is shortening effectively CP times NP TOTAPOL causes shorter effective CP times TOTAPOL-conzentration [mm] multi dimensional experiments difficult lower signal intensities

31 DNP as a Tool for Structural Biology NP TOTAPOL leads to a reduction of detectable nuclei: measured, normalized integral modell with r = 10 Å modell with r = 9 Å a i overlapping factor a i = V i V m i 1 j=1 D j V (i V m ) V r = V V bb V e r [TTT] [TOT] = TOTAPOL-concentration

32 DNP as a Tool for Structural Biology NP PRE effect creates holes in the cheese

33 DNP as a Tool for Structural Biology, ACh- Receptor Neurotoxin II (Naja naja oxiana; NOR1) on nachr (Torpedo californica) nicotinic AChR: ionotropic (ligand gated ion-channels) parasympathetic autonomic nervous system, neuromuscular junction

34 DNP as a Tool for Structural Biology, ACh- Receptor inactivation of TOTAPOL in close proximity Linden, Oschkinat et al. J. Am. Chem. Soc. 2011

35 DNP as a Tool for Structural Biology, ACh- Receptor inactivation of TOTAPOL close proximity can help

36 DNP as a Tool for Structural Biology, ACh- Receptor just 6% of the measurement time needed 10 days 10 hours

37 DNP as a Tool for Structural Biology, RNCs ic Nul with DNP we could investigate something small in something very big and nature-like 9/26/

38 DNP as a Tool for Structural Biology, RNCs Auflösung: ca. 7,3Å Bhushan, Beckmann et al. Nature Structural & Molecular Biology (2010) we investigated the folding state of a signal peptide within the ribosomal exit tunnel is there one specific conformation of the nascent chain? what is the helix content? 9/26/

39 DNP as a Tool for Structural Biology, RNCs the ribosome is times bigger compared to the NC 10 nmol nascent chain = ca. 37 µg 10 nmol ribosomes = ca. 25mg 9/26/

40 DNP as a Tool for Structural Biology, RNCs 9/26/

41 DNP as a Tool for Structural Biology, RNCs 9/26/

42 DNP as a Tool for Structural Biology, RNCs 1 MKKIWLALAG LVLAFSASAA FATPVWISQ AQGIRSGP 37 9/26/

43 DNP as a Tool for Structural Biology??? there are lot of barriers - line broadening is a very big issue (DNP is still blobby) - short CP times prevent multi-dimensional experiments - de novo assignements ar nearly impossible - cryo hardware is difficult to maintain and construction sites - new radicals with longer electron relaxation - deuteration of samples - sample preparation (glas matrix) - new systems (more suitable) - coupling of the radical 9/26/