Remarks on methyl protonation in large molecules. Peter Schmieder
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1 Remarks on methyl protonation in large molecules
2 NMR on large proteins 2/43 If the size of proteins under investigation by solution state NMR increases, several problems arise: The number of resonances increases without an increase in spectral dispersion The relaxation of the nuclei involved becomes increasingly efficient, the lines get broader and the transfer of magnetisation necessary during the NMR experiments becomes less efficient (since the J couplings do not change)
3 NMR on large proteins 3/43 The number of signals increases spectrin-sh3 (62 aa) Cph1-2 (514 aa)
4 NMR on large proteins 4/43 The lines get broader, making magnetization transfer inefficient 1 Hz 10 Hz 50 Hz ppm ppm ppm
5 NMR on large proteins 5/43 Recipes against the increasing number of signals are higher dimensionality and selective labeling, those against increasingly faster relaxation are deuteration TROSY Which can be used independently or jointly
6 Deuteration and TROSY 6/43 The main source of relaxation is different for the different nuclei involved protons ( 1 H) carbon ( 13 C) nitrogen ( 15 N) other protons directly bound proton directly bound proton An important difference between the protons bound to carbon and to nitrogen is the exchange with water
7 Deuteration and TROSY 7/43 Deuteration normal protein deuterated protein = H - C = H -N
8 Deuteration and TROSY 8/43 Deuteration Proton-spins are diluted, the carbons loose their main relaxation source H H H N D D H N H H N H H C H H H D D H N D D C D D D / H ~ 1/6.5 C C D=1 D=0,02
9 Deuteration and TROSY 9/43 But deuteration does not help with the nitrogen nuclei, they still have there main source of relaxation. With TROSY (Transverse Relaxation Optimized SpectroscopY) we use relaxation interference to obtain narrower lines for nitrogen and nitrogen-bound protons
10 Deuteration and TROSY 10/43 The interference between CSA and dipolar relaxation is difficult to see with small molecules 15 N-HSQC 15 N-HSQC no decoupling
11 Deuteration and TROSY 11/43 But we know the four components of an HN-multiplet represent different spin states ( and ). As it turns out the interaction between CSA and DD is different for each component N R H ~ (D HN + CSA H ) R H ~ (D HN -CSA H ) R N ~ (D HN + CSA N ) R N ~ (D HN -CSA N ) H
12 Deuteration and TROSY 12/43 And indeed: with large molecules one line each of 1 H and 15 N is narrow, so one of the four components will be particularly narrow as well 15 N-HSQC 15 N-HSQC no decoupling 15 N(ppm) H(ppm) H(ppm)
13 Deuteration and TROSY 13/43 The rates are field-dependent and thus the maximum effect is achieved at 950 MHz 900 MHz 900 MHz
14 Deuteration and TROSY 14/43 To obtain a TROSY- spectrum we have to eliminate three lines which can be done by appropriate phase cycling 15 N-HSQC no decoupling 15 N(ppm) TROSY 15 N(ppm) H(ppm)
15 Methyl protonation: precursors 15/43 But having thus eliminated all the carbon bound protons there is also the problem of a lack of restraints in structure calculation An initial solution was a deuteration of 75%, but that caused problems with isotopomers and sensitivity A better solution was methyl protonation
16 Methyl protonation: precursors 16/43 The original idea was to use pyruvate Labeling of Val Leu Ile ( -CH 3 ) Ala at different amount + scrambeling Rosen et al. J.Mol.Biol. 263, (1996)
17 Methyl protonation: precursors 17/43 To avoid scrambeling other keto acids were used Labeling of Val Leu Ile ( -CH 3 ) -keto butyric acid -keto valeric acid
18 Methyl protonation: precursors 18/43 Other pattern -keto butyric acid -keto valeric acid relaxation studies linear chain
19 Methyl protonation: SH3 19/43 SH3(CN) SH3(DCN) SH3(DCN, 1 H-CH3)
20 Methyl protonation: SH3 20/43 SH3(DCN, 1 H-CH3) The degree of deuteration
21 Methyl protonation: SH3 21/43 SH3(DCN, 1 H-CH3) High-resolution HSQC ct-hsqc
22 Methyl protonation: SH3 22/43 random coil shifts Val, Leu, Ile 32.7 ppm 21.4 ppm 26.8 ppm 13.5 ppm 17.5 ppm 42.3 ppm 38.6 ppm 24.4 ppm 27.7 ppm
23 Methyl protonation: SH3 23/43 Experimental schemes for assignment Tugarinov and Kay J. Am. Chem. Soc. 125, (2003) straight-through Leu, Ile-(HM)CM(CGCBCA)NNH Val-(HM)CM(CBCA)NNH here the linear chain becomes important CH 3 CH 3 12 CD 3 CD 2 CD CH 3 CD 12 CD 3 CD 3 NH CD CD CO NH CD 2 CD CO NH CD CO
24 Methyl protonation: SH3 24/43 Val-(HM)CM(CBCA)NNH TROSY HN-plane Val-53 Val-9 Glu-45 Lys-59 Val-58 Val-23 Val-44 Asn-47 Leu-10 Val-46 Thr-24 Pro-54!
25 Methyl protonation: SH3 25/43 Val-(HM)CM(CBCA)NNH CH 3 -region HC-plane
26 Methyl protonation: SH3 26/43 Leu,Ile-(HM)CM(CGCBCA)NNH TROSY HN-plane
27 Methyl protonation: SH3 27/43 Leu,Ile-(HM)CM(CGCBCA)NNH CH 3 -region HC-plane
28 Methyl protonation: SH3 28/43 Experimental schemes for assignment Tugarinov and Kay J. Am. Chem. Soc. 125, (2003) out-and-back HMCM(CG)CBCA HMCM(CGCBCA)CO here the linear chain becomes important CH 3 CH 3 12 CD 3 CD 2 CD CH 3 CD 12 CD 3 CD 3 NH CD CD CO NH CD 2 CD CO NH CD CO
29 Methyl protonation: SH3 29/43 no step one step two steps three steps Val/Ile/Leu-CH 3 Val-C Ile/Leu-C Ile/Leu-C Val-C Ile/Leu-C
30 Methyl protonation: SH3 30/43 no step one step two steps three steps Val/Ile/Leu-CH 3 Val-C Ile/Leu-C Ile/Leu-C Val-C Ile/Leu-C
31 Methyl protonation: SH3 31/43 Val Leu Ile HMCM[CG]CBCA C C C C C? C C C V53 V58 L8 L12 L33 I30
32 Methyl protonation: SH3 32/43 HMCM(CGCBCA)CO HNCO Val Leu, Ile
33 Methyl protonation: real examples Expression YtvA G LOV Jα STAS 33/43 HCDF DCN using 16 g d C-Glucose, 4 g 15 N-NH4Cl 36 mg protein from 1 l DCN-Met mit 16 g d C-Glucose, 4 g 15 N-NH4Cl 400 mg 2-ketobutyrate, 200 mg 2-ketoisovalerate 70 mg protein from 1 l
34 Methyl protonation: real examples 34/43 YtvA unlabeled DN DN-Met- 1 H ω 1 { 1 H} (ppm)
35 Methyl protonation: real examples 35/43 Expression B2709 high yield shaking flask DCN using 5 g d C-Glucose, 1 g 15 N-NH4Cl 115 mg protein from 1 l DCN-Met mit 5 g d C-Glucose, 1 g 15 N-NH4Cl 50 mg 2-ketobutyrate, 200 mg 2-ketoisovalerate 70 mg protein from 1 l
36 Methyl protonation: real examples 36/43 B Val, 21 Leu, 7 Ile = 75 CH 3 -groups 13 C-HSQC 13 C-ct-HSQC
37 Methyl protonation: real examples 37/43 B2709 HMCM[CG]CBCA
38 Methyl protonation: real examples 38/43 B2709
39 Methyl protonation: real examples 39/43 The ratio between butyric and isovaleric acid should be calculated from the abundance of the amino acids in the protein: B2709: 13 Val, 21 Leu, 7 Ile = 75 CH3-groups YtvA: 19 Val, 28 Leu, 24 Ile = 118 CH3-groups It should be mentioned that the experiments presented above do not work for proteins of all sizes. Several alternative approaches have been utilized, e.g. mutations, use of X-ray-structures etc.
40 Methyl protonation: more options 40/43 There are also other amino acids that are of interest for the study of dynamics and interaction of proteins and several further labeling options have been presented: Alanine Methionine 2 -Isoleucin pro-r and pro-s Valine and Leucine Some of them require more complicated precursor compositions and not all work without scambeling
41 Methyl protonation: more options 41/43 Most of the precursors that have been introduced over the years are commercially available by now $ 950 $ 995
42 Acknowledgement 42/43 FMP Monika Beerbaum Martin Ballaschk Marcel Jurk Matthias Dorn Anne Diehl Natalja Erdmann Kristina Rehbein Charité B. Uchanska-Ziegler A. Ziegler C. Schnick Bruker Wolfgang Bermel Rainer Kerssebaum
43 43/43 That s it
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