1
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
2
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
5
|
Wagner JT, Knapp MJ, Podrabsky JE. Antioxidant capacity and anoxia-tolerance in Austrofundulus limnaeus embryos. J Exp Biol 2019; 222:jeb.204347. [DOI: 10.1242/jeb.204347] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/28/2019] [Indexed: 12/19/2022]
Abstract
Embryos of Austrofundulus limnaeus can tolerate extreme environmental stresses by entering into a state of metabolic and developmental arrest known as diapause. Oxidative stress is ubiquitous in aerobic organisms and the unique biology and ecology of A. limnaeus likely results in frequent and repeated exposures to oxidative stress during development. Antioxidant capacity of A. limnaeus was explored during development by measuring antioxidant capacity due to small molecules and several enzymatic antioxidant systems. Diapause II embryos can survive for several days in 1% hydrogen peroxide without indications of negative effects. Surprisingly, both small and large molecule antioxidant systems are highest during early development and may be due to maternal provisioning. Antioxidant capacity is largely invested in small molecules during early development and in enzymatic systems during late development. The switch in antioxidant mechanisms and decline in small molecule antioxidants during development correlates with the loss of extreme anoxia tolerance.
Collapse
Affiliation(s)
- Josiah T. Wagner
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207, USA
- Knight Cancer Institute Cancer Early Detection Advanced Research Center, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Mailcode: KR-CEDR, Portland, OR 97239, USA
| | - Michael J. Knapp
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207, USA
| | - Jason E. Podrabsky
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207, USA
| |
Collapse
|
6
|
Chaplin VD, Hangasky JA, Huang HT, Duan R, Maroney MJ, Knapp MJ. Chloride Supports O 2 Activation in the D201G Facial Triad Variant of Factor-Inhibiting Hypoxia Inducible Factor, an α-Ketoglutarate Dependent Oxygenase. Inorg Chem 2018; 57:12588-12595. [PMID: 30252455 DOI: 10.1021/acs.inorgchem.8b01736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
α-Ketoglutarate (αKG) dependent oxygenases comprise a large superfamily of enzymes that activate O2 for varied reactions. While most of these enzymes contain a nonheme Fe bound by a His2(Asp/Glu) facial triad, a small number of αKG-dependent halogenases require only the two His ligands to bind Fe and activate O2. The enzyme "factor inhibiting HIF" (FIH) contains a His2Asp facial triad and selectively hydroxylates polypeptides; however, removal of the Asp ligand in the Asp201→Gly variant leads to a highly active enzyme, seemingly without a complete facial triad. Herein, we report on the formation of an Fe-Cl cofactor structure for the Asp201→Gly FIH variant using X-ray absorption spectroscopy (XAS), which provides insight into the structure of the His2Cl facial triad found in halogenases. The Asp201→Gly variant supports anion dependent peptide hydroxylation, demonstrating the requirement for a complete His2X facial triad to support O2 reactivity. Our results indicated that exogenous ligand binding to form a complete His2X facial triad was essential for O2 activation and provides a structural model for the His2Cl-bound nonheme Fe found in halogenases.
Collapse
Affiliation(s)
- Vanessa D Chaplin
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - John A Hangasky
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - Hsin-Ting Huang
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - Ran Duan
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - Michael J Maroney
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - Michael J Knapp
- Department of Chemistry , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| |
Collapse
|
7
|
Iyer SR, Chaplin VD, Knapp MJ, Solomon EI. O 2 Activation by Nonheme Fe II α-Ketoglutarate-Dependent Enzyme Variants: Elucidating the Role of the Facial Triad Carboxylate in FIH. J Am Chem Soc 2018; 140:11777-11783. [PMID: 30148961 PMCID: PMC6146021 DOI: 10.1021/jacs.8b07277] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
FIH [factor inhibiting HIF (hypoxia inducible factor)] is an α-ketoglutarate (αKG)-dependent nonheme iron enzyme that catalyzes the hydroxylation of the C-terminal transactivation domain (CAD) asparagine residue in HIF-1α to regulate cellular oxygen levels. The role of the facial triad carboxylate ligand in O2 activation and catalysis was evaluated by replacing the Asp201 residue with Gly (D201G), Ala (D201A), and Glu (D201E). Magnetic circular dichroism (MCD) spectroscopy showed that the (FeII)FIH variants were all 6-coordinate (6C) and the αKG plus CAD bound FIH variants were all 5-coordinate (5C), mirroring the behavior of the wild-type ( wt) enzyme. When only αKG is bound, all FIH variants exhibited weaker FeII-OH2 bonds for the sixth ligand compared to wt, and for αKG-bound D201E this is either extremely weak or the site is 5C, demonstrating that the Asp201 residue plays an important role in the wt enzyme in ensuring that the (FeII/αKG)FIH site remains 6C. Variable-temperature, variable-field (VTVH) MCD spectroscopy showed that all of the αKG- and CAD-bound FIH variants, though 5C, have different ground-state geometric and electronic structures, which impair their oxygen activation rates. Comparison of O2 consumption to substrate hydroxylation kinetics revealed uncoupling between the two half reactions in the variants. Thus, the Asp201 residue also ensures fidelity between CAD substrate binding and oxygen activation, enabling tightly coupled turnover.
Collapse
Affiliation(s)
- Shyam R. Iyer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Vanessa D. Chaplin
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Michael J. Knapp
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
8
|
Chaplin VD, Valliere MA, Hangasky JA, Knapp MJ. Investigations on the role of a solvent tunnel in the α-ketoglutarate dependent oxygenase factor inhibiting HIF (FIH). J Inorg Biochem 2017; 178:63-69. [PMID: 29078149 DOI: 10.1016/j.jinorgbio.2017.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 09/27/2017] [Accepted: 10/06/2017] [Indexed: 01/25/2023]
Abstract
Non-heme Fe(II)/α-ketoglutarate (αKG)-dependent oxygenases catalyze a wide array of reactions through coupling oxidative decarboxylation of αKG to substrate oxygenation. This class of enzymes follows a sequential mechanism in which O2 reacts only after binding primary substrate, raising questions over how protein structure tailors molecular access to the Fe(II) cofactor. The enzyme "factor inhibiting hypoxia inducible factor" (FIH) senses pO2 in human cells by hydroxylating the C-terminal transactivation domain (CTAD), suggesting that structural elements limiting molecular access to the active site may limit the pO2 response. In this study, we tested the impact of a solvent-accessible tunnel in FIH on molecular access to the active site in FIH. The size of the tunnel was increased through alanine point mutagenesis (Y93A, E105A, and Q147A), followed by a suite of mechanistic and spectroscopic probes. Steady-state kinetics varying O2 or CTAD indicated that O2 passage through the tunnel was not affected by Ala substitutions, allowing us to conclude that this narrow tunnel did not impact pO2 sensing by FIH. Steady-state kinetics with varied αKG concentrations revealed increased substrate inhibition for the Ala variants, suggesting that a second αKG molecule may bind near the active site of FIH. If this solvent-accessible tunnel is the O2 entry tunnel, it may be narrow in order to permit O2 access while preventing metabolic intermediates, such as αKG, from inhibiting FIH under physiological conditions.
Collapse
Affiliation(s)
- Vanessa D Chaplin
- Department of Chemistry, University of Massachusetts, Amherst, United States
| | - Meaghan A Valliere
- Department of Chemistry, University of Massachusetts, Amherst, United States
| | - John A Hangasky
- Department of Chemistry, University of Massachusetts, Amherst, United States
| | - Michael J Knapp
- Department of Chemistry, University of Massachusetts, Amherst, United States.
| |
Collapse
|
9
|
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.
Collapse
Affiliation(s)
- Cornelius Y Taabazuing
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Justin Fermann
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Scott Garman
- 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
| |
Collapse
|
10
|
Pektas S, Taabazuing CY, Knapp MJ. Increased Turnover at Limiting O2 Concentrations by the Thr(387) → Ala Variant of HIF-Prolyl Hydroxylase PHD2. Biochemistry 2015; 54:2851-7. [PMID: 25857330 DOI: 10.1021/bi501540c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PHD2 is a 2-oxoglutarate, non-heme Fe(2+)-dependent oxygenase that senses O2 levels in human cells by hydroxylating two prolyl residues in the oxygen-dependent degradation domain (ODD) of HIF1α. Identifying the active site contacts that determine the rate of reaction at limiting O2 concentrations is crucial for understanding how this enzyme senses pO2 and may suggest methods for chemically altering hypoxia responses. A hydrogen bonding network extends from the Fe(II) cofactor through ordered waters to the Thr(387) residue in the second coordination sphere. Here we tested the impact of the side chain of Thr(387) on the reactivity of PHD2 toward O2 through a combination of point mutagenesis, steady state kinetic experiments and {FeNO}(7) EPR spectroscopy. The steady state kinetic parameters for Thr(387) → Asn were very similar to those of wild-type (WT) PHD2, but kcat and kcat/KM(O2) for Thr(387) → Ala were increased by roughly 15-fold. X-Band electron paramagnetic resonance spectroscopy of the {FeNO}(7) centers of the (Fe+NO+2OG) enzyme forms showed the presence of a more rhombic line shape in Thr(387) → Ala than in WT PHD2, indicating an altered conformation for bound gas in this variant. Here we show that the side chain of residue Thr(387) plays a significant role in determining the rate of turnover by PHD2 at low O2 concentrations.
Collapse
Affiliation(s)
- Serap Pektas
- 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
| |
Collapse
|
11
|
Hangasky JA, Gandhi H, Valliere MA, Ostrom NE, Knapp MJ. The rate-limiting step of O2 activation in the α-ketoglutarate oxygenase factor inhibiting hypoxia inducible factor. Biochemistry 2014; 53:8077-84. [PMID: 25423620 PMCID: PMC4283935 DOI: 10.1021/bi501246v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
Factor
inhibiting HIF (FIH) is a cellular O2-sensing enzyme, which
hydroxylates the hypoxia inducible factor-1α. Previously reported
inverse solvent kinetic isotope effects indicated that FIH limits
its overall turnover through an O2 activation step (HangaskyJ. A., SabanE.,
and KnappM. J. (2013) 52, 1594−160223351038). Here we characterize the rate-limiting step for O2 activation by FIH using a suite of mechanistic probes on
the second order rate constant kcat/KM(O2). Steady-state kinetics showed
that the rate constant for O2 activation was slow (kcat/KM(O2)app = 3500 M–1 s–1) compared with other non-heme iron oxygenases,
and solvent viscosity assays further excluded diffusional encounter
with O2 from being rate limiting on kcat/KM(O2). Competitive
oxygen-18 kinetic isotope effect measurements (18kcat/KM(O2) = 1.0114(5)) indicated that the transition state for O2 activation resembled a cyclic peroxohemiketal, which precedes the
formation of the ferryl intermediate observed in related enzymes.
We interpret this data to indicate that FIH limits its overall activity
at the point of the nucleophilic attack of Fe-bound O2— on the C-2 carbon of αKG. Overall, these results
show that FIH follows the consensus mechanism for αKG oxygenases,
suggesting that FIH may be an ideal enzyme to directly access steps
involved in O2 activation among the broad family of αKG
oxygenases.
Collapse
Affiliation(s)
- John A Hangasky
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | | | | | | | | |
Collapse
|
12
|
Abstract
![]()
Nonheme Fe(II)/αKG-dependent
oxygenases catalyze diverse
reactions, typically inserting an O atom from O2 into a
C–H bond. Although the key to their catalytic cycle is the
fact that binding and positioning of primary substrate precede O2 activation, the means by which substrate binding stimulates
turnover is not well understood. Factor Inhibiting HIF (FIH) is a
Fe(II)/αKG-dependent oxygenase that acts as a cellular oxygen
sensor in humans by hydroxylating the target residue Asn803, found in the C-terminal transactivation domain (CTAD) of hypoxia
inducible factor-1. FIH-Gln239 makes two hydrogen bonds
with CTAD-Asn803, positioning this target residue over
the Fe(II). We hypothesized the positioning of the side chain of CTAD-Asn803 by FIH-Gln239 was critical for stimulating O2 activation and subsequent substrate hydroxylation. The steady-state
characterization of five FIH-Gln239 variants (Ala, Asn,
Glu, His, and Leu) tested the role of hydrogen bonding potential and
sterics near the target residue. Each variant exhibited a 20–1200-fold
decrease in kcat and kcat/KM(CTAD), but no change
in KM(CTAD), indicating that the step
after CTAD binding was affected by point mutation. Uncoupled O2 activation was prominent in these variants, as shown by large
coupling ratios (C = [succinate]/[CTAD-OH] = 3–5)
for each of the FIH-Gln239 → X variants. The coupling
ratios decreased in D2O, indicating an isotope-sensitive
inactivation for variants, not observed in the wild type. The data
presented indicate that the proper positioning of CTAD-Asn803 by FIH-Gln239 is necessary to suppress uncoupled turnover
and to support substrate hydroxylation, suggesting substrate positioning
may be crucial for directing O2 reactivity within the broader
class of αKG hydroxylases.
Collapse
Affiliation(s)
- John A Hangasky
- Department of Chemistry, University of Massachusetts at Amherst , Amherst, Massachusetts 01003, United States
| | | | | |
Collapse
|
13
|
Light KM, Hangasky JA, Knapp MJ, Solomon EI. First- and second-sphere contributions to Fe(II) site activation by cosubstrate binding in non-heme Fe enzymes. Dalton Trans 2014; 43:1505-8. [PMID: 24292428 DOI: 10.1039/c3dt53201a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Non-heme Fe(II) enzymes exhibit a general mechanistic strategy where binding all cosubstrates opens a coordination site on the Fe(II) for O2 activation. This study shows that strong-donor ligands, steric interactions with the substrate and second-sphere H-bonding to the facial triad carboxylate allow for five-coordinate site formation in this enzyme superfamily.
Collapse
Affiliation(s)
- Kenneth M Light
- Department of Chemistry, Stanford University, Stanford, USA.
| | | | | | | |
Collapse
|
14
|
Abstract
The ability to sense and adapt to changes in pO2 is crucial for basic metabolism in most organisms, leading to elaborate pathways for sensing hypoxia (low pO2). This review focuses on the mechanisms utilized by mammals and bacteria to sense hypoxia. While responses to acute hypoxia in mammalian tissues lead to altered vascular tension, the molecular mechanism of signal transduction is not well understood. In contrast, chronic hypoxia evokes cellular responses that lead to transcriptional changes mediated by the hypoxia inducible factor (HIF), which is directly controlled by post-translational hydroxylation of HIF by the non-heme Fe(II)/αKG-dependent enzymes FIH and PHD2. Research on PHD2 and FIH is focused on developing inhibitors and understanding the links between HIF binding and the O2 reaction in these enzymes. Sulfur speciation is a putative mechanism for acute O2-sensing, with special focus on the role of H2S. This sulfur-centered model is discussed, as are some of the directions for further refinement of this model. In contrast to mammals, bacterial O2-sensing relies on protein cofactors that either bind O2 or oxidatively decompose. The sensing modality for bacterial O2-sensors is either via altered DNA binding affinity of the sensory protein, or else due to the actions of a two-component signaling cascade. Emerging data suggests that proteins containing a hemerythrin-domain, such as FBXL5, may serve to connect iron sensing to O2-sensing in both bacteria and humans. As specific molecular machinery becomes identified, these hypoxia sensing pathways present therapeutic targets for diseases including ischemia, cancer, or bacterial infection.
Collapse
Affiliation(s)
| | - John A Hangasky
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States
| | - Michael J Knapp
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States.
| |
Collapse
|
15
|
Pektas S, Knapp MJ. Substrate preference of the HIF-prolyl hydroxylase-2 (PHD2) and substrate-induced conformational change. J Inorg Biochem 2013; 126:55-60. [PMID: 23787140 PMCID: PMC4046702 DOI: 10.1016/j.jinorgbio.2013.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 04/04/2013] [Accepted: 05/15/2013] [Indexed: 12/22/2022]
Abstract
HIF prolyl-4-hydroxylase 2 (PHD2) is a non-heme Fe, 2-oxoglutarate (2OG) dependent dioxygenase that regulates the hypoxia inducible transcription factor (HIF) by hydroxylating two conserved prolyl residues in N-terminal oxygen degradation domain (NODD) and C-terminal oxygen degradation domain (CODD) of HIF-1α. Prior studies have suggested that the substrate preference of PHD2 arises from binding contacts with the β2β3 loop of PHD2. In this study we tested the substrate selectivity of PHD2 by kinetic competition assays, varied ionic strength, and global protein flexibility using amide H/D exchange (HDX). Our results revealed that PHD2 preferred CODD by 20-fold over NODD and that electrostatics influenced this effect. Global HDX monitored by mass spectrometry indicated that binding of Fe(II) and 2OG stabilized the overall protein structure but the saturating concentrations of either NODD or CODD caused an identical change in protein flexibility. These observations imply that both substrates stabilize the β2β3 loop to the same extent. Under unsaturated substrate conditions NODD led to a higher HDX rate than CODD due to its lower binding affinity to PHD2. Our results suggest that loop closure is the dominant contributor to substrate selectivity in PHD2.
Collapse
Affiliation(s)
- Serap Pektas
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, Voice 413-545-4001, FAX 413-545-4490
| | - Michael J. Knapp
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, Voice 413-545-4001, FAX 413-545-4490
| |
Collapse
|
16
|
Light KM, Hangasky JA, Knapp MJ, Solomon EI. Spectroscopic studies of the mononuclear non-heme Fe(II) enzyme FIH: second-sphere contributions to reactivity. J Am Chem Soc 2013; 135:9665-74. [PMID: 23742069 DOI: 10.1021/ja312571m] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Factor inhibiting hypoxia-inducible factor (FIH) is an α-ketoglutarate (αKG)-dependent enzyme which catalyzes hydroxylation of residue Asn803 in the C-terminal transactivation domain (CAD) of hypoxia-inducible factor 1α (HIF-1α) and plays an important role in cellular oxygen sensing and hypoxic response. Circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature, variable-field (VTVH) MCD spectroscopies are used to determine the geometric and electronic structures of FIH in its (Fe(II)), (Fe(II)/αKG), and (Fe(II)/αKG/CAD) forms. (Fe(II))FIH and (Fe(II)/αKG)FIH are found to be six-coordinate (6C), whereas (Fe(II)/αKG/CAD)FIH is found to be a 5C/6C mixture. Thus, FIH follows the general mechanistic strategy of non-heme Fe(II) enzymes. Modeling shows that, when Arg238 of FIH is removed, the facial triad carboxylate binds to Fe(II) in a bidentate mode with concomitant lengthening of the Fe(II)/αKG carbonyl bond, which would inhibit the O2 reaction. Correlations over α-keto acid-dependent enzymes and with the extradiol dioxygenases show that members of these families (where both the electron source and O2 bind to Fe(II)) have a second-sphere residue H-bonding to the terminal oxygen of the carboxylate, which stays monodentate. Alternatively, structures of the pterin-dependent and Rieske dioxygenases, which do not have substrate binding to Fe(II), lack H-bonds to the carboxylate and thus allow its bidentate coordination which would direct O2 reactivity. Finally, vis-UV MCD spectra show an unusually high-energy Fe(II) → αKG π* metal-to-ligand charge transfer transition in (Fe(II)/αKG)FIH which is red-shifted upon CAD binding. This red shift indicates formation of H-bonds to the αKG that lower the energy of its carbonyl LUMO, activating it for nucleophilic attack by the Fe-O2 intermediate formed along the reaction coordinate.
Collapse
Affiliation(s)
- Kenneth M Light
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | | | | |
Collapse
|
17
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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).
Collapse
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
| |
Collapse
|
18
|
Hangasky JA, Saban E, Knapp MJ. Inverse solvent isotope effects arising from substrate triggering in the factor inhibiting hypoxia inducible factor. Biochemistry 2013; 52:1594-602. [PMID: 23351038 DOI: 10.1021/bi3015482] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oxygen homeostasis plays a critical role in angiogenesis, erythropoiesis, and cell metabolism. Oxygen homeostasis is set by the hypoxia inducible factor-1α (HIF-1α) pathway, which is controlled by factor inhibiting HIF-1α (FIH). FIH is a non-heme Fe(II), α-ketoglutarate (αKG)-dependent dioxygenase that inhibits HIF-1α by hydroxylating the C-terminal transactivation domain (CTAD) of HIF-1α at HIF-Asn(803). A tight coupling between CTAD binding and O2 activation is essential for hypoxia sensing, making changes in the coordination geometry of Fe(II) upon CTAD encounter a crucial feature of this enzyme. Although the consensus chemical mechanism for FIH proposes that CTAD binding triggers O2 activation by causing the Fe(II) cofactor to release an aquo ligand, experimental evidence of this has been absent. More broadly, this proposed coordination change at Fe(II) has not been observed during steady-state turnover in any αKG oxygenase to date. In this work, solvent isotope effects (SIEs) were used as a direct mechanistic probe of substrate-triggered aquo release in FIH, as inverse SIEs (SIE < 1) are signatures for pre-equilibrium aquo release from metal ions. Our mechanistic studies of FIH have revealed inverse solvent isotope effects in the steady-state rate constants at limiting concentrations of CTAD or αKG [(D2O)kcat/KM(CTAD) = 0.40 ± 0.07, and (D2O)kcat/KM(αKG) = 0.32 ± 0.08], providing direct evidence of aquo release during steady-state turnover. Furthermore, the SIE at saturating concentrations of CTAD and αKG was inverse ((D2O)kcat = 0.51 ± 0.07), indicating that aquo release occurs after CTAD binds. The inverse kinetic SIEs observed in the steady state for FIH can be explained by a strong Fe-OH2 bond. The stable Fe-OH2 bond plays an important part in FIH's regulatory role over O2 homeostasis in humans and points toward a strategy for tightly coupling O2 activation with CTAD hydroxylation that relies on substrate triggering.
Collapse
Affiliation(s)
- John A Hangasky
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | | | | |
Collapse
|
19
|
Flagg SC, Giri N, Pektas S, Maroney MJ, Knapp MJ. Inverse solvent isotope effects demonstrate slow aquo release from hypoxia inducible factor-prolyl hydroxylase (PHD2). Biochemistry 2012; 51:6654-66. [PMID: 22747465 PMCID: PMC3525350 DOI: 10.1021/bi300229y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Prolyl hydroxylase domain 2 (PHD2) is deemed a primary oxygen sensor in humans, yet many details of its underlying mechanism are still not fully understood. (Fe(2+) + αKG)PHD2 is 6-coordinate, with a 2His/1Asp facial triad occupying three coordination sites, a bidentate α-ketoglutarate occupying two sites, and an aquo ligand in the final site. Turnover is thought to be initiated upon release of the aquo ligand, creating a site for O(2) to bind at the iron. Herein we show that steady-state turnover is faster under acidic conditions, with k(cat) exhibiting a kinetic pK(a) = 7.22. A variety of spectroscopic probes were employed to identify the active-site acid, through comparison of (Fe(2+) + αKG)PHD2 at pH 6.50 with pH 8.50. The near-UV circular dichroism spectrum was virtually unchanged at elevated pH, indicating that the secondary structure did not change as a function of pH. UV-visible and Fe X-ray absorption spectroscopy indicated that the primary coordination sphere of Fe(2+) changed upon increasing the pH; extended X-ray absorption fine structure analysis found a short Fe-(O/N) bond length of 1.96 Å at pH 8.50, strongly suggesting that the aquo ligand was deprotonated at this pH. Solvent isotope effects were measured during steady-sate turnover over a wide pH-range, with an inverse solvent isotope effect (SIE) of k(cat) observed ((D(2)O)k(cat) = 0.91 ± 0.03) for the acid form; a similar SIE was observed for the basic form of the enzyme ((D(2)O)k(cat) = 0.9 ± 0.1), with an acid equilibrium offset of ΔpK(a) = 0.67 ± 0.04. The inverse SIE indicated that aquo release from the active site Fe(2+) immediately precedes a rate-limiting step, suggesting that turnover in this enzyme may be partially limited by the rate of O(2) binding or activation, and suggesting that aquo release is relatively slow. The unusual kinetic pK(a) further suggested that PHD2 might function physiologically to sense both intracellular pO(2) as well as pH, which could provide for feedback between anaerobic metabolism and hypoxia sensing.
Collapse
Affiliation(s)
- Shannon C. Flagg
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003
| | - Nitai Giri
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003
| | - Serap Pektas
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003
| | - Michael J. Maroney
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, 01003
| | - Michael J. Knapp
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, 01003
| |
Collapse
|
20
|
Flagg SC, Martin CB, Taabazuing CY, Holmes BE, Knapp MJ. Screening chelating inhibitors of HIF-prolyl hydroxylase domain 2 (PHD2) and factor inhibiting HIF (FIH). J Inorg Biochem 2012; 113:25-30. [PMID: 22687491 DOI: 10.1016/j.jinorgbio.2012.03.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 02/04/2012] [Accepted: 03/09/2012] [Indexed: 12/12/2022]
Abstract
Two primary O(2)-sensors for humans are the HIF-hydroxylases, enzymes that hydroxylate specific residues of the hypoxia inducible factor-α (HIF). These enzymes are factor inhibiting HIF (FIH) and prolyl hydroxylase-2 (PHD2), each an α-ketoglutarate (αKG) dependent, non-heme Fe(II) dioxygenase. Although the two enzymes have similar active sites, FIH hydroxylates Asn(803) of HIF-1α while PHD2 hydroxylates Pro(402) and/or Pro(564) of HIF-1α. The similar structures but unique functions of FIH and PHD2 make them prime targets for selective inhibition leading to regulatory control of diseases such as cancer and stroke. Three classes of iron chelators were tested as inhibitors for FIH and PHD2: pyridines, hydroxypyrones/hydroxypyridinones and catechols. An initial screen of the ten small molecule inhibitors at varied [αKG] revealed a non-overlapping set of inhibitors for PHD2 and FIH. Dose response curves at moderate [αKG] ([αKG]~K(M)) showed that the hydroxypyrones/hydroxypyridinones were selective inhibitors, with IC(50) in the μM range, and that the catechols were generally strong inhibitors of both FIH and PHD2, with IC(50) in the low μM range. As support for binding at the active site of each enzyme as the mode of inhibition, electron paramagnetic resonance (EPR) spectroscopy were used to demonstrate inhibitor binding to the metal center of each enzyme. This work shows some selective inhibition between FIH and PHD2, primarily through the use of simple aromatic or pseudo-aromatic chelators, and suggests that hydroxypyrones and hydroxypyridones may be promising chelates for FIH or PHD2 inhibition.
Collapse
Affiliation(s)
- Shannon C Flagg
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | | | | | | | | |
Collapse
|
21
|
Abstract
The factor inhibiting HIF (FIH) is a proximate oxygen sensor for human cells, hydroxylating Asn(803) within the α-subunit of the hypoxia inducible factor (HIF). FIH is an α-ketoglutatrate (αKG)-dependent, non-heme Fe(II) dioxygenase, in which Fe(II) is coordinated by a (His(2)Asp) facial triad, αKG, and H(2)O. Hydrogen bonding among the facial triad, the HIF-Asn(803) side chain, and various second-sphere residues suggests a functional role for the second coordination sphere in tuning the chemistry of the Fe(II) center. Point mutants of FIH were prepared to test the functional role of the αKG-centered (Asn(205) and Asn(294)) or HIF-Asn(803)-centered (Arg(238) and Gln(239)) second-sphere residues. The second sphere was tested for local effects on priming Fe(II) to react with O(2), oxidative decarboxylation, and substrate positioning. Steady-sate kinetics were used to test for overall catalytic effects; autohydroxylation rates were used to test for priming and positioning, and electronic spectroscopy was used to assess the primary coordination sphere and the electrophilicity of αKG. Asn(205) → Ala and Asn(294) → Ala mutants exhibited diminished rates of steady-state turnover, while minimally affecting autohydroxylation, consistent with impaired oxidative decarboxylation. Blue-shifted metal to ligand charge transfer transitions for (Fe+αKG)FIH indicated that these point mutations destabilized the π* orbitals of αKG, further supporting a slowed rate of oxidative decarboxylation. The Arg(238) → Met mutant exhibited steady-state rates too low to measure and diminished product yields, suggesting impaired substrate positioning or priming; the Arg(238) → Met mutant was capable of O(2) activation for the autohydroxylation reaction. The Gln(239) → Asn mutant exhibited significantly slowed steady-state kinetics and diminished product yields, suggesting impaired substrate positioning or priming. As HIF binding to the Gln(239) → Asn mutant stimulated autohydroxylation, it is more likely that this point mutant simply mispositions the HIF-Asn(803) side chain. This work combines kinetics and spectroscopy to show that these second-sphere hydrogen bonds play roles in promoting oxidative decarboxylation, priming Fe(II) to bind O(2), and positioning HIF-Asn(803).
Collapse
Affiliation(s)
- Evren Saban
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003
| | - Yuan-Han Chen
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, 01003
| | - John Hangasky
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003
| | | | - Breanne E. Holmes
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003
| | - Michael J. Knapp
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, 01003
| |
Collapse
|
22
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- Evren Saban
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States
| | | | | |
Collapse
|
23
|
Carver AM, De M, Bayraktar H, Rana S, Rotello VM, Knapp MJ. Intermolecular electron-transfer catalyzed on nanoparticle surfaces. J Am Chem Soc 2009; 131:3798-9. [PMID: 19243185 DOI: 10.1021/ja806064t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Surface-functionalized nanoparticles enhance the rate of electron transfer (ET) between Cyt c(Fe(2+)) and Co(phen)(3)(3+) by a factor of 10(5) through simultaneous electrostatic binding of an ET donor and acceptor.
Collapse
Affiliation(s)
- Adrienne M Carver
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | | | | | | | | | | |
Collapse
|
24
|
Chambers JJ, Knapp MJ. Peer to peer mentoring for pre‐tenure faculty in the chemical biology field. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.lb308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
25
|
|
26
|
Affiliation(s)
- Meaghan E. Germain
- Department of Chemistry and Program in Molecular and Cellular Biology, University of Massachusetts at Amherst, Amherst, Massachusetts 01003
| | - Michael J. Knapp
- Department of Chemistry and Program in Molecular and Cellular Biology, University of Massachusetts at Amherst, Amherst, Massachusetts 01003
| |
Collapse
|
27
|
|
28
|
Chen YH, Comeaux LM, Eyles SJ, Knapp MJ. Auto-hydroxylation of FIH-1: an Fe(ii), alpha-ketoglutarate-dependent human hypoxia sensor. Chem Commun (Camb) 2008:4768-70. [PMID: 18830487 DOI: 10.1039/b809099h] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
HIF-asparaginyl hydroxylase (FIH-1) normally couples O(2)-activation to hydroxylation of Asn(803) on the alpha-subunit of the hypoxia-inducible factor (HIFalpha), a key step in pO(2) sensing; in the absence of HIFalpha, O(2)-activation becomes uncoupled, leading to self-hydroxylation at Trp(296) and a purple Fe(iii)-O-Trp chromophore-this alternative reactivity may affect human hypoxia sensing.
Collapse
Affiliation(s)
- Yuan-Han Chen
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | | | | | | |
Collapse
|
29
|
Chen YH, Comeaux LM, Herbst RW, Saban E, Kennedy DC, Maroney MJ, Knapp MJ. Coordination changes and auto-hydroxylation of FIH-1: uncoupled O2-activation in a human hypoxia sensor. J Inorg Biochem 2008; 102:2120-9. [PMID: 18805587 DOI: 10.1016/j.jinorgbio.2008.07.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Revised: 07/29/2008] [Accepted: 07/31/2008] [Indexed: 01/09/2023]
Abstract
Hypoxia sensing is the generic term for pO2-sensing in humans and other higher organisms. These cellular responses to pO2 are largely controlled by enzymes that belong to the Fe(II) alpha-ketoglutarate (alphaKG) dependent dioxygenase superfamily, including the human enzyme called the factor inhibiting HIF (FIH-1), which couples O2-activation to the hydroxylation of the hypoxia inducible factor alpha (HIFalpha). Uncoupled O2-activation by human FIH-1 was studied by exposing the resting form of FIH-1 (alphaKG + Fe)FIH-1, to air in the absence of HIFalpha. Uncoupling lead to two distinct enzyme oxidations, one a purple chromophore (lambda(max) = 583 nm) arising from enzyme auto-hydroxylation of Trp296, forming an Fe(III)-O-Trp296 chromophore [Y.-H. Chen, L.M. Comeaux, S.J. Eyles, M.J. Knapp, Chem. Commun. (2008), doi:10.1039/B809099H]; the other a yellow chromophore due to Fe(III) in the active site, which under some conditions also contained variable levels of an oxygenated surface residue (oxo)Met275. The kinetics of purple FIH-1 formation were independent of Fe(II) and alphaKG concentrations, however, product yield was saturable with increasing [alphaKG] and required excess Fe(II). Yellow FIH-1 was formed from (succinate+Fe)FIH-1, or by glycerol addition to (alphaKG+Fe)FIH-1, suggesting that glycerol could intercept the active oxidant from the FIH-1 active site and prevent hydroxylation. Both purple and yellow FIH-1 contained high-spin, rhombic Fe(III) centers, as shown by low temperature EPR. XAS indicated distorted octahedral Fe(III) geometries, with subtle differences in inner-shell ligands for yellow and purple FIH-1. EPR of Co(II)-substituted FIH-1 (alphaKG + Co)FIH-1, indicated a mixture of 5-coordinate and 6-coordinate enzyme forms, suggesting that resting FIH-1 can readily undergo uncoupled O2-activation by loss of an H2O ligand from the metal center.
Collapse
Affiliation(s)
- Yuan-Han Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | | | | | | | | | | | | |
Collapse
|
30
|
Germain ME, Vargo TR, McClure BA, Rack JJ, Van Patten PG, Odoi M, Knapp MJ. Quenching Mechanism of Zn(Salicylaldimine) by Nitroaromatics. Inorg Chem 2008; 47:6203-11. [DOI: 10.1021/ic702469q] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
31
|
Germain ME, Knapp MJ. Discrimination of Nitroaromatics and Explosives Mimics by a Fluorescent Zn(salicylaldimine) Sensor Array. J Am Chem Soc 2008; 130:5422-3. [DOI: 10.1021/ja800403k] [Citation(s) in RCA: 206] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Meaghan E. Germain
- Department of Chemistry and Program in Molecular and Cellular Biology, University of Massachusetts at Amherst, Amherst, Massachusetts 01003
| | - Michael J. Knapp
- Department of Chemistry and Program in Molecular and Cellular Biology, University of Massachusetts at Amherst, Amherst, Massachusetts 01003
| |
Collapse
|
32
|
Bayraktar H, Srivastava S, You CC, Rotello VM, Knapp MJ. Controlled nanoparticleassembly through protein conformational changes. Soft Matter 2008; 4:751-756. [PMID: 32907180 DOI: 10.1039/b716386j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Selective surface recognition by proteins provides programmed bottom-up assembly of synthetic nanomaterials. We have investigated the controlled self-assembly of functionalized gold nanoparticles (Au-TAsp) with cytochrome c (Cyt c) and apoCyt c through complementary electrostatic interactions. Au-TAsp formed discrete, water-soluble adducts with native Cyt c, whereas unfolded apoCyt c induced nanocomposite formation at high Cyt c : Au-TAsp ratios. The binding of random-coil apoCyt c to Au-TAsp at low ratios induced α-helix formation in soluble nanocomposites, but at elevated ratios insoluble micron-scale aggregates were formed. The local structure of the assemblies was critically dependent on the Cyt c : Au-TAsp ratio. The dispersibility of apoCyt c-Au-TAsp was pH dependent, providing rapid and reversible control over nanocomposite assembly. The apoCyt c-Au-TAsp aggregates could likewise be disassembled through proteolytic cleavage of apoCyt c, demonstrating the ability to selectively remodel these hybrid materials.
Collapse
Affiliation(s)
- Halil Bayraktar
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA.
| | - Sudhanshu Srivastava
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA.
| | - Chang-Cheng You
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA.
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA. and Program in Molecular and Cellular Biology, University of Massachusetts, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
| | - Michael J Knapp
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA. and Program in Molecular and Cellular Biology, University of Massachusetts, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
| |
Collapse
|
33
|
You CC, Agasti SS, De M, Knapp MJ, Rotello VM. Modulation of the catalytic behavior of alpha-chymotrypsin at monolayer-protected nanoparticle surfaces. J Am Chem Soc 2007; 128:14612-8. [PMID: 17090046 DOI: 10.1021/ja064433z] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino-acid-functionalized gold clusters modulate the catalytic behavior of alpha-chymotrypsin (ChT) toward cationic, neutral, and anionic substrates. Kinetic studies reveal that the substrate specificity (k(cat)/K(M)) of ChT-nanoparticle complexes increases by approximately 3-fold for the cationic substrate but decreases by 95% for the anionic substrate as compared with that of free ChT, providing enhanced substrate selectivity. Concurrently, the catalytic constants (k(cat)) of ChT show slight augmentation for the cationic substrate and significant attenuation for the anionic substrate in the presence of amino-acid-functionalized nanoparticles. The amino acid monolayer on the nanoparticle is proposed to control both the capture of substrate by the active site and release of product through electrostatic interactions, leading to the observed substrate specificities and catalytic constants.
Collapse
Affiliation(s)
- Chang-Cheng You
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
| | | | | | | | | |
Collapse
|
34
|
Germain ME, Vargo TR, Khalifah PG, Knapp MJ. Fluorescent Detection of Nitroaromatics and 2,3-Dimethyl- 2,3-dinitrobutane (DMNB) by a Zinc Complex: (salophen)Zn. Inorg Chem 2007; 46:4422-9. [PMID: 17472370 DOI: 10.1021/ic062012c] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescent sensors for the detection of chemical explosives are in great demand. It is shown herein that the fluorescence of ZnL* (H2L=N,N'-phenylene-bis-(3,5-di-tert-butylsalicylideneimine)) is quenched in solution by nitroaromatics and 2,3-dimethyl-2,3-dinitrobutane (DMNB), chemical signatures of explosives. The relationship between the structure and fluorescence of ZnL is explored, and crystal structures of three forms of ZnL(base), (base=ethanol, tetrahydrofuran, pyridine) are reported, with the base=ethanol structure exhibiting a four-centered hydrogen bonding array. Solution structures are monitored by 1H NMR and molecular weight determination, revealing a dimeric structure in poor donor solvents which converts to a monomeric structure in the presence of good donor solvents or added Lewis bases to form five-coordinate ZnL(base). Fluorescence wavelengths and quantum yields in solution are nearly insensitive to monomer-dimer interconversion, as well as to the identity of the Lewis base; in contrast, the emission wavelength in the solid state varies for different ZnL(base) due to pi-stacking. Nitroaromatics and DMNB are moderately efficient quenchers of ZnL*, with Stern-Volmer constants KSV=2-49 M-1 in acetonitrile solution.
Collapse
Affiliation(s)
- Meaghan E Germain
- Department of Chemistry and Program in Molecular and Cellular Biology, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, USA
| | | | | | | |
Collapse
|
35
|
Sandanaraj BS, Bayraktar H, Krishnamoorthy K, Knapp MJ, Thayumanavan S. Recognition and modulation of cytochrome c's redox properties using an amphiphilic homopolymer. Langmuir 2007; 23:3891-7. [PMID: 17315896 DOI: 10.1021/la063063p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
An amphiphilic homopolymer scaffold has been used to bind to the protein, cytochrome c. This interaction is analyzed using cyclic voltammetry, native gel electrophoresis, UV-visible absorption, and circular dichroism spectroscopy. The polymer binds to cytochrome c with micromolar affinity and the association of polymer with cytochrome c leads to a structural change of the protein. This conformational change exposes the heme unit of the protein, which affords an opportunity to reversibly modulate its electron-transfer properties. We have also shown that the electrostatic binding of polymer to cytochrome c can be used to disrupt its interaction with its natural partner, cytochrome c peroxidase.
Collapse
Affiliation(s)
- Britto S Sandanaraj
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | | | | | | | | |
Collapse
|
36
|
Affiliation(s)
- Halil Bayraktar
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
| | | | | | | |
Collapse
|
37
|
Bayraktar H, Ghosh PS, Rotello VM, Knapp MJ. Disruption of protein–protein interactions using nanoparticles: inhibition of cytochrome c peroxidase. Chem Commun (Camb) 2006:1390-2. [PMID: 16550276 DOI: 10.1039/b516096k] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Functionalized gold nanoparticles bind selectively to cytochrome c or cytochrome c peroxidase and inhibit enzyme turnover.
Collapse
Affiliation(s)
- Halil Bayraktar
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | | | | | | |
Collapse
|
38
|
Abstract
The reactivity of O(2) with soybean lipoxygenase-1 (SLO) has been examined using a range of kinetic probes. We are able to rule out diffusional encounter of O(2) with protein, an outer-sphere electron transfer to O(2), and proton transfer as rate-limiting steps in k(cat)/K(M)(O(2)) for wild-type enzyme (WT SLO); this restricts the rate-limiting step to either the combination of O(2) with L(*) or a subsequent conformational change. In the Ile(553) --> Phe mutant, which constricts the putative O(2) binding channel [Knapp et al. (2001) J. Am. Chem. Soc. 123, 2931-2932], k(cat)/K(M)(O(2)) decreases by over a factor of 20; yet, this mutant appears to have the same rate-limiting step as WT SLO. It is argued that the slow step on k(cat)/K(M)(O(2)) is the combination of O(2) with L(*), with proximal protein effects determining the rate of reaction. The available data for SLO support the view that enzymes can affect O(2) reactivity without a direct involvement of metal cofactors. The primary role of the Fe(3+) cofactor is to generate an enzyme-bound radical, while the protein is concluded to control the stereo- and regiochemistry of O(2) encounter with this radical.
Collapse
Affiliation(s)
- Michael J Knapp
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | |
Collapse
|
39
|
Abstract
The temperature dependence of the primary and secondary intrinsic isotope effects for the C-H bond cleavage catalyzed by peptidylglycine alpha-hydroxylating monooxygenase has been determined. Analysis of the magnitude and Arrhenius behavior of the intrinsic isotope effects provides strong evidence for the use of tunneling as a primary catalytic strategy for this enzyme. Modeling of the isotope effect data allows for a comparison to the hydrogen transfer catalyzed by soybean lipoxygenase in terms of environmental reorganization energy and frequency of the protein vibration that controls the hydrogen transfer.
Collapse
Affiliation(s)
- Wilson A Francisco
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
| | | | | | | |
Collapse
|
40
|
Abstract
Many biological C-H activation reactions exhibit nonclassical kinetic isotope effects (KIEs). These nonclassical KIEs are too large (kH/kD > 7) and/or exhibit unusual temperature dependence such that the Arrhenius prefactor KIEs (AH/AD) fall outside of the semiclassical range near unity. The focus of this minireview is to discuss such KIEs within the context of the environmentally coupled hydrogen tunneling model. Full tunneling models of hydrogen transfer assume that protein or solvent fluctuations generate a reactive configuration along the classical, heavy-atom coordinate, from which the hydrogen transfers via nuclear tunneling. Environmentally coupled tunneling also invokes an environmental vibration (gating) that modulates the tunneling barrier, leading to a temperature-dependent KIE. These properties directly link enzyme fluctuations to the reaction coordinate for hydrogen transfer, making a quantum view of hydrogen transfer necessarily a dynamic view of catalysis. The environmentally coupled hydrogen tunneling model leads to a range of magnitudes of KIEs, which reflect the tunneling barrier, and a range of AH/AD values, which reflect the extent to which gating modulates hydrogen transfer. Gating is the primary determinant of the temperature dependence of the KIE within this model, providing insight into the importance of this motion in modulating the reaction coordinate. The potential use of variable temperature KIEs as a direct probe of coupling between environmental dynamics and the reaction coordinate is described. The evolution from application of a tunneling correction to a full tunneling model in enzymatic H transfer reactions is discussed in the context of a thermophilic alcohol dehydrogenase and soybean lipoxygenase-1.
Collapse
Affiliation(s)
- Michael J Knapp
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | | |
Collapse
|
41
|
Sañudo EC, Grillo VA, Knapp MJ, Bollinger JC, Huffman JC, Hendrickson DN, Christou G. Tetranuclear manganese complexes with dimer-of-dimer and ladder structures from the use of a bis-bipyridyl ligand. Inorg Chem 2002; 41:2441-50. [PMID: 11978111 DOI: 10.1021/ic011262k] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction of the bis-chelating ligand 1,2-bis(2,2'-bipyridine-6-yl)ethane (L) with the trinuclear species of formula [Mn(3)O(O(2)CR)(6)(py)(3)](ClO(4)) (R = Me (1); R = Et (2); R = Ph (3)) has afforded the new tetranuclear mixed-valent complexes [Mn(4)O(2)(O(2)CR)(4)L(2)](ClO(4))(2) (R = Me (4); R = Et (5); R = Ph (6)) and [Mn(4)O(2)(OMe)(3)(O(2)CR)(2)L(2)(MeOH)](ClO(4))(2) (R = Me (7); R = Et (8); R = Ph (9)). Complexes 4-6 were obtained in yields of 20%, 44%, and 37%, respectively. They are mixed-valent, with an average Mn oxidation state of +2.5. Complexes 7-9 were obtained in yields of 57%, 65%, and 70%, respectively. They are also mixed-valent, but with an average Mn oxidation state of +2.75. Complexes 4 x 2THF and 9 x 3MeOH x H(2)O crystallize in the triclinic space group P1 macro and contain [Mn(4)(mu(3)-O)(2)](6+) and [Mn(4)(mu(3)-O)(2)(mu-OMe)(2)](5+) cores, respectively, the latter being a new structural type in the family of Mn(4) complexes. Reactivity studies of 4-9 have shown that 4-6 can be converted into 7-9, respectively, and vice versa. The magnetic properties of 5 and 9 have been studied by dc and ac magnetic susceptibility techniques. Complex 5 displays antiferromagnetic coupling between its Mn ions resulting in a spin ground state of S = 0. Complex 9 also displays antiferromagnetic coupling, but the resulting ground state is S = (7)/(2), as confirmed by fitting magnetization versus field data collected for 9 at low temperatures, which gave S = (7)/(2), D = -0.77 cm(-1), and g = 1.79. Complex 9 exhibits a frequency-dependent out-of-phase ac susceptibility peak, indicative of the slow magnetization relaxation that is diagnostic of single-molecule magnetism behavior.
Collapse
Affiliation(s)
- E Carolina Sañudo
- Department of Chemistry and Molecular Structure Center, Indiana University, Bloomington, Indiana 47405-7102, USA
| | | | | | | | | | | | | |
Collapse
|
42
|
Knapp MJ, Rickert K, Klinman JP. Temperature-dependent isotope effects in soybean lipoxygenase-1: correlating hydrogen tunneling with protein dynamics. J Am Chem Soc 2002; 124:3865-74. [PMID: 11942823 DOI: 10.1021/ja012205t] [Citation(s) in RCA: 395] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hydrogen-atom transfer in soybean lipoxygenase-1 (SLO) exhibits a large kinetic isotope effect on k(cat) (KIE = 81) near room temperature and a very weak temperature dependence (E(act) = 2.1 kcal/mol). These properties are consistent with H small middle dot transfer that occurs entirely by a tunneling event. Mutants of SLO were prepared, and the temperature dependence of the KIE was measured, to test for alterations in the tunneling behavior. All mutants studied exhibit KIEs of similar, large magnitude at 30 degrees C, despite an up to 3 orders of magnitude change in k(cat). E(act) for two of the mutants (Leu(754) --> Ala, Leu(546) --> Ala) is larger than for wild-type (WT), and the KIE becomes slightly more temperature dependent. In contrast, Ile(553) --> Ala exhibits k(cat) and E(act) parameters similar to wild-type soybean lipoxygenase-1 (WT-SLO) for protiated substrate; however, the KIE is markedly temperature dependent. The behavior of the former two mutants could reflect increased reorganization energies (lambda), but the behavior of the latter mutant is inconsistent with this description. We have invoked a full H* tunneling model (Kuznetsov, A. M.; Ulstrup, J. Can. J. Chem. 1999, 77, 1085-1096) to explain the temperature dependence of the KIE, which is indicative of the extent to which distance sampling (gating) modulates hydrogen transfer. WT-SLO exhibits a very small E(act) and a nearly temperature-independent KIE, which was modeled as arising from a compressed hydrogen transfer distance with little modulation of the hydrogen transfer distance. The observations on the Leu(754) --> Ala and Leu(546) --> Ala mutants were modeled as arising from a slightly less compressed active site with greater modulation of the hydrogen transfer distance by environmental dynamics. Finally, the observed behavior of the Ile(553) --> Ala mutant indicates a relaxed active site with extensive involvement of gating to facilitate hydrogen transfer. We conclude that WT-SLO has an active site structure that is well organized to support hydrogen tunneling and that mutations perturb structural elements that support hydrogen tunneling. Modest alterations in active site residues increase lambda and/or increase the hydrogen transfer distance, thereby affecting the probability that tunneling can occur. These studies allow the detection and characterization of a protein-gating mode in catalysis.
Collapse
Affiliation(s)
- Michael J Knapp
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | | |
Collapse
|
43
|
|
44
|
Maes EM, Knapp MJ, Czernuszewicz RS, Hendrickson DN. Ligand Conformational Effects on the Resonance Raman Signature of [Fe4S4(SAryl)4]2- Clusters. J Phys Chem B 2000. [DOI: 10.1021/jp0003104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Estelle M. Maes
- Departments of Chemistry, University of Houston, Houston, Texas 77204, and University of California at San Diego, La Jolla, California 92093
| | - Michael J. Knapp
- Departments of Chemistry, University of Houston, Houston, Texas 77204, and University of California at San Diego, La Jolla, California 92093
| | - Roman S. Czernuszewicz
- Departments of Chemistry, University of Houston, Houston, Texas 77204, and University of California at San Diego, La Jolla, California 92093
| | - David N. Hendrickson
- Departments of Chemistry, University of Houston, Houston, Texas 77204, and University of California at San Diego, La Jolla, California 92093
| |
Collapse
|
45
|
Abstract
High-frequency (94-371 GHz) EPR data are reported for powdered samples of [PPh4]2[Fe(SPh)4], an accurate model for the reduced site of rubredoxins. This is the first HFEPR investigation of an S = 2 ferrous complex, illustrating the utility of this technique for the investigation of integer-spin systems. A full-matrix diagonalization approach is used to simulate spectra over the 94-371 GHz frequency range, providing the spin-Hamiltonian parameters g, D, and E. It is observed that g is anisotropic, characterized by gx = gy = 2.08 and gz = 2.00, and that D = +5.84 cm(-1) and E = +1.42 cm(-1), where the uncertainty in each parameter is estimated as +/- 2%. The spin-Hamiltonian for [PPh4]2[Fe(SPh)4] is related to fundamental properties, such as the crystal-field splitting and the spin-orbit coupling of Fe2+. It is shown that the conventional spin-Hamiltonian accurately represents the electronic structure of the Fe2+ ion in this molecule. Through a comparison with Fe(SPh)4(PPh4)2, the zero-field splitting of the Fe2+ site in reduced rubredoxin is estimated to be D = +5.3 cm(-1) and E = +1.5 cm(-1). This is one of the few HFEPR investigations of a rhombic, high-spin system; as such, it is a step toward the eventual investigation of similar Fe2+ sites in proteins.
Collapse
Affiliation(s)
- M J Knapp
- Department of Chemistry and Biochemistry-0358, University of California at San Diego, La Jolla 92093, USA
| | | | | | | |
Collapse
|
46
|
Brechin EK, Knapp MJ, Huffman JC, Hendrickson* DN, Christou* G. New hexanuclear and octanuclear iron(III) oxide clusters: octahedral [Fe6O2]14+ species and core isomerism in [Fe8O4]16+ complexes. Inorganica Chim Acta 2000. [DOI: 10.1016/s0020-1693(99)00377-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
47
|
Abstract
High-frequency EPR data are reported for the Fe(II/III) valence delocalized dinuclear complex [Fe(2)(OH)(3)(tmtacn)(2)](2+). A full-matrix diagonalization approach is used to derive the spin-Hamiltonian parameters for this S(T) = (9)/(2) complex. At high fields (up to 14.5 T) and high frequencies (189-433 GHz) fine structure peaks due to resonances between the Kramers doublets (M(s) = (9)/(2), (7)/(2),.) are observed. The spacing of the fine structure reveals that the axial zero-field splitting (ZFS) parameter D is +1.08(1) cm(-)(1); a very small rhombic ZFS (|E| </= 0.01 cm(-)(1)) is suggested by line broadening of these interdoublet resonances. Simulations reveal that g is close to 2.00, and very nearly isotropic: g(x)() = g(y)() = g(z)() = 2.00(2). This complex is a model for the valence-delocalized [Fe(2)S(2)](+) pairs found in larger iron-sulfur clusters, such as the cofactors from the nitrogenase system. This work indicates that HFEPR is a viable technique for the study of high-spin centers in proteins.
Collapse
Affiliation(s)
- Michael J. Knapp
- Department of Chemistry and Biochemistry-0358, University of California at San Diego, La Jolla, California 92093, and the Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, Florida 32310
| | | | | | | |
Collapse
|
48
|
Aromí G, Knapp MJ, Claude JP, Huffman JC, Hendrickson DN, Christou G. High-Spin Molecules: Hexanuclear MnIII Clusters with [Mn6O4X4]6+ (X = Cl-, Br-) Face-Capped Octahedral Cores and S = 12 Ground States. J Am Chem Soc 1999. [DOI: 10.1021/ja983446c] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guillem Aromí
- Contribution from the Department of Chemistry and Molecular Structure Center, Indiana University, Bloomington, Indiana 47405-4001, and Department of Chemistry-0358, University of California at San Diego, La Jolla, California 93093-0358
| | - Michael J. Knapp
- Contribution from the Department of Chemistry and Molecular Structure Center, Indiana University, Bloomington, Indiana 47405-4001, and Department of Chemistry-0358, University of California at San Diego, La Jolla, California 93093-0358
| | - Juan-Pablo Claude
- Contribution from the Department of Chemistry and Molecular Structure Center, Indiana University, Bloomington, Indiana 47405-4001, and Department of Chemistry-0358, University of California at San Diego, La Jolla, California 93093-0358
| | - John C. Huffman
- Contribution from the Department of Chemistry and Molecular Structure Center, Indiana University, Bloomington, Indiana 47405-4001, and Department of Chemistry-0358, University of California at San Diego, La Jolla, California 93093-0358
| | - David N. Hendrickson
- Contribution from the Department of Chemistry and Molecular Structure Center, Indiana University, Bloomington, Indiana 47405-4001, and Department of Chemistry-0358, University of California at San Diego, La Jolla, California 93093-0358
| | - George Christou
- Contribution from the Department of Chemistry and Molecular Structure Center, Indiana University, Bloomington, Indiana 47405-4001, and Department of Chemistry-0358, University of California at San Diego, La Jolla, California 93093-0358
| |
Collapse
|
49
|
Grant CM, Stamper BJ, Knapp MJ, Folting K, Huffman JC, Hendrickson DN, Christou G. Syntheses, crystal structures and properties of mononuclear chromium(III) and dinuclear vanadium(III) and copper(II) complexes with a bis-bipyridyl ligand †. ACTA ACUST UNITED AC 1999. [DOI: 10.1039/a905280a] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
50
|
Grant CM, Knapp MJ, Streib WE, Huffman JC, Hendrickson DN, Christou G. Dinuclear and Hexanuclear Iron(III) Oxide Complexes with a Bis(bipyridine) Ligand: A New [Fe(6)(&mgr;(3)-O)(4)](10+) Core. Inorg Chem 1998; 37:6065-6070. [PMID: 11670744 DOI: 10.1021/ic980686k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of the bis(bipyridine) ligand L (1,2-bis(2,2'-bipyridyl-6-yl)ethane) has yielded new dinuclear and hexanuclear complexes. The FeCl(3)/NaO(2)CPh/L (4:4:1) reaction system in MeCN gives red-brown [Fe(6)O(4)Cl(4)(O(2)CPh)(4)L(2)][FeCl(4)](2) (1). The same reaction system in a 3:3:1 ratio in MeOH gives orange [Fe(2)(OMe)(2)Cl(2)(O(2)CPh)L][FeCl(4)] (2). Complex 1.2MeCN: monoclinic, P2(1)/a, a = 15.317(2) Å, b = 18.303(3) Å, c = 16.168(3) Å, beta = 108.91(1) degrees, and Z = 2. Complex 2: triclinic, P&onemacr;, a = 14.099(6) Å, b = 18.510(7) Å, c = 7.108(3) Å, alpha = 96.77(2) degrees, beta = 99.45(2) degrees, gamma = 81.16(2) degrees, and Z = 2. The cation of 1 consists of a near-planar [Fe(6)(&mgr;(3)-O)(4)](10+) core that can be described as three edge-fused [Fe(2)O(2)] rhombs to which are attached two additional Fe atoms. The cation of 2 contains a [Fe(2)(&mgr;-OMe)(2)(&mgr;-O(2)CPh)](3+) core. In both cations, the L group acts as a bridging ligand across an Fe(2) unit, with the bpy rings essentially parallel. Variable-temperature solid-state magnetic-susceptibility studies of 1 and 2 in the 2.00-300 K range reveal that for both complexes the data are consistent with an S = 0 cation and S = (5)/(2) [FeCl(4)](-) anions. These conclusions were confirmed by magnetization vs field studies in the 2.00-4.00 K and 10.0-50.0 kG ranges. Fitting of the data for 2 to the appropriate theoretical equation for an equimolar composition of Fe(2) cations and [FeCl(4)](-) anions allowed the exchange interaction in the cation to be determined as J = -10.5 cm(-)(1) (H = -2JS(1)S(2)) with g held at 2.00. The obtained J value is consistent with that predicted by a previously published magnetostructural relationship.
Collapse
Affiliation(s)
- Craig M. Grant
- Department of Chemistry and Molecular Structure Center, Indiana University, Bloomington, Indiana 47405-4001, and Department of Chemistry, University of California at San Diego, La Jolla, California 92093-0358
| | | | | | | | | | | |
Collapse
|