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Ma L, Zheng JJ, Zhou N, Zhang R, Fang L, Yang Y, Gao X, Chen C, Yan X, Fan K. A natural biogenic nanozyme for scavenging superoxide radicals. Nat Commun 2024; 15:233. [PMID: 38172125 PMCID: PMC10764798 DOI: 10.1038/s41467-023-44463-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Biominerals, the inorganic minerals of organisms, are known mainly for their physical property-related functions in modern living organisms. Our recent discovery of the enzyme-like activities of nanomaterials, coined as nanozyme, inspires the hypothesis that nano-biominerals might function as enzyme-like catalyzers in cells. Here we report that the iron cores of biogenic ferritins act as natural nanozymes to scavenge superoxide radicals. Through analyzing eighteen representative ferritins from three living kingdoms, we find that the iron core of prokaryote ferritin possesses higher superoxide-diminishing activity than that of eukaryotes. Further investigation reveals that the differences in catalytic capability result from the iron/phosphate ratio changes in the iron core, which is mainly determined by the structures of ferritins. The phosphate in the iron core switches the iron core from single crystalline to amorphous iron phosphate-like structure, resulting in decreased affinity to the hydrogen proton of the ferrihydrite-like core that facilitates its reaction with superoxide in a manner different from that of ferric ions. Furthermore, overexpression of ferritins with high superoxide-diminishing activities in E. coli increases the resistance to superoxide, whereas bacterioferritin knockout or human ferritin knock-in diminishes free radical tolerance, highlighting the physiological antioxidant role of this type of nanozymes.
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Affiliation(s)
- Long Ma
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100408, China
| | - Jia-Jia Zheng
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Ning Zhou
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruofei Zhang
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Long Fang
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yili Yang
- China Regional Research Centre, International Centre for Genetic Engineering and Biotechnology, Taizhou, Jiangsu, 225316, China
| | - Xingfa Gao
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Xiyun Yan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100408, China.
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Nanozyme Laboratory in Zhongyuan, Zhengzhou, Henan, 451163, China.
| | - Kelong Fan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100408, China.
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Nanozyme Laboratory in Zhongyuan, Zhengzhou, Henan, 451163, China.
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Reutovich AA, Srivastava AK, Smith GL, Foucher A, Yates DM, Stach EA, Papaefthymiou GC, Arosio P, Bou-Abdallah F. Effect of Phosphate and Ferritin Subunit Composition on the Kinetics, Structure, and Reactivity of the Iron Core in Human Homo- and Heteropolymer Ferritins. Biochemistry 2022; 61:2106-2117. [PMID: 36099002 PMCID: PMC9548343 DOI: 10.1021/acs.biochem.2c00354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ferritins are highly conserved supramolecular protein nanostructures that play a key role in iron homeostasis. Thousands of iron atoms can be stored inside their hollow cavity as a hydrated ferric oxyhydroxide mineral. Although phosphate associates with the ferritin iron nanoparticles, the effect of physiological concentrations on the kinetics, structure, and reactivity of ferritin iron cores has not yet been explored. Here, the iron loading and mobilization kinetics were studied in the presence of 1-10 mM phosphate using homopolymer and heteropolymer ferritins having different H to L subunit ratios. In the absence of ferritin, phosphate enhances the rate of ferrous ion oxidation and forms large and soluble polymeric Fe(III)-phosphate species. In the presence of phosphate, Fe(II) oxidation and core formation in ferritin is significantly accelerated with oxidation rates several-fold higher than with phosphate alone. High-angle annular dark-field scanning transmission electron microscopy measurements revealed a strong phosphate effect on both the size and morphology of the iron mineral in H-rich (but not L-rich) ferritins. While iron nanoparticles in L-rich ferritins have spherical shape in the absence and presence of phosphate, iron nanoparticles in H-rich ferritins change from irregular shapes in the absence of phosphate to spherical particles in the presence of phosphate with larger size distribution and smaller particle size. In the presence of phosphate, the kinetics of iron-reductive mobilization from ferritin releases twice as much iron than in its absence. Altogether, our results demonstrate an important role for phosphate, and the ferritin H and L subunit composition toward the kinetics of iron oxidation and removal from ferritin, as well as the structure and reactivity of the iron mineral, and may have an important implication on ferritin iron management in vivo.
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Affiliation(s)
- Aliaksandra A Reutovich
- Department of Chemistry, State University of New York, Potsdam, New York 13676, United States
| | - Ayush K Srivastava
- Department of Chemistry, State University of New York, Potsdam, New York 13676, United States
| | - Gideon L Smith
- Department of Chemistry, State University of New York, Potsdam, New York 13676, United States
| | - Alexandre Foucher
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Douglas M Yates
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Eric A Stach
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | - Paolo Arosio
- Department of Molecular and Translational Medicine, University of Brescia, 25121 Brescia, Italy
| | - Fadi Bou-Abdallah
- Department of Chemistry, State University of New York, Potsdam, New York 13676, United States
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3
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Morphological difference of Escherichia coli non-heme ferritin iron cores reconstituted in the presence and absence of inorganic phosphate. J Biol Inorg Chem 2022; 27:583-594. [DOI: 10.1007/s00775-022-01952-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/28/2022] [Indexed: 10/15/2022]
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4
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Melman A, Bou-Abdallah F. Iron mineralization and core dissociation in mammalian homopolymeric H-ferritin: Current understanding and future perspectives. Biochim Biophys Acta Gen Subj 2020; 1864:129700. [DOI: 10.1016/j.bbagen.2020.129700] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 01/13/2023]
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Bou-Abdallah F, Flint N, Wilkinson T, Salim S, Srivastava AK, Poli M, Arosio P, Melman A. Ferritin exhibits Michaelis-Menten behavior with oxygen but not with iron during iron oxidation and core mineralization. Metallomics 2020; 11:774-783. [PMID: 30720039 DOI: 10.1039/c9mt00001a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The excessively high and inconsistent literature values for Km,Fe and Km,O2 prompted us to examine the iron oxidation kinetics in ferritin, the major iron storage protein in mammals, and to determine whether a traditional Michaelis-Menten enzymatic behavior is obeyed. The kinetics of Fe(ii) oxidation and mineralization catalyzed by three different types of ferritins (recombinant human homopolymer 24H, HuHF, human heteropolymer ∼21H:3L, HL, and horse spleen heteropolymer ∼3.3H:20.7L, HosF) were therefore studied under physiologically relevant O2 concentrations, but also in the presence of excess Fe(ii) and O2 concentrations. The observed iron oxidation kinetics exhibited two distinct phases (phase I and phase II), neither of which obeyed Michaelis-Menten kinetics. While phase I was very rapid and corresponded to the oxidation of approximately 2 Fe(ii) ions per H-subunit, phase II was much slower and varied linearly with the concentration of iron(ii) cations in solution, independent of the size of the iron core. Under low oxygen concentration close to physiological, the iron uptake kinetics revealed a Michaelis-Menten behavior with Km,O2 values in the low μM range (i.e. ∼1-2 μM range). Our experimental Km,O2 values are significantly lower than typical cellular oxygen concentration, indicating that iron oxidation and mineralization in ferritin should not be affected by the oxygenation level of cells, and should proceed even under hypoxic events. A kinetic model is proposed in which the inhibition of the protein's activity is caused by bound iron(iii) cations at the ferroxidase center, with the rate limiting step corresponding to an exchange or a displacement reaction between incoming Fe(ii) cations and bound Fe(iii) cations.
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Affiliation(s)
- Fadi Bou-Abdallah
- Department of Chemistry, State University of New York, Potsdam, NY 13676, USA.
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Parida A, Mohanty A, Kansara BT, Behera RK. Impact of Phosphate on Iron Mineralization and Mobilization in Nonheme Bacterioferritin B from Mycobacterium tuberculosis. Inorg Chem 2019; 59:629-641. [DOI: 10.1021/acs.inorgchem.9b02894] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Akankshika Parida
- Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Abhinav Mohanty
- Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Bharat T. Kansara
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Rabindra K. Behera
- Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India
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Hagen WR, Hagedoorn PL, Honarmand Ebrahimi K. The workings of ferritin: a crossroad of opinions. Metallomics 2018; 9:595-605. [PMID: 28573266 DOI: 10.1039/c7mt00124j] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Biochemistry of the essential element iron is complicated by radical chemistry associated with Fe(ii) ions and by the extremely low solubility of the Fe(iii) ion in near-neutral water. To mitigate these problems cells from all domains of life synthesize the protein ferritin to take up and oxidize Fe(ii) and to form a soluble storage of Fe(iii) from which iron can be made available for physiology. A long history of studies on ferritin has not yet resulted in a generally accepted mechanism of action of this enzyme. In fact strong disagreement exists between extant ideas on several key steps in the workings of ferritin. The scope of this review is to explain the experimental background of these controversies and to indicate directions towards their possible resolution.
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Affiliation(s)
- Wilfred R Hagen
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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Ebrahimi KH, Bill E, Hagedoorn PL, Hagen WR. Spectroscopic evidence for the role of a site of the di-iron catalytic center of ferritins in tuning the kinetics of Fe(ii) oxidation. MOLECULAR BIOSYSTEMS 2017; 12:3576-3588. [PMID: 27722502 DOI: 10.1039/c6mb00235h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ferritin is a nanocage protein made of 24 subunits. Its major role is to manage intracellular concentrations of free Fe(ii) and Fe(iii) ions, which is pivotal for iron homeostasis across all domains of life. This function of the protein is regulated by a conserved di-iron catalytic center and has been the subject of extensive studies over the past 50 years. Yet, it has not been fully understood how Fe(ii) is oxidized in the di-iron catalytic center and it is not known why eukaryotic and microbial ferritins oxidize Fe(ii) with different kinetics. In an attempt to obtain a new insight into the mechanism of Fe(ii) oxidation and understand the origin of the observed differences in the catalysis of Fe(ii) oxidation among ferritins we studied and compared the mechanism of Fe(ii) oxidation in the eukaryotic human H-type ferritin (HuHF) and the archaeal ferritin from Pyrococcus furiosus (PfFtn). The results show that the spectroscopic characteristics of the intermediate of Fe(ii) oxidation and the Fe(iii)-products are the same in these two ferritins supporting the proposal of unity in the mechanism of Fe(ii) oxidation among eukaryotic and microbial ferritins. Moreover, we observed that a site in the di-iron catalytic center controls the distribution of Fe(ii) among subunits of HuHF and PfFtn differently. This observation explains the reported differences between HuHF and PfFtn in the kinetics of Fe(ii) oxidation and the amount of O2 consumed per Fe(ii) oxidized. These results provide a fresh understanding of the mechanism of Fe(ii) oxidation by ferritins.
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Affiliation(s)
- Kourosh Honarmand Ebrahimi
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion (MPI-CEC), Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Wilfred R Hagen
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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Honarmand Ebrahimi K, Bill E, Hagedoorn P, Hagen WR. Spectroscopic evidence for the presence of a high-valent Fe(IV) species in the ferroxidase reaction of an archaeal ferritin. FEBS Lett 2017; 591:1712-1719. [PMID: 28542723 PMCID: PMC5519934 DOI: 10.1002/1873-3468.12697] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/10/2017] [Accepted: 05/21/2017] [Indexed: 12/20/2022]
Abstract
A high‐valent Fe(IV) species is proposed to be generated from the decay of a peroxodiferric intermediate in the catalytic cycle at the di‐iron cofactor center of dioxygen‐activating enzymes such as methane monooxygenase. However, it is believed that this intermediate is not formed in the di‐iron substrate site of ferritin, where oxidation of Fe(II) substrate to Fe(III) (the ferroxidase reaction) occurs also via a peroxodiferric intermediate. In opposition to this generally accepted view, here we present evidence for the occurrence of a high‐valent Fe(IV) in the ferroxidase reaction of an archaeal ferritin, which is based on trapped intermediates obtained with the freeze‐quench technique and combination of spectroscopic characterization. We hypothesize that a Fe(IV) intermediate catalyzes oxidation of excess Fe(II) nearby the ferroxidase center.
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Affiliation(s)
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion (MPI‐CEC)MülheimGermany
| | | | - Wilfred R. Hagen
- Department of BiotechnologyDelft University of TechnologyThe Netherlands
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Genome-wide comparison of ferritin family from Archaea, Bacteria, Eukarya, and Viruses: its distribution, characteristic motif, and phylogenetic relationship. Naturwissenschaften 2015; 102:64. [DOI: 10.1007/s00114-015-1314-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/07/2015] [Accepted: 09/09/2015] [Indexed: 01/06/2023]
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Honarmand Ebrahimi K, Hagedoorn PL, Hagen WR. Unity in the Biochemistry of the Iron-Storage Proteins Ferritin and Bacterioferritin. Chem Rev 2014; 115:295-326. [DOI: 10.1021/cr5004908] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Kourosh Honarmand Ebrahimi
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628
BC Delft, The Netherlands
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628
BC Delft, The Netherlands
| | - Wilfred R. Hagen
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628
BC Delft, The Netherlands
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Honarmand Ebrahimi K, Dienemann C, Hoefgen S, Than ME, Hagedoorn PL, Hagen WR. The amyloid precursor protein (APP) does not have a ferroxidase site in its E2 domain. PLoS One 2013; 8:e72177. [PMID: 23977245 PMCID: PMC3747053 DOI: 10.1371/journal.pone.0072177] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 07/02/2013] [Indexed: 02/07/2023] Open
Abstract
The ubiquitous 24-meric iron-storage protein ferritin and multicopper oxidases such as ceruloplasmin or hephaestin catalyze oxidation of Fe(II) to Fe(III), using molecular oxygen as oxidant. The ferroxidase activity of these proteins is essential for cellular iron homeostasis. It has been reported that the amyloid precursor protein (APP) also has ferroxidase activity. The activity is assigned to a ferroxidase site in the E2 domain of APP. A synthetic 22-residue peptide that carries the putative ferroxidase site of E2 domain (FD1 peptide) has been claimed to encompass the same activity. We previously tested the ferroxidase activity of the synthetic FD1 peptide but we did not observe any activity above the background oxidation of Fe(II) by molecular oxygen. Here we used isothermal titration calorimetry to study Zn(II) and Fe(II) binding to the natural E2 domain of APP, and we employed the transferrin assay and oxygen consumption measurements to test the ferroxidase activity of the E2 domain. We found that this domain neither in the presence nor in the absence of the E1 domain binds Fe(II) and it is not able to catalyze the oxidation of Fe(II). Binding of Cu(II) to the E2 domain did not induce ferroxidase activity contrary to the presence of redox active Cu(II) centers in ceruloplasmin or hephaestin. Thus, we conclude that E2 or E1 domains of APP do not have ferroxidase activity and that the potential involvement of APP as a ferroxidase in the pathology of Alzheimer’s disease must be re-evaluated.
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