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1.
Small ; : e2310768, 2024 Feb 11.
Article in English | MEDLINE | ID: mdl-38342671

ABSTRACT

There is a noticeable gap in the literature regarding research on halogen-substitution-regulated ferroelectric semiconductors featuring multiple phase transitions. Here, a new category of 1D perovskite ferroelectrics (DFP)2 SbX5 (DFP+ = 3,3-difluoropyrrolidium, X- = I- , Br- , abbreviated as I-1 and Br-2) with twophase transitions (PTs) is reported. The first low-temperature PT is a mmmFmm2 ferroelectric PT, while the high-temperature PT is a counterintuitive inverse temperature symmetry-breaking PT. By the substitution of iodine with bromine, the Curie temperature (Tc) significantly increases from 348 K of I-1 to 374 K of Br-2. Their ferroelectricity and pyroelectricity are improved (Ps value from 1.3 to 4.0 µC cm-2 , pe value from 0.2 to 0.48 µC cm-2  K-1 for I-1 and Br-2), while their optical bandgaps increased from 2.1 to 2.7 eV. A critical slowing down phenomenon is observed in the dielectric measurement of I-1 while Br-2 exhibits the ferroelastic domain. Structural and computational analyses elucidate that the order-disorder movement of cations and the distortion of the chain perovskite [SbX5 ]2- anions skeleton lead to PT. The semiconductor properties are determined by [SbX5 ]2- anions. The findings contribute to the development of ferroelectric semiconductors and materials with multiple PTs and provide materials for potential applications in the optoelectronic field.

2.
Opt Express ; 32(2): 1231-1245, 2024 Jan 15.
Article in English | MEDLINE | ID: mdl-38297679

ABSTRACT

Comprehensive optical imaging of the intensity, phase, and birefringent information of the biological sample is important because important physical or pathological changes always accompany the changes in multiple optical parameters. Current studies lack such a metric that can present the comprehensive optical property of the sample in one figure. In this paper, a polarization state synthesis tomography (PoST) method, which is based on the principle of polarization state coherent synthesis and demodulation, is proposed to achieve full-field tomographic imaging of the comprehensive information (i.e., intensity, phase, and birefringence) of the biological sample. In this method, the synthesis of the polarization state is achieved by the time-domain full-field low coherence interferometer, where the polarization states of the sample beam and the reference beam are set to be orthogonal for the synthesis of the polarization state. The synthesis of the polarization state enables two functions of the PoST system: (1) Depth information of the sample can be encoded by the synthesized polarization state because only when the optical path length difference between the two arms is within the coherence length, a new polarization state can be synthesized; (2) Since the scattering coefficient, refractive index and the birefringent property of the sample can modulate the intensity and phase of the sample beam, the synthesized polarization state is sensitive to all these three parameters and can provide the comprehensive optical information of the sample. In this work, the depth-resolved ability and the comprehensive optical imaging metric have been demonstrated by the standard samples and the onion cells, demonstrating the potential application value of this method for further investigation of the important physical or pathological process of the biological tissues.

3.
Opt Lett ; 48(7): 1878-1881, 2023 Apr 01.
Article in English | MEDLINE | ID: mdl-37221789

ABSTRACT

To achieve non-invasive and high effective resolution microvascular imaging in vivo, photothermal modulation speckle optical coherence tomography (PMS-OCT) imaging technology is proposed in this Letter to enhance the speckle signal of the bloodstream for improving the imaging contrast and image quality in the deeper depth of Fourier domain optical coherence tomography (FD-OCT). The results of simulation experiments proved that this photothermal effect could disturb and enhance the speckle signals, because the photothermal effect could modulate the sample volume to expand and change the refractive index of tissues, leading to the change in the phase of interference light. Therefore, the speckle signal of the bloodstream will also change. With this technology we obtain a clear cerebral vascular nondestructive image of a chicken embryo at a certain imaging depth. This technology expands the application fields of optical coherence tomography (OCT) especially in more complex biological structures and tissues, such as the brain, and provides a new way, to the best of our knowledge, for the application of OCT in brain science.


Subject(s)
Brain , Tomography, Optical Coherence , Chick Embryo , Animals , Chickens , Computer Simulation , Embryo, Mammalian
4.
Opt Lett ; 48(18): 4757-4760, 2023 Sep 15.
Article in English | MEDLINE | ID: mdl-37707895

ABSTRACT

To achieve accurate selection and synchronous imaging of blood vessels and lymph, a speckle spectrum contrast method (SSC) based on spectral-domain optical coherence tomography (SD-OCT) is proposed in this Letter. In this method, the time-lapse optical coherence tomography (OCT) intensity signal is transformed to the Fourier frequency domain. By analyzing the frequency spectrum of the time-lapse OCT intensity signal, a parameter called SSC signal, which represents the ratio of different intervals of the high frequency to the low frequency, is utilized to extract and contrast different types of the vessels in the biological tissues. In the SSC spectrum, the SSC signals of the static tissue, lymphatic vessels, and vascular vessels can be separated in three different frequency intervals, enabling differentiation and synchronous imaging of the lymphatic-vascular vessels. A mouse ear was used to demonstrate the feasibility and efficiency of this method. By using the SSC signal as the imaging parameter, the lymphatic and blood vessels of the mouse ear are differentiated and visualized simultaneously. This study shows the feasibility of the three-dimensional (3D) synchronous angio-lymphography based on the SSC method, which provides a tool to improve the understanding for disease research and treatment.


Subject(s)
Lymphography , Tomography, Optical Coherence , Animals , Mice
5.
BMC Microbiol ; 22(1): 189, 2022 08 02.
Article in English | MEDLINE | ID: mdl-35918663

ABSTRACT

Despite the known influence of continuous cropping on soil microorganisms, little is known about the associated difference in the effects of continuous cropping on the community compositions of soil bacteria and fungi. Here, we assessed soil physicochemical property, as well as bacterial and fungal compositions across different years (Uncropped control, 1, 6, 11, 16, and 21 years) and in the watermelon system of a gravel mulch field in the Loess Plateau of China. Our results showed that long-term continuous cropping led to substantial shifts in soil bacterial and fungal compositions. The relative abundances of dominant bacterial and fungal genera (average relative abundance > 1.0%) significantly varied among different continuous cropping years (P < 0.05). Structural equation models demonstrated that continuous cropping alter soil bacterial and fungal compositions mainly by causing substantial variations in soil attributes. Variations in soil pH, nutrient, salinity, and moisture content jointly explained 73% and 64% of the variation in soil bacterial and fungal compositions, respectively. Variations in soil moisture content and pH caused by continuous cropping drove the shifts in soil bacterial and fungal compositions, respectively (Mantel R = 0.74 and 0.54, P < 0.01). Furthermore, the variation in soil bacterial and fungal composition showed significant correlation with watermelon yield reduction (P < 0.01). Together, long-term continuous cropping can alter soil microbial composition, and thereby influencing watermelon yield. Our findings are useful for alleviating continuous cropping obstacles and guiding agricultural production.


Subject(s)
Citrullus , Mycobiome , Bacteria/genetics , Biodiversity , Fungi/genetics , Rhizosphere , Soil/chemistry , Soil Microbiology
6.
Toxicol Appl Pharmacol ; 367: 62-70, 2019 03 15.
Article in English | MEDLINE | ID: mdl-30742845

ABSTRACT

Arsenic exposure increases the risk of various bone disorders. For instance, chronic exposure to low level arsenic can cause bone resorption by promoting osteoclast differentiation. Osteoclast precursor cells produce hydrogen peroxide after low level arsenic exposure and then undergo differentiation, producing cells which break down bone matrix. Nuclear factor E2-related factor 2 (Nrf2) regulates receptor activator of nuclear factor-κB dependent osteoclastogenesis by modulating intracellular reactive oxygen species (ROS) signaling via expression of cytoprotective enzymes. Here we tested the hypothesis that loss of Nrf2 will increase arsenic-induced bone loss. We treated 40 week-old Nrf2+/+ and Nrf2-/- mice with 5 ppm arsenic in the drinking water, which produces a blood arsenic level similar to humans living in areas where arsenic exposure is endemic. After 4 months, Micro-CT and dual-energy x-ray analysis revealed a drastic overall decrease in the bone volume with arsenic treatment in mice lacking Nrf2. Deficiency of Nrf2 in RAW 264.7 cells or bone marrow-derived macrophages (BMMs) promoted arsenic-induced osteoclast differentiation. Lack of Nrf2 increases arsenic-induced ROS levels and phosphorylation of p38. N-Acetyl-cysteine and SB203580 pretreatment essentially abolished arsenic-induced phosphorylation of p38 and reversed arsenic-induced increased osteoclast differentiation in Nrf2 deficiency. Taken together, our data suggest that loss of Nrf2 causes increased oxidative stress and enhanced susceptibility to arsenic-induced bone loss.


Subject(s)
Arsenites/toxicity , Bone Remodeling/drug effects , Femur/drug effects , NF-E2-Related Factor 2/deficiency , Osteoclasts/drug effects , Osteogenesis/drug effects , Osteoporosis/chemically induced , Sodium Compounds/toxicity , Animals , Female , Femur/metabolism , Femur/pathology , Mice , Mice, Inbred C57BL , Mice, Knockout , NF-E2-Related Factor 2/genetics , Osteoclasts/metabolism , Osteoclasts/pathology , Osteoporosis/genetics , Osteoporosis/metabolism , Osteoporosis/pathology , Oxidative Stress/drug effects , RAW 264.7 Cells , Signal Transduction/drug effects
8.
J Biol Chem ; 290(30): 18293-303, 2015 Jul 24.
Article in English | MEDLINE | ID: mdl-26041781

ABSTRACT

Electron transfer reactions among three prominent colored proteins in intact cells of Acidithiobacillus ferrooxidans were monitored using an integrating cavity absorption meter that permitted the acquisition of accurate absorbance data in suspensions of cells that scattered light. The concentrations of proteins in the periplasmic space were estimated to be 350 and 25 mg/ml for rusticyanin and cytochrome c, respectively; cytochrome a was present as one molecule for every 91 nm(2) in the cytoplasmic membrane. All three proteins were rapidly reduced to the same relative extent when suspensions of live bacteria were mixed with different concentrations of ferrous ions at pH 1.5. The subsequent molecular oxygen-dependent oxidation of the multicenter respiratory chain occurred with a single macroscopic rate constant, regardless of the proteins' in vitro redox potentials or their putative positions in the aerobic iron respiratory chain. The crowded electron transport proteins in the periplasm of the organism constituted an electron conductive medium where the network of protein interactions functioned in a concerted fashion as a single ensemble with a standard reduction potential of 650 mV. The appearance of product ferric ions was correlated with the reduction levels of the periplasmic electron transfer proteins; the limiting first-order catalytic rate constant for aerobic respiration on iron was 7,400 s(-1). The ability to conduct direct spectrophotometric studies under noninvasive physiological conditions represents a new and powerful approach to examine the extent and rates of biological events in situ without disrupting the complexity of the live cellular environment.


Subject(s)
Acidithiobacillus/metabolism , Electron Transport , Iron/metabolism , Oxidation-Reduction , Acidithiobacillus/chemistry , Aerobiosis , Cytochromes a/metabolism , Cytochromes c/metabolism , Iron/chemistry , Kinetics
9.
Proteins ; 83(1): 178-87, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25392945

ABSTRACT

Human α-amino-ß-carboxymuconate-ε-semialdehyde decarboxylase determines the fate of tryptophan metabolites in the kynurenine pathway by controlling the quinolinate levels for de novo nicotinamide adenine dinucleotide biosynthesis. The unstable nature of its substrate has made gaining insight into its reaction mechanism difficult. Our electron paramagnetic resonance (EPR) spectroscopic study on the Cu-substituted human enzyme suggests that the native substrate does not directly ligate to the metal ion. Substrate binding did not result in a change of either the hyperfine structure or the super-hyperfine structure of the EPR spectrum. We also determined the crystal structure of the human enzyme in its native catalytically active state (at 1.99 Å resolution), a substrate analogue-bound form (2.50 Å resolution), and a selected active site mutant form with one of the putative substrate binding residues altered (2.32 Å resolution). These structures illustrate that each asymmetric unit contains three pairs of dimers. Consistent with the EPR findings, the ligand-bound complex structure shows that the substrate analogue does not directly coordinate to the metal ion but is bound to the active site by two arginine residues through noncovalent interactions.


Subject(s)
Carboxy-Lyases/chemistry , Carboxy-Lyases/metabolism , Models, Molecular , Biocatalysis , Catalytic Domain , Crystallography, X-Ray , Electron Spin Resonance Spectroscopy , Escherichia coli/metabolism , Humans , Protein Multimerization , Substrate Specificity , Temperature , Zinc/metabolism
10.
J Virol ; 88(17): 9605-15, 2014 Sep 01.
Article in English | MEDLINE | ID: mdl-24920818

ABSTRACT

UNLABELLED: Helper T-cell epitope dominance in human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp120 is not adequately explained by peptide binding to major histocompatibility complex (MHC) proteins. Antigen processing potentially influences epitope dominance, but few, if any, studies have attempted to reconcile the influences of antigen processing and MHC protein binding for all helper T-cell epitopes of an antigen. Epitopes of gp120 identified in both humans and mice occur on the C-terminal flanks of flexible segments that are likely to be proteolytic cleavage sites. In this study, the influence of gp120 conformation on the dominance pattern in gp120 from HIV strain 89.6 was examined in CBA mice, whose MHC class II protein has one of the most well defined peptide-binding preferences. Only one of six dominant epitopes contained the most conserved element of the I-Ak binding motif, an aspartic acid. Destabilization of the gp120 conformation by deletion of single disulfide bonds preferentially enhanced responses to the cryptic I-Ak motif-containing sequences, as reported by T-cell proliferation or cytokine secretion. Conversely, inclusion of CpG in the adjuvant with gp120 enhanced responses to the dominant CD4+ T-cell epitopes. The gp120 destabilization affected secretion of some cytokines more than others, suggesting that antigen conformation could modulate T-cell functions through mechanisms of antigen processing. IMPORTANCE: CD4+ helper T cells play an essential role in protection against HIV and other pathogens. Thus, the sites of helper T-cell recognition, the dominant epitopes, are targets for vaccine design; and the corresponding T cells may provide markers for monitoring infection and immunity. However, T-cell epitopes are difficult to identify and predict. It is also unclear whether CD4+ T cells specific for one epitope are more protective than T cells specific for other epitopes. This work shows that the three-dimensional (3D) structure of an HIV protein partially determines which epitopes are dominant, most likely by controlling the breakdown of HIV into peptides. Moreover, some types of signals from CD4+ T cells are affected by the HIV protein 3D structure; and thus the protectiveness of a particular peptide vaccine could be related to its location in the 3D structure.


Subject(s)
Epitopes/chemistry , Epitopes/immunology , HIV Envelope Protein gp120/chemistry , HIV Envelope Protein gp120/immunology , Histocompatibility Antigens Class II/metabolism , Animals , Epitopes/metabolism , Female , HIV Envelope Protein gp120/metabolism , Mice, Inbred CBA , Protein Binding , Protein Conformation , Protein Stability
11.
Biochemistry ; 51(29): 5811-21, 2012 Jul 24.
Article in English | MEDLINE | ID: mdl-22746257

ABSTRACT

The previously reported crystal structures of α-amino-ß-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD) show a five-coordinate Zn(II)(His)(3)(Asp)(OH(2)) active site. The water ligand is H-bonded to a conserved His228 residue adjacent to the metal center in ACMSD from Pseudomonas fluorescens (PfACMSD). Site-directed mutagenesis of His228 to tyrosine and glycine in this study results in a complete or significant loss of activity. Metal analysis shows that H228Y and H228G contain iron rather than zinc, indicating that this residue plays a role in the metal selectivity of the protein. As-isolated H228Y displays a blue color, which is not seen in wild-type ACMSD. Quinone staining and resonance Raman analyses indicate that the blue color originates from Fe(III)-tyrosinate ligand-to-metal charge transfer. Co(II)-substituted H228Y ACMSD is brown in color and exhibits an electron paramagnetic resonance spectrum showing a high-spin Co(II) center with a well-resolved (59)Co (I = 7/2) eight-line hyperfine splitting pattern. The X-ray crystal structures of as-isolated Fe-H228Y (2.8 Å) and Co-substituted (2.4 Å) and Zn-substituted H228Y (2.0 Å resolution) support the spectroscopic assignment of metal ligation of the Tyr228 residue. The crystal structure of Zn-H228G (2.6 Å) was also determined. These four structures show that the water ligand present in WT Zn-ACMSD is either missing (Fe-H228Y, Co-H228Y, and Zn-H228G) or disrupted (Zn-H228Y) in response to the His228 mutation. Together, these results highlight the importance of His228 for PfACMSD's metal specificity as well as maintaining a water molecule as a ligand of the metal center. His228 is thus proposed to play a role in activating the metal-bound water ligand for subsequent nucleophilic attack on the substrate.


Subject(s)
Carboxy-Lyases/genetics , Carboxy-Lyases/metabolism , Histidine/genetics , Histidine/metabolism , Pseudomonas fluorescens/enzymology , Pseudomonas fluorescens/genetics , Carboxy-Lyases/chemistry , Catalytic Domain , Crystallography, X-Ray , Dihydroxyphenylalanine/metabolism , Ferric Compounds/chemistry , Ferric Compounds/metabolism , Histidine/chemistry , Metals/metabolism , Models, Molecular , Mutagenesis, Site-Directed , Point Mutation , Pseudomonas fluorescens/chemistry , Substrate Specificity
12.
Bioorg Chem ; 43: 2-14, 2012 Aug.
Article in English | MEDLINE | ID: mdl-22534166

ABSTRACT

This review examines the mechanisms propelling cofactor-independent, organic cofactor-dependent and metal-dependent decarboxylase chemistry. Decarboxylation, the removal of carbon dioxide from organic acids, is a fundamentally important reaction in biology. Numerous decarboxylase enzymes serve as key components of aerobic and anaerobic carbohydrate metabolism and amino acid conversion. In the past decade, our knowledge of the mechanisms enabling these crucial decarboxylase reactions has continued to expand and inspire. This review focuses on the organic cofactors biotin, flavin, NAD, pyridoxal 5'-phosphate, pyruvoyl, and thiamin pyrophosphate as catalytic centers. Significant attention is also placed on the metal-dependent decarboxylase mechanisms.


Subject(s)
Carboxy-Lyases/metabolism , Amino Acids/metabolism , Animals , Biotin/metabolism , Carbohydrate Metabolism , Carboxy-Lyases/chemistry , Decarboxylation , Flavins/metabolism , Free Radicals/metabolism , Metals/chemistry , Metals/metabolism , NAD/metabolism , Pyridoxal Phosphate/metabolism , Thiamine Pyrophosphate/metabolism
13.
Biomed Opt Express ; 13(10): 5390-5399, 2022 Oct 01.
Article in English | MEDLINE | ID: mdl-36425642

ABSTRACT

Lymphatic vessels are structurally similar to blood vessels, and the lymphatic fluid flowing within the lymphatic vessels is distributed throughout the body and plays a vital role in the human immune system. Visualization of the lymphatic vessels is clinically important in the diagnosis of tumor cell metastasis and related immune system diseases, but lymph is difficult to image due to its near-transparent nature and low flow rate. In this paper, we present a lymphography method based on time-autocorrelated optical coherence tomography. By using the minimum value difference of the autocorrelation function of the time-varying interference intensity between the lymph and the surrounding tissues, the non-invasive and high-sensitivity imaging of lymph vessels can be achieved. The method proposed in this paper has potential significance for the research and treatment of immune system diseases.

14.
J Biol Chem ; 285(28): 21679-88, 2010 Jul 09.
Article in English | MEDLINE | ID: mdl-20448033

ABSTRACT

The Escherichia coli Hsp40 DnaJ uses its J-domain (Jd) to couple ATP hydrolysis and client protein capture in Hsp70 DnaK. Fusion of the Jd to peptide p5 (as in Jdp5) dramatically increases the apparent affinity of the p5 moiety for DnaK in the presence of ATP, and Jdp5 stimulates ATP hydrolysis in DnaK by several orders of magnitude. NMR experiments with [(15)N]Jdp5 demonstrated that the peptide tethers the Jd to the ATPase domain. Thus, ATP hydrolysis and client protein binding in DnaK are coupled principally through the association of the client with DnaJ. Overexpression of a recombinant Jd was specifically toxic to cells that simultaneously expressed DnaK. No toxicity was observed when overexpressing Jdp5 or mutant Jd or when co-overexpressing the Jd and the nucleotide exchange factor GrpE. The results suggest that the Jd shifts DnaK to a client-bound form by stimulating the DnaK ATPase but only when the Jd is brought to DnaK by a client-Hsp40 complex.


Subject(s)
Adenosine Triphosphatases/chemistry , Escherichia coli/enzymology , HSP40 Heat-Shock Proteins/chemistry , HSP70 Heat-Shock Proteins/chemistry , Chaperonins/chemistry , Escherichia coli Proteins/chemistry , Hydrolysis , Magnetic Resonance Spectroscopy , Molecular Chaperones , Mutation , Protein Binding , Protein Structure, Tertiary , Recombinant Proteins/chemistry
15.
Biochemistry ; 45(35): 10412-21, 2006 Sep 05.
Article in English | MEDLINE | ID: mdl-16939194

ABSTRACT

Alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase (ACMSD) is a widespread enzyme found in many bacterial species and all currently sequenced eukaryotic organisms. It occupies a key position at the branching point of two metabolic pathways: the tryptophan to quinolinate pathway and the bacterial 2-nitrobenzoic acid degradation pathway. The activity of ACMSD determines whether the metabolites in both pathways are converted to quinolinic acid for NAD biosynthesis or to acetyl-CoA for the citric acid cycle. Here we report the first high-resolution crystal structure of ACMSD from Pseudomonas fluorescens which validates our previous predictions that this enzyme is a member of the metal-dependent amidohydrolase superfamily of the (beta/alpha)(8) TIM barrel fold. The structure of the enzyme in its native form, determined at 1.65 A resolution, reveals the precise spatial arrangement of the active site metal center and identifies a potential substrate-binding pocket. The identity of the native active site metal was determined to be Zn. Also determined was the structure of the enzyme complexed with cobalt at 2.50 A resolution. The hydrogen bonding network around the metal center suggests that Arg51 and His228 may play important roles in catalysis. The metal center configuration of PfACMSD is very similar to that of Zn-dependent adenosine deaminase and Fe-dependent cytosine deaminase, suggesting that ACMSD may share certain similarities in its catalytic mechanism with these enzymes. These data enable us to propose possible catalytic mechanisms for ACMSD which appear to be unprecedented among all currently characterized decarboxylases.


Subject(s)
Carboxy-Lyases/chemistry , Carboxy-Lyases/genetics , Pseudomonas fluorescens/enzymology , Binding Sites , Carboxy-Lyases/physiology , Catalysis , Coenzymes/chemistry , Crystallography, X-Ray , Decarboxylation , Metals , Models, Chemical , Molecular Sequence Data , Protein Structure, Secondary , Sequence Homology, Amino Acid , Structure-Activity Relationship
16.
Biochemistry ; 45(21): 6628-34, 2006 May 30.
Article in English | MEDLINE | ID: mdl-16716073

ABSTRACT

The enzymatic activity of Pseudomonas fluorescens alpha-amino-beta-carboxymuconic-epsilon-semialdehyde decarboxylase (ACMSD) is critically dependent on a transition metal ion [Li, T., Walker, A. L., Iwaki, H., Hasegawa, Y., and Liu, A. (2005) J. Am. Chem. Soc. 127, 12282-12290]. Sequence analysis in this study further suggests that ACMSD belongs to the amidohydrolase superfamily, whose structurally characterized members comprise a catalytically essential metal cofactor. To identify ACMSD's metal ligands and assess their functions in catalysis, a site-directed mutagenesis analysis was conducted. Alteration of His-9, His-177, and Asp-294 resulted in a dramatic loss of enzyme activity, substantial reduction of the metal-binding ability, and an altered metallocenter electronic structure. Thus, these residues are confirmed to be the endogenous metal ligands. His-11 is implicated in metal binding because of the strictly conserved HxH motif with His-9. Mutations at the 228 site yielded nearly inactive enzyme variants H228A and H228E. The two His-228 mutant proteins, however, exhibited full metal-binding ability and a metal center similar to that of the wild-type enzyme as shown by EPR spectroscopy. Kinetic analysis on the mutants indicates that His-228 is a critical catalytic residue along with the metal cofactor. Since the identified metal ligands and His-228 are present in all known ACMSD sequences, it is likely that ACMSD proteins from other organisms contain the same cofactor and share similar catalytic mechanisms. ACMSD is therefore the first characterized member in the amidohydrolase superfamily that represents a C-C breaking activity.


Subject(s)
Amidohydrolases/chemistry , Carboxy-Lyases/metabolism , Amino Acid Sequence , Base Sequence , Carboxy-Lyases/chemistry , Carboxy-Lyases/genetics , DNA Primers , Escherichia coli/growth & development , Molecular Sequence Data , Mutagenesis, Site-Directed , Plasmids , Sequence Homology, Amino Acid
17.
J Am Chem Soc ; 127(35): 12282-90, 2005 Sep 07.
Article in English | MEDLINE | ID: mdl-16131206

ABSTRACT

The enzyme alpha-amino-beta-carboxy-muconic-epsilon-semialdehyde decarboxylase (ACMSD) plays an important role in the biodegradation of 2-nitrobenzoic acid in microorganisms and in tryptophan catabolism in humans. We report that the overexpressed ACMSD enzyme from Pseudomonas fluorescens requires a divalent metal, such as Co(II), Fe(II), Cd(II), or Mn(II), for catalytic activity and that neither a redox reagent nor an organic cofactor is required for the catalytic function. The metal ions can be taken up in either cell or cell-free preparations for generating the active form of ACMSD. The kinetic parameters and enzyme specific activity are shown to depend on the metal ion present in the enzyme, suggesting a catalytic role of the metal center. EPR spectrum of Co(II)-ACMSD provides a high-spin (S = 3/2 mononuclear metal ion in a non-heme, noncorrinoid environment with a mixed nitrogen/oxygen ligand field. We observe hyperfine interactions due to 59Co nucleus at temperatures below 5 K but not at higher temperatures. Ten hyperfine lines are present in the g(perpendicular) region, and three equivalent nitrogen hyperfine couplings are required to simulate the resonances in the EPR spectrum. The results for the metal binding site are also assessed using the copper-substituted enzyme, and the EPR spectral assignments for both cobalt and copper proteins give strong support for a distorted trigonal bipyramidal geometry of the metal center. Ultimately, these results suggest for the first time that ACMSD is a metal-dependent enzyme that catalyzes a novel nonoxidative decarboxylation.


Subject(s)
Carboxy-Lyases/chemistry , Metals/chemistry , Pseudomonas fluorescens/chemistry , Binding Sites , Cadmium/chemistry , Cadmium/metabolism , Carboxy-Lyases/metabolism , Catalysis , Cations, Divalent/chemistry , Cations, Divalent/metabolism , Cobalt/chemistry , Cobalt/metabolism , Decarboxylation , Electron Spin Resonance Spectroscopy/methods , Enzyme Activation , Humans , Iron/chemistry , Iron/metabolism , Kinetics , Ligands , Manganese/chemistry , Manganese/metabolism , Metals/metabolism , Oxidation-Reduction , Temperature
18.
Arch Biochem Biophys ; 442(1): 82-91, 2005 Oct 01.
Article in English | MEDLINE | ID: mdl-16150418

ABSTRACT

(S)-2-Hydroxylpropanylphosphonic acid epoxidase (HppE) is a novel type of mononuclear non-heme iron-dependent enzyme that catalyzes the O2 coupled, oxidative epoxide ring closure of HPP to form fosfomycin, which is a clinically useful antibiotic. Sequence alignment of the only two known HppE sequences led to the speculation that the conserved residues His138, Glu142, and His180 are the metal binding ligands of the Streptomyces wedmorensis enzyme. Substitution of these residues with alanine resulted in significant reduction of metal binding affinity, as indicated by EPR analysis of the enzyme-Fe(II)-substrate-nitrosyl complex and the spectral properties of the Cu(II)-reconstituted mutant proteins. The catalytic activities for both epoxidation and self-hydroxylation were also either eliminated or diminished in proportion to the iron content in these mutants. The complete loss of enzymatic activity for the E142A and H180A mutants in vivo and in vitro is consistent with the postulated roles of the altered residues in metal binding. The H138A mutant is also inactive in vivo, but in vitro it retains 27% of the active site iron and nearly 20% of the wild-type activity. Thus, it cannot be unequivocally stated whether H138 is an iron ligand or simply facilitates iron binding due to proximity. The results reported herein provide initial evidence implicating an unusual histidine/carboxylate iron ligation in HppE. By analogy with other well-characterized enzymes from the 2-His-1-carboxylate family, this type of iron core is consistent with a mechanism in which both oxygen and HPP bind to the iron as a first step in the in the conversion of HPP to fosfomycin.


Subject(s)
Iron/metabolism , Mutagenesis, Site-Directed , Oxidoreductases/metabolism , Streptomyces/enzymology , Amino Acid Sequence , Amino Acids/chemistry , Amino Acids/metabolism , Base Sequence , Binding Sites , Catalysis , Copper/chemistry , Copper/metabolism , Electron Spin Resonance Spectroscopy , Enzyme Activation , Fosfomycin/biosynthesis , Fosfomycin/chemistry , Iron/chemistry , Ligands , Molecular Sequence Data , Mutation , Oxidoreductases/chemistry , Oxidoreductases/genetics , Oxygen/chemistry , Oxygen/metabolism
19.
Biochemistry ; 44(21): 7623-31, 2005 May 31.
Article in English | MEDLINE | ID: mdl-15909977

ABSTRACT

3-Hydroxyanthranilate-3,4-dioxygenase (HAD) is a non-heme Fe(II) dependent enzyme that catalyzes the oxidative ring-opening of 3-hydroxyanthranilate to 2-amino-3-carboxymuconic semialdehyde. The enzymatic product subsequently cyclizes to quinolinate, an intermediate in the biosynthesis of nicotinamide adenine dinucleotide. Quinolinate has also been implicated in important neurological disorders. Here, we describe the mechanism by which 4-chloro-3-hydroxyanthranilate inhibits the HAD catalyzed reaction. Using overexpressed and purified bacterial HAD, we demonstrate that 4-chloro-3-hydroxyanthranilate functions as a mechanism-based inactivating agent. The inactivation results in the consumption of 2 +/- 0.8 equiv of oxygen and the production of superoxide. EPR analysis of the inactivation reaction demonstrated that the inhibitor stimulated the oxidation of the active site Fe(II) to the catalytically inactive Fe(III) oxidation state. The inactivated enzyme can be reactivated by treatment with DTT and Fe(II). High resolution ESI-FTMS analysis of the inactivated enzyme demonstrated that the inhibitor did not form an adduct with the enzyme and that four conserved cysteines were oxidized to two disulfides (Cys125-Cys128 and Cys162-Cys165) during the inactivation reaction. These results are consistent with a mechanism in which the enzyme, complexed to the inhibitor and O2, generates superoxide which subsequently dissociates, leaving the inhibitor and the oxidized iron center at the active site.


Subject(s)
3-Hydroxyanthranilic Acid/analogs & derivatives , 3-Hydroxyanthranilic Acid/chemistry , Dioxygenases/antagonists & inhibitors , Enzyme Inhibitors/chemistry , Ralstonia/enzymology , 3-Hydroxyanthranilate 3,4-Dioxygenase , Amino Acid Sequence , Dioxygenases/biosynthesis , Dioxygenases/genetics , Dioxygenases/isolation & purification , Disulfides/chemistry , Dithionitrobenzoic Acid , Enzyme Activation/genetics , Escherichia coli/enzymology , Escherichia coli/genetics , Mass Spectrometry , Molecular Sequence Data , Oxygen Consumption/genetics , Spectrometry, Mass, Electrospray Ionization , Substrate Specificity/genetics , Superoxides/metabolism
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