1
|
Chen JR, Ke TX, Frey PA, Ke SC. Electron Spin Echo Envelope Modulation Spectroscopy Reveals How Adenosylcobalamin-Dependent Lysine 5,6-Aminomutase Positions the Radical Pair Intermediates and Modulates Their Stabilities for Efficient Catalysis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun-Ru Chen
- Physics Department, National Dong Hwa University, Hualien 974301, Taiwan
| | - Ting-Xi Ke
- Physics Department, National Dong Hwa University, Hualien 974301, Taiwan
| | - Perry A. Frey
- Department of Biochemistry, University of Wisconsin−Madison, Madison, Wisconsin 53726, United States
| | - Shyue-Chu Ke
- Physics Department, National Dong Hwa University, Hualien 974301, Taiwan
| |
Collapse
|
2
|
Krzyaniak MD, Eser BE, Ellis HR, Fitzpatrick PF, McCracken J. Pulsed EPR study of amino acid and tetrahydropterin binding in a tyrosine hydroxylase nitric oxide complex: evidence for substrate rearrangements in the formation of the oxygen-reactive complex. Biochemistry 2013; 52:8430-41. [PMID: 24168553 DOI: 10.1021/bi4010914] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosine hydroxylase is a nonheme iron enzyme found in the nervous system that catalyzes the hydroxylation of tyrosine to form l-3,4-dihydroxyphenylalanine, the rate-limiting step in the biosynthesis of the catecholamine neurotransmitters. Catalysis requires the binding of three substrates: tyrosine, tetrahydrobiopterin, and molecular oxygen. We have used nitric oxide as an O₂ surrogate to poise Fe(II) at the catalytic site in an S = 3/2, {FeNO}⁷ form amenable to EPR spectroscopy. ²H-electron spin echo envelope modulation was then used to measure the distance and orientation of specifically deuterated substrate tyrosine and cofactor 6-methyltetrahydropterin with respect to the magnetic axes of the {FeNO}⁷ paramagnetic center. Our results show that the addition of tyrosine triggers a conformational change in the enzyme that reduces the distance from the {FeNO}⁷ center to the closest deuteron on 6,7-²H-6-methyltetrahydropterin from >5.9 Å to 4.4 ± 0.2 Å. Conversely, the addition of 6-methyltetrahydropterin to enzyme samples treated with 3,5-²H-tyrosine resulted in reorientation of the magnetic axes of the S = 3/2, {FeNO}⁷ center with respect to the deuterated substrate. Taken together, these results show that the coordination of both substrate and cofactor direct the coordination of NO to Fe(II) at the active site. Parallel studies of a quaternary complex of an uncoupled tyrosine hydroxylase variant, E332A, show no change in the hyperfine coupling to substrate tyrosine and cofactor 6-methyltetrahydropterin. Our results are discussed in the context of previous spectroscopic and X-ray crystallographic studies done on tyrosine hydroxylase and phenylalanine hydroxylase.
Collapse
Affiliation(s)
- Matthew D Krzyaniak
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | | | | | | | | |
Collapse
|
3
|
Casey TM, Grzyska PK, Hausinger RP, McCracken J. Measuring the orientation of taurine in the active site of the non-heme Fe(II)/α-ketoglutarate-dependent taurine hydroxylase (TauD) using electron spin echo envelope modulation (ESEEM) spectroscopy. J Phys Chem B 2013; 117:10384-94. [PMID: 23937570 PMCID: PMC3854568 DOI: 10.1021/jp404743d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The position and orientation of taurine near the non-heme Fe(II) center of the α-ketoglutarate (α-KG)-dependent taurine hydroxylase (TauD) was measured using Electron Spin Echo Envelope Modulation (ESEEM) spectroscopy. TauD solutions containing Fe(II), α-KG, and natural abundance taurine or specifically deuterated taurine were prepared anaerobically and treated with nitric oxide (NO) to make an S = 3/2 {FeNO}(7) complex that is suitable for robust analysis with EPR spectroscopy. Using ratios of ESEEM spectra collected for TauD samples having natural abundance taurine or deuterated taurine, (1)H and (14)N modulations were filtered out of the spectra and interactions with specific deuterons on taurine could be studied separately. The Hamiltonian parameters used to calculate the amplitudes and line shapes of frequency spectra containing isolated deuterium ESEEM were obtained with global optimization algorithms. Additional statistical analysis was performed to validate the interpretation of the optimized parameters. The strongest (2)H hyperfine coupling was to a deuteron on the C1 position of taurine and was characterized by an effective dipolar distance of 3.90 ± 0.25 Å from the {FeNO}(7) paramagnetic center. The principal axes of this C1-(2)H hyperfine coupling and nuclear quadrupole interaction tensors were found to make angles of 26 ± 5 and 52 ± 17°, respectively, with the principal axis of the {FeNO}(7) zero-field splitting tensor. These results are discussed within the context of the orientation of substrate taurine prior to the initiation of hydrogen abstraction.
Collapse
Affiliation(s)
- Thomas M. Casey
- Department of Chemistry, Michigan State University, East Lansing MI-48824
| | - Piotr K. Grzyska
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing MI-48824
| | - Robert P. Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI-48824
| | - John McCracken
- Department of Chemistry, Michigan State University, East Lansing MI-48824
| |
Collapse
|
4
|
Sun L, Savory JJ, Warncke K. Design and implementation of an FPGA-based timing pulse programmer for pulsed-electron paramagnetic resonance applications. CONCEPTS IN MAGNETIC RESONANCE. PART B, MAGNETIC RESONANCE ENGINEERING 2013; 43:100-109. [PMID: 25076864 PMCID: PMC4112105 DOI: 10.1002/cmr.b.21240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The design, construction and implementation of a field-programmable gate array (FPGA) -based pulse programmer for pulsed-electron paramagnetic resonance (EPR) experiments is described. The FPGA pulse programmer offers advantages in design flexibility and cost over previous pulse programmers, that are based on commercial digital delay generators, logic pattern generators, and application-specific integrated circuit (ASIC) designs. The FPGA pulse progammer features a novel transition-based algorithm and command protocol, that is optimized for the timing structure required for most pulsed magnetic resonance experiments. The algorithm was implemented by using a Spartan-6 FPGA (Xilinx), which provides an easily accessible and cost effective solution for FPGA interfacing. An auxiliary board was designed for the FPGA-instrument interface, which buffers the FPGA outputs for increased power consumption and capacitive load requirements. Device specifications include: Nanosecond pulse formation (transition edge rise/fall times, ≤3 ns), low jitter (≤150 ps), large number of channels (16 implemented; 48 available), and long pulse duration (no limit). The hardware and software for the device were designed for facile reconfiguration to match user experimental requirements and constraints. Operation of the device is demonstrated and benchmarked by applications to 1-D electron spin echo envelope modulation (ESEEM) and 2-D hyperfine sublevel correlation (HYSCORE) experiments. The FPGA approach is transferrable to applications in nuclear magnetic resonance (NMR; magnetic resonance imaging, MRI), and to pulse perturbation and detection bandwidths in spectroscopies up through the optical range.
Collapse
Affiliation(s)
- Li Sun
- Department of Physics, N201 Mathematics and Science Center, 400 Dowman Drive, Emory University, Atlanta, Georgia 30322-2430
| | - Joshua J. Savory
- Department of Physics, N201 Mathematics and Science Center, 400 Dowman Drive, Emory University, Atlanta, Georgia 30322-2430
| | - Kurt Warncke
- Department of Physics, N201 Mathematics and Science Center, 400 Dowman Drive, Emory University, Atlanta, Georgia 30322-2430
| |
Collapse
|
5
|
Warncke K. Characterization of the product radical structure in the Co(II)-product radical pair state of coenzyme B12-dependent ethanolamine deaminase by using three-pulse 2H ESEEM spectroscopy. Biochemistry 2005; 44:3184-93. [PMID: 15736929 DOI: 10.1021/bi048196t] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular structural features of the product radical in the Co(II)-product radical pair catalytic intermediate state in coenzyme B(12)- (adenosylcobalamin-) dependent ethanolamine deaminase from Salmonella typhimurium have been characterized by using X-band three-pulse electron spin-echo envelope modulation (ESEEM) spectroscopy in the disordered solid state. The Co(II)-product radical pair state was prepared by cryotrapping holoenzyme during steady-state turnover on excess 1,1,2,2-(2)H(4)-aminoethanol or natural abundance, (1)H(4)-aminoethanol. Simulation of the (2)H/(1)H quotient ESEEM (obtained at two microwave frequencies, 8.9 and 10.9 GHz) from the interaction of the unpaired electron localized at C2 of the product radical with nearby (2)H nuclei requires four types of coupled (2)H, which are assigned as follows: (a) a single strongly coupled (effective dipole distance, r(eff) = 2.3 A) (2)H in the C5' methyl group of 5'-deoxyadenosine, (b) two weakly coupled (r(eff) = 4.2 A) (2)H in the C5' methyl group, (c) one (2)H coupling from a beta-(2)H bonded to C1 of the product radical (isotropic hyperfine coupling, A(iso) = 4.7 MHz), and (d) a second type of C1 beta-(2)H coupling (A(iso) = 7.7 MHz). The two beta-(2)H couplings are proposed to arise from two C1-C2 rotamer states of the product radical that are present in approximately equal proportion. A model is presented, in which C5' is positioned at a distance of 3.3 A from C2, which is comparable with the C1-C5' distance in the Co(II)-substrate radical pair intermediate. Therefore, the C5'methyl group remains in close (van der Waals) contact with the substrate and product radical species during the radical rearrangement step of the catalytic cycle, and the C5' center is the sole mediator of radical pair recombination in ethanolamine deaminase.
Collapse
Affiliation(s)
- Kurt Warncke
- Department of Physics, N201 Mathematics and Science Center, 400 Dowman Drive, Emory University, Atlanta, Georgia 30322, USA.
| |
Collapse
|
6
|
Clemens KL, Force DA, Britt RD. Acetate binding at the photosystem II oxygen evolving complex: an S(2)-state multiline signal ESEEM study. J Am Chem Soc 2002; 124:10921-33. [PMID: 12207548 DOI: 10.1021/ja012036c] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previously, using acetate deuterated in the methyl hydrogen positions, we showed that acetate binds in close proximity to the Mn cluster/Y(.)(z) tyrosine dual spin complex in acetate-inhibited photosystem II (PSII) preparations exhibiting the "split" EPR signal arising from the S(2)-Y(.)(z) interaction [Force, D. A.; Randall, D. W.; Britt, R. D. Biochemistry 1997, 36, 12062-12070]. By using paramagnetic NO to quench the paramagnetism of Y(.)(z), we are able to observe the ESEEM spectrum of deuterated acetate interacting with only the Mn cluster. A good fit of the ESEEM data indicates two (2)H dipolar hyperfine couplings of 0.097 MHz and one of 0.190 MHz. Modeling of these dipolar interactions, using our "dangler" 3 + 1 model for the S(2)-state of the Mn cluster, reveals distances consistent with direct ligation of acetate to the Mn cluster. As acetate inhibition is competitive with the essential cofactor Cl(-), this suggests that Cl(-) ligates directly to the Mn cluster. The effect of acetate binding on the structure of the Mn cluster is investigated by comparing the Mn-histidine coupling in NO/acetate-treated PSII and untreated PSII using ESEEM. We find that the addition of acetate and NO does not affect the histidine ligation to the Mn cluster. We also investigate the ability of acetate to access Y(.)(z) in Mn-depleted PSII, a PSII preparation expected to be more solvent accessible than intact PSII. We detect no coupling between Y(.)(z) and acetate. We have previously shown that small alcohols such as methanol can ligate to the Mn cluster with ease, while larger alcohols such as 2-propanol, as well as DMSO, are excluded [Force, D. A.; Randall, D. W.; Lorigan, G. A.; Clemens, K. L.; Britt, R. D. J. Am. Chem. Soc. 1998, 120, 13321-13333]. We probe the effect of acetate binding on the ability of methanol and DMSO to bind to the Mn cluster. We find that methanol is able to bind to the Mn cluster in the presence of acetate. We detect no DMSO binding in the presence of acetate. Thus, acetate binding does not increase the affinity or accessibility for DMSO binding at the Mn cluster. We also explore the possibility that the acetate binding site is also a binding site for substrate water. By comparing the ratioed three-pulse ESEEM spectra of a control, untreated PSII sample in 50% D(2)O to an NO/acetate-treated PSII sample in 50% D(2)O, we find that the binding of acetate to the oxygen evolving complex of photosystem II displaces deuterons bound very closely to the Mn cluster.
Collapse
Affiliation(s)
- Keri L Clemens
- Department of Chemistry, University of California, Davis, CA 95616-0935, USA
| | | | | |
Collapse
|
7
|
Warncke K, Perry MS. Redox state dependence of rotamer distributions in tyrosine and neutral tyrosyl radical. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1545:1-5. [PMID: 11342025 DOI: 10.1016/s0167-4838(00)00289-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Redox state-dependent changes in the relative orientation of the phenol side chain and the peptide group in model tyrosine have been characterized using specific 2H isotopic labelling and X-band electron paramagnetic resonance (EPR) spectroscopy. Tyrosyl radicals were generated by UV photolysis of tyrosine trapped in rigid polycrystalline basic-aqueous medium at T < or = 170 K. Ring-2H(4) and beta-2H(2) substitutions on tyrosine were used to enhance the lineshape contributions from beta-hydrogen or ring-hydrogen hyperfine interactions, respectively. The EPR lineshape at 120 K of the trapped ring-2H(4)-tyrosyl radical is altered dramatically after annealing at 235 K. In contrast, the lineshape of the beta-2H(2)-tyrosyl radical is impervious to annealing. The effect of annealing on the lineshape therefore arises from a change in the isotropic hyperfine coupling between unpaired pi-electron spin density at the ring carbon atom C(1) and the beta-hydrogen nuclei, which is caused by rotational relaxation of the ring and peptide group about the C(1)-C(beta) bond. EPR simulations indicate angular distributions of the peptide group (R-) of 0 degrees < or = theta(R) < or = 30 degrees and 0 degrees < or = theta(R)< or = 18 degrees in the rigid and relaxed radical states, respectively. Redox-induced changes in the C(1)-C(beta) rotamer distribution must be accounted for in assessments of stable amino acid side chain equilibrium structures, and may influence catalytic tyrosyl radical/tyrosine function in enzymes.
Collapse
Affiliation(s)
- K Warncke
- Department of Physics, 1001 Rollins Research Center, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA.
| | | |
Collapse
|
8
|
Hulsebosch RJ, van den Brink JS, Nieuwenhuis SAM, Gast P, Raap J, Lugtenburg J, Hoff AJ. Electronic Structure of the Neutral Tyrosine Radical in Frozen Solution. Selective 2H-, 13C-, and 17O-Isotope Labeling and EPR Spectroscopy at 9 and 35 GHz. J Am Chem Soc 1997. [DOI: 10.1021/ja9707872] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. J. Hulsebosch
- Contribution from the Department of Biophysics, Huygens Laboratory, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - J. S. van den Brink
- Contribution from the Department of Biophysics, Huygens Laboratory, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - S. A. M. Nieuwenhuis
- Contribution from the Department of Biophysics, Huygens Laboratory, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - P. Gast
- Contribution from the Department of Biophysics, Huygens Laboratory, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - J. Raap
- Contribution from the Department of Biophysics, Huygens Laboratory, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - J. Lugtenburg
- Contribution from the Department of Biophysics, Huygens Laboratory, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - A. J. Hoff
- Contribution from the Department of Biophysics, Huygens Laboratory, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| |
Collapse
|
9
|
Erickson R, Benetis NP, Lund A, Lindgren M. Radical Cation of Naphthalene on H−ZSM-5 Zeolite and in CFCl3 Matrix. A Theoretical and Experimental EPR, ENDOR, and ESEEM Study. J Phys Chem A 1997. [DOI: 10.1021/jp9631994] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Roland Erickson
- Chemical Physics Laboratory, Department of Physics and Measurement Technology, IFM, Linköping University, S-581 83 Linköping, Sweden
| | - Nikolas P. Benetis
- Chemical Physics Laboratory, Department of Physics and Measurement Technology, IFM, Linköping University, S-581 83 Linköping, Sweden
| | - Anders Lund
- Chemical Physics Laboratory, Department of Physics and Measurement Technology, IFM, Linköping University, S-581 83 Linköping, Sweden
| | - Mikael Lindgren
- Chemical Physics Laboratory, Department of Physics and Measurement Technology, IFM, Linköping University, S-581 83 Linköping, Sweden
| |
Collapse
|
10
|
Warncke K, McCracken J. Analysis of static distributions in hydrogen hyperfine interactions in randomly oriented radicals in the solid state by using2H electron spin echo envelope modulation spectroscopy: Conformational dispersion of β ‐2H coupling in the model tyrosyl radical. J Chem Phys 1995. [DOI: 10.1063/1.470363] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|