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Quaye J, Ouedraogo D, Gadda G. Targeted Mutation of a Non-catalytic Gating Residue Increases the Rate of Pseudomonas aeruginosa d-Arginine Dehydrogenase Catalytic Turnover. J Agric Food Chem 2023; 71. [PMID: 37933126 PMCID: PMC10655190 DOI: 10.1021/acs.jafc.3c05328] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023]
Abstract
Commercial food and l-amino acid industries rely on bioengineered d-amino acid oxidizing enzymes to detect and remove d-amino acid contaminants. However, the bioengineering of enzymes to generate faster biological catalysts has proven difficult as a result of the failure to target specific kinetic steps that limit enzyme turnover, kcat, and the poor understanding of loop dynamics critical for catalysis. Pseudomonas aeruginosa d-arginine dehydrogenase (PaDADH) oxidizes most d-amino acids and is a good candidate for application in the l-amino acid and food industries. The side chain of the loop L2 E246 residue located at the entrance of the PaDADH active site pocket potentially favors the closed active site conformation and secures the substrate upon binding. This study used site-directed mutagenesis, steady-state, and rapid reaction kinetics to generate the glutamine, glycine, and leucine variants and investigate whether increasing the rate of product release could translate to an increased enzyme turnover rate. Upon E246 mutation to glycine, there was an increased rate of d-arginine turnover kcat from 122 to 500 s-1. Likewise, the kcat values increased 2-fold for the glutamine or leucine variants. Thus, we have engineered a faster biocatalyst for industrial applications by selectively increasing the rate of the PaDADH product release.
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Affiliation(s)
- Joanna
Afokai Quaye
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United
States
| | - Daniel Ouedraogo
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United
States
| | - Giovanni Gadda
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United
States
- Department
of Biology, Georgia State University, Atlanta, Georgia 30302-3965, United
States
- Center
for Diagnostics and Therapeutics, Georgia
State University, Atlanta, Georgia 30302-3965, United States
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2
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Ouedraogo D, Souffrant M, Yao XQ, Hamelberg D, Gadda G. Non-active Site Residue in Loop L4 Alters Substrate Capture and Product Release in d-Arginine Dehydrogenase. Biochemistry 2023; 62:1070-1081. [PMID: 36795942 PMCID: PMC9996824 DOI: 10.1021/acs.biochem.2c00697] [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: 02/18/2023]
Abstract
Numerous studies demonstrate that enzymes undergo multiple conformational changes during catalysis. The malleability of enzymes forms the basis for allosteric regulation: residues located far from the active site can exert long-range dynamical effects on the active site residues to modulate catalysis. The structure of Pseudomonas aeruginosa d-arginine dehydrogenase (PaDADH) shows four loops (L1, L2, L3, and L4) that span the substrate and the FAD-binding domains. Loop L4 comprises residues 329-336, spanning over the flavin cofactor. The I335 residue on loop L4 is ∼10 Å away from the active site and ∼3.8 Å from N(1)-C(2)═O atoms of the flavin. In this study, we used molecular dynamics and biochemical techniques to investigate the effect of the mutation of I335 to histidine on the catalytic function of PaDADH. Molecular dynamics showed that the conformational dynamics of PaDADH are shifted to a more closed conformation in the I335H variant. In agreement with an enzyme that samples more in a closed conformation, the kinetic data of the I335H variant showed a 40-fold decrease in the rate constant of substrate association (k1), a 340-fold reduction in the rate constant of substrate dissociation from the enzyme-substrate complex (k2), and a 24-fold decrease in the rate constant of product release (k5), compared to that of the wild-type. Surprisingly, the kinetic data are consistent with the mutation having a negligible effect on the reactivity of the flavin. Altogether, the data indicate that the residue at position 335 has a long-range dynamical effect on the catalytic function in PaDADH.
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Affiliation(s)
- Daniel Ouedraogo
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Michael Souffrant
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Xin-Qiu Yao
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
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3
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Moni BM, Quaye JA, Gadda G. Mutation of a distal gating residue modulates NADH binding in NADH:Quinone oxidoreductase from Pseudomonas aeruginosa PAO1. J Biol Chem 2023; 299:103044. [PMID: 36803963 PMCID: PMC10033279 DOI: 10.1016/j.jbc.2023.103044] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/07/2023] [Accepted: 02/11/2023] [Indexed: 02/19/2023] Open
Abstract
Enzymes require flexible regions to adopt multiple conformations during catalysis. The mobile regions of enzymes include gates that modulate the passage of molecules in and out of the enzyme's active site. The enzyme PA1024 from Pseudomonas aeruginosa PA01 is a recently discovered flavin-dependent NADH:quinone oxidoreductase (NQO, EC 1.6.5.9). Q80 in loop 3 (residues 75-86) of NQO is ∼15 Å away from the flavin and creates a gate that seals the active site through a hydrogen bond with Y261 upon NADH binding. In this study, we mutated Q80 to glycine, leucine, or glutamate to investigate the mechanistic significance of distal residue Q80 in NADH binding in the active site of NQO. The UV-visible absorption spectrum reveals that the mutation of Q80 minimally affects the protein microenvironment surrounding the flavin. The anaerobic reductive half-reaction of the NQO-mutants yields a ≥25-fold increase in the Kd value for NADH compared to the WT enzyme. However, we determined that the kred value was similar in the Q80G, Q80L, and wildtype enzymes and only ∼25% smaller in the Q80E enzyme. Steady-state kinetics with NQO-mutants and NQO-WT at varying concentrations of NADH and 1,4-benzoquinone establish a ≤5-fold decrease in the kcat/KNADH value. Moreover, there is no significant difference in the kcat/KBQ (∼1 × 106 M-1s-1) and kcat (∼24 s-1) values in NQO-mutants and NQO-WT. These results are consistent with the distal residue Q80 being mechanistically essential for NADH binding to NQO with minimal effect on the quinone binding to the enzyme and hydride transfer from NADH to flavin.
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Affiliation(s)
- Bilkis Mehrin Moni
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Joanna A Quaye
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA; Department of Biology, Georgia State University, Atlanta, Georgia, USA; The Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA.
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Kabir MP, Ouedraogo D, Orozco-Gonzalez Y, Gadda G, Gozem S. Alternative Strategy for Spectral Tuning of Flavin-Binding Fluorescent Proteins. J Phys Chem B 2023; 127:1301-1311. [PMID: 36740810 PMCID: PMC9940217 DOI: 10.1021/acs.jpcb.2c06475] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
iLOV is an engineered flavin-binding fluorescent protein (FbFP) with applications for in vivo cellular imaging. To expand the range of applications of FbFPs for multicolor imaging and FRET-based biosensing, it is desirable to understand how to modify their absorption and emission wavelengths (i.e., through spectral tuning). There is particular interest in developing FbFPs that absorb and emit light at longer wavelengths, which has proven challenging thus far. Existing spectral tuning strategies that do not involve chemical modification of the flavin cofactor have focused on placing positively charged amino acids near flavin's C4a and N5 atoms. Guided by previously reported electrostatic spectral tunning maps (ESTMs) of the flavin cofactor and by quantum mechanical/molecular mechanical (QM/MM) calculations reported in this work, we suggest an alternative strategy: placing a negatively charged amino acid near flavin's N1 atom. We predict that a single-point mutant, iLOV-Q430E, has a slightly red-shifted absorption and fluorescence maximum wavelength relative to iLOV. To validate our theoretical prediction, we experimentally expressed and purified iLOV-Q430E and measured its spectral properties. We found that the Q430E mutation results in a slight change in absorption and a 4-8 nm red shift in the fluorescence relative to iLOV, in good agreement with the computational predictions. Molecular dynamics simulations showed that the carboxylate side chain of the glutamate in iLOV-Q430E points away from the flavin cofactor, which leads to a future expectation that further red shifting may be achieved by bringing the side chain closer to the cofactor.
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Quaye JA, Gadda G. The Pseudomonas aeruginosa PAO1 metallo flavoprotein d-2-hydroxyglutarate dehydrogenase requires Zn 2+ for substrate orientation and activation. J Biol Chem 2023; 299:103008. [PMID: 36775127 PMCID: PMC10034468 DOI: 10.1016/j.jbc.2023.103008] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Pseudomonas aeruginosa PAO1 d-2-hydroxyglutarate (D2HG) dehydrogenase (PaD2HGDH) oxidizes D2HG to 2-ketoglutarate during the vital l-serine biosynthesis and is a potential therapeutic target against P. aeruginosa. PaD2HGDH, which oxidizes d-malate as an alternative substrate, has been demonstrated to be a metallo flavoprotein that requires Zn2+ for activity. However, the role of Zn2+ in the enzyme has not been elucidated, making it difficult to rationalize why nature employs both a redox center and a metal ion for catalysis in PaD2HGDH and other metallo flavoenzymes. In this study, recombinant His-tagged PaD2HGDH was purified to high levels in the presence of Zn2+ or Co2+ to investigate the metal's role in catalysis. We found that the flavin reduction step was reversible and partially rate limiting for the enzyme's turnover at pH 7.4 with either D2HG or d-malate with similar rate constants for both substrates, irrespective of whether Zn2+ or Co2+ was bound to the enzyme. The steady-state pL profiles of the kcat and kcat/Km values with d-malate demonstrate that Zn2+ mediates the activation of water coordinated to the metal. Our data are consistent with a dual role for the metal, which orients the hydroxy acid substrate in the enzyme's active site and rapidly deprotonates the substrate to yield an alkoxide species for hydride transfer to the flavin. Thus, we propose a catalytic mechanism for PaD2HGDH oxidation that establishes Zn2+ as a cofactor required for substrate orientation and activation during enzymatic turnover.
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Affiliation(s)
- Joanna A Quaye
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA; Department of Biology, Georgia State University, Atlanta, Georgia, USA; Department of The Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA.
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6
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Quaye JA, Gadda G. Uncovering Zn 2+ as a cofactor of FAD-dependent Pseudomonas aeruginosa PAO1 D-2-hydroxyglutarate dehydrogenase. J Biol Chem 2023; 299:103007. [PMID: 36775126 PMCID: PMC10025160 DOI: 10.1016/j.jbc.2023.103007] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Pseudomonas aeruginosa couples the oxidation of D-2-hydroxyglutarate (D2HG) to L-serine biosynthesis for survival, using D-2-hydroxyglutarate dehydrogenase (PaD2HGDH). Knockout of PaD2HGDH impedes P. aeruginosa growth, making PaD2HGDH a potential target for therapeutics. Previous studies showed that the enzyme's activity is increased in the presence of Zn2+, Co2+, or Mn2+ but did not establish the enzyme's metal composition and whether the metal is an activator or a required cofactor for the enzyme, which we addressed in this study. Comparable to the human enzyme, PaD2HGDH showed only 15% flavin reduction with D2HG or D-malate. Upon purifying PaD2HGDH with 1 mM Zn2+, the Zn2+:protein stoichiometry was 2:1, yielding an enzyme with ∼40 s-1 kcat for D-malate. Treatment with 1 mM EDTA decreased the Zn2+:protein ratio to 1:1 without changing the kinetic parameters with D-malate. We observed complete enzyme inactivation for the Metallo-apoenzyme with 100 mM EDTA treatment, suggesting that Zn2+ is essential for PaD2HGDH activity. The presence of Zn2+ increased the flavin N3 atom pKa value to 11.9, decreased the flavin ε450 at pH 7.4 from 13.5 to 11.8 mM-1cm-1, and yielded a charged transfer complex with a broad absorbance band >550 nm, consistent with a Zn2+-hydrate species altering the electronic properties of the enzyme-bound FAD. The exogenous addition of Zn2+, Co2+, Cd2+, Mn2+, or Ni2+ to the metallo-apoenzyme reactivated the enzyme in a sigmoidal pattern, consistent with an induced fit rapid-rearrangement mechanism. Collectively, our data demonstrate that PaD2HGDH is a Zn2+-dependent metallo flavoprotein, which requires Zn2+ as an essential cofactor for enzyme activity.
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Affiliation(s)
- Joanna A Quaye
- Departments of Chemistry, Georgia State University, Atlanta, GA 30302-3965
| | - Giovanni Gadda
- Departments of Chemistry, Georgia State University, Atlanta, GA 30302-3965; Departments of Biology, Georgia State University, Atlanta, GA 30302-3965; Departments of The Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965.
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7
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Quaye JA, Ball J, Gadda G. Kinetic solvent viscosity effects uncover an internal isomerization of the enzyme-substrate complex in Pseudomonas aeruginosa PAO1 NADH:Quinone oxidoreductase. Arch Biochem Biophys 2022; 727:109342. [PMID: 35777523 DOI: 10.1016/j.abb.2022.109342] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 11/02/2022]
Abstract
NAD(P)H:quinone oxidoreductases (NQOs) play an essential protective role as antioxidants in the detoxification of quinones in both Prokaryotes and Eukaryotes. NQO from Pseudomonas aeruginosa PAO1 uses FMN to catalyze the two-electron reduction of various quinones with NADH. In this study, steady-state kinetics, kinetic solvent viscosity effects, and rapid reaction kinetics were used to determine which kinetic steps control the overall turnover of the enzyme with benzoquinone or juglone. The rate constant for flavin reduction (kred) at pH 6.0 was 12.9 ± 0.3 s-1, and the Kd for NADH was at least an order of magnitude lower than 90 μM. With benzoquinone, the kcat value was 11.7 ± 0.3 s-1, consistent with flavin reduction being almost entirely rate-limiting for overall turnover. With juglone, a kcat value of 10.0 ± 0.5 s-1 was recorded. The normalized plot of the relative solvent viscosity effects on the kcat values established that hydride transfer from NADH to the FMN and quinol product release, with a calculated rate constant (kP-rel) of 52 s-1, are partially rate-limiting for the overall turnover of NQO. Kinetic solvent viscosity effects with glucose or sucrose revealed a hyperbolic dependence on the kcat and kcat/Km values with benzoquinone or juglone, respectively, consistent with the presence of a solvent-sensitive internal isomerization of the enzyme-substrate complex (ES). The data demonstrate opposing effects of benzoquinone and juglone on the equilibrium of the NQO ES isomerization with glucose or sucrose. Thus, our study demonstrates how quinol substrate properties alter the equilibrium of NQO ES isomerization.
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Affiliation(s)
- Joanna A Quaye
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA, 30302, USA
| | - Jacob Ball
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA, 30302, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA, 30302, USA; Department of Biology, Georgia State University, Atlanta, GA, 30302, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302, USA.
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8
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Iyer A, Reis RAG, Agniswamy J, Weber IT, Gadda G. Discovery of a new flavin N5-adduct in a tyrosine to phenylalanine variant of d-Arginine dehydrogenase. Arch Biochem Biophys 2022; 715:109100. [PMID: 34864048 DOI: 10.1016/j.abb.2021.109100] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/02/2022]
Abstract
d-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) catalyzes the flavin-dependent oxidation of d-arginine and other d-amino acids. Here, we report the crystal structure at 1.29 Å resolution for PaDADH-Y249F expressed and co-crystallized with d-arginine. The overall structure of PaDADH-Y249F resembled PaDADH-WT, but the electron density for the flavin cofactor was ambiguous, suggesting the presence of modified flavins. Electron density maps and mass spectrometric analysis confirmed the presence of both N5-(4-guanidino-oxobutyl)-FAD and 6-OH-FAD in a single crystal of PaDADH-Y249F and helped with the further refinement of the X-ray crystal structure. The versatility of the reduced flavin is apparent in the PaDADH-Y249F structure and is evidenced by the multiple functions it can perform in the same active site.
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Affiliation(s)
- Archana Iyer
- Department of Chemistry, Georgia State University, Atlanta, GA, 30302, USA
| | - Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, GA, 30302, USA
| | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Irene T Weber
- Department of Chemistry, Georgia State University, Atlanta, GA, 30302, USA; Department of Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, GA, 30302, USA; Department of Biology, Georgia State University, Atlanta, GA, 30302, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302, USA.
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9
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Mohammadyari P, Gadda G, del Cerro JM, Taibi A. Head rotation effects on head and neck hemodynamics by 4D-PC MR imaging and mathematical modelling. Phys Med 2021. [DOI: 10.1016/s1120-1797(22)00231-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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10
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Deng X, Yao XQ, Berglund K, Dong B, Ouedraogo D, Ghane MA, Zhuo Y, McBean C, Wei ZZ, Gozem S, Yu SP, Wei L, Fang N, Mabb AM, Gadda G, Hamelberg D, Yang JJ. Tuning Protein Dynamics to Sense Rapid Endoplasmic-Reticulum Calcium Dynamics. Angew Chem Int Ed Engl 2021; 60:23289-23298. [PMID: 34436811 DOI: 10.1002/anie.202108443] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Indexed: 11/11/2022]
Abstract
Multi-scale calcium (Ca2+ ) dynamics, exhibiting wide-ranging temporal kinetics, constitutes a ubiquitous mode of signal transduction. We report a novel endoplasmic-reticulum (ER)-targeted Ca2+ indicator, R-CatchER, which showed superior kinetics in vitro (koff ≥2×103 s-1 , kon ≥7×106 M-1 s-1 ) and in multiple cell types. R-CatchER captured spatiotemporal ER Ca2+ dynamics in neurons and hotspots at dendritic branchpoints, enabled the first report of ER Ca2+ oscillations mediated by calcium sensing receptors (CaSRs), and revealed ER Ca2+ -based functional cooperativity of CaSR. We elucidate the mechanism of R-CatchER and propose a principle to rationally design genetically encoded Ca2+ indicators with a single Ca2+ -binding site and fast kinetics by tuning rapid fluorescent-protein dynamics and the electrostatic potential around the chromophore. The design principle is supported by the development of G-CatchER2, an upgrade of our previous (G-)CatchER with improved dynamic range. Our work may facilitate protein design, visualizing Ca2+ dynamics, and drug discovery.
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Affiliation(s)
- Xiaonan Deng
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, 50 Decatur Street, 552 NSC, Atlanta, GA, 30303, USA
| | - Xin-Qiu Yao
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, 50 Decatur Street, 552 NSC, Atlanta, GA, 30303, USA
| | - Ken Berglund
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Bin Dong
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, 50 Decatur Street, 552 NSC, Atlanta, GA, 30303, USA
| | - Daniel Ouedraogo
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, 50 Decatur Street, 552 NSC, Atlanta, GA, 30303, USA
| | - Mohammad A Ghane
- Neuroscience Institute, Georgia State University, Atlanta, GA, 30303, USA.,Center for Behavioral Neuroscience, Georgia State University, Atlanta, GA, 30303, USA
| | - You Zhuo
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, 50 Decatur Street, 552 NSC, Atlanta, GA, 30303, USA
| | - Cheyenne McBean
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, 50 Decatur Street, 552 NSC, Atlanta, GA, 30303, USA
| | - Zheng Zachory Wei
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Samer Gozem
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, 50 Decatur Street, 552 NSC, Atlanta, GA, 30303, USA
| | - Shan P Yu
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Ling Wei
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Ning Fang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, 50 Decatur Street, 552 NSC, Atlanta, GA, 30303, USA
| | - Angela M Mabb
- Neuroscience Institute, Georgia State University, Atlanta, GA, 30303, USA.,Center for Behavioral Neuroscience, Georgia State University, Atlanta, GA, 30303, USA
| | - Giovanni Gadda
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, 50 Decatur Street, 552 NSC, Atlanta, GA, 30303, USA
| | - Donald Hamelberg
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, 50 Decatur Street, 552 NSC, Atlanta, GA, 30303, USA
| | - Jenny J Yang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, 50 Decatur Street, 552 NSC, Atlanta, GA, 30303, USA
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11
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Deng X, Yao X, Berglund K, Dong B, Ouedraogo D, Ghane MA, Zhuo Y, McBean C, Wei ZZ, Gozem S, Yu SP, Wei L, Fang N, Mabb AM, Gadda G, Hamelberg D, Yang JJ. Tuning Protein Dynamics to Sense Rapid Endoplasmic‐Reticulum Calcium Dynamics. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xiaonan Deng
- Department of Chemistry Center for Diagnostics and Therapeutics Advanced Translational Imaging Facility Georgia State University 50 Decatur Street, 552 NSC Atlanta GA 30303 USA
| | - Xin‐Qiu Yao
- Department of Chemistry Center for Diagnostics and Therapeutics Advanced Translational Imaging Facility Georgia State University 50 Decatur Street, 552 NSC Atlanta GA 30303 USA
| | - Ken Berglund
- Department of Neurosurgery Emory University School of Medicine Atlanta GA 30322 USA
| | - Bin Dong
- Department of Chemistry Center for Diagnostics and Therapeutics Advanced Translational Imaging Facility Georgia State University 50 Decatur Street, 552 NSC Atlanta GA 30303 USA
| | - Daniel Ouedraogo
- Department of Chemistry Center for Diagnostics and Therapeutics Advanced Translational Imaging Facility Georgia State University 50 Decatur Street, 552 NSC Atlanta GA 30303 USA
| | - Mohammad A. Ghane
- Neuroscience Institute Georgia State University Atlanta GA 30303 USA
- Center for Behavioral Neuroscience Georgia State University Atlanta GA 30303 USA
| | - You Zhuo
- Department of Chemistry Center for Diagnostics and Therapeutics Advanced Translational Imaging Facility Georgia State University 50 Decatur Street, 552 NSC Atlanta GA 30303 USA
| | - Cheyenne McBean
- Department of Chemistry Center for Diagnostics and Therapeutics Advanced Translational Imaging Facility Georgia State University 50 Decatur Street, 552 NSC Atlanta GA 30303 USA
| | - Zheng Zachory Wei
- Department of Anesthesiology Emory University School of Medicine Atlanta GA 30322 USA
| | - Samer Gozem
- Department of Chemistry Center for Diagnostics and Therapeutics Advanced Translational Imaging Facility Georgia State University 50 Decatur Street, 552 NSC Atlanta GA 30303 USA
| | - Shan P. Yu
- Department of Anesthesiology Emory University School of Medicine Atlanta GA 30322 USA
| | - Ling Wei
- Department of Anesthesiology Emory University School of Medicine Atlanta GA 30322 USA
| | - Ning Fang
- Department of Chemistry Center for Diagnostics and Therapeutics Advanced Translational Imaging Facility Georgia State University 50 Decatur Street, 552 NSC Atlanta GA 30303 USA
| | - Angela M. Mabb
- Neuroscience Institute Georgia State University Atlanta GA 30303 USA
- Center for Behavioral Neuroscience Georgia State University Atlanta GA 30303 USA
| | - Giovanni Gadda
- Department of Chemistry Center for Diagnostics and Therapeutics Advanced Translational Imaging Facility Georgia State University 50 Decatur Street, 552 NSC Atlanta GA 30303 USA
| | - Donald Hamelberg
- Department of Chemistry Center for Diagnostics and Therapeutics Advanced Translational Imaging Facility Georgia State University 50 Decatur Street, 552 NSC Atlanta GA 30303 USA
| | - Jenny J. Yang
- Department of Chemistry Center for Diagnostics and Therapeutics Advanced Translational Imaging Facility Georgia State University 50 Decatur Street, 552 NSC Atlanta GA 30303 USA
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12
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Dratch BD, Orozco-Gonzalez Y, Gadda G, Gozem S. Ionic Atmosphere Effect on the Absorption Spectrum of a Flavoprotein: A Reminder to Consider Solution Ions. J Phys Chem Lett 2021; 12:8384-8396. [PMID: 34435784 DOI: 10.1021/acs.jpclett.1c02173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 06/13/2023]
Abstract
This study utilizes the FMN-dependent NADH:quinone oxidoreductase from Pseudomonas aeruginosa PAO1 to investigate the effect of introducing an active site negative charge on the flavin absorption spectrum both in the absence and presence of a long-range electrostatic potential coming from solution ions. There were no observed changes in the flavin UV-visible spectrum when an active site tyrosine (Y277) becomes deprotonated in vitro. These results could only be reproduced computationally using average solvent electrostatic configuration (ASEC) QM/MM simulations that include both positive and negative solution ions. The same calculations performed with minimal ions to neutralize the total protein charge predicted that deprotonating Y277 would significantly alter the flavin absorption spectrum. Analyzing the distribution of solution ions indicated that the ions reorganize around the protein surface upon Y277 deprotonation to cancel the effect of the tyrosinate on the flavin absorption spectrum. Additional biochemical experiments were performed to test this hypothesis.
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Affiliation(s)
- Benjamin D Dratch
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | | | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
- Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
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13
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Iyer A, Reis RAG, Gannavaram S, Momin M, Spring-Connell AM, Orozco-Gonzalez Y, Agniswamy J, Hamelberg D, Weber IT, Gozem S, Wang S, Germann MW, Gadda G. A Single-Point Mutation in d-Arginine Dehydrogenase Unlocks a Transient Conformational State Resulting in Altered Cofactor Reactivity. Biochemistry 2021; 60:711-724. [PMID: 33630571 DOI: 10.1021/acs.biochem.1c00054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Proteins are inherently dynamic, and proper enzyme function relies on conformational flexibility. In this study, we demonstrated how an active site residue changes an enzyme's reactivity by modulating fluctuations between conformational states. Replacement of tyrosine 249 (Y249) with phenylalanine in the active site of the flavin-dependent d-arginine dehydrogenase yielded an enzyme with both an active yellow FAD (Y249F-y) and an inactive chemically modified green FAD, identified as 6-OH-FAD (Y249F-g) through various spectroscopic techniques. Structural investigation of Y249F-g and Y249F-y variants by comparison to the wild-type enzyme showed no differences in the overall protein structure and fold. A closer observation of the active site of the Y249F-y enzyme revealed an alternative conformation for some active site residues and the flavin cofactor. Molecular dynamics simulations probed the alternate conformations observed in the Y249F-y enzyme structure and showed that the enzyme variant with FAD samples a metastable conformational state, not available to the wild-type enzyme. Hybrid quantum/molecular mechanical calculations identified differences in flavin electronics between the wild type and the alternate conformation of the Y249F-y enzyme. The computational studies further indicated that the alternate conformation in the Y249F-y enzyme is responsible for the higher spin density at the C6 atom of flavin, which is consistent with the formation of 6-OH-FAD in the variant enzyme. The observations in this study are consistent with an alternate conformational space that results in fine-tuning the microenvironment around a versatile cofactor playing a critical role in enzyme function.
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Affiliation(s)
- Archana Iyer
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Swathi Gannavaram
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Mohamed Momin
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | | | | | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Irene T Weber
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Siming Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States
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14
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Reddish FN, Miller CL, Deng X, Dong B, Patel AA, Ghane MA, Mosca B, McBean C, Wu S, Solntsev KM, Zhuo Y, Gadda G, Fang N, Cox DN, Mabb AM, Treves S, Zorzato F, Yang JJ. Rapid subcellular calcium responses and dynamics by calcium sensor G-CatchER . iScience 2021; 24:102129. [PMID: 33665552 PMCID: PMC7900224 DOI: 10.1016/j.isci.2021.102129] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 12/14/2020] [Accepted: 01/26/2021] [Indexed: 12/15/2022] Open
Abstract
The precise spatiotemporal characteristics of subcellular calcium (Ca2+) transients are critical for the physiological processes. Here we report a green Ca2+ sensor called "G-CatchER+" using a protein design to report rapid local ER Ca2+ dynamics with significantly improved folding properties. G-CatchER+ exhibits a superior Ca2+ on rate to G-CEPIA1er and has a Ca2+-induced fluorescence lifetimes increase. G-CatchER+ also reports agonist/antagonist triggered Ca2+ dynamics in several cell types including primary neurons that are orchestrated by IP3Rs, RyRs, and SERCAs with an ability to differentiate expression. Upon localization to the lumen of the RyR channel (G-CatchER+-JP45), we report a rapid local Ca2+ release that is likely due to calsequestrin. Transgenic expression of G-CatchER+ in Drosophila muscle demonstrates its utility as an in vivo reporter of stimulus-evoked SR local Ca2+ dynamics. G-CatchER+ will be an invaluable tool to examine local ER/SR Ca2+ dynamics and facilitate drug development associated with ER dysfunction.
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Affiliation(s)
- Florence N Reddish
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA
| | - Cassandra L Miller
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA
| | - Xiaonan Deng
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA
| | - Bin Dong
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA
| | - Atit A Patel
- Neuroscience Institute, Georgia State University, Atlanta, GA 30303, USA.,Center for Behavioral Neuroscience, Georgia State University, Atlanta, GA 30303, USA
| | - Mohammad A Ghane
- Neuroscience Institute, Georgia State University, Atlanta, GA 30303, USA.,Center for Behavioral Neuroscience, Georgia State University, Atlanta, GA 30303, USA
| | - Barbara Mosca
- Department of Life Sciences, General Pathology, University of Ferrara, Ferrara, Italy
| | - Cheyenne McBean
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA
| | - Shengnan Wu
- Center for Molecular and Translational Medicine, Georgia State University, Atlanta, GA 30303, USA
| | - Kyril M Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - You Zhuo
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA
| | - Giovanni Gadda
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA
| | - Ning Fang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA
| | - Daniel N Cox
- Neuroscience Institute, Georgia State University, Atlanta, GA 30303, USA.,Center for Behavioral Neuroscience, Georgia State University, Atlanta, GA 30303, USA
| | - Angela M Mabb
- Neuroscience Institute, Georgia State University, Atlanta, GA 30303, USA.,Center for Behavioral Neuroscience, Georgia State University, Atlanta, GA 30303, USA
| | - Susan Treves
- Department of Life Sciences, General Pathology, University of Ferrara, Ferrara, Italy.,Department of Biomedicine, Basel University, Hebelstrasse 20, 4031 Basel, Switzerland
| | - Francesco Zorzato
- Department of Life Sciences, General Pathology, University of Ferrara, Ferrara, Italy.,Department of Biomedicine, Basel University, Hebelstrasse 20, 4031 Basel, Switzerland
| | - Jenny J Yang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA
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15
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Quaye JA, Gadda G. Kinetic and Bioinformatic Characterization of d-2-Hydroxyglutarate Dehydrogenase from Pseudomonas aeruginosa PAO1. Biochemistry 2020; 59:4833-4844. [PMID: 33301690 DOI: 10.1021/acs.biochem.0c00832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
d-2-Hydroxyglutarate dehydrogenase from Pseudomonas aeruginosa PAO1 (PaD2HGDH) catalyzes the oxidation of d-2-hydroxyglutarate to 2-ketoglutarate, which is a necessary step in the serine biosynthetic pathway. The dependence of P. aeruginosa on PaD2HGDH makes the enzyme a potential therapeutic target against P. aeruginosa. In this study, recombinant His-tagged PaD2HGDH was expressed and purified to high levels from gene PA0317, which was previously annotated as an FAD-binding PCMH-type domain-containing protein. The enzyme cofactor was identified as FAD with fluorescence emission after phosphodiesterase treatment and with mass spectrometry analysis. PaD2HGDH had a kcat value of 11 s-1 and a Km value of 60 μM with d-2-hydroxyglutarate at pH 7.4 and 25 °C. The enzyme was also active with d-malate but did not react with molecular oxygen. Steady-state kinetics with d-malate and phenazine methosulfate as an electron acceptor established a mechanism that was consistent with ping-pong bi-bi steady-state kinetics at pH 7.4. A comparison of the kcat/Km values with d-2-hydroxyglutarate and d-malate suggested that the C5 carboxylate of d-2-hydroxyglutarate is important for the substrate specificity of the enzyme. Other homologues of the enzyme have been previously grouped in the VAO/PMCH family of flavoproteins. PaD2HGDH shares fully conserved residues with other α-hydroxy acid oxidizing enzymes, and these conserved residues are found in the active site of the PaD2HDGH homology model. An Enzyme Function Initiative-Enzyme Similarity Tool Sequence Similarity Network analysis suggests a functional difference between PaD2HGDH and human D2HGDH, and no relationship with VAO. A phylogenetic tree analysis of PaD2HGDH, VAO, and human D2HGDH establishes genetic diversity among these enzymes.
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16
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Vodovoz M, Gadda G. Kinetic solvent viscosity effects reveal a protein isomerization in the reductive half-reaction of Neurospora crassa class II nitronate monooxygenase. Arch Biochem Biophys 2020; 695:108625. [DOI: 10.1016/j.abb.2020.108625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/27/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022]
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17
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Abstract
Choline oxidase catalyzes the four-electron, two-step, flavin-mediated oxidation of choline to glycine betaine. The enzyme is important both for medical and biotechnological reasons, because glycine betaine is one among a limited number of compatible solutes used by cells to counteract osmotic pressure. From a fundamental standpoint, choline oxidase has emerged as one of the paradigm enzymes for the oxidation of alcohols catalyzed by flavoproteins. Mechanistic, structural, and computational studies have elucidated the mechanism of action of the enzyme from Arthrobacter globiformis at the molecular level. Both choline and oxygen access to the active site cavity are gated and tightly controlled. Amino acid residues involved in substrate binding, and their contribution, have been identified. The mechanism of choline oxidation, with a hydride transfer reaction, an asynchronous transition state, the formation and stabilization of an alkoxide transient species, and a quantum mechanical mode of reaction, has been elucidated. The importance of nonpolar side chains for oxygen localization and of the positive charge harbored on the substrate for activation of oxygen for reaction with the reduced flavin have been recognized. Interesting phenomena, like the formation of a metastable photoinduced flavin-protein adduct, the reversible formation of a bicovalent flavoprotein, and the trapping of the enzyme in inactive conformations, have been described. This review summarizes the current status of our understanding on the structure-function-dynamics of choline oxidase.
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Affiliation(s)
- Giovanni Gadda
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, United States; Department of Biology, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, United States.
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18
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Su D, Smitherman C, Gadda G. A Metastable Photoinduced Protein–Flavin Adduct in Choline Oxidase, an Enzyme Not Involved in Light-Dependent Processes. J Phys Chem B 2020; 124:3936-3943. [DOI: 10.1021/acs.jpcb.0c02633] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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19
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Su D, Aguillon C, Gadda G. Characterization of conserved active site residues in class I nitronate monooxygenase. Arch Biochem Biophys 2019; 672:108058. [PMID: 31356775 DOI: 10.1016/j.abb.2019.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 01/08/2023]
Abstract
Propionate 3-nitronate (P3N) is a natural toxin that irreversibly inhibits mitochondrial succinate dehydrogenase. P3N poisoning leads to a variety of neurological disorders and even death. Nitronate monooxygenase (NMO) from Pseudomonas aeruginosa PAO1 was the first NMO characterized in bacteria and serves as a paradigm for Class I NMO. Here, we hypothesized that the carboxylate group of P3N might form a hydrogen bond with one or more of the four tyrosine or a lysine residues that are conserved in the active site of the enzyme. In the wild-type enzyme, the kcat value was pH independent between pH 6.0 and 11.0, while the kcat/KP3N value decreased at high pH, suggesting that a protonated group with a pKa value of 9.5 is required for binding the anionic substrate. A pH titration of the UV-visible absorption spectrum of the enzyme showed an increased absorbance at 297 nm with increasing pH, defining a pKa value of 9.5 and a Δε297 nm of 2.4 M-1cm-1, consistent with a tyrosine being important for substrate binding. The N3 atom of the oxidized flavin, instead, did not ionize likely because its pKa was perturbed by the ionization of a tyrosine in the active site of the enzyme. The Y109F, Y254F, Y299F, Y303F, and K307 M, substitutions had small effects (i.e., <3.5-fold) on the steady-state kinetic parameters of the enzyme. With all mutated enzymes, the kcat/KP3N value was less than 2.5-fold different from the wild-type enzyme, suggesting that none of the residues is solely essential for substrate binding.
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20
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Su D, Kabir MP, Orozco‐Gonzalez Y, Gozem S, Gadda G. Cover Feature: Fluorescence Properties of Flavin Semiquinone Radicals in Nitronate Monooxygenase (ChemBioChem 13/2019). Chembiochem 2019. [DOI: 10.1002/cbic.201900373] [Citation(s) in RCA: 1] [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: 11/09/2022]
Affiliation(s)
- Dan Su
- Department of ChemistryGeorgia State University 50 Decatur St. SE Atlanta GA 30302 USA
| | - Mohammad Pabel Kabir
- Department of ChemistryGeorgia State University 50 Decatur St. SE Atlanta GA 30302 USA
| | | | - Samer Gozem
- Department of ChemistryGeorgia State University 50 Decatur St. SE Atlanta GA 30302 USA
| | - Giovanni Gadda
- Department of ChemistryGeorgia State University 50 Decatur St. SE Atlanta GA 30302 USA
- Department of BiologyGeorgia State University 100 Piedmond Ave. Atlanta GA 30303 USA
- Center for Diagnostics and TherapeuticsGeorgia State University P.O. Box 5090 Atlanta GA 30303 USA
- Center for Biotechnology and Drug DesignGeorgia State University Atlanta GA 30302 USA
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21
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Reis RAG, Salvi F, Williams I, Gadda G. Kinetic Investigation of a Presumed Nitronate Monooxygenase from Pseudomonas aeruginosa PAO1 Establishes a New Class of NAD(P)H:Quinone Reductases. Biochemistry 2019; 58:2594-2607. [PMID: 31075192 DOI: 10.1021/acs.biochem.9b00207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PA0660 from Pseudomonas aeruginosa PAO1 is currently classified as a hypothetical nitronate monooxygenase (NMO), but no evidence at the transcript or protein level has been presented. In this study, PA0660 was purified and its biochemical and kinetic properties were characterized. Absorption spectroscopy and mass spectrometry demonstrated a tightly, noncovalently bound FMN in the active site of the enzyme. Analytical ultracentrifugation showed that the enzyme exists as a dimer in solution. Despite its annotation, PA0660 did not exhibit nitronate monooxygenase activity. The enzyme could be reduced with NADPH or NADH with a marked preference for NADPH, as indicated by ∼30-fold larger kcat/ Km and kred/ Kd values. Turnover could be sustained with NAD(P)H and quinones, DCPIP, and to a lesser extent molecular oxygen. However, PA0660 did not turn over with methyl red, consistent with a lack of azoreductase activity. The enzyme turned over through a ping-pong bi-bi steady-state kinetic mechanism with NADPH and 1,4-benzoquinone showing a kcat value of 90 s-1. The rate constant for flavin reduction with saturating NADPH was 360 s-1, whereas that for flavin oxidation with 1,4-benzoquinone was 270 s-1, consistent with both hydride transfers from the pyridine nucleotide to the flavin and from the flavin to 1,4-benzoquinone being partially rate-limiting for enzyme turnover. A BlastP search and a multiple-sequence alignment analysis of PA0660 highlighted the presence of six conserved motifs in >1000 open reading frames currently annotated as hypothetical NMOs. Our results suggest that PA0660 should be classified as an NAD(P)H:quinone reductase and serve as a paradigm enzyme for a new class of enzymes.
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22
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Su D, Kabir MP, Orozco-Gonzalez Y, Gozem S, Gadda G. Fluorescence Properties of Flavin Semiquinone Radicals in Nitronate Monooxygenase. Chembiochem 2019; 20:1646-1652. [PMID: 30748074 DOI: 10.1002/cbic.201900016] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Indexed: 11/09/2022]
Abstract
Fluorescent cofactors like flavins can be exploited to probe their local environment with spatial and temporal resolution. Although the fluorescence properties of the oxidized and two-electron-reduced states of flavins have been studied extensively, this is not the case for the one-electron-reduced state. Both the neutral and anionic semiquinones have proven particularly challenging to examine, as they are unstable in solution and are transient, short-lived species in many catalytic cycles. Here, we report that the nitronate monooxygenase (NMO) from Pseudomonas aeruginosa PAO1 is capable of stabilizing both semiquinone forms anaerobically for hours, thus enabling us to study their spectroscopy in a constant protein environment. We found that in the active site of NMO, the anionic semiquinone exhibits no fluorescence, whereas the neutral semiquinone radical shows a relatively strong fluorescence, with a behavior that violates the Kasha-Vavilov rule. These fluorescence properties are discussed in the context of time-dependent density functional theory calculations, which reveal low-lying dark states in both systems.
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Affiliation(s)
- Dan Su
- Department of Chemistry, Georgia State University, 50 Decatur St. SE, Atlanta, GA, 30302, USA
| | - Mohammad Pabel Kabir
- Department of Chemistry, Georgia State University, 50 Decatur St. SE, Atlanta, GA, 30302, USA
| | - Yoelvis Orozco-Gonzalez
- Department of Chemistry, Georgia State University, 50 Decatur St. SE, Atlanta, GA, 30302, USA
| | - Samer Gozem
- Department of Chemistry, Georgia State University, 50 Decatur St. SE, Atlanta, GA, 30302, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, 50 Decatur St. SE, Atlanta, GA, 30302, USA.,Department of Biology, Georgia State University, 100 Piedmond Ave., Atlanta, GA, 30303, USA.,Center for Diagnostics and Therapeutics, Georgia State University, P.O. Box 5090, Atlanta, GA, 30303, USA.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, 30302, USA
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23
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Ball J, Reis RAG, Agniswamy J, Weber IT, Gadda G. Steric hindrance controls pyridine nucleotide specificity of a flavin-dependent NADH:quinone oxidoreductase. Protein Sci 2018; 28:167-175. [PMID: 30246917 DOI: 10.1002/pro.3514] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 02/04/2023]
Abstract
The crystal structure of the NADH:quinone oxidoreductase PA1024 has been solved in complex with NAD+ to 2.2 Å resolution. The nicotinamide C4 is 3.6 Å from the FMN N5 atom, with a suitable orientation for facile hydride transfer. NAD+ binds in a folded conformation at the interface of the TIM-barrel domain and the extended domain of the enzyme. Comparison of the enzyme-NAD+ structure with that of the ligand-free enzyme revealed a different conformation of a short loop (75-86) that is part of the NAD+ -binding pocket. P78, P82, and P84 provide internal rigidity to the loop, whereas Q80 serves as an active site latch that secures the NAD+ within the binding pocket. An interrupted helix consisting of two α-helices connected by a small three-residue loop binds the pyrophosphate moiety of NAD+ . The adenine moiety of NAD+ appears to π-π stack with Y261. Steric constraints between the adenosine ribose of NAD+ , P78, and Q80, control the strict specificity of the enzyme for NADH. Charged residues do not play a role in the specificity of PA1024 for the NADH substrate.
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Affiliation(s)
- Jacob Ball
- Department of Chemistry, Georgia State University, Atlanta, Georgia, 30302-3965
| | - Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, Georgia, 30302-3965
| | - Johnson Agniswamy
- School of Biology, Centers for Georgia State University, Atlanta, Georgia, 30302-3965
| | - Irene T Weber
- Department of Chemistry, Georgia State University, Atlanta, Georgia, 30302-3965.,School of Biology, Centers for Georgia State University, Atlanta, Georgia, 30302-3965.,Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia, 30302-3965.,Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, 30302-3965
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia, 30302-3965.,School of Biology, Centers for Georgia State University, Atlanta, Georgia, 30302-3965.,Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia, 30302-3965.,Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, 30302-3965
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24
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Ball J, Gannavaram S, Gadda G. Structural determinants for substrate specificity of flavoenzymes oxidizing d-amino acids. Arch Biochem Biophys 2018; 660:87-96. [PMID: 30312594 DOI: 10.1016/j.abb.2018.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/01/2018] [Accepted: 10/08/2018] [Indexed: 12/26/2022]
Abstract
The oxidation of d-amino acids is relevant to neurodegenerative diseases, detoxification, and nutrition in microorganisms and mammals. It is also important for the resolution of racemic amino acid mixtures and the preparation of chiral building blocks for the pharmaceutical and food industry. Considerable biochemical and structural knowledge has been accrued in recent years on the enzymes that carry out the oxidation of the Cα-N bond of d-amino acids. These enzymes contain FAD as a required coenzyme, share similar overall three-dimensional folds and highly conserved active sites, but differ in their specificity for substrates with neutral, anionic, or cationic side-chains. Here, we summarize the current biochemical and structural knowledge regarding substrate specificity on d-amino acid oxidase, d-aspartate oxidase, and d-arginine dehydrogenase for which a wealth of biochemical and structural studies is available.
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Affiliation(s)
- Jacob Ball
- Departments of Chemistry, Georgia State University, Atlanta, GA, 30302-3965, USA
| | - Swathi Gannavaram
- Departments of Chemistry, Georgia State University, Atlanta, GA, 30302-3965, USA
| | - Giovanni Gadda
- Departments of Chemistry, Georgia State University, Atlanta, GA, 30302-3965, USA; Departments of Biology, Georgia State University, Atlanta, GA, 30302-3965, USA; Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, 30302-3965, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302-3965, USA.
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25
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Robbins JM, Geng J, Barry BA, Gadda G, Bommarius AS. Photoirradiation Generates an Ultrastable 8-Formyl FAD Semiquinone Radical with Unusual Properties in Formate Oxidase. Biochemistry 2018; 57:5818-5826. [PMID: 30226367 DOI: 10.1021/acs.biochem.8b00571] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Formate oxidase (FOX) was previously shown to contain a noncovalently bound 8-formyl FAD (8-fFAD) cofactor. However, both the absorption spectra and the kinetic parameters previously reported for FOX are inconsistent with more recent reports. The ultraviolet-visible (UV-vis) absorption spectrum reported in early studies closely resembles the spectra observed for protein-bound 8-formyl flavin semiquinone species, thus suggesting FOX may be photosensitive. Therefore, the properties of dark and light-exposed FOX were investigated using steady-state kinetics and site-directed mutagenesis analysis along with inductively coupled plasma optical emission spectroscopy, UV-vis absorption spectroscopy, circular dichroism spectroscopy, liquid chromatography and mass spectrometry, and electron paramagnetic resonance (EPR) spectroscopy. Surprisingly, these experimental results demonstrate that FOX is deactivated in the presence of light through generation of an oxygen stable, anionic (red) 8-fFAD semiquinone radical capable of persisting either in an aerobic environment for multiple weeks or in the presence of a strong reducing agent like sodium dithionite. Herein, we study the photoinduced formation of the 8-fFAD semiquinone radical in FOX and report the first EPR spectrum of this radical species. The stability of the 8-fFAD semiquinone radical suggests FOX to be a model enzyme for probing the structural and mechanistic features involved in stabilizing flavin semiquinone radicals. It is likely that the photoinduced formation of a stable 8-fFAD semiquinone radical is a defining characteristic of 8-formyl flavin-dependent enzymes. Additionally, a better understanding of the radical stabilization process may yield a FOX enzyme with more robust activity and broader industrial usefulness.
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Affiliation(s)
- John M Robbins
- School of Chemical and Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332-0100 , United States.,Engineered Biosystems Building (EBB) , Georgia Institute of Technology , Atlanta , Georgia 30332-2000 , United States
| | - Jiafeng Geng
- School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332-0363 , United States
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332-0363 , United States
| | - Giovanni Gadda
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30302-3965 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Atlanta , Georgia 30302-3965 , United States.,Center for Biotechnology and Drug Design , Georgia State University , Atlanta , Georgia 30302-3965 , United States.,Department of Biology , Georgia State University , Atlanta , Georgia 30302-3965 , United States
| | - Andreas S Bommarius
- School of Chemical and Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332-0100 , United States.,Engineered Biosystems Building (EBB) , Georgia Institute of Technology , Atlanta , Georgia 30332-2000 , United States.,School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332-0363 , United States
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26
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Affiliation(s)
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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27
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Flores E, Gadda G. Kinetic Characterization of PA1225 from Pseudomonas aeruginosa PAO1 Reveals a New NADPH:Quinone Reductase. Biochemistry 2018; 57:3050-3058. [PMID: 29715013 DOI: 10.1021/acs.biochem.8b00090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The pa1225 gene of Pseudomonas aeruginosa strain PAO1 was cloned, and the resulting enzyme (PA1225) was purified and revealed to be an NADPH:quinone reductase. By using kinetics, fluorescence, and mass spectrometric analyses, PA1225 was shown to utilize FAD to transfer a hydride ion from NADPH to quinones. The enzyme could also use NADH, but with an efficiency that was 40-fold lower than that of NADPH as suggested by the kcat/ Km values at pH 6.0. Similar initial rates of reaction were determined with 1,4-benzoquinone and 2,6-dimethoxy-1,4-benzoquinone in the range between 25 and 200 μM, suggesting a low Km value for the quinone-oxidizing substrate. The lack of inhibition by NADP+ versus NADPH at saturating concentrations of 1,4-benzoquinone was consistent with a ping-pong bi-bi mechanism. The reductive half-reaction at pH 6.0 had Kd values of 0.07 mM with NADPH and 1.8 mM with NADH; the kred for flavin reduction was independent of pH with values of ∼10 s-1 with NADPH and ∼5 s-1 with NADH. Thus, the enzyme specificity for the reducing substrate arises primarily from a tighter binding of NADPH than of NADH. At pH 6.0, the kcat value with NADPH and 1,4-benzoquinone was 10.1 s-1, consistent with the hydride transfer from NADPH to FAD being fully rate limiting for the overall turnover of the enzyme. The enzyme showed negligible NADPH oxidase and azoreductase activities. This study enables annotation of the pa1225 gene as NADPH:quinone reductase, elucidates the enzymatic function of PA1225 in P. aeruginosa PAO1, and establishes that PA1225 is not an azoreductase as previously proposed.
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28
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Robbins JM, Bommarius AS, Gadda G. Mechanistic studies of formate oxidase from Aspergillus oryzae : A novel member of the glucose-Methanol-choline oxidoreductase enzyme superfamily that oxidizes carbon acids. Arch Biochem Biophys 2018; 643:24-31. [DOI: 10.1016/j.abb.2018.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/18/2018] [Accepted: 02/13/2018] [Indexed: 10/18/2022]
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Carro J, Ferreira P, Martínez AT, Gadda G. Stepwise Hydrogen Atom and Proton Transfers in Dioxygen Reduction by Aryl-Alcohol Oxidase. Biochemistry 2018; 57:1790-1797. [DOI: 10.1021/acs.biochem.8b00106] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Juan Carro
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Patricia Ferreira
- Departament of Biochemistry and Cellular and Molecular Biology and Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, E-50009 Zaragoza, Spain
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Giovanni Gadda
- Department of Chemistry, Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
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30
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Agniswamy J, Reis RA, Wang Y, Smitherman C, Su D, Weber I, Gadda G. Crystal structure of yeast nitronate monooxygenase from
Cyberlindnera saturnus. Proteins 2018; 86:599-605. [DOI: 10.1002/prot.25470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/12/2018] [Accepted: 01/23/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Johnson Agniswamy
- Department of BiologyGeorgia State UniversityAtlanta Georgia30302‐3965
| | - Renata A.G. Reis
- Department of ChemistryGeorgia State UniversityAtlanta Georgia30302‐3965
| | - Yuan‐Fang Wang
- Department of BiologyGeorgia State UniversityAtlanta Georgia30302‐3965
| | - Crystal Smitherman
- Department of ChemistryGeorgia State UniversityAtlanta Georgia30302‐3965
- Center for Diagnostics and Therapeutics, Georgia State UniversityAtlanta Georgia30302‐3965
| | - Dan Su
- Department of ChemistryGeorgia State UniversityAtlanta Georgia30302‐3965
| | - Irene Weber
- Department of BiologyGeorgia State UniversityAtlanta Georgia30302‐3965
- Department of ChemistryGeorgia State UniversityAtlanta Georgia30302‐3965
- Center for Biotechnology and Drug Design, Georgia State UniversityAtlanta Georgia30302‐3965
| | - Giovanni Gadda
- Department of BiologyGeorgia State UniversityAtlanta Georgia30302‐3965
- Department of ChemistryGeorgia State UniversityAtlanta Georgia30302‐3965
- Center for Diagnostics and Therapeutics, Georgia State UniversityAtlanta Georgia30302‐3965
- Center for Biotechnology and Drug Design, Georgia State UniversityAtlanta Georgia30302‐3965
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31
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Affiliation(s)
- Elvira Romero
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - J. Rubén Gómez Castellanos
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Giovanni Gadda
- Departments of Chemistry and Biology, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
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32
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Affiliation(s)
- Dan Su
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hongling Yuan
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
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33
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Gadda G, Yuan H. Substitutions of S101 decrease proton and hydride transfers in the oxidation of betaine aldehyde by choline oxidase. Arch Biochem Biophys 2017; 634:76-82. [PMID: 29029877 DOI: 10.1016/j.abb.2017.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 11/25/2022]
Abstract
Choline oxidase oxidizes choline to glycine betaine, with two flavin-mediated reactions to convert the alcohol substrate to the carbon acid product. Proton abstraction from choline or hydrated betaine aldehyde in the wild-type enzyme occurs in the mixing time of the stopped-flow spectrophotometer, thereby precluding a mechanistic investigation. Mutagenesis of S101 rendered the proton transfer reaction amenable to study. Here, we have investigated the aldehyde oxidation reaction catalyzed by the mutant enzymes using steady-state and rapid kinetics with betaine aldehyde. Stopped-flow traces for the reductive half-reaction of the S101T/V/C variants were biphasic, corresponding to the reactions of proton abstraction and hydride transfer. In contrast, the S101A enzyme yielded monophasic traces like wild-type choline oxidase. The rate constants for proton transfer in the S101T/C/V variants decreased logarithmically with increasing hydrophobicity of residue 101, indicating a behavior different from that seen previously with choline for which no correlation was determined. The rate constants for hydride transfer also showed a logarithmic decrease with increasing hydrophobicity at position 101, which was similar to previous results with choline as a substrate for the enzyme. Thus, the hydrophilic character of S101 is necessary not only for efficient hydride transfer but also for the proton abstraction reaction.
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Affiliation(s)
- Giovanni Gadda
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, United States; Department of Biology, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, United States; Center for Biotechnology and Drug Design, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, United States.
| | - Hongling Yuan
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, United States
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34
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Abstract
OBJECTIVE The gravitational gradient is the major component to face when considering the physiology of venous return, and there is a growing interest in understanding the mechanisms ensuring the heart filling, in the absence of gravity, for astronauts who perform long-term space missions. APPROACH The purpose of the Drain Brain project was to monitor the cerebral venous outflow of a crew member during an experiment on the International Space Station (ISS), so as to study the compensatory mechanisms that facilitate this essential physiological action in subjects living in a microgravity environment. Such venous function has been characterized by means of a novel application of strain-gauge plethysmography which uses a capacitive sensor. MAIN RESULTS In this contribution, preliminary results of our investigation have been presented. In particular, comparison of plethysmography data confirmed that long duration spaceflights lead to a redistribution of venous blood volume, and showed interesting differences in the amplitude of cardiac oscillations measured at the level of the neck veins. SIGNIFICANCE The success of the experiment has also demonstrated that thanks to its easy portability, non-invasiveness, and non-operator dependence, the proposed device can be considered as a novel tool for use aboard the ISS. Further trials are now under way to complete the investigation on the drainage function of the neck veins in microgravity.
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Affiliation(s)
- A Taibi
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Ferrara and INFN, Sezione di Ferrara, via Saragat 1, 44122 Ferrara, Italy
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35
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36
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Sethi SK, Daugherty AM, Gadda G, Utriainen DT, Jiang J, Raz N, Haacke EM. Jugular Anomalies in Multiple Sclerosis Are Associated with Increased Collateral Venous Flow. AJNR Am J Neuroradiol 2017; 38:1617-1622. [PMID: 28546249 DOI: 10.3174/ajnr.a5219] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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] [Received: 01/15/2017] [Accepted: 03/13/2017] [Indexed: 01/08/2023]
Abstract
BACKGROUND AND PURPOSE To date, research on extracranial venous collaterals has been focused on structure, with relatively little attention paid to hemodynamics. We addressed this limitation by quantitatively comparing collateral flow in patients with multiple sclerosis and healthy controls by using phase-contrast MR imaging. We hypothesize that patients with MS with structurally anomalous internal jugular veins will have elevated collateral venous flow compared with healthy controls. MATERIALS AND METHODS The sample consisted of 276 patients with MS and 106 healthy controls. We used MRV to classify internal jugular veins as stenotic and nonstenotic based on an absolute cross-sectional area threshold in 276 patients with MS and 60 healthy controls; 46 healthy controls lacked this imaging. Individual and total vessel flows were quantified by using phase-contrast MR imaging on all patients. Veins were classified by extracranial drainage type: internal jugular veins (I), paraspinal (II), and superficial (III). Differences among healthy controls, patients with MS, nonstenotic patients, and stenotic subgroups in total venous flow by vessel type were evaluated in a general linear model for statistical analysis. RESULTS In the MS group, 153 patients (55%) evidenced stenosis, whereas 12 (20%) healthy controls were classified as stenotic (P < .001). Compared with healthy controls, the MS group showed lower type I flow and increased type II flow. Stenosis was associated with reduced flow in the type I vessels [F(1272) = 68; P < .001]. The stenotic MS group had increased flow in the type II vessels compared with the nonstenotic MS group [F(1272) = 67; P < .001]. CONCLUSIONS Compared with healthy controls, patients with MS exhibit reduced venous flow in the main extracerebral drainage vein (internal jugular vein). In contrast, flow in the paraspinal venous collaterals is elevated in patients with MS and exacerbated by venous stenosis. Collateral drainage may be a compensatory response to internal jugular vein flow reduction.
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Affiliation(s)
- S K Sethi
- From The MRI Institute for Biomedical Research (S.K.S., D.T.U., J.J., E.M.H.), Detroit, Michigan
| | | | - G Gadda
- Department of Physics and Earth Sciences (G.G.), University of Ferrara, Ferrara, Italy
| | - D T Utriainen
- From The MRI Institute for Biomedical Research (S.K.S., D.T.U., J.J., E.M.H.), Detroit, Michigan
| | - J Jiang
- From The MRI Institute for Biomedical Research (S.K.S., D.T.U., J.J., E.M.H.), Detroit, Michigan
| | - N Raz
- Institute of Gerontology (A.M.D., N.R.)
- Departments of Psychology (N.R.)
| | - E M Haacke
- From The MRI Institute for Biomedical Research (S.K.S., D.T.U., J.J., E.M.H.), Detroit, Michigan
- Radiology (E.M.H.), Wayne State University, Detroit, Michigan
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37
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Robbins JM, Souffrant MG, Hamelberg D, Gadda G, Bommarius AS. Enzyme-Mediated Conversion of Flavin Adenine Dinucleotide (FAD) to 8-Formyl FAD in Formate Oxidase Results in a Modified Cofactor with Enhanced Catalytic Properties. Biochemistry 2017. [PMID: 28640638 DOI: 10.1021/acs.biochem.7b00335] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Flavins, including flavin adenine dinucleotide (FAD), are fundamental catalytic cofactors that are responsible for the redox functionality of a diverse set of proteins. Alternatively, modified flavin analogues are rarely found in nature as their incorporation typically results in inactivation of flavoproteins, thus leading to the disruption of important cellular pathways. Here, we report that the fungal flavoenzyme formate oxidase (FOX) catalyzes the slow conversion of noncovalently bound FAD to 8-formyl FAD and that this conversion results in a nearly 10-fold increase in formate oxidase activity. Although the presence of an enzyme-bound 8-formyl FMN has been reported previously as a result of site-directed mutagenesis studies of lactate oxidase, FOX is the first reported case of 8-formyl FAD in a wild-type enzyme. Therefore, the formation of the 8-formyl FAD cofactor in formate oxidase was investigated using steady-state kinetics, site-directed mutagenesis, ultraviolet-visible, circular dichroism, and fluorescence spectroscopy, liquid chromatography with mass spectrometry, and computational analysis. Surprisingly, the results from these studies indicate not only that 8-formyl FAD forms spontaneously and results in the active form of FOX but also that its autocatalytic formation is dependent on a nearby arginine residue, R87. Thus, this work describes a new enzyme cofactor and provides insight into the little-understood mechanism of enzyme-mediated 8α-flavin modifications.
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Affiliation(s)
- John M Robbins
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0100, United States.,Engineered Biosystems Building (EBB), Georgia Institute of Technology , Atlanta, Georgia 30332-2000, United States
| | - Michael G Souffrant
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Molecular Basis of Disease Program, Georgia State University , Atlanta, Georgia 30303, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Molecular Basis of Disease Program, Georgia State University , Atlanta, Georgia 30303, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Center for Biotechnology and Drug Design, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Department of Biology, Georgia State University , Atlanta, Georgia 30302-3965, United States
| | - Andreas S Bommarius
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0100, United States.,Engineered Biosystems Building (EBB), Georgia Institute of Technology , Atlanta, Georgia 30332-2000, United States.,School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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38
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Abstract
d-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is a flavin-dependent oxidoreductase, which is part of a novel two-enzyme racemization system that functions to convert d-arginine to l-arginine. PaDADH contains a noncovalently linked FAD that shows the highest activity with d-arginine. The enzyme exhibits broad substrate specificity towards d-amino acids, particularly with cationic and hydrophobic d-amino acids. Biochemical studies have established the structure and the mechanistic properties of the enzyme. The enzyme is a true dehydrogenase because it displays no reactivity towards molecular oxygen. As established through solvent and multiple kinetic isotope studies, PaDADH catalyzes an asynchronous CH and NH bond cleavage via a hydride transfer mechanism. Steady-state kinetic studies with d-arginine and d-histidine are consistent with the enzyme following a ping-pong bi-bi mechanism. As shown by a combination of crystallography, kinetic and computational data, the shape and flexibility of loop L1 in the active site of PaDADH are important for substrate capture and broad substrate specificity.
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Affiliation(s)
- Daniel Ouedraogo
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Jacob Ball
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Archana Iyer
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Maria Vodovoz
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States; Department of Biology, Georgia State University, Atlanta, GA 30302, United States; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302, United States; Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302, United States.
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39
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Ouedraogo D, Souffrant M, Vasquez S, Hamelberg D, Gadda G. Importance of Loop L1 Dynamics for Substrate Capture and Catalysis in Pseudomonas aeruginosa d-Arginine Dehydrogenase. Biochemistry 2017; 56:2477-2487. [DOI: 10.1021/acs.biochem.7b00098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Daniel Ouedraogo
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Michael Souffrant
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Sheena Vasquez
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
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40
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Saxena R, Yang C, Rao M, Turaga RC, Garlapati C, Gundala SR, Myers K, Ghareeb A, Bhattarai S, Kamalinia G, Bristi S, Su D, Gadda G, Rida PCG, Cantuaria GH, Aneja R. Preclinical Development of a Nontoxic Oral Formulation of Monoethanolamine, a Lipid Precursor, for Prostate Cancer Treatment. Clin Cancer Res 2017; 23:3781-3793. [PMID: 28167510 DOI: 10.1158/1078-0432.ccr-16-1716] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 01/10/2017] [Accepted: 01/22/2017] [Indexed: 12/27/2022]
Abstract
Purpose: Most currently available chemotherapeutic agents target rampant cell division in cancer cells, thereby affecting rapidly dividing normal cells resulting in toxic side-effects. This nonspecificity necessitates identification of novel cellular pathways that are reprogrammed selectively in cancer cells and can be exploited to develop pharmacologically superior and less toxic therapeutics. Despite growing awareness on dysregulation of lipid metabolism in cancer cells, targeting lipid biosynthesis is still largely uncharted territory. Herein, we report development of a novel nontoxic orally deliverable anticancer formulation of monoethanolamine (Etn) for prostate cancer by targeting the Kennedy pathway of phosphatidylethanolamine (PE) lipid biosynthesis.Experimental Design: We first evaluated gastrointestinal tract stability, drug-drug interaction liability, pharmacokinetic, and toxicokinetic properties of Etn to evaluate its suitability as a nontoxic orally deliverable agent. We next performed in vitro and in vivo experiments to investigate efficacy and mechanism of action.Results: Our data demonstrate that Etn exhibits excellent bioavailability, gastrointestinal tract stability, and no drug-drug interaction liability. Remarkably, orally fed Etn inhibited tumor growth in four weeks by approximately 67% in mice bearing human prostate cancer PC-3 xenografts without any apparent toxicity. Mechanistically, Etn exploits selective overexpression of choline kinase in cancer cells, resulting in accumulation of phosphoethanolamine (PhosE), accompanied by downregulation of HIF-1α that induces metabolic stress culminating into cell death.Conclusions: Our study provides first evidence for the superior anticancer activity of Etn, a simple lipid precursor formulation, whose nontoxicity conforms to FDA-approved standards, compelling its clinical development for prostate cancer management. Clin Cancer Res; 23(14); 3781-93. ©2017 AACR.
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Affiliation(s)
- Roopali Saxena
- Department of Biology, Georgia State University, Atlanta, Georgia
| | - Chunhua Yang
- Department of Biology, Georgia State University, Atlanta, Georgia
| | - Mukkavilli Rao
- Department of Biology, Georgia State University, Atlanta, Georgia
| | | | | | | | - Kimberly Myers
- Department of Biology, Georgia State University, Atlanta, Georgia
| | - Ahmed Ghareeb
- Department of Biology, Georgia State University, Atlanta, Georgia
| | | | - Golnaz Kamalinia
- Department of Biology, Georgia State University, Atlanta, Georgia
| | - Sangina Bristi
- Department of Biology, Georgia State University, Atlanta, Georgia
| | - Dan Su
- Department of Chemistry, Georgia State University, Atlanta, Georgia
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia
| | | | - Guilherme H Cantuaria
- Department of Gynecologic Oncology, Northside Hospital Cancer Institute, Atlanta, Georgia
| | - Ritu Aneja
- Department of Biology, Georgia State University, Atlanta, Georgia.
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41
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Ball J, Salvi F, Gadda G. Functional Annotation of a Presumed Nitronate Monoxygenase Reveals a New Class of NADH:Quinone Reductases. J Biol Chem 2016; 291:21160-21170. [PMID: 27502282 PMCID: PMC5076524 DOI: 10.1074/jbc.m116.739151] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Indexed: 12/12/2022] Open
Abstract
The protein PA1024 from Pseudomonas aeruginosa PAO1 is currently classified as 2-nitropropane dioxygenase, the previous name for nitronate monooxygenase in the GenBankTM and PDB databases, but the enzyme was not kinetically characterized. In this study, PA1024 was purified to high levels, and the enzymatic activity was investigated by spectroscopic and polarographic techniques. Purified PA1024 did not exhibit nitronate monooxygenase activity; however, it displayed NADH:quinone reductase and a small NADH:oxidase activity. The enzyme preferred NADH to NADPH as a reducing substrate. PA1024 could reduce a broad spectrum of quinone substrates via a Ping Pong Bi Bi steady-state kinetic mechanism, generating the corresponding hydroquinones. The reductive half-reaction with NADH showed a kred value of 24 s-1 and an apparent Kd value estimated in the low micromolar range. The enzyme was not able to reduce the azo dye methyl red, routinely used in the kinetic characterization of azoreductases. Finally, we revisited and modified the existing six conserved motifs of PA1024, which define a new class of NADH:quinone reductases and are present in more than 490 hypothetical proteins in the GenBankTM, the vast majority of which are currently misannotated as nitronate monooxygenase.
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Affiliation(s)
| | | | - Giovanni Gadda
- From the Departments of Chemistry and Biology, Center for Biotechnology and Drug Design, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965
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42
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Gadda G, Taibi A, Sisini F, Gambaccini M, Sethi SK, Utriainen DT, Haacke EM, Zamboni P, Ursino M. Validation of a Hemodynamic Model for the Study of the Cerebral Venous Outflow System Using MR Imaging and Echo-Color Doppler Data. AJNR Am J Neuroradiol 2016; 37:2100-2109. [PMID: 27444939 DOI: 10.3174/ajnr.a4860] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/09/2016] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE A comprehensive parameter model was developed to investigate correlations between cerebral hemodynamics and alterations in the extracranial venous circulation due to posture changes and/or extracranial venous obstruction (stenosis). The purpose of this work was to validate the simulation results by using MR imaging and echo-color Doppler experimental blood flow data in humans. MATERIALS AND METHODS To validate the model outcomes, we used supine average arterial and venous extracerebral blood flow, obtained by using phase-contrast MR imaging from 49 individuals with stenosis in the acquisition plane at the level of the disc between the second and third vertebrae of the left internal jugular vein, 20 with stenosis in the acquisition plane at the level of the disc between the fifth and sixth vertebrae of the right internal jugular vein, and 38 healthy controls without stenosis. Average data from a second group of 10 healthy volunteers screened with an echo-color Doppler technique were used to evaluate flow variations due to posture change. RESULTS There was excellent agreement between experimental and simulated supine flows. Every simulated CBF fell inside the standard error from the corresponding average experimental value, as well as most of the simulated extracerebral arterial flow (extracranial blood flow from the head and face, measured at the level of the disc between second and third vertebrae) and venous flows. Simulations of average jugular and vertebral blood flow variations due to a change of posture from supine to upright also matched the experimental data. CONCLUSIONS The good agreement between simulated and experimental results means that the model can correctly reproduce the main factors affecting the extracranial circulation and could be used to study other types of stenotic conditions not represented by the experimental data.
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Affiliation(s)
- G Gadda
- From the Department of Physics and Earth Sciences (G.G., A.T., F.S., M.G.)
| | - A Taibi
- From the Department of Physics and Earth Sciences (G.G., A.T., F.S., M.G.)
| | - F Sisini
- From the Department of Physics and Earth Sciences (G.G., A.T., F.S., M.G.)
| | - M Gambaccini
- From the Department of Physics and Earth Sciences (G.G., A.T., F.S., M.G.)
| | - S K Sethi
- MRI Institute for Biomedical Research (S.K.S., D.T.U., E.M.H.), Detroit, Michigan
| | - D T Utriainen
- MRI Institute for Biomedical Research (S.K.S., D.T.U., E.M.H.), Detroit, Michigan
| | - E M Haacke
- MRI Institute for Biomedical Research (S.K.S., D.T.U., E.M.H.), Detroit, Michigan
| | - P Zamboni
- Vascular Diseases Center (P.Z.), University of Ferrara, Ferrara, Italy
| | - M Ursino
- Department of Electrical, Electronic and Information Engineering (M.U.), University of Bologna, Bologna, Italy
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Sachla AJ, Ouattara M, Romero E, Agniswamy J, Weber IT, Gadda G, Eichenbaum Z. In vitro heme biotransformation by the HupZ enzyme from Group A streptococcus. Biometals 2016; 29:593-609. [PMID: 27154580 DOI: 10.1007/s10534-016-9937-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 05/01/2016] [Indexed: 01/14/2023]
Abstract
In Group A streptococcus (GAS), the metallorepressor MtsR regulates iron homeostasis. Here we describe a new MtsR-repressed gene, which we named hupZ (heme utilization protein). A recombinant HupZ protein was purified bound to heme from Escherichia coli grown in the presence of 5-aminolevulinic acid and iron. HupZ specifically binds heme with stoichiometry of 1:1. The addition of NADPH to heme-bound HupZ (in the presence of cytochrome P450 reductase, NADPH-regeneration system and catalase) triggered progressive decrease of the HupZ Soret band and the appearance of an absorption peak at 660 nm that was resistance to hydrolytic conditions. No spectral changes were observed when ferredoxin and ferredoxin reductase were used as redox partners. Differential spectroscopy with myoglobin or with the ferrous chelator, ferrozine, confirmed that carbon monoxide and free iron are produced during the reaction. ApoHupZ was crystallized as a homodimer with a split β-barrel conformation in each monomer comprising six β strands and three α helices. This structure resembles the split β-barrel domain shared by the members of a recently described family of heme degrading enzymes. However, HupZ is smaller and lacks key residues found in the proteins of the latter group. Phylogenetic analysis places HupZ on a clade separated from those for previously described heme oxygenases. In summary, we have identified a new GAS enzyme-containing split β-barrel and capable of heme biotransformation in vitro; to the best of our knowledge, this is the first enzyme among Streptococcus species with such activity.
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Affiliation(s)
- Ankita J Sachla
- Department of Biology, College of Arts and Sciences, Georgia State University, P.O. Box 4010, Atlanta, GA, 30302-4010, USA
| | - Mahamoudou Ouattara
- Department of Biology, College of Arts and Sciences, Georgia State University, P.O. Box 4010, Atlanta, GA, 30302-4010, USA
| | - Elvira Romero
- Department of Chemistry, College of Arts and Sciences, Georgia State University, Atlanta, GA, 30302-3965, USA
| | - Johnson Agniswamy
- Department of Biology, College of Arts and Sciences, Georgia State University, P.O. Box 4010, Atlanta, GA, 30302-4010, USA
| | - Irene T Weber
- Department of Biology, College of Arts and Sciences, Georgia State University, P.O. Box 4010, Atlanta, GA, 30302-4010, USA.,Department of Chemistry, College of Arts and Sciences, Georgia State University, Atlanta, GA, 30302-3965, USA.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, 30303, USA
| | - Giovanni Gadda
- Department of Biology, College of Arts and Sciences, Georgia State University, P.O. Box 4010, Atlanta, GA, 30302-4010, USA.,Department of Chemistry, College of Arts and Sciences, Georgia State University, Atlanta, GA, 30302-3965, USA.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, 30303, USA.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA
| | - Zehava Eichenbaum
- Department of Biology, College of Arts and Sciences, Georgia State University, P.O. Box 4010, Atlanta, GA, 30302-4010, USA.
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Abstract
Choline oxidase from Arthrobacter globiformis catalyzes the oxidation of choline to glycine betaine by using oxygen as an electron acceptor. A partially rate limiting isomerization of the reduced wild-type enzyme during the reaction with oxygen was previously detected using solvent viscosity effects. In this study, we hypothesized that the side chains of M62 and F357, located at the entrance to the active site of choline oxidase, may be related to the slow isomerization detected. We engineered a double-variant enzyme M62A/F357A. The kinetic characterization of the double-variant enzyme showed a lack of the isomerization detected in wild-type choline oxidase, and a lack of saturation with an oxygen concentration as high as 1 mM, while most other kinetic parameters were similar to those of wild-type choline oxidase. The kinetic characterization of the single-variant enzymes established that only the side chain of F357 plays a role in the isomerization of choline oxidase in the oxidative half-reaction. Molecular dynamics studies suggest that the slow isomerization related to F357 is possibly due to the participation of the phenyl ring in a newly proposed gating mechanism for a narrow tunnel, assumed to regulate the access of oxygen to the reduced cofactor.
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Affiliation(s)
- Francesca Salvi
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
| | - Isela Rodriguez
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
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Affiliation(s)
- Elvira Romero
- Department of Chemistry, ¶Department of Biology, ∥Center for Biotechnology
and Drug
Design, and #Center
for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Safieh Tork Ladani
- Department of Chemistry, ¶Department of Biology, ∥Center for Biotechnology
and Drug
Design, and #Center
for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department of Chemistry, ¶Department of Biology, ∥Center for Biotechnology
and Drug
Design, and #Center
for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Giovanni Gadda
- Department of Chemistry, ¶Department of Biology, ∥Center for Biotechnology
and Drug
Design, and #Center
for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
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Gadda G, Taibi A, Sisini F, Gambaccini M, Sethi SK, Utriainen D, Haacke EM, Zamboni P, Ursino M. A simulation model to study the role of the extracranial venous drainage pathways in intracranial hemodynamics. Annu Int Conf IEEE Eng Med Biol Soc 2016; 2015:7800-3. [PMID: 26738101 DOI: 10.1109/embc.2015.7320201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Alterations in the extracranial venous circulation due to posture changes, and/or extracranial venous obstructions in patients with vascular diseases, can have important implications on cerebral hemodynamics. A hemodynamic model for the study of cerebral venous outflow was developed to investigate the correlations between extracranial blood redistributions and changes in the intracranial environment. Flow data obtained with both magnetic resonance (MR) and Echo-Color Doppler (ECD) technique are used to validate the model. The very good agreement between simulated supine and upright flows and experimental results means that the model can correctly reproduce the main factors affecting the extracranial venous circulation.
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Barman A, Smitherman C, Souffrant M, Gadda G, Hamelberg D. Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins. J Chem Inf Model 2015; 56:139-47. [DOI: 10.1021/acs.jcim.5b00560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Arghya Barman
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Crystal Smitherman
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Michael Souffrant
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Giovanni Gadda
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
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Ball J, Bui QV, Gannavaram S, Gadda G. Importance of glutamate 87 and the substrate α-amine for the reaction catalyzed by d-arginine dehydrogenase. Arch Biochem Biophys 2015; 568:56-63. [DOI: 10.1016/j.abb.2015.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/16/2015] [Accepted: 01/20/2015] [Indexed: 10/24/2022]
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Smitherman C, Rungsrisuriyachai K, Germann MW, Gadda G. Identification of the Catalytic Base for Alcohol Activation in Choline Oxidase. Biochemistry 2014; 54:413-21. [DOI: 10.1021/bi500982y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Crystal Smitherman
- Department
of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug
Design, ∥Center for Diagnostics and Therapeutics, and ⊥Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Kunchala Rungsrisuriyachai
- Department
of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug
Design, ∥Center for Diagnostics and Therapeutics, and ⊥Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Markus W. Germann
- Department
of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug
Design, ∥Center for Diagnostics and Therapeutics, and ⊥Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Giovanni Gadda
- Department
of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug
Design, ∥Center for Diagnostics and Therapeutics, and ⊥Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-3965, United States
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Abstract
We developed a mathematical model of the cerebral venous outflow for the simulation of the average blood flows and pressures in the main drainage vessels of the brain. The main features of the model are that it includes a validated model for the simulation of the intracranial circulation and it accounts for the dependence of the hydraulic properties of the jugular veins with respect to the gravity field, which makes it an useful tool for the study of the correlations between extracranial blood redistributions and changes in the intracranial environment. The model is able to simulate the average pressures and flows in different points of the jugular ducts, taking into account the amount of blood coming from the anastomotic connections; simulate how the blood redistribution due to change of posture affects flows and pressures in specific points of the system; and simulate redistributions due to stenotic patterns. Sensitivity analysis to check the robustness of the model was performed. The model reproduces average physiologic behavior of the jugular, vertebral, and cerebral ducts in terms of pressures and flows. In fact, jugular flow drops from ∼11.7 to ∼1.4 ml/s in the passage from supine to standing. At the same time, vertebral flow increases from 0.8 to 3.4 ml/s, while cerebral blood flow, venous sinuses pressure, and intracranial pressure are constant around the average value of 12.5 ml/s, 6 mmHg, and 10 mmHg, respectively. All these values are in agreement with literature data.
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Affiliation(s)
- G Gadda
- Department of Physics and Earth Sciences, University of Ferrara, Ferrara, Italy;
| | - A Taibi
- Department of Physics and Earth Sciences, University of Ferrara, Ferrara, Italy
| | - F Sisini
- Department of Physics and Earth Sciences, University of Ferrara, Ferrara, Italy
| | - M Gambaccini
- Department of Physics and Earth Sciences, University of Ferrara, Ferrara, Italy
| | - P Zamboni
- Vascular Diseases Center, University of Ferrara, Ferrara, Italy; and
| | - M Ursino
- Department of Electrical, Electronic and Information Engineering, University of Bologna, Bologna, Italy
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