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Amirahmadi M, Hosseinkhani S, Hosseini M, Yaghmei P, Heydari A. Fe 3O 4@SiO 2@NiAl-LDH microspheres implication in separation, kinetic and structural properties of phenylalanine dehydrogenase. Heliyon 2023; 9:e19429. [PMID: 37809670 PMCID: PMC10558515 DOI: 10.1016/j.heliyon.2023.e19429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/12/2023] [Accepted: 08/22/2023] [Indexed: 10/10/2023] Open
Abstract
Fe3O4@SiO2@NiAl-LDH three-components microsphere contains a Fe3O4@SiO2 magnetic core and a layered double hydroxide with nickel cation provide the binding ability to (His)-tagged-protein and exhibits high performance in protein separation and purification. The morphology and chemistry of the synthesized Fe3O4@SiO2@NiAl-LDH microspheres were characterized by energy-dispersive X-ray spectroscopy (EDX), scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared (FTIR), vibrating sample magnetometer (VSM), Dynamic light scattering (DLS). Purified enzyme was assesed with SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis and intrinsic fluorescence spectroscopy. In this study, the separation of phenylalanine dehydrogenase (PheDH) by Fe3O4@SiO2@NiAl -LDH was performed and the effect of microsphere was investigated on the kinetic and structural properties of PheDH. After purification, kinetic parameters such as Km, Vmax, Kcat, kcat/Km, optimum temperature, thermal stability, and and activation energy were evaluated and compared according to the mentioned methods. The interaction between the enzyme and the microsphere displayed a high performance in protein binding capacity. The results also revealed that the kinetic parameters of the enzyme changed in a dose-dependent manner in the presence of a microsphere. Moreover, the results of intrinsic fluorescence and Circular Dichroism (CD) confirmed the structural changes of the protein in the interaction with the microsphere.
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Affiliation(s)
- Mozhgan Amirahmadi
- Department of Biochemistry, Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-175, Iran
| | - Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran 1417614418, Iran
| | - Paricher Yaghmei
- Department of Biochemistry, Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Akbar Heydari
- Chemistry Department, Tarbiat Modares University, P.O. Box 14155-4838, Tehran, Iran
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Vedel IM, Prestel A, Zhang Z, Skawinska NT, Stark H, Harris P, Kragelund BB, Peters GHJ. Structural characterization of human tryptophan hydroxylase 2 reveals that L-Phe is superior to L-Trp as the regulatory domain ligand. Structure 2023:S0969-2126(23)00127-2. [PMID: 37119821 DOI: 10.1016/j.str.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/03/2023] [Accepted: 04/04/2023] [Indexed: 05/01/2023]
Abstract
Tryptophan hydroxylase 2 (TPH2) catalyzes the rate-limiting step in serotonin biosynthesis in the brain. Consequently, regulation of TPH2 is relevant for serotonin-related diseases, yet the regulatory mechanism of TPH2 is poorly understood and structural and dynamical insights are missing. We use NMR spectroscopy to determine the structure of a 47 N-terminally truncated variant of the regulatory domain (RD) dimer of human TPH2 in complex with L-Phe, and show that L-Phe is the superior RD ligand compared with the natural substrate, L-Trp. Using cryo-EM, we obtain a low-resolution structure of a similarly truncated variant of the complete tetrameric enzyme with dimerized RDs. The cryo-EM two-dimensional (2D) class averages additionally indicate that the RDs are dynamic in the tetramer and likely exist in a monomer-dimer equilibrium. Our results provide structural information on the RD as an isolated domain and in the TPH2 tetramer, which will facilitate future elucidation of TPH2's regulatory mechanism.
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Affiliation(s)
- Ida M Vedel
- Department of Chemistry, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Andreas Prestel
- Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark
| | - Zhenwei Zhang
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Natalia T Skawinska
- Department of Chemistry, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Pernille Harris
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Birthe B Kragelund
- Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark.
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
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Fitzpatrick PF. The aromatic amino acid hydroxylases: Structures, catalysis, and regulation of phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase. Arch Biochem Biophys 2023; 735:109518. [PMID: 36639008 DOI: 10.1016/j.abb.2023.109518] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/01/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023]
Abstract
The aromatic amino acid hydroxylases phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase are non-heme iron enzymes that catalyze key physiological reactions. This review discusses the present understanding of the common catalytic mechanism of these enzymes and recent advances in understanding the relationship between their structures and their regulation.
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Affiliation(s)
- Paul F Fitzpatrick
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, 78229, USA.
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Arturo EC, Merkel GW, Hansen MR, Lisowski S, Almeida D, Gupta K, Jaffe EK. Manipulation of a cation-π sandwich reveals conformational flexibility in phenylalanine hydroxylase. Biochimie 2021; 183:63-77. [PMID: 33221376 PMCID: PMC9856217 DOI: 10.1016/j.biochi.2020.11.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/04/2020] [Accepted: 11/10/2020] [Indexed: 01/24/2023]
Abstract
Phenylalanine hydroxylase (PAH) is an allosteric enzyme that maintains phenylalanine (Phe) below neurotoxic levels; its failure results in phenylketonuria, an inborn error of amino acid metabolism. Wild type (WT) PAH equilibrates among resting-state (RS-PAH) and activated (A-PAH) conformations, whose equilibrium position depends upon allosteric Phe binding. The RS-PAH conformation of WT rat PAH (rPAH) contains a cation-π sandwich involving Phe80 that cannot exist in the A-PAH conformation. Phe80 variants F80A, F80D, F80L, and F80R were prepared and evaluated using native PAGE, size exclusion chromatography, ion exchange behavior, intrinsic protein fluorescence, enzyme kinetics, and limited proteolysis, each as a function of [Phe]. Like WT rPAH, F80A and F80D show allosteric activation by Phe while F80L and F80R are constitutively active. Maximal activity of all variants suggests relief of a rate-determining conformational change. Limited proteolysis of WT rPAH (minus Phe) reveals facile cleavage within a 4-helix bundle that is buried in the RS-PAH tetramer interface, reflecting dynamic dissociation of that tetramer. This cleavage is not seen for the Phe80 variants, which all show proteolytic hypersensitivity in a linker that repositions during the RS-PAH to A-PAH interchange. Hypersensitivity is corrected by addition of Phe such that all variants become like WT rPAH and achieve the A-PAH conformation. Thus, manipulation of Phe80 perturbs the conformational space sampled by PAH, increasing sampling of on-pathway intermediates in the RS-PAH and A-PAH interchange. The behavior of the Phe80 variants mimics that of disease-associated R68S and suggests a molecular basis for proteolytic susceptibility in PKU-associated human PAH variants.
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Affiliation(s)
- Emilia C. Arturo
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, 10111,Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102
| | - George W. Merkel
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, 10111
| | - Michael R. Hansen
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, 10111
| | - Sophia Lisowski
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, 10111
| | - Deeanne Almeida
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, 10111
| | - Kushol Gupta
- Department pf Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Eileen K. Jaffe
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, 10111,To whom correspondence should be addressed: Eileen K. Jaffe: Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111; ; Tel.(215) 728-3695; Fax. (215) 728-2412
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Arturo EC, Gupta K, Hansen MR, Borne E, Jaffe EK. Biophysical characterization of full-length human phenylalanine hydroxylase provides a deeper understanding of its quaternary structure equilibrium. J Biol Chem 2019; 294:10131-10145. [PMID: 31076506 PMCID: PMC6664189 DOI: 10.1074/jbc.ra119.008294] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/09/2019] [Indexed: 11/06/2022] Open
Abstract
Dysfunction of human phenylalanine hydroxylase (hPAH, EC 1.14.16.1) is the primary cause of phenylketonuria, the most common inborn error of amino acid metabolism. The dynamic domain rearrangements of this multimeric protein have thwarted structural study of the full-length form for decades, until now. In this study, a tractable C29S variant of hPAH (C29S) yielded a 3.06 Å resolution crystal structure of the tetrameric resting-state conformation. We used size-exclusion chromatography in line with small-angle X-ray scattering (SEC-SAXS) to analyze the full-length hPAH solution structure both in the presence and absence of Phe, which serves as both substrate and allosteric activators. Allosteric Phe binding favors accumulation of an activated PAH tetramer conformation, which is biophysically distinct in solution. Protein characterization with enzyme kinetics and intrinsic fluorescence revealed that the C29S variant and hPAH are otherwise equivalent in their response to Phe, further supported by their behavior on various chromatography resins and by analytical ultracentrifugation. Modeling of resting-state and activated forms of C29S against SAXS data with available structural data created and evaluated several new models for the transition between the architecturally distinct conformations of PAH and highlighted unique intra- and inter-subunit interactions. Three best-fitting alternative models all placed the allosteric Phe-binding module 8-10 Å farther from the tetramer center than do all previous models. The structural insights into allosteric activation of hPAH reported here may help inform ongoing efforts to treat phenylketonuria with novel therapeutic approaches.
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Affiliation(s)
- Emilia C Arturo
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111
- the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, and
| | - Kushol Gupta
- the Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Michael R Hansen
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111
| | - Elias Borne
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111
| | - Eileen K Jaffe
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111,
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