3.1 Materials
D2O (99.8% isotopically enriched) and 25MgO (95.75% isotopically enriched) was purchased from Euriso-Top. Glycerol-D3, di-sodium ethylenediaminetetraacetic acid (EDTA), tris(hydroxymethyl)aminomethane (TRIS) was purchased from Cambridge Isotope Laboratories, Fluka, and J.T.Baker, respectively. 4-(2-Hydroxyethyl)-1-piperazineethanesulfonic acid (Hepes), adenosine-5’-triphosphate (ATP), cytidine-5’-diphosphate (CDP), Sephadex® G-25, 2-methylbutan, hydrochloric acid solution (molecular biology grade, 36.5-38%) and sodium hydroxide were purchased from Sigma-Aldrich. Amicon® Ultra concentration device (30 kDa filter) was bought from Merck KGaA, whereas Glycerol and Magnesiumsulfate was used from Roth. Polyacrylamid Gels (PAGE, 7.5%, Tris-HCl) were bought from Biorad.
The following buffers were used:
i. Α buffer consists of TRIS (50 mM), EDTA (1 mM) and glycerol (5% v/v) adjusted to pH 7.6
ii. Assay buffer consists of HEPES, MgSO4 (15 mM), EDTA (1 mM) adjusted to pH 8.0
iii. Desalt buffer consists of TRIS (30 mM) and glycerol (5% v/v) adjusted to pH 7.6
Sample Preparation The following EPR tubes were used:
i. 263 GHz: Vitrocom CV2033S/Q (Ø 0.33 mm)
ii. W band: Bruker E600-213/ST9O (Ø 0.9/0.5 mm)and Wilmad glass quartz tubes (Ø 0.9/0.5 mm); Bruker
iii. Q Band: Bruker quartz tubes ER221TUB-Q-10 (Ø 1.6/1.1 mm).
3.2 Sample Preparation
α-NH2Y730, α-NH2Y731 and β-NH2Y356 were prepared and purified as previously described,44,
67 beside the absence of DTT in the final Sephadex column.253 These preparations were performed by T. Argirević form our group and for β-NH2Y356 by E. Minnihan from the Stubbe lab at the MIT. For α-NH2Y731 the truncated form was removed by an additional an anion exchange column (MonoQ, equilibrated in α-buffer) against a NaCl gradient (2.5-400 mM) over 50 mL. This step was performed with the help of Florian Brodhun in the Feussner lab (Georg August University, Göttingen). All NH2Y mutated subunits were mixed in equimolar ratios with their corresponding wt (prereduced α/β) and spin concentrated to 100-200 µM (α2β2) in D2O (>99 %) and H2O assay buffer.134 The concentration was checked by UV-vis spectroscopy on tyrosine and tryptophan absorption bands ε280 nm ≅ 320 mM-1cm-1 (α244≅189 mM-1 cm-1 + β269≅131 mM-1 cm-1). The samples were stored in 0.5 mL Eppendorf tubes per 10 μL aliquots in liquid N2. The double mutant samples were directly obtained as a 1:1 complex by Wankyu Lee from the Stubbe lab at MIT.254
β-2,3,5-F3Y122• mixed with α-wt or α-Y731F was prepared by Kanchana Ravichandran from the Stubbe lab at the MIT, as described previously.120 The samples in D2O (>99 %) and H2O assay buffer were stored in 100 µL aliquots at 80K. pBAD-nrdB122TAG and pBAD-FnYRS-E3 were co-transformed into E. coli TOP10 chemically competent cells and grown at 37°C on LB-agar plates containing 100 µg/mL ampicillin (Amp) and 35 µg/mL chloramphenicol (Cm). A starter culture (2 mL) supplemented with the antibiotics was inoculated with a single colony and grown until saturation (37°C, 12 h). This starter culture was diluted 100-fold into fresh 2X YT media containing Amp and Cm. After 16 h, the cultures were diluted 100-fold into 4 x 2 L of 2X YT with antibiotics and 0.7 mM 2,3,5-F3Y (500 mM stock solution in water, NH4OH solubilized). At an OD600 of 0.5, 100 µM o-phenanthroline (100 mM stock solution in 0.1 M HCl) was added to chelate iron. 30 min
later, 0.05% (w/v) L-arabinose (10% w/v stock solution in water) was added to induce the FnYRS and NrdB. Growth was continued for an additional 5 h and the cells were harvested by centrifugation (3500 x g, 15 min).
Apo β2-Y122(2,3,5-)F3Y was purified using anion-exchange chromatography as previously described.255 Typical yields of 10-15 mg pure protein/g cell paste were obtained.
Reconstitution of Apo β2-Y122(2,3,5-)F3Y. Apo β2-Y122(2,3,5-)F3Y was deoxygenated and taken into an anaerobic chamber maintained at 4°C. 5 equiv. of FeII(NH4)2(SO4)2 was incubated with the protein for 15 min. The sample was brought out of the chamber sealed, and O2 in the form of O2-saturated 50 mM hepes pH 7.6, 5% glycerol was added to reconstitute the cluster. 250 µL of β2-Y122(2,3,5-)F3Y was frozen in an EPR tube immediately after reconstitution to quantitate radical content. Typical yields of 0.6-1.0 2,3,5-F3Y122•/β2 were obtained for the reconstituted protein.
25Mg2+-samples were prepared by first washing the protein in 5 concentration (to 20% v/v) dilution steps with desalt buffer and buffer exchanged the sample with a 25MgCl2
(15 mM) assay buffer with additional 5 steps. The 25MgCl2 was obtained quantitatively by dissolving 25MgO (12.3 mg, 30 mM) in concentrated hydrochloric acid solution (98.4 µL, 120 mM) in test tube overnight, similarly as described previously.256 Milli-Q® water was added and the HCl was allowed to evaporate in a desiccator and afterwards the product was dried under high vacuum. ESI-MS of the product dissolved in Methanol showed mass shift of 1 m/z compared to MgCl2 in natural abundance. 4% of 24Mg(II) could be observed.
EPR samples were prepared by thawing each aliquot at 4°C and followed equilibration at 25°C for 10 min. The reaction was initiated by adding CDP and ATP in H2O/D2O assay buffer with final concentration 2 and 6 mM, into the reaction mixture (1 µL 263 GHz, 2.5 µL W band and 6 µL Q band) with final complex concentrations of 90-100 µM. Each reaction was allowed to proceed for 10-20 s and manually freeze quenched inside an EPR tube with liquid N2. For Q-band PELDOR samples glycerol-D3 (20 % v/v) was added after 10-20 s, and then the reaction was frozen in ice cold 2-propanol (≈185 K).
The quench times were varied based on the individual kinetic rates of the different samples as measured by UV-vis stopped flow44, 67, 254 or Rapid Freeze Quench.28 This should ensure a maximum radical yield.
X/Q-Band Spectroscopy
3.3 X/Q-Band Spectroscopy
Q-Band spectra were obtained by a Bruker Elexsys E 580 spectrometer with a nominal output power of 3 W. The ESE traces and PELDOR traces were recorded in a Bruker (EN5107D2) cavity. The cooling of the cavity was achieved within a liquid Helium continuous flow cryostat (CF95550, Oxford Instruments). PELDOR257 (πMW1/2−τ1−πMW1− [τ1+x]−πMW2−[τ2-x]−πMW1−τ1−echo) spectroscopy is a constant time 4 pulse experiment.
PELDOR uses pulses at a pump (MW2) and detect microwave (MW1) frequency and was carried out by measuring the dipolar evolution over the time x in steps of 8 ns. Experimental details are given in the figure captions.
X-Band measurements were performed on a Bruker Elexsys E500 spectrometer, with a HighQ CW-resonator (4122SHQE, Bruker) in an ESR900 (Oxford Instruments) cryostat.
3.4 W-Band Spectroscopy
The EPR and ENDOR spectra were recorded on an Elexsys® E680 with 400 mW output power and typical π/2 pulse length of 16 ns at 70 K. The cooling was performed under continuous Helium flow in Oxford Instruments cryostat. A pulsed ENDOR probehead (1021H, Bruker) was used as a resonator.
Mims-ENDOR183 (π/2−τ−π/2−RF−π/2− τ−echo) spectroscopy was carried out with a 40 µs RF pulse amplified by a 250 W RF amplifier (250A250A, Amplifier Research). All obtained ENDOR spectra were normalized to compare with simulations.