1
|
Podgorski MN, Lee JHZ, Harbort JS, Nguyen GTH, Doherty DZ, Donald WA, Harmer JR, Bruning JB, Bell SG. Characterisation of the heme aqua-ligand coordination environment in an engineered peroxygenase cytochrome P450 variant. J Inorg Biochem 2023; 249:112391. [PMID: 37837941 DOI: 10.1016/j.jinorgbio.2023.112391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023]
Abstract
The cytochrome P450 enzymes (CYPs) are heme-thiolate monooxygenases that catalyse the insertion of an oxygen atom into the C-H bonds of organic molecules. In most CYPs, the activation of dioxygen by the heme is aided by an acid-alcohol pair of residues located in the I-helix of the enzyme. Mutation of the threonine residue of this acid-alcohol pair of CYP199A4, from the bacterium Rhodospeudomonas palustris HaA2, to a glutamate residue induces peroxygenase activity. In the X-ray crystal structures of this variant an interaction of the glutamate side chain and the distal aqua ligand of the heme was observed and this results in this ligand not being readily displaced in the peroxygenase mutant on the addition of substrate. Here we use a range of bulky hydrophobic and nitrogen donor containing ligands in an attempt to displace the distal aqua ligand of the T252E mutant of CYP199A4. Ligand binding was assessed by UV-visible absorbance spectroscopy, native mass spectrometry, electron paramagnetic resonance and X-ray crystallography. None of the ligands tested, even the nitrogen donor ligands which bind directly to the iron in the wild-type enzyme, resulted in displacement of the aqua ligand. Therefore, modification of the I-helix threonine residue to a glutamate residue results in a significant strengthening of the ferric distal aqua ligand. This ligand was not displaced using any of the ligands during this study and this provides a rationale as to why this mutant can shutdown the monooxygenase pathway of this enzyme and switch to peroxygenase activity.
Collapse
Affiliation(s)
- Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Joel H Z Lee
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Joshua S Harbort
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia
| | - Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Daniel Z Doherty
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jeffrey R Harmer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia.
| |
Collapse
|
2
|
Frkic RL, Pederick JL, Horsfall AJ, Jovcevski B, Crame EE, Kowalczyk W, Pukala TL, Chang MR, Zheng J, Blayo AL, Abell AD, Kamenecka TM, Harbort JS, Harmer JR, Griffin PR, Bruning JB. PPARγ Corepression Involves Alternate Ligand Conformation and Inflation of H12 Ensembles. ACS Chem Biol 2023; 18:1115-1123. [PMID: 37146157 DOI: 10.1021/acschembio.2c00917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/07/2023]
Abstract
Inverse agonists of peroxisome proliferator activated receptor γ (PPARγ) have emerged as safer alternatives to full agonists for their reduced side effects while still maintaining impressive insulin-sensitizing properties. To shed light on their molecular mechanism, we characterized the interaction of the PPARγ ligand binding domain with SR10221. X-ray crystallography revealed a novel binding mode of SR10221 in the presence of a transcriptionally repressing corepressor peptide, resulting in much greater destabilization of the activation helix, H12, than without corepressor peptide. Electron paramagnetic resonance provided in-solution complementary protein dynamic data, which revealed that for SR10221-bound PPARγ, H12 adopts a plethora of conformations in the presence of corepressor peptide. Together, this provides the first direct evidence for corepressor-driven ligand conformation for PPARγ and will allow the development of safer and more effective insulin sensitizers suitable for clinical use.
Collapse
Affiliation(s)
- Rebecca L Frkic
- The Institute for Photonics and Advanced Sensing and School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jordan L Pederick
- The Institute for Photonics and Advanced Sensing and School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Aimee J Horsfall
- ARC Centre of Excellence for Nanoscale Biophotonics, The Institute for Photonics and Advanced Sensing, and School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Blagojce Jovcevski
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Elise E Crame
- Discipline of Physiology, School of Biomedicine, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - Tara L Pukala
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Mi Ra Chang
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, UF Scripps Biomolecular Research, University of Florida, Jupiter, Florida 33458, United States
| | - Jie Zheng
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, UF Scripps Biomolecular Research, University of Florida, Jupiter, Florida 33458, United States
| | - Anne-Laure Blayo
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, UF Scripps Biomolecular Research, University of Florida, Jupiter, Florida 33458, United States
| | - Andrew D Abell
- ARC Centre of Excellence for Nanoscale Biophotonics, The Institute for Photonics and Advanced Sensing, and School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Theodore M Kamenecka
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, UF Scripps Biomolecular Research, University of Florida, Jupiter, Florida 33458, United States
| | - Joshua S Harbort
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jeffrey R Harmer
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, UF Scripps Biomolecular Research, University of Florida, Jupiter, Florida 33458, United States
| | - John B Bruning
- The Institute for Photonics and Advanced Sensing and School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| |
Collapse
|
3
|
Liang J, Johannessen B, Wu Z, Webster RF, Yong J, Zulkifli MYB, Harbort JS, Cheok YR, Wen H, Ao Z, Kong B, Chang SLY, Scott J, Liang K. Regulating the Coordination Environment of Mesopore-Confined Single Atoms from Metalloprotein-MOFs for Highly Efficient Biocatalysis. Adv Mater 2022; 34:e2205674. [PMID: 36073657 DOI: 10.1002/adma.202205674] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Single-atom catalysts (SACs) exhibit unparalleled atomic utilization and catalytic efficiency, yet it is challenging to modulate SACs with highly dispersed single-atoms, mesopores, and well-regulated coordination environment simultaneously and ultimately maximize their catalytic efficiency. Here, a generalized strategy to construct highly active ferric-centered SACs (Fe-SACs) is developed successfully via a biomineralization strategy that enables the homogeneous encapsulation of metalloproteins within metal-organic frameworks (MOFs) followed by pyrolysis. The results demonstrate that the constructed metalloprotein-MOF-templated Fe-SACs achieve up to 23-fold and 47-fold higher activity compared to those using metal ions as the single-atom source and those with large mesopores induced by Zn evaporation, respectively, as well as up to a 25-fold and 1900-fold higher catalytic efficiency compared to natural enzymes and natural-enzyme-immobilized MOFs. Furthermore, this strategy can be generalized to a variety of metal-containing metalloproteins and enzymes. The enhanced catalytic activity of Fe-SACs benefits from the highly dispersed atoms, mesopores, as well as the regulated coordination environment of single-atom active sites induced by metalloproteins. Furthermore, the developed Fe-SACs act as an excellent and effective therapeutic platform for suppressing tumor cell growth. This work advances the development of highly efficient SACs using metalloproteins-MOFs as a template with diverse biotechnological applications.
Collapse
Affiliation(s)
- Jieying Liang
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | | | - Zhibin Wu
- State Key Laboratory of Powder Metallurgy, Central South University, Changsha, 410083, P. R. China
| | - Richard F Webster
- Electron Microscope Unit, Mark Wainwright Analytical Centre and School of Materials Science and Engineering, Faculty of Science, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Joel Yong
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales, 2052, Australia
- Graduate School of Biomedical Engineering, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Muhammad Yazid Bin Zulkifli
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Joshua S Harbort
- Centre for Advanced Imaging, The University of Queensland, Queensland, 4072, Australia
| | - You Rou Cheok
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Haotian Wen
- Electron Microscope Unit, Mark Wainwright Analytical Centre and School of Materials Science and Engineering, Faculty of Science, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Zhimin Ao
- Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhuhai, 519087, P. R. China
| | - Biao Kong
- Laboratory of Advanced Materials, Department of Chemistry, Shanghai Key Lab of Molecular Catalysis and Innovative Materials, Collaborative Innovation Centre of Chemistry for Energy Materials, Fudan University, Shanghai, 200438, P. R. China
| | - Shery L Y Chang
- Electron Microscope Unit, Mark Wainwright Analytical Centre and School of Materials Science and Engineering, Faculty of Science, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Jason Scott
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Kang Liang
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales, 2052, Australia
- Graduate School of Biomedical Engineering, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| |
Collapse
|
4
|
Podgorski MN, Harbort JS, Lee JHZ, Nguyen GT, Bruning JB, Donald WA, Bernhardt PV, Harmer JR, Bell SG. An Altered Heme Environment in an Engineered Cytochrome P450 Enzyme Enables the Switch from Monooxygenase to Peroxygenase Activity. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05877] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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)
- Matthew N. Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Joshua S. Harbort
- Center for Advanced Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joel H. Z. Lee
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Giang T.H. Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - John B. Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - William A. Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jeffrey R. Harmer
- Center for Advanced Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stephen G. Bell
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| |
Collapse
|
5
|
Coleman T, Kirk AM, Chao RR, Podgorski MN, Harbort JS, Churchman LR, Bruning JB, Bernhardt PV, Harmer JR, Krenske EH, De Voss JJ, Bell SG. Understanding the Mechanistic Requirements for Efficient and Stereoselective Alkene Epoxidation by a Cytochrome P450 Enzyme. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04872] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Tom Coleman
- Department of Chemistry, University Adelaide, Adelaide, South Australia 5005, Australia
| | - Alicia M. Kirk
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Rebecca R. Chao
- Department of Chemistry, University Adelaide, Adelaide, South Australia 5005, Australia
| | - Matthew N. Podgorski
- Department of Chemistry, University Adelaide, Adelaide, South Australia 5005, Australia
| | - Joshua S. Harbort
- Center for Advanced Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Luke R. Churchman
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - John B. Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jeffrey R. Harmer
- Center for Advanced Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Elizabeth H. Krenske
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stephen G. Bell
- Department of Chemistry, University Adelaide, Adelaide, South Australia 5005, Australia
| |
Collapse
|
6
|
Podgorski MN, Harbort JS, Coleman T, Stok JE, Yorke JA, Wong LL, Bruning JB, Bernhardt PV, De Voss JJ, Harmer JR, Bell SG. Biophysical Techniques for Distinguishing Ligand Binding Modes in Cytochrome P450 Monooxygenases. Biochemistry 2020; 59:1038-1050. [PMID: 32058707 DOI: 10.1021/acs.biochem.0c00027] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The cytochrome P450 superfamily of heme monooxygenases catalyzes important chemical reactions across nature. The changes in the optical spectra of these enzymes, induced by the addition of substrates or inhibitors, are critical for assessing how these molecules bind to the P450, enhancing or inhibiting the catalytic cycle. Here we use the bacterial CYP199A4 enzyme (Uniprot entry Q2IUO2), from Rhodopseudomonas palustris HaA2, and a range of substituted benzoic acids to investigate different binding modes. 4-Methoxybenzoic acid elicits an archetypal type I spectral response due to a ≥95% switch from the low- to high-spin state with concomitant dissociation of the sixth aqua ligand. 4-(Pyridin-3-yl)- and 4-(pyridin-2-yl)benzoic acid induced different type II ultraviolet-visible (UV-vis) spectral responses in CYP199A4. The former induced a greater red shift in the Soret wavelength (424 nm vs 422 nm) along with a larger overall absorbance change and other differences in the α-, β-, and δ-bands. There were also variations in the ferrous UV-vis spectra of these two substrate-bound forms with a spectrum indicative of Fe-N bond formation with 4-(pyridin-3-yl)benzoic acid. The crystal structures of CYP199A4, with the pyridinyl compounds bound, revealed that while the nitrogen of 4-(pyridin-3-yl)benzoic acid is coordinated to the heme, with 4-(pyridin-2-yl)benzoic acid an aqua ligand remains. Continuous wave and pulse electron paramagnetic resonance data in frozen solution revealed that the substrates are bound in the active site in a form consistent with the crystal structures. The redox potential of each CYP199A4-substrate combination was measured, allowing correlation among binding modes, spectroscopic properties, and the observed biochemical activity.
Collapse
Affiliation(s)
- Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Joshua S Harbort
- Center for Advanced Imaging, University of Queensland, Brisbane, QLD 4072, Australia
| | - Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Jake A Yorke
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K
| | - Luet-Lok Wong
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Paul V Bernhardt
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - James J De Voss
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Jeffrey R Harmer
- Center for Advanced Imaging, University of Queensland, Brisbane, QLD 4072, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| |
Collapse
|
7
|
Zerk TJ, Moore PW, Harbort JS, Chow S, Byrne L, Koutsantonis GA, Harmer JR, Martínez M, Williams CM, Bernhardt PV. Elucidating the mechanism of the Ley-Griffith (TPAP) alcohol oxidation. Chem Sci 2017; 8:8435-8442. [PMID: 29619191 PMCID: PMC5863698 DOI: 10.1039/c7sc04260d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 10/16/2017] [Indexed: 01/14/2023] Open
Abstract
The Ley-Griffith reaction is utilized extensively in the selective oxidation of alcohols to aldehydes or ketones. The central catalyst is commercially available tetra-n-propylammonium perruthenate (TPAP, n-Pr4N[RuO4]) which is used in combination with the co-oxidant N-methylmorpholine N-oxide (NMO). Although this reaction has been employed for more than 30 years, the mechanism remains unknown. Herein we report a comprehensive study of the oxidation of diphenylmethanol using the Ley-Griffith reagents to show that the rate determining step involves a single alcohol molecule, which is oxidised by a single perruthenate anion; NMO does not appear in rate law. A key finding of this study is that when pure n-Pr4N[RuO4] is employed in anhydrous solvent, alcohol oxidation initially proceeds very slowly. After this induction period, water produced by alcohol oxidation leads to partial formation of insoluble RuO2, which dramatically accelerates catalysis via a heterogeneous process. This is particularly relevant in a synthetic context where catalyst degradation is usually problematic. In this case a small amount of n-Pr4N[RuO4] must decompose to RuO2 to facilitate catalysis.
Collapse
Affiliation(s)
- Timothy J Zerk
- School of Chemistry and Molecular Biosciences , University of Queensland , Brisbane 4072 , Queensland , Australia . ;
| | - Peter W Moore
- School of Chemistry and Molecular Biosciences , University of Queensland , Brisbane 4072 , Queensland , Australia . ;
| | - Joshua S Harbort
- Centre for Advanced Imaging , University of Queensland , Brisbane 4072 , Australia
| | - Sharon Chow
- School of Chemistry and Molecular Biosciences , University of Queensland , Brisbane 4072 , Queensland , Australia . ;
| | - Lindsay Byrne
- Centre for Microscopy, Characterisation and Analysis , University of Western Australia , Crawley , Western Australia 6009 , Australia
| | - George A Koutsantonis
- School of Molecular Sciences , University of Western Australia , Crawley , Western Australia 6009 , Australia
| | - Jeffrey R Harmer
- Centre for Advanced Imaging , University of Queensland , Brisbane 4072 , Australia
| | - Manuel Martínez
- Departament de Química Inorgànica I Orgànica , Secció de Química Inorgànica , Universitat de Barcelona , Martí i Franquès 1-11 , E-08028 Barcelona , Spain
| | - Craig M Williams
- School of Chemistry and Molecular Biosciences , University of Queensland , Brisbane 4072 , Queensland , Australia . ;
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences , University of Queensland , Brisbane 4072 , Queensland , Australia . ;
| |
Collapse
|