Supporting Information. Interphase Enzyme Kinetics of an Integral Membrane Kinase by. Time-Resolved Solid-state NMR. contributed equally

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1 Supporting Information Interphase Enzyme Kinetics of an Integral Membrane Kinase by Time-Resolved Solid-state NMR Sandra J. Ullrich 1,2, Ute A. Hellmich 1,2, Stefan Ullrich 3 and Clemens Glaubitz 1,2* contributed equally Institute for Biophysical Chemistry (1) Centre for Biomolecular Magnetic Resonance (2) Institute for Organic Chemistry and Chemical Biology (3) Goethe University, Frankfurt am Main, Germany (*) Correspondence: Clemens Glaubitz Institute for Biophysical Chemistry Goethe University Frankfurt Max-von-Laue-Str Frankfurt am Main glaubitz@em.uni-frankfurt.de Tel.: /28 Fax.:

2 1. Supplementary Results 1.1. Membrane Partitioning of DAG and PA Tab. S1: Predicted logp values and octanol/water partitioning for selected diacylglycerols (DAG) of different acyl chain lengths (n), the corresponding phosphatidylic acid (PA). logp calculations where performed with html DAG (n = acyl chain length) DAG logp octanol/water logp octanol/water PA DBG (n=4) 1.38 ± : ± : 1 DHG (n=6) 3.27 ± *10 3 : ± : 1 DOG (n=8) 5.17 ± *10 5 : ± *10 3 : 1 DLG (n=12) 8.64 ± *10 8 : ± *10 6 :1 DAG (n = acyl chain length) 31 P Chemical Shift [ppm] DP DAG-PA Peak integrals (normalized to DOPC) CP DBG (n=4) ± ± 0.21 DHG (n=6) ± ± 0.26 DOG (n=8) ± ± 0.16 DLG (n=12) ± ± 0.12 Fig. S1: Comparison between 31 P-CP and DP spectra obtained from DGK proteoliposomes containing DBG (a) and DOG (b) acquired at the end of the enzymatic reaction, when all ATP was consumed and DBG-PA and 2

3 DOG-PA have been generated by DGK. In the CP spectrum all resonances of soluble components are suppressed while in the DP spectrum all species in all phases are visible (see also Fig. 1). The signal of DBG-PA is reduced but not completely removed, indicating an equilibrium between water and lipid phase. Analyzing the integral peak intensities reveals a DP:CP ratio of 1.97:0.5. This means that approx. 1/3 of DBG-PA is membrane bound. The same experimental analysis has been carried out for DOG (b). Here, approx. 90% of DOG-PA is found to be membrane bound. The values of DHG (approx. 45%) and DLG (100%) correspond to the expected trend of increasing lipophilicity with a longer acyl chain length (data not shown). The 31 P chemical shifts show a monotonic dependence on the number of acyl chain segments. Our data show that all DAG-PA species partition into the membrane. This is an expected observation except for DBG, which is often assumed to be completely soluble. Therefore, an amount of 1/3 of membrane bound DBG- PA cannot be neglected when analyzing DGK activity data. Only MAS NMR allows the observation of both the soluble and membrane bound fraction of DBG-PA. Based on logp predictions (Tab. S1), it can be assumed that the membrane population of DBG is even larger than for DBG-PA. The large differences between calculated partition coefficients and values obtained from our 31 P NMR spectra is probably due to the limited applicability of the octanol-water model. The experimental conditions were identical to those described in the Material and Methods section. All samples were prepared in the same way and contained the same amount of DAG analogue (2 µmol). Errors were calculated from the S/N-ratio and the difference between experimental and simulated spectra. The ability to quantify and compare integral peak intensities in the 31 P CP experiments has been evaluated by comparison of 1 H and 31 P-T1ρ measurements for the bulk lipid and DBG-PA resonance (data not shown). Similar values were obtained which means that both membrane components show a similar CP dynamic, allowing a quantitative comparison. 3

4 1.2. Fitting Parameters for Time-Resolved Data Sets Tab. S2a: Fitting parameters for the non-stimulated, time-resolved 31 P-MAS-NMR data set shown in Fig. 2a Exponential Rates (1) k (min -1 ) R 2 α P-ATP 1.51(5)* α P-ADP 1.68(2)* β P-ATP 1.42(4)* β P-ADP 1.66(2)* γ P-ATP 1.42(4)* DGK (2.1mg, 0.15 µmol), DOPC (18µmol), MgATP (30mM, 2 µmol), T=303K Tab. S2b: Fitting parameters for the substrate stimulated, time-resolved 31 P-MAS-NMR data set shown in Figs. 2b Exponential Rates (1) k (min -1 ) R 2 αp-atp 7.57(2)* αp-adp 6.44(3)* βp-atp 6.84(2)* βp-adp 6.99(2)* γp-atp 6.60(2)* DBG-PA 5.69(2)* DGK (2.1 mg, 0.15 µmol), DOPC (18 µmol), MgATP (30 mm, 2 µmol), DBG (2.5 mm, µmol), T = 303K. (1) αp-, βp- and γp-atp resonances are well described by I=I 0 *Exp(-t*k), while αp-, βp-adp and DBG-PA could be approximated using I=I 0 *(1-Exp(-t*k)). Peak integrals were normalized to the initial amount of ATP. 4

5 1.3. Supporting Data for the Kinetic Analysis of DGK Activity Fig. S2: ATP hydrolysis rates obtained from time resolved 31 P-DP MAS NMR data sets as shown in Fig. S2 are plotted as a function of [ATP] and [DBG] in a double reciprocal manner. The data show that ATP and DBG bind independently from one another. This agrees with a mechanism in which DGK follows a random-equilibrium ATP mechanism.the x-axis intercept allows an estimation of thek M value for ATP ( K M,ATP =1.9 ± 1.3 mm) and DBG ATP ATP ( K M,DBG =3.7 ± 1.3 mm, 1.4 ± 0.5 mol%).a more precise valueof K M,DBG =2.8±0.3 mm (1.1 ± 0.1 mol%) was obtained from Fig. 3 in which hydrolysis as well as phosphorlyation rates over a larger concentration range is shown. From these data, also K DBG-PA M,DBG =4.7±0.3mM (1.8 ± 0.1 mol%) could be determined Supporting Data for the Kinetic Analysis of DGK Activity in the Presence of Salt Fig. S3: Control experiments were carried out in order to investigate the effect of salt on the stimulated ATP hydrolysis rate of DGK. Activities were determined from time-resolved NMR data as described in this paper in the presence of 22.5 mm NaCl and 52.5 mm NaCl. Finally, salt-free TrisATP instead of NaATP was used to completely exclude salt in the reaction mixture. Otherwise, kinetic measurements were performed under identical conditions, compared to column 1 (NaATP). Rates for ATP hydrolysis were normalized to column 1. The addition of NaCl as well as the salt-free ATP-Tris showed no significant effect on the ATP hydrolysis rate (data not shown). 5

6 2. Supplementary Methods 2.1. Complete Deconvolution of Time-Resolved 31P-NMR Data Sets Time-resolved 2D data sets were subjected to a complete peak deconvolution using the mdcon routine built into TopSpin 2.1 in combination with an automatisation script (Bruker, Karlsruhe). Chemical shifts, line widths, intensities and line shapes (Lorentzian/Gaussian) were fitted simultaneously to each resonance in each time slice. A total of 9 resonances were included into this analysis, covering αp, βp, γp-atp, αp, βp-adp, DBG-PA, free Pi, DOPC and a small signal stemming from lipids which have been co-purified with DGK.The resulting peak integrals were used for further kinetic analysis. Data analysis was aided by scripts written in Python 2.5 ( with the help of modules PyLab ( and SciPy ( Kinetic analysis was carried out with OriginPro 8.0 (OriginLab Corporation, USA). Figure S4:Complete deconvolution of a timeresolved 31P-MAS NMR data set showing the phosphorylation of DBG (DBG-PA) by DGK at the expense of ATP. The best fit is subtracted from the original experimental data set. The difference spectrum shows that an excellent fit is achieved with this deconvolution procedure. The deconvolution procedure yields the peak integrals for the individual reaction components. This allows the direct analysis of the rates of DBG phosphorylation and DBGPA:ATP stoichiometries (as shown in Figs. 1, 2 and 4c,d). 6