1
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Bopp C, Bernet NM, Meyer F, Khan R, Robinson SL, Kohler HPE, Buller R, Hofstetter TB. Elucidating the Role of O 2 Uncoupling for the Adaptation of Bacterial Biodegradation Reactions Catalyzed by Rieske Oxygenases. ACS ENVIRONMENTAL AU 2024; 4:204-218. [PMID: 39035869 PMCID: PMC11258757 DOI: 10.1021/acsenvironau.4c00016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 07/23/2024]
Abstract
Oxygenation of aromatic and aliphatic hydrocarbons by Rieske oxygenases is the initial step of various biodegradation pathways for environmental organic contaminants. Microorganisms carrying Rieske oxygenases are able to quickly adapt their substrate spectra to alternative carbon and energy sources that are structurally related to the original target substrate, yet the molecular events responsible for this rapid adaptation are not well understood. Here, we evaluated the hypothesis that reactive oxygen species (ROS) generated by unproductive activation of O2, the so-called O2 uncoupling, in the presence of the alternative substrate exert a selective pressure on the bacterium for increasing the oxygenation efficiency of Rieske oxygenases. To that end, we studied wild-type 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42 and five enzyme variants that have evolved from adaptive laboratory evolution experiments with 3- and 4-nitrotoluene as alternative growth substrates. The enzyme variants showed a substantially increased oxygenation efficiency toward the new target substrates concomitant with a reduction of ROS production, while mechanisms and kinetics of enzymatic O2 activation remained unchanged. Structural analyses and docking studies suggest that amino acid substitutions in enzyme variants occurred at residues lining both substrate and O2 transport tunnels, enabling tighter binding of the target substrates in the active site. Increased oxygenation efficiencies measured in vitro for the various enzyme (variant)-substrate combinations correlated linearly with in vivo changes in growth rates for evolved Acidovorax strains expressing the variants. Our data suggest that the selective pressure from oxidative stress toward more efficient oxygenation by Rieske oxygenases was most notable when O2 uncoupling exceeded 60%.
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Affiliation(s)
- Charlotte
E. Bopp
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute
of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Nora M. Bernet
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute
of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Fabian Meyer
- Competence
Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Riyaz Khan
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Serina L. Robinson
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Hans-Peter E. Kohler
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Rebecca Buller
- Competence
Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Thomas B. Hofstetter
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute
of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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2
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Paris JC, Hei Cheung Y, Zhang T, Chang WC, Liu P, Guo Y. New Frontiers in Nonheme Enzymatic Oxyferryl Species. Chembiochem 2024:e202400307. [PMID: 38900645 DOI: 10.1002/cbic.202400307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 06/22/2024]
Abstract
Non-heme mononuclear iron dependent (NHM-Fe) enzymes exhibit exceedingly diverse catalytic reactivities. Despite their catalytic versatilities, the mononuclear iron centers in these enzymes show a relatively simple architecture, in which an iron atom is ligated with 2-4 amino acid residues, including histidine, aspartic or glutamic acid. In the past two decades, a common high-valent reactive iron intermediate, the S=2 oxyferryl (Fe(IV)-oxo or Fe(IV)=O) species, has been repeatedly discovered in NHM-Fe enzymes containing a 2-His-Fe or 2-His-1-carboxylate-Fe center. However, for 3-His/4-His-Fe enzymes, no common reactive intermediate has been identified. Recently, we have spectroscopically characterized the first S=1 Fe(IV) intermediate in a 3-His-Fe containing enzyme, OvoA, which catalyzes a novel oxidative carbon-sulfur bond formation. In this review, we summarize the broad reactivities demonstrated by S=2 Fe(IV)-oxo intermediates, the discovery of the first S=1 Fe(IV) intermediate in OvoA and the mechanistic implication of such a discovery, and the intrinsic reactivity differences of the S=2 and the S=1 Fe(IV)-oxo species. Finally, we postulate the possible reasons to utilize an S=1 Fe(IV) species in OvoA and their implications to other 3-His/4-His-Fe enzymes.
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Affiliation(s)
- Jared C Paris
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA, 15213, USA
| | - Yuk Hei Cheung
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA, 02215, USA
| | - Tao Zhang
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA, 02215, USA
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC, 27695, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA, 02215, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA, 15213, USA
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3
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Bopp CE, Bernet NM, Pati SG, Hofstetter TB. Characterization of O 2 uncoupling in biodegradation reactions of nitroaromatic contaminants catalyzed by rieske oxygenases. Methods Enzymol 2024; 703:3-28. [PMID: 39261002 DOI: 10.1016/bs.mie.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Rieske oxygenases are known as catalysts that enable the cleavage of aromatic and aliphatic C-H bonds in structurally diverse biomolecules and recalcitrant organic environmental pollutants through substrate oxygenations and oxidative heteroatom dealkylations. Yet, the unproductive O2 activation, which is concomitant with the release of reactive oxygen species (ROS), is typically not taken into account when characterizing Rieske oxygenase function. Even if considered an undesired side reaction, this O2 uncoupling allows for studying active site perturbations, enzyme mechanisms, and how enzymes evolve as environmental microorganisms adapt their substrates to alternative carbon and energy sources. Here, we report on complementary methods for quantifying O2 uncoupling based on mass balance or kinetic approaches that relate successful oxygenations to total O2 activation and ROS formation. These approaches are exemplified with data for two nitroarene dioxygenases (nitrobenzene and 2-nitrotoluene dioxygenase) which have been shown to mono- and dioxygenate substituted nitroaromatic compounds to substituted nitrobenzylalcohols and catechols, respectively.
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Affiliation(s)
- Charlotte E Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, Zürich, Switzerland
| | - Nora M Bernet
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, Zürich, Switzerland
| | - Sarah G Pati
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Thomas B Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, Zürich, Switzerland.
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4
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Martin CB, Taabazuing CY, Knapp MJ. Dynamic Domain Links Substrate Binding and Catalysis in the Factor-Inhibiting-HIF-1. Biochemistry 2023; 62:2442-2449. [PMID: 37526986 DOI: 10.1021/acs.biochem.3c00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
The interplay between active-site chemistry and functionally relevant enzyme motions can provide useful insights into selective enzyme modulation. Modulation of the hypoxia-sensing function of factor-inhibiting-HIF-1 (FIH) enzyme is a potential therapeutic strategy in disease states such as ischemia and cancer. The hypoxia-sensing function of FIH relies in major part on the tight coupling of the first half of the catalytic mechanism which involves O2 activation and eventual succinate production to the second half which involves HIF-1α/CTAD substrate hydroxylation. In this study, we demonstrate the role of a loop hinge domain in FIH (FIH102-118) called the 100s loop in maintaining this particular tight coupling. Molecular dynamics patterns from Gaussian Network Model (iGNM) database analysis of FIH identified the 100s loop as one dynamic domain containing a hinge residue (Tyr102) with a potential substrate positioning role. Enzymological and biophysical studies of the 100s loop point mutants revealed altered enzyme kinetics with the exception of the conservative FIH mutant Y102F, which suggests a sterics-related role for this residue. Removal of the bulk of Tyr102 (Y102A) resulted in succinate production, autohydroxylation, and an O2 binding environment comparable to wild-type FIH. However, the HIF-1α/CTAD substrate hydroxylation of this mutant was significantly reduced which implies that (1) the FIH loop hinge residue Tyr102 does not affect O2 activation, (2) the stacking steric interaction of Tyr102 is important in substrate positioning for productive hydroxylation, and (3) Tyr102 is important for the synchronization of O2 activation and substrate hydroxylation.
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Affiliation(s)
- Cristina B Martin
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Cornelius Y Taabazuing
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Michael J Knapp
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
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5
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Mingroni MA, Chaplin Momaney V, Barlow AN, Jaen Maisonet I, Knapp MJ. Measurement of kinetic isotope effects on peptide hydroxylation using MALDI-MS. Methods Enzymol 2022; 679:363-380. [PMID: 36682871 DOI: 10.1016/bs.mie.2022.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Primary kinetic isotope effects (KIEs) provide unique insight into enzymatic reactions, as they can reveal rate-limiting steps and detailed chemical mechanisms. HIF hydroxylases, part of a family of 2-oxoglutarate (2OG) oxygenases are central to the regulation of many crucial biological processes through O2-sensing, but present a challenge to monitor due to the large size of the protein substrate and the similarity between native and hydroxylated substrate. MALDI-TOF MS is a convenient tool to measure peptide masses, which can also be used to measure the discontinuous kinetics of peptide hydroxylation for Factor Inhibiting HIF (FIH). Using this technique, rate data can be observed from the mole-fraction of CTAD and CTAD-OH in small volumes, allowing noncompetitive H/D KIEs to be measured. Slow dCTAD substrate leads to extensive uncoupling of O2 consumption from peptide hydroxylation, leading to enzyme autohydroxylation, which is observed using UV-vis spectroscopy. Simultaneously measuring both the normal product, CTAD-OH, and the uncoupled product, autohydroxylated enzyme, the KIE on the microscopic step of hydrogen atom transfer (HAT) can be estimated. MALDI-MS analysis is a strong method for monitoring reactions that hydroxylate peptides, and can be generalized to other similar reactions, and simultaneous kinetic detection of branched products can provide valuable insight on microscopic KIEs at intermediate mechanistic steps.
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Affiliation(s)
- Michael A Mingroni
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States
| | | | - Alexandra N Barlow
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States
| | | | - Michael J Knapp
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States.
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6
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Bopp CE, Bernet NM, Kohler HPE, Hofstetter TB. Elucidating the Role of O 2 Uncoupling in the Oxidative Biodegradation of Organic Contaminants by Rieske Non-heme Iron Dioxygenases. ACS ENVIRONMENTAL AU 2022; 2:428-440. [PMID: 36164353 PMCID: PMC9502038 DOI: 10.1021/acsenvironau.2c00023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Oxygenations of aromatic
soil and water contaminants with molecular
O2 catalyzed by Rieske dioxygenases are frequent initial
steps of biodegradation in natural and engineered environments. Many
of these non-heme ferrous iron enzymes are known to be involved in
contaminant metabolism, but the understanding of enzyme–substrate
interactions that lead to successful biodegradation is still elusive.
Here, we studied the mechanisms of O2 activation and substrate
hydroxylation of two nitroarene dioxygenases to evaluate enzyme- and
substrate-specific factors that determine the efficiency of oxygenated
product formation. Experiments in enzyme assays of 2-nitrotoluene
dioxygenase (2NTDO) and nitrobenzene dioxygenase (NBDO) with methyl-,
fluoro-, chloro-, and hydroxy-substituted nitroaromatic substrates
reveal that typically 20–100% of the enzyme’s activity
involves unproductive paths of O2 activation with generation
of reactive oxygen species through so-called O2 uncoupling.
The 18O and 13C kinetic isotope effects of O2 activation and nitroaromatic substrate hydroxylation, respectively,
suggest that O2 uncoupling occurs after generation of FeIII-(hydro)peroxo species in the catalytic cycle. While 2NTDO
hydroxylates ortho-substituted nitroaromatic substrates
more efficiently, NBDO favors meta-substituted, presumably
due to distinct active site residues of the two enzymes. Our data
implies, however, that the O2 uncoupling and hydroxylation
activity cannot be assessed from simple structure–reactivity
relationships. By quantifying O2 uncoupling by Rieske dioxygenases,
our work provides a mechanistic link between contaminant biodegradation,
the generation of reactive oxygen species, and possible adaptation
strategies of microorganisms to the exposure of new contaminants.
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Affiliation(s)
- Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Nora M. Bernet
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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7
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Pati SG, Bopp CE, Kohler HPE, Hofstetter TB. Substrate-Specific Coupling of O 2 Activation to Hydroxylations of Aromatic Compounds by Rieske Non-heme Iron Dioxygenases. ACS Catal 2022; 12:6444-6456. [PMID: 35692249 PMCID: PMC9171724 DOI: 10.1021/acscatal.2c00383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/09/2022] [Indexed: 02/07/2023]
Abstract
![]()
Rieske dioxygenases
catalyze the initial steps in the hydroxylation
of aromatic compounds and are critical for the metabolism of xenobiotic
substances. Because substrates do not bind to the mononuclear non-heme
FeII center, elementary steps leading to O2 activation
and substrate hydroxylation are difficult to delineate, thus making
it challenging to rationalize divergent observations on enzyme mechanisms,
reactivity, and substrate specificity. Here, we show for nitrobenzene
dioxygenase, a Rieske dioxygenase capable of transforming nitroarenes
to nitrite and substituted catechols, that unproductive O2 activation with the release of the unreacted substrate and reactive
oxygen species represents an important path in the catalytic cycle.
Through correlation of O2 uncoupling for a series of substituted
nitroaromatic compounds with 18O and 13C kinetic
isotope effects of dissolved O2 and aromatic substrates,
respectively, we show that O2 uncoupling occurs after the
rate-limiting formation of FeIII-(hydro)peroxo species
from which substrates are hydroxylated. Substituent effects on the
extent of O2 uncoupling suggest that the positioning of
the substrate in the active site rather than the susceptibility of
the substrate for attack by electrophilic oxygen species is responsible
for unproductive O2 uncoupling. The proposed catalytic
cycle provides a mechanistic basis for assessing the very different
efficiencies of substrate hydroxylation vs unproductive O2 activation and generation of reactive oxygen species in reactions
catalyzed by Rieske dioxygenases.
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Affiliation(s)
- Sarah G. Pati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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8
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Mingroni MA, Knapp MJ. Kinetic Studies of the Hydrogen Atom Transfer in a Hypoxia-Sensing Enzyme, FIH-1: KIE and O 2 Reactivity. Biochemistry 2021; 60:3315-3322. [PMID: 34714626 DOI: 10.1021/acs.biochem.1c00476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cellular hypoxia plays a crucial role in tissue development and adaptation to pO2. Central to cellular oxygen sensing is factor-inhibiting HIF-1α (FIH), an α-ketoglutarate (αKG)/non-heme iron(II)-dependent dioxygenase that hydroxylates a specific asparagine residue of hypoxia inducible factor-1α (HIF-1α). The high KM(O2) and rate-limiting decarboxylation step upon O2 activation are key features of the enzyme that classify it as an oxygen sensor and set it apart from other αKG/Fe(II)-dependent dioxygenases. Although the chemical intermediates following decarboxylation are presumed to follow the consensus mechanism of other αKG/Fe(II)-dependent dioxygenases, experiments have not previously demonstrated these canonical steps in FIH. In this work, a deuterated peptide substrate was used as a mechanistic probe for the canonical hydrogen atom transfer (HAT). Our data show a large kinetic isotope effect (KIE) in steady-state kinetics (Dkcat = 10 ± 1), revealing that the HAT occurs and is partially rate limiting on kcat. Kinetic studies showed that the deuterated peptide led FIH to uncouple O2 activation and provided the opportunity to spectroscopically observe the ferryl intermediate. This enzyme uncoupling was used as an internal competition with respect to the fate of the ferryl intermediate, demonstrating a large observed KIE on the uncoupling (Dk5 = 1.147 ± 0.005) and an intrinsic KIE on the HAT step (Dk > 15). The close energy barrier between αKG decarboxylation and HAT distinguishes FIH as an O2-sensing enzyme and is crucial for ensuring substrate specificity in the regulation of cellular O2 homeostasis.
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Affiliation(s)
- Michael A Mingroni
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Michael J Knapp
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
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9
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Chaturvedi S, Ramanan R, Lehnert N, Schofield CJ, Karabencheva-Christova TG, Christov CZ. Catalysis by the Non-Heme Iron(II) Histone Demethylase PHF8 Involves Iron Center Rearrangement and Conformational Modulation of Substrate Orientation. ACS Catal 2020; 10:1195-1209. [PMID: 31976154 PMCID: PMC6970271 DOI: 10.1021/acscatal.9b04907] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/10/2019] [Indexed: 02/07/2023]
Abstract
PHF8 (KDM7B) is a human non-heme 2-oxoglutarate (2OG) JmjC domain oxygenase that catalyzes the demethylation of the di/mono-Nε-methylated K9 residue of histone H3. Altered PHF8 activity is linked to genetic diseases and cancer; thus, it is an interesting target for epigenetic modulation. We describe the use of combined quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations to explore the mechanism of PHF8, including dioxygen activation, 2OG binding modes, and substrate demethylation steps. A PHF8 crystal structure manifests the 2OG C-1 carboxylate bound to iron in a nonproductive orientation, i.e., trans to His247. A ferryl-oxo intermediate formed by activating dioxygen bound to the vacant site in this complex would be nonproductive, i.e., "off-line" with respect to reaction with Nε-methylated K9. We show rearrangement of the "off-line" ferryl-oxo intermediate to a productive "in-line" geometry via a solvent exchange reaction (called "ferryl-flip") is energetically unfavorable. The calculations imply that movement of the 2OG C-1 carboxylate prior to dioxygen binding at a five-coordination stage in catalysis proceeds with a low barrier, suggesting that two possible 2OG C-1 carboxylate geometries can coexist at room temperature. We explored alternative mechanisms for hydrogen atom transfer and show that second sphere interactions orient the Nε-methylated lysine in a conformation where hydrogen abstraction from a methyl C-H bond is energetically more favorable than hydrogen abstraction from the N-H bond of the protonated Nε-methyl group. Using multiple HAT reaction path calculations, we demonstrate the crucial role of conformational flexibility in effective hydrogen transfer. Subsequent hydroxylation occurs through a rebound mechanism, which is energetically preferred compared to desaturation, due to second sphere interactions. The overall mechanistic insights reveal the crucial role of iron-center rearrangement, second sphere interactions, and conformational flexibility in PHF8 catalysis and provide knowledge useful for the design of mechanism-based PHF8 inhibitors.
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Affiliation(s)
- Shobhit
S. Chaturvedi
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Rajeev Ramanan
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Nicolai Lehnert
- Department
of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | - Christo Z. Christov
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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10
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Martin CB, Chaplin VD, Eyles SJ, Knapp MJ. Protein Flexibility of the α-Ketoglutarate-Dependent Oxygenase Factor-Inhibiting HIF-1: Implications for Substrate Binding, Catalysis, and Regulation. Biochemistry 2019; 58:4047-4057. [PMID: 31499004 DOI: 10.1021/acs.biochem.9b00619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein dynamics are crucial for the mechanistically ordered enzymes to bind to their substrate in the correct sequence and perform catalysis. Factor-inhibiting HIF-1 (FIH) is a nonheme Fe(II) α-ketoglutarate-dependent oxygenase that is a key hypoxia (low pO2) sensor in humans. As these hypoxia-sensing enzymes follow a multistep chemical mechanism consuming α-ketoglutarate, a protein substrate that is hydroxylated, and O2, understanding protein flexibility and the order of substrate binding may aid in the development of strategies for selective targeting. The primary substrate of FIH is the C-terminal transactivation domain (CTAD) of hypoxia-inducible factor 1α (HIF) that is hydroxylated on the side chain of Asn803. We assessed changes in protein flexibility connected to metal and αKG binding, finding that (M+αKG) binding significantly stabilized the cupin barrel core of FIH as evidenced by enhanced thermal stability and decreased protein dynamics as assessed by global amide hydrogen/deuterium exchange mass spectrometry and limited proteolysis. Confirming predictions of the consensus mechanism, (M+αKG) increased the affinity of FIH for CTAD as measured by titrations monitoring intrinsic tryptophan fluorescence. The decreased protein dynamics caused by (M+αKG) enforces a sequentially ordered substrate binding sequence in which αKG binds before CTAD, suggesting that selective inhibition may require inhibitors that target the binding sites of both αKG and the prime substrate. A consequence of the correlation between dynamics and αKG binding is that all relevant ligands must be included in binding-based inhibitor screens, as shown by testing permutations of M, αKG, and inhibitor.
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Affiliation(s)
- Cristina B Martin
- Department of Chemistry , University of Massachusetts , Amherst , Massachusetts 01003 , United States
| | - Vanessa D Chaplin
- Department of Chemistry , University of Massachusetts , Amherst , Massachusetts 01003 , United States
| | - Stephen J Eyles
- Department of Biochemistry and Molecular Biology , University of Massachusetts , Amherst , Massachusetts 01003 , United States
| | - Michael J Knapp
- Department of Chemistry , University of Massachusetts , Amherst , Massachusetts 01003 , United States
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11
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Xue J, Lu J, Lai W. Mechanistic insights into a non-heme 2-oxoglutarate-dependent ethylene-forming enzyme: selectivity of ethylene-formation versusl-Arg hydroxylation. Phys Chem Chem Phys 2019; 21:9957-9968. [PMID: 31041955 DOI: 10.1039/c9cp00794f] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ethylene-forming enzyme (EFE) is a unique member of the Fe(ii)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases. It converts 2OG into ethylene plus three CO2 molecules (ethylene-forming reaction) and also catalyzes the C5 hydroxylation of l-arginine coupled to the oxidative decarboxylation of 2OG (l-Arg hydroxylation reaction). To uncover the mechanisms of the dual transformations by EFE, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out. Based on the results, a branched mechanism was proposed. An FeII-peroxysuccinate complex with a dissociated CO2 generated through the nucleophilic attack of the superoxo moiety of the Fe-O2 species on the keto carbon of 2OG is the key common intermediate in both reactions. A competition between the subsequent CO2 insertion (a key step in the ethylene-forming pathway) and the O-O bond cleavage (leading to the formation of succinate) governs the product selectivity. The calculated reaction barriers suggested that the CO2 insertion is favored over the O-O bond cleavage. This is consistent with the product preference observed in experiments. By comparison with the results of AsqJ (an Fe/2OG oxygenase that leads to substrate oxidation exclusively), the protein environment was found to be crucial for the selectivity. Further calculations demonstrated that the local electric field of the protein environment in EFE promotes ethylene formation by acting as a charge template, exemplifying the importance of the electrostatic interaction in enzyme catalysis. These findings offer mechanistic insights into the EFE catalysis and provide important clues for better understanding the unique ethylene-forming capability of EFE compared with other Fe/2OG oxygenases.
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Affiliation(s)
- Junqin Xue
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
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12
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Klinman JP, Offenbacher AR. Understanding Biological Hydrogen Transfer Through the Lens of Temperature Dependent Kinetic Isotope Effects. Acc Chem Res 2018; 51:1966-1974. [PMID: 30152685 DOI: 10.1021/acs.accounts.8b00226] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Hydrogen atom transfer (HAT) is a salient feature of many enzymatic C-H cleavage mechanisms. In systems where kinetic isolation of HAT is achieved, selective labeling of substrate with hydrogen isotopes, such as deuterium, enables the determination of intrinsic kinetic isotope effects (KIEs). While the magnitude of the KIE is itself informative, ultimately the size of the temperature dependence of the KIE, Δ Ea = Ea(D) - Ea(H), serves as a critical, and often misinterpreted (or even ignored) descriptor of the reaction coordinate. As will be highlighted in this Account, Δ Ea is one of the most robust parameters to emerge from studies of enzyme catalyzed hydrogen transfer. Kinetic parameters for C-H reactions via HAT can appear consistent with either classical "over-the-barrier" or "Bell-like tunneling correction" models. However, neither of these models is able to explain the observation of near-zero Δ Ea values with many native enzymes that increase upon extrinsic or intrinsic perturbations to function. Instead, a full tunneling model has been developed that can account for the aggregate trends in the temperature dependence of the KIE. This model is reminiscent of Marcus-like theory for electron tunneling, with the additional incorporation of an H atom donor-acceptor distance (DAD) sampling term for effective wave function overlap; the role of the latter term is manifested in the experimentally determined Δ Ea. Three enzyme systems from this laboratory that illustrate different aspects of HAT are presented: taurine dioxygenase, the dual copper β-monooxygenases, and soybean lipoxygenase (SLO). The latter provides a particularly compelling system for understanding the properties of hydrogen tunneling, showing systematic increases in Δ Ea upon reduction in the size of hydrophobic residues both proximal and distal from the active site iron cofactor. Of note, recent ENDOR-based studies of enzyme-substrate complexes with SLO indicate an increase in DAD for mutants with increased Δ Ea, observations that are inconsistent with "Bell-like correction" models. Overall, the surmounting kinetic and biophysical evidence corroborates a multidimensional approach for understanding HAT, offering a robust mechanistic explanation for the magnitude and trends of the KIE and Δ Ea. Recent DFT and QM/MM computations on SLO are compared to the developed nonadiabatic analytical constructs, providing considerable insight into ground state structures and reactivity. However, QM/MM is unable to readily reproduce the small Δ Ea values characteristic of native enzymes. Future theoretical developments to capture these experimental observations may necessitate a parsing of protein motions for local, substrate deuteration-sensitive modes from isotope-insensitive modes within the larger conformational landscape, in the process providing deeper understanding of how native enzymes have evolved to transiently optimize their active site configurations.
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Affiliation(s)
- Judith P. Klinman
- Department of Chemistry, Department of Molecular and Cell Biology and California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Adam R. Offenbacher
- Department of Chemistry, Department of Molecular and Cell Biology and California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
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13
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Mechanisms of Bacterial Tolerance and Persistence in the Gastrointestinal and Respiratory Environments. Clin Microbiol Rev 2018; 31:31/4/e00023-18. [PMID: 30068737 DOI: 10.1128/cmr.00023-18] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Pathogens that infect the gastrointestinal and respiratory tracts are subjected to intense pressure due to the environmental conditions of the surroundings. This pressure has led to the development of mechanisms of bacterial tolerance or persistence which enable microorganisms to survive in these locations. In this review, we analyze the general stress response (RpoS mediated), reactive oxygen species (ROS) tolerance, energy metabolism, drug efflux pumps, SOS response, quorum sensing (QS) bacterial communication, (p)ppGpp signaling, and toxin-antitoxin (TA) systems of pathogens, such as Escherichia coli, Salmonella spp., Vibrio spp., Helicobacter spp., Campylobacter jejuni, Enterococcus spp., Shigella spp., Yersinia spp., and Clostridium difficile, all of which inhabit the gastrointestinal tract. The following respiratory tract pathogens are also considered: Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Burkholderia cenocepacia, and Mycobacterium tuberculosis Knowledge of the molecular mechanisms regulating the bacterial tolerance and persistence phenotypes is essential in the fight against multiresistant pathogens, as it will enable the identification of new targets for developing innovative anti-infective treatments.
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14
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Pan J, Bhardwaj M, Zhang B, Chang WC, Schardl CL, Krebs C, Grossman RB, Bollinger JM. Installation of the Ether Bridge of Lolines by the Iron- and 2-Oxoglutarate-Dependent Oxygenase, LolO: Regio- and Stereochemistry of Sequential Hydroxylation and Oxacyclization Reactions. Biochemistry 2018. [PMID: 29537853 PMCID: PMC5895980 DOI: 10.1021/acs.biochem.8b00157] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The core of the loline
family of insecticidal alkaloids is the
bicyclic pyrrolizidine unit with an additional strained ether bridge
between carbons 2 and 7. Previously reported genetic and in
vivo biochemical analyses showed that the presumptive iron-
and 2-oxoglutarate-dependent (Fe/2OG) oxygenase, LolO, is required
for installation of the ether bridge upon the pathway intermediate,
1-exo-acetamidopyrrolizidine (AcAP). Here we show
that LolO is, in fact, solely responsible for this biosynthetic four-electron
oxidation. In sequential 2OG- and O2-consuming steps, LolO
removes hydrogens from C2 and C7 of AcAP to form both carbon–oxygen
bonds in N-acetylnorloline (NANL), the precursor
to all other lolines. When supplied with substoichiometric 2OG, LolO
only hydroxylates AcAP. At higher 2OG:AcAP ratios, the enzyme further
processes the alcohol to the tricyclic NANL. Characterization of the
alcohol intermediate by mass spectrometry and nuclear magnetic resonance
spectroscopy shows that it is 2-endo-hydroxy-1-exo-acetamidopyrrolizidine (2-endo-OH-AcAP).
Kinetic and spectroscopic analyses of reactions with site-specifically
deuteriated AcAP substrates confirm that the C2–H bond is cleaved
first and that the responsible intermediate is, as expected, an FeIV–oxo (ferryl) complex. Analyses of the loline products
from cultures fed with stereospecifically deuteriated AcAP precursors,
proline and aspartic acid, establish that LolO removes the endo hydrogens
from C2 and C7 and forms both new C–O bonds with retention
of configuration. These findings delineate the pathway to an important
class of natural insecticides and lay the foundation for mechanistic
dissection of the chemically challenging oxacyclization reaction.
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Affiliation(s)
- Juan Pan
- Department of Chemistry and Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | | | - Bo Zhang
- Department of Chemistry and Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Wei-Chen Chang
- Department of Chemistry and Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | | | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | | | - J Martin Bollinger
- Department of Chemistry and Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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15
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Song X, Lu J, Lai W. Mechanistic insights into dioxygen activation, oxygen atom exchange and substrate epoxidation by AsqJ dioxygenase from quantum mechanical/molecular mechanical calculations. Phys Chem Chem Phys 2018; 19:20188-20197. [PMID: 28726913 DOI: 10.1039/c7cp02687k] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Herein, we use in-protein quantum mechanical/molecular mechanical (QM/MM) calculations to elucidate the mechanism of dioxygen activation, oxygen atom exchange and substrate epoxidation processes by AsqJ, an FeII/α-ketoglutarate-dependent dioxygenase (α-KGD) using a 2-His-1-Asp facial triad. Our results demonstrated that the whole reaction proceeds through a quintet surface. The dioxygen activation by AsqJ leads to a quintet penta-coordinated FeIV-oxo species, which has a square pyramidal geometry with the oxo group trans to His134. This penta-coordinated FeIV-oxo species is not the reactive one in the substrate epoxidation reaction since its oxo group is pointing away from the target C[double bond, length as m-dash]C bond. Instead, it can undergo the oxo group isomerization followed by water binding or the water binding followed by oxygen atom exchange to form the reactive hexa-coordinated FeIV-oxo species with the oxo group trans to His211. The calculated parameters of Mössbauer spectra for this hexa-coordinated FeIV-oxo intermediate are in excellent agreement with the experimental values, suggesting that it is most likely the experimentally trapped species. The calculated energetics indicated that the rate-limiting step is the substrate C[double bond, length as m-dash]C bond activation. This work improves our understanding of the dioxygen activation by α-KGD and provides important structural information about the reactive FeIV-oxo species.
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Affiliation(s)
- Xudan Song
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
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16
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Goswami A, Liu X, Cai W, Wyche TP, Bugni TS, Meurillon M, Peyrottes S, Perigaud C, Nonaka K, Rohr J, Van Lanen SG. Evidence that oxidative dephosphorylation by the nonheme Fe(II), α-ketoglutarate:UMP oxygenase occurs by stereospecific hydroxylation. FEBS Lett 2017; 591:468-478. [PMID: 28074470 DOI: 10.1002/1873-3468.12554] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 12/23/2016] [Accepted: 12/25/2016] [Indexed: 11/08/2022]
Abstract
LipL and Cpr19 are nonheme, mononuclear Fe(II)-dependent, α-ketoglutarate (αKG):UMP oxygenases that catalyze the formation of CO2 , succinate, phosphate, and uridine-5'-aldehyde, the last of which is a biosynthetic precursor for several nucleoside antibiotics that inhibit bacterial translocase I (MraY). To better understand the chemistry underlying this unusual oxidative dephosphorylation and establish a mechanistic framework for LipL and Cpr19, we report herein the synthesis of two biochemical probes-[1',3',4',5',5'-2 H]UMP and the phosphonate derivative of UMP-and their activity with both enzymes. The results are consistent with a reaction coordinate that proceeds through the loss of one 2 H atom of [1',3',4',5',5'-2 H]UMP and stereospecific hydroxylation geminal to the phosphoester to form a cryptic intermediate, (5'R)-5'-hydroxy-UMP. Thus, these enzyme catalysts can additionally be assigned as UMP hydroxylase-phospholyases.
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Affiliation(s)
- Anwesha Goswami
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Xiaodong Liu
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Wenlong Cai
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Thomas P Wyche
- Department of Pharmaceutical Sciences, University of Wisconsin-Madison, WI, USA
| | - Tim S Bugni
- Department of Pharmaceutical Sciences, University of Wisconsin-Madison, WI, USA
| | - Maïa Meurillon
- Nucleosides and Phosphorylated Effectors Team, IBMM, UMR5247 CNRS University Montpellier, France
| | - Suzanne Peyrottes
- Nucleosides and Phosphorylated Effectors Team, IBMM, UMR5247 CNRS University Montpellier, France
| | - Christian Perigaud
- Nucleosides and Phosphorylated Effectors Team, IBMM, UMR5247 CNRS University Montpellier, France
| | - Koichi Nonaka
- Biologics Technology Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., Gunma, Japan
| | - Jürgen Rohr
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
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17
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Proshlyakov DA, McCracken J, Hausinger RP. Spectroscopic analyses of 2-oxoglutarate-dependent oxygenases: TauD as a case study. J Biol Inorg Chem 2016; 22:367-379. [PMID: 27812832 DOI: 10.1007/s00775-016-1406-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/25/2016] [Indexed: 11/28/2022]
Abstract
A wide range of spectroscopic approaches have been used to interrogate the mononuclear iron metallocenter in 2-oxoglutarate (2OG)-dependent oxygenases. The results from these spectroscopic studies have provided valuable insights into the structural changes at the active site during substrate binding and catalysis, thus providing critical information that complements investigations of these enzymes by X-ray crystallography, biochemical, and computational approaches. This mini-review highlights taurine hydroxylase (taurine:2OG dioxygenase, TauD) as a case study to illustrate the wealth of knowledge that can be generated by applying a diverse array of spectroscopic investigations to a single enzyme. In particular, electronic absorption, circular dichroism, magnetic circular dichroism, conventional and pulse electron paramagnetic, Mössbauer, X-ray absorption, and resonance Raman methods have been exploited to uncover the properties of the metal site in TauD.
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Affiliation(s)
- Denis A Proshlyakov
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - John McCracken
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Robert P Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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18
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Electron flow through biological molecules: does hole hopping protect proteins from oxidative damage? Q Rev Biophys 2016; 48:411-20. [PMID: 26537399 DOI: 10.1017/s0033583515000062] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Biological electron transfers often occur between metal-containing cofactors that are separated by very large molecular distances. Employing photosensitizer-modified iron and copper proteins, we have shown that single-step electron tunneling can occur on nanosecond to microsecond timescales at distances between 15 and 20 Å. We also have shown that charge transport can occur over even longer distances by hole hopping (multistep tunneling) through intervening tyrosines and tryptophans. In this perspective, we advance the hypothesis that such hole hopping through Tyr/Trp chains could protect oxygenase, dioxygenase, and peroxidase enzymes from oxidative damage. In support of this view, by examining the structures of P450 (CYP102A) and 2OG-Fe (TauD) enzymes, we have identified candidate Tyr/Trp chains that could transfer holes from uncoupled high-potential intermediates to reductants in contact with protein surface sites.
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19
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Wetzl D, Bolsinger J, Nestl BM, Hauer B. α-Hydroxylation of Carboxylic Acids Catalyzed by Taurine Dioxygenase. ChemCatChem 2016. [DOI: 10.1002/cctc.201501244] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dennis Wetzl
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany), Fax
| | - Jennifer Bolsinger
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany), Fax
| | - Bettina M. Nestl
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany), Fax
| | - Bernhard Hauer
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany), Fax
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20
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Taabazuing CY, Fermann J, Garman S, Knapp MJ. Substrate Promotes Productive Gas Binding in the α-Ketoglutarate-Dependent Oxygenase FIH. Biochemistry 2016; 55:277-86. [PMID: 26727884 PMCID: PMC4793777 DOI: 10.1021/acs.biochem.5b01003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Fe(2+)/α-ketoglutarate (αKG)-dependent oxygenases use molecular oxygen to conduct a wide variety of reactions with important biological implications, such as DNA base excision repair, histone demethylation, and the cellular hypoxia response. These enzymes follow a sequential mechanism in which O2 binds and reacts after the primary substrate binds, making those structural factors that promote productive O2 binding central to their chemistry. A large challenge in this field is to identify strategies that engender productive turnover. Factor inhibiting HIF (FIH) is a Fe(2+)/αKG-dependent oxygenase that forms part of the O2 sensing machinery in human cells by hydroxylating the C-terminal transactivation domain (CTAD) found within the HIF-1α protein. The structure of FIH was determined with the O2 analogue NO bound to Fe, offering the first direct insight into the gas binding geometry in this enzyme. Through a combination of density functional theory calculations, {FeNO}(7) electron paramagnetic resonance spectroscopy, and ultraviolet-visible absorption spectroscopy, we demonstrate that CTAD binding stimulates O2 reactivity by altering the orientation of the bound gas molecule. Although unliganded FIH binds NO with moderate affinity, the bound gas can adopt either of two orientations with similar stability; upon CTAD binding, NO adopts a single preferred orientation that is appropriate for supporting oxidative decarboxylation. Combined with other studies of related enzymes, our data suggest that substrate-induced reorientation of bound O2 is the mechanism utilized by the αKG oxygenases to tightly couple O2 activation to substrate hydroxylation.
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Affiliation(s)
| | - Justin Fermann
- Department of Chemistry, University of Massachusetts, Amherst
| | - Scott Garman
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst
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21
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Chang WC, Guo Y, Wang C, Butch SE, Rosenzweig AC, Boal AK, Krebs C, Bollinger JM. Mechanism of the C5 stereoinversion reaction in the biosynthesis of carbapenem antibiotics. Science 2014; 343:1140-4. [PMID: 24604200 PMCID: PMC4160820 DOI: 10.1126/science.1248000] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The bicyclic β-lactam/2-pyrrolidine precursor to all carbapenem antibiotics is biosynthesized by attachment of a carboxymethylene unit to C5 of L-proline followed by β-lactam ring closure. Carbapenem synthase (CarC), an Fe(II) and 2-(oxo)glutarate (Fe/2OG)-dependent oxygenase, then inverts the C5 configuration. Here we report the structure of CarC in complex with its substrate and biophysical dissection of its reaction to reveal the stereoinversion mechanism. An Fe(IV)-oxo intermediate abstracts the hydrogen (H•) from C5, and tyrosine 165, a residue not visualized in the published structures of CarC lacking bound substrate, donates H• to the opposite face of the resultant radical. The reaction oxidizes the Fe(II) cofactor to Fe(III), limiting wild-type CarC to one turnover, but substitution of the H•-donating tyrosine disables stereoinversion and confers to CarC the capacity for catalytic substrate oxidation.
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Affiliation(s)
- Wei-chen Chang
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yisong Guo
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chen Wang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Susan E. Butch
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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22
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Sogi KM, Gartner ZJ, Breidenbach MA, Appel MJ, Schelle MW, Bertozzi CR. Mycobacterium tuberculosis Rv3406 is a type II alkyl sulfatase capable of sulfate scavenging. PLoS One 2013; 8:e65080. [PMID: 23762287 PMCID: PMC3675115 DOI: 10.1371/journal.pone.0065080] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 04/22/2013] [Indexed: 11/19/2022] Open
Abstract
The genome of Mycobacterium tuberculosis (Mtb) encodes nine putative sulfatases, none of which have a known function or substrate. Here, we characterize Mtb’s single putative type II sulfatase, Rv3406, as a non-heme iron (II) and α-ketoglutarate-dependent dioxygenase that catalyzes the oxidation and subsequent cleavage of alkyl sulfate esters. Rv3406 was identified based on its homology to the alkyl sulfatase AtsK from Pseudomonas putida. Using an in vitro biochemical assay, we confirmed that Rv3406 is a sulfatase with a preference for alkyl sulfate substrates similar to those processed by AtsK. We determined the crystal structure of the apo Rv3406 sulfatase at 2.5 Å. The active site residues of Rv3406 and AtsK are essentially superimposable, suggesting that the two sulfatases share the same catalytic mechanism. Finally, we generated an Rv3406 mutant (Δrv3406) in Mtb to study the sulfatase’s role in sulfate scavenging. The Δrv3406 strain did not replicate in minimal media with 2-ethyl hexyl sulfate as the sole sulfur source, in contrast to wild type Mtb or the complemented strain. We conclude that Rv3406 is an iron and α-ketoglutarate-dependent sulfate ester dioxygenase that has unique substrate specificity that is likely distinct from other Mtb sulfatases.
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Affiliation(s)
- Kimberly M. Sogi
- Department of Chemistry, University of California, Berkeley, California, United States of America
| | - Zev J. Gartner
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Mark A. Breidenbach
- Department of Chemistry, University of California, Berkeley, California, United States of America
| | - Mason J. Appel
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Michael W. Schelle
- Department of Chemistry, University of California, Berkeley, California, United States of America
| | - Carolyn R. Bertozzi
- Department of Chemistry, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
- * E-mail:
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23
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Phelan RM, Townsend CA. Mechanistic insights into the bifunctional non-heme iron oxygenase carbapenem synthase by active site saturation mutagenesis. J Am Chem Soc 2013; 135:7496-502. [PMID: 23611403 PMCID: PMC3683866 DOI: 10.1021/ja311078s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The carbapenem class of β-lactam antibiotics is known for its remarkable potency, antibacterial spectrum, and resistance to β-lactamase-mediated inactivation. While the biosynthesis of structurally "complex" carbapenems, such as thienamycin, share initial biochemical steps with carbapenem-3-carboxylate ("simple" carbapenem), the requisite inversion at C5 and formation of the characteristic α,β-unsaturated carboxylate are different in origin between the two groups. Here, we consider carbapenem synthase, a mechanistically distinct bifunctional non-heme iron α-ketoglutarate-dependent enzyme responsible for the terminal reactions, C5 epimerization and desaturation, in simple carbapenem production. Interestingly, this enzyme accepts two stereoisomeric substrates and transforms each to a common active antibiotic. Owing both to enzyme and product instability, resorting to saturation mutagenesis of active site and selected second-sphere residues gave clearly differing profiles of CarC tolerance to structural modification. Guided by a crystal structure and the mutational data, in silico docking was used to suggest the positioning of each disastereomeric substrate in the active site. The two orientations relative to the reactive iron-oxo center are manifest in the two distinct reactions, C5-epimerization and C2/3-desaturation. These observations favor a two-step reaction scheme involving two complete oxidative cycles as opposed to a single catalytic cycle in which an active site tyrosine, Tyr67, after hydrogen donation to achieve bicyclic ring inversion, is further hypothesized to serve as a radical carrier.
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Affiliation(s)
- Ryan M. Phelan
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218
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24
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Hangasky JA, Taabazuing CY, Valliere MA, Knapp MJ. Imposing function down a (cupin)-barrel: secondary structure and metal stereochemistry in the αKG-dependent oxygenases. Metallomics 2013; 5:287-301. [PMID: 23446356 PMCID: PMC4109655 DOI: 10.1039/c3mt20153h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Fe(ii)/αketoglutarate (αKG) dependent oxygenases catalyze a diverse range of reactions significant in biological processes such as antibiotic biosynthesis, lipid metabolism, oxygen sensing, and DNA and RNA repair. Although functionally diverse, the eight-stranded β-barrel (cupin) and HX(D/E)XnH facial triad motifs are conserved in this super-family of enzymes. Crystal structure analysis of 25 αKG oxygenases reveals two stereoisomers of the Fe cofactor, Anti and Clock, which differ in the relative position of the exchangeable ligand position and the primary substrate. Herein, we discuss the relationship between the chemical mechanism and the secondary coordination sphere of the αKG oxygenases, within the constraints of the stereochemistry of the Fe cofactor. Sequence analysis of the cupin barrel indicates that a small subset of positions constitute the second coordination sphere, which has significant ramifications for the structure of the ferryl intermediate. The competence of both Anti and Clock stereoisomers of Fe points to a ferryl intermediate that is 5 coordinate. The small number of conserved close contacts within the active sites of αKG oxygenases can be extended to chemically related enzymes, such as the αKG-dependent halogenases SyrB2 and CytC3, and the non-αKG dependent dioxygenases isopenicillin N synthase (IPNS) and cysteine dioxygenase (CDO).
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Affiliation(s)
- John A. Hangasky
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | | | - Meaghan A. Valliere
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Michael J. Knapp
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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25
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Knauer SH, Hartl-Spiegelhauer O, Schwarzinger S, Hänzelmann P, Dobbek H. The Fe(II)/α-ketoglutarate-dependent taurine dioxygenases from Pseudomonas putida and Escherichia coli are tetramers. FEBS J 2012; 279:816-31. [PMID: 22221834 DOI: 10.1111/j.1742-4658.2012.08473.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Fe(II)/α-ketoglutarate-dependent oxygenases are versatile catalysts associated with a number of different biological functions in which they use the oxidizing power of activated dioxygen to convert a variety of substrates. A mononuclear nonheme iron center is used to couple the decarboxylation of the cosubstrate α-ketoglutarate with a two-electron oxidation of the substrate, which is a hydroxylation in most cases. Although Fe(II)/α-ketoglutarate-dependent oxygenases have diverse amino acid sequences and substrate specifity, it is assumed that they share a common mechanism. One representative of this enzyme family is the Fe(II)/α-ketoglutarate-dependent taurine dioxygenase that catalyzes the hydroxylation of taurine yielding sulfite and aminoacetaldehyde. Its mechanism has been studied in detail becoming a model system for the whole enzyme family. However, its oligomeric state and architecture have been disputed. Here, we report the biochemical and kinetic characterization of the Fe(II)/α-ketoglutarate-dependent taurine dioxygenase from Pseudomonas putida KT2440 (TauD(Pp) ). We also present three crystal structures of the apo form of this enzyme. Comparisons with taurine dioxygenase from Escherichia coli (TauD(Ec) ) demonstrate that both enzymes are quite similar regarding their spectra, structure and kinetics, and only minor differences for the accumulation of intermediates during the reaction have been observed. Structural data and analytical gel filtration, as well as sedimentation velocity analytical ultracentrifugation, show that both TauD(Pp) and TauD(Ec) are tetramers in solution and in the crystals, which is in contrast to the earlier description of taurine dioxygenase from E. coli as a dimer. Database The atomic coordinates and structure factors have been deposited with the Brookhaven Protein Data Bank (entry 3PVJ, 3V15, 3V17) Structured digital abstract • tauDpp and tauDpp bind by molecular sieving (View interaction) • tauDpp and tauDpp bind by x-ray crystallography (View interaction) • tauDEc and tauDEc bind by molecular sieving (View interaction).
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Affiliation(s)
- Stefan H Knauer
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Germany
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Meyer MP, Klinman JP. Investigating inner-sphere reorganization via secondary kinetic isotope effects in the C-H cleavage reaction catalyzed by soybean lipoxygenase: tunneling in the substrate backbone as well as the transferred hydrogen. J Am Chem Soc 2011; 133:430-9. [PMID: 21192631 PMCID: PMC3090704 DOI: 10.1021/ja1050742] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work describes the application of NMR to the measurement of secondary deuterium (2° (2)H) and carbon-13 ((13)C) kinetic isotope effects (KIEs) at positions 9-13 within the substrate linoleic acid (LA) of soybean lipoxygenase-1. The KIEs have been measured using LA labeled with either protium (11,11-h2-LA) or deuterium (11,11-d2-LA) at the reactive C11 position, which has been previously shown to yield a primary deuterium isotope effect of ca. 80. The conditions of measurement yield the intrinsic 2° (2)H and (13)C KIEs on k(cat)/K(m) directly for 11,11-d2-LA, whereas the values for the 2° (2)H KIEs for 11,11-h2-LA are obtained after correction for a kinetic commitment. The pattern of the resulting 2° (2)H and (13)C isotope effects reveals values that lie far above those predicted from changes in local force constants. Additionally, many of the experimental values cannot be modeled by electronic effects, torsional strain, or the simple inclusion of a tunneling correction to the rate. Although previous studies have shown the importance of extensive tunneling for cleavage of the primary hydrogen at C11 of LA, the present findings can only be interpreted by extending the conclusion of nonclassical behavior to the secondary hydrogens and carbons that flank the position undergoing C-H bond cleavage. A quantum mechanical method introduced by Buhks et al. [J. Phys. Chem. 1981, 85, 3763] to model the inner-sphere reorganization that accompanies electron transfer has been shown to be able to reproduce the scale of the 2° (2)H KIEs.
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Affiliation(s)
- Matthew P. Meyer
- To whom correspondence should be addressed. J.P.K.: Tel: 510-642-2668; Fax: 510-643-6232; . MPM: Tel: 209-228-2983; Fax: 209-675-8042;
| | - Judith P. Klinman
- Departments of Chemistry and of Molecular and Cell Biology and the California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
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Saban E, Flagg SC, Knapp MJ. Uncoupled O2-activation in the human HIF-asparaginyl hydroxylase, FIH, does not produce reactive oxygen species. J Inorg Biochem 2011; 105:630-6. [PMID: 21443853 DOI: 10.1016/j.jinorgbio.2011.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 01/07/2011] [Accepted: 01/10/2011] [Indexed: 12/22/2022]
Abstract
The factor inhibiting HIF (FIH) is one of the primary oxygen sensors in human cells, controlling gene expression by hydroxylating the α-subunit of the hypoxia inducible transcription factor (HIF). As FIH is an alpha-ketoglutarate dependent non-heme iron dioxygenase, oxygen activation is thought to precede substrate hydroxylation. The coupling between oxygen activation and substrate hydroxylation was hypothesized to be very tight, in order for FIH to fulfill its function as a regulatory enzyme. Coupling was investigated by looking for reactive oxygen species production during turnover. We used alkylsulfatase (AtsK), a metabolic bacterial enzyme with a related mechanism and similar turnover frequency, for comparison, and tested both FIH and AtsK for H(2)O(2), O(2)(-) and OH formation under steady and substrate-depleted conditions. Coupling ratios were determined by comparing the ratio of substrate consumed to product formed. We found that AtsK reacted with O(2) on the seconds timescale in the absence of prime substrate, and uncoupled during turnover to produce H(2)O(2); neither O(2)(-) nor OH were detected. In contrast, FIH was unreactive toward O(2) on the minutes timescale in the absence of prime substrate, and tightly coupled during steady-state turnover; we were unable to detect any reactive oxygen species produced by FIH. We also investigated the inactivation mechanisms of these enzymes and found that AtsK likely inactivated due to deoligomerizion, whereas FIH inactivated by slow autohydroxylation. Autohydroxylated FIH could not be reactivated by dithiothreitol (DTT) nor ascorbate, suggesting that autohydroxylation is likely to be irreversible under physiological conditions.
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Affiliation(s)
- Evren Saban
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States
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Yang Z, Chi X, Funabashi M, Baba S, Nonaka K, Pahari P, Unrine J, Jacobsen JM, Elliott GI, Rohr J, Van Lanen SG. Characterization of LipL as a non-heme, Fe(II)-dependent α-ketoglutarate:UMP dioxygenase that generates uridine-5'-aldehyde during A-90289 biosynthesis. J Biol Chem 2011; 286:7885-7892. [PMID: 21216959 DOI: 10.1074/jbc.m110.203562] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fe(II)- and α-ketoglutarate (α-KG)-dependent dioxygenases are a large and diverse superfamily of mononuclear, non-heme enzymes that perform a variety of oxidative transformations typically coupling oxidative decarboxylation of α-KG with hydroxylation of a prime substrate. The biosynthetic gene clusters for several nucleoside antibiotics that contain a modified uridine component, including the lipopeptidyl nucleoside A-90289 from Streptomyces sp. SANK 60405, have recently been reported, revealing a shared open reading frame with sequence similarity to proteins annotated as α-KG:taurine dioxygenases (TauD), a well characterized member of this dioxygenase superfamily. We now provide in vitro data to support the functional assignment of LipL, the putative TauD enzyme from the A-90289 gene cluster, as a non-heme, Fe(II)-dependent α-KG:UMP dioxygenase that produces uridine-5'-aldehyde to initiate the biosynthesis of the modified uridine component of A-90289. The activity of LipL is shown to be dependent on Fe(II), α-KG, and O(2), stimulated by ascorbic acid, and inhibited by several divalent metals. In the absence of the prime substrate UMP, LipL is able to catalyze oxidative decarboxylation of α-KG, although at a significantly reduced rate. The steady-state kinetic parameters using optimized conditions were determined to be K(m)(α-KG) = 7.5 μM, K(m)(UMP) = 14 μM, and k(cat) ≈ 80 min(-1). The discovery of this new activity not only sets the stage to explore the mechanism of LipL and related dioxygenases further but also has critical implications for delineating the biosynthetic pathway of several related nucleoside antibiotics.
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Affiliation(s)
- Zhaoyong Yang
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536
| | - Xiuling Chi
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536
| | - Masanori Funabashi
- Biopharmaceutical Research Group I, Biopharmaceutical Technology Research Laboratories, Pharmaceutical Technology Division, Daiichi Sankyo Co., Ltd., 389-4, Aza-ohtsurugi, Shimokawa, Izumi-machi, Iwaki-shi, Fukushima 971-8183, Japan, and
| | - Satoshi Baba
- Biopharmaceutical Research Group I, Biopharmaceutical Technology Research Laboratories, Pharmaceutical Technology Division, Daiichi Sankyo Co., Ltd., 389-4, Aza-ohtsurugi, Shimokawa, Izumi-machi, Iwaki-shi, Fukushima 971-8183, Japan, and
| | - Koichi Nonaka
- Biopharmaceutical Research Group I, Biopharmaceutical Technology Research Laboratories, Pharmaceutical Technology Division, Daiichi Sankyo Co., Ltd., 389-4, Aza-ohtsurugi, Shimokawa, Izumi-machi, Iwaki-shi, Fukushima 971-8183, Japan, and
| | - Pallab Pahari
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536
| | - Jason Unrine
- the Department of Plant and Soil Sciences, College of Agriculture, University of Kentucky, Lexington, Kentucky 40536
| | - Jesse M Jacobsen
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536
| | - Gregory I Elliott
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536
| | - Jürgen Rohr
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536
| | - Steven G Van Lanen
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536,.
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McCusker KP, Klinman JP. An active-site phenylalanine directs substrate binding and C-H cleavage in the alpha-ketoglutarate-dependent dioxygenase TauD. J Am Chem Soc 2010; 132:5114-20. [PMID: 20302299 DOI: 10.1021/ja909416z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes that cleave C-H bonds are often found to depend on well-packed hydrophobic cores that influence the distance between the hydrogen donor and acceptor. Residue F159 in taurine alpha-ketoglutarate dioxygenase (TauD) is demonstrated to play an important role in the binding and orientation of its substrate, which undergoes a hydrogen atom transfer to the active site Fe(IV)=O. Mutation of F159 to smaller hydrophobic side chains (L, V, A) leads to substantially reduced rates for substrate binding and for C-H bond cleavage, as well as increased contribution of the chemical step to k(cat) under steady-state turnover conditions. The greater sensitivity of these substrate-dependent processes to mutation at position 159 than observed for the oxygen activation process supports a previous conclusion of modularity of function within the active site of TauD (McCusker, K. P.; Klinman, J. P. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 19791-19795). Extraction of intrinsic deuterium kinetic isotope effects (KIEs) using single turnover transients shows 2- to 4-fold increase in the size of the KIE for F159V in relation to wild-type and F159L. It appears that there is a break in behavior following removal of a single methylene from the side chain of F159L to generate F159V, whereby the protein active site loses its ability to restore the internuclear distance between substrate and Fe(IV)=O that supports optimal hydrogenic wave function overlap.
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Affiliation(s)
- Kevin P McCusker
- Department of Chemistry, California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
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