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Bonomi F, Iametti S, Barbiroli A. Protein interactions in the biological assembly of iron-sulfur clusters in Escherichia coli: Molecular and mechanistic aspects of the earliest assembly steps. IUBMB Life 2022; 74:723-732. [PMID: 35611886 PMCID: PMC9321986 DOI: 10.1002/iub.2622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/24/2022] [Indexed: 11/11/2022]
Abstract
This contribution focuses on the earliest steps of the assembly of FeS clusters and their insertion into acceptor apoproteins, that call for transient formation of a 2Fe2S cluster on a scaffold protein from sulfide and iron salts. For the sake of simplicity, this report is essentially limited to the Escherichia coli isc-encoded proteins and does not take into account agents that modulate the enzymatic synthesis of sulfide by protein in the same operon or the redox events associated with both sulfide generation and conversion of 2Fe2S structures in clusters of higher nuclearity. Therefore, the results discussed here are based on chemical reconstitution systems using inorganic sulfide, ferric salts, and excess thiols. This simplification offers the possibility to address some mechanistic issues related to the role of protein/protein interaction as for modulating: (a) the rate of cluster assembly on scaffold proteins; (b) the stability of the cluster on the scaffold protein; and (c) the rate of transfer to acceptor apoproteins as also influenced by the acceptor concentration. The emerging picture highlights the mechanistic versatility of the systems, that is discussed in terms of the capability of such an apparently simple combination of proteins to cope with various physiological situation. The hypothetical mechanism presented here may represent an additional way of modulating the rate and outcome of the overall process while avoiding potential toxicity issues.
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Affiliation(s)
- Francesco Bonomi
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| | - Stefania Iametti
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
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2
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Iametti S, Bonomi F, Barbiroli A. Circular Dichroism to Probe the Synthesis, Transfer, and Stability of Fe-S Clusters. Methods Mol Biol 2021; 2353:209-229. [PMID: 34292552 DOI: 10.1007/978-1-0716-1605-5_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
All Fe-S proteins are characterized by distinctive circular dichroism (CD) features in the visible region of the spectrum due to chiral interaction between the cluster itself and the protein backbone. Therefore, the presence of a CD signal in the visible region relates to the presence of the cluster, whereas the disappearance of the signal refers to cluster breakdown or redox changes. The position of the CD features in the spectrum and the intensity of individual components of the CD signal show great variations among different Fe-S proteins. This feature can provide information on transfer processes between proteins, as well as on possible changes in cluster nuclearity. This method can also be used to detect changes in the chemical nature or spatial organization of cluster ligands that may be concurrent with cluster transfer and associated events.
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Affiliation(s)
- Stefania Iametti
- Section of Chemistry and Biomolecular Sciences, DeFENS, University of Milan, Milan, Italy
| | - Francesco Bonomi
- Section of Chemistry and Biomolecular Sciences, DeFENS, University of Milan, Milan, Italy.
| | - Alberto Barbiroli
- Section of Chemistry and Biomolecular Sciences, DeFENS, University of Milan, Milan, Italy
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3
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Campbell IJ, Olmos JL, Xu W, Kahanda D, Atkinson JT, Sparks ON, Miller MD, Phillips GN, Bennett GN, Silberg JJ. Prochlorococcus phage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases. J Biol Chem 2020; 295:10610-10623. [PMID: 32434930 DOI: 10.1074/jbc.ra120.013501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/15/2020] [Indexed: 01/13/2023] Open
Abstract
Marine cyanobacteria are infected by phages whose genomes encode ferredoxin (Fd) electron carriers. These Fds are thought to redirect the energy harvested from light to phage-encoded oxidoreductases that enhance viral fitness, but it is unclear how the biophysical properties and partner specificities of phage Fds relate to those of photosynthetic organisms. Here, results of a bioinformatics analysis using a sequence similarity network revealed that phage Fds are most closely related to cyanobacterial Fds that transfer electrons from photosystems to oxidoreductases involved in nutrient assimilation. Structural analysis of myovirus P-SSM2 Fd (pssm2-Fd), which infects the cyanobacterium Prochlorococcus marinus, revealed high levels of similarity to cyanobacterial Fds (root mean square deviations of ≤0.5 Å). Additionally, pssm2-Fd exhibited a low midpoint reduction potential (-336 mV versus a standard hydrogen electrode), similar to other photosynthetic Fds, although it had lower thermostability (Tm = 28 °C) than did many other Fds. When expressed in an Escherichia coli strain deficient in sulfite assimilation, pssm2-Fd complemented bacterial growth when coexpressed with a P. marinus sulfite reductase, revealing that pssm2-Fd can transfer electrons to a host protein involved in nutrient assimilation. The high levels of structural similarity with cyanobacterial Fds and reactivity with a host sulfite reductase suggest that phage Fds evolved to transfer electrons to cyanobacterially encoded oxidoreductases.
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Affiliation(s)
- Ian J Campbell
- Biochemistry and Cell Biology Graduate Program, Rice University, Houston, Texas, USA.,Department of Biosciences, Rice University, Houston, Texas, USA
| | - Jose Luis Olmos
- Biochemistry and Cell Biology Graduate Program, Rice University, Houston, Texas, USA.,Department of Biosciences, Rice University, Houston, Texas, USA
| | - Weijun Xu
- Department of Biosciences, Rice University, Houston, Texas, USA
| | | | | | | | | | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas, USA.,Department of Chemistry, Rice University, Houston, Texas, USA
| | - George N Bennett
- Department of Biosciences, Rice University, Houston, Texas, USA.,Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Jonathan J Silberg
- Department of Biosciences, Rice University, Houston, Texas, USA .,Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA.,Department of Bioengineering, Rice University, Houston, Texas, USA
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4
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Yan R, Adinolfi S, Iannuzzi C, Kelly G, Oregioni A, Martin S, Pastore A. Cluster and fold stability of E. coli ISC-type ferredoxin. PLoS One 2013; 8:e78948. [PMID: 24265733 PMCID: PMC3827102 DOI: 10.1371/journal.pone.0078948] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/22/2013] [Indexed: 11/25/2022] Open
Abstract
Iron-sulfur clusters are essential protein prosthetic groups that provide their redox potential to several different metabolic pathways. Formation of iron-sulfur clusters is assisted by a specialised machine that comprises, among other proteins, a ferredoxin. As a first step to elucidate the precise role of this protein in cluster assembly, we have studied the factors governing the stability and the dynamic properties of E. coli ferredoxin using different spectroscopic techniques. The cluster-loaded protein is monomeric and well structured with a flexible C-terminus but is highly oxygen sensitive so that it readily loses the cluster leading to an irreversible unfolding under aerobic conditions. This process is slowed down by reducing conditions and high ionic strengths. NMR relaxation experiments on the cluster-loaded protein also show that, once the cluster is in place, the protein forms a globular and relatively rigid domain. These data indicate that the presence of the iron-sulfur cluster is the switch between a functional and a non-functional state.
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Affiliation(s)
- Robert Yan
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Salvatore Adinolfi
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Clara Iannuzzi
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Geoff Kelly
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Alain Oregioni
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Stephen Martin
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Annalisa Pastore
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
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5
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Kaas Q, Craik DJ. NMR of plant proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 71:1-34. [PMID: 23611313 DOI: 10.1016/j.pnmrs.2013.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 01/21/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Quentin Kaas
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
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6
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Grzyb J, Bojko M, Waloszek A, Strzałka K. Ferredoxin:NADP+ oxidoreductase as a target of Cd2+ inhibitory action--biochemical studies. PHYTOCHEMISTRY 2011; 72:14-20. [PMID: 21071046 DOI: 10.1016/j.phytochem.2010.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 10/14/2010] [Accepted: 10/18/2010] [Indexed: 05/30/2023]
Abstract
The ferredoxin:NADP+ oxidoreductase (FNR) catalyses the ferredoxin-dependent reduction of NADP+ to NADPH in linear photosynthetic electron transport. The enzyme also transfers electrons from reduced ferredoxin (Fd) or NADPH to the cytochrome b(6)f complex in cyclic electron transport. In vitro, the enzyme catalyses the NADPH-dependent reduction of various substrates, including ferredoxin, the analogue of its redox centre - ferricyanide, and the analogue of quinones, which is dibromothymoquinone. This paper presents results on the cadmium-induced inhibition of FNR. The K(i) value calculated for research condition was 1.72 mM. FNR molecule can bind a large number of cadmium ions, as shown by the application of cadmium-selective electrode, but just one ion remains bound after dialysis. The effect of cadmium binding is significant disturbance in the electron transfer process from flavin adenine dinucleotide (FAD) to dibromothymoqinone, but less interference with the reduction of ferricyanide. However, it caused a strong inhibition of Fd reduction, indicating that Cd-induced changes in the FNR structure disrupt Fd binding. Additionally, the protonation of the thiol groups is shown to be of great importance in the inhibition process. A mechanism for cadmium-caused inhibition is proposed and discussed with respect to the in vitro and in vivo situation.
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Affiliation(s)
- Joanna Grzyb
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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Sárvári E, Gáspár L, Solti A, Mészáros I, Záray G, Fodor F. Cd-Fe interactions: comparison of the effects of iron deficiency and cadmium on growth and photosynthetic performance in poplar. ACTA BIOLOGICA HUNGARICA 2010; 61 Suppl:136-48. [PMID: 21565772 DOI: 10.1556/abiol.61.2010.suppl.14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
To check the importance of Cd-induced iron deficiency in Cd stress, symptoms of Cd stress were compared with those of iron deficiency or the combination of these two stresses. Poplar plants grown in hydroponics with Fe-EDTA (e) or Fe-citrate (c) up to four-leaf stage were treated for two weeks either by the withdrawal of iron (Fedef), or supplying 10 μM Cd(NO3)2 in the presence (Cad) or absence of an iron source (Fedef + Cad). Cadmium and iron content of leaves developing under the stress was in the order of cCad > eCad > cFedef + Cad and cCad ≈ eFedef ≈ cFedef + Cad < eCad < cFedef, respectively. Growth inhibition was much stronger in Cad than Fedef plants. The inhibitory effects on CO2 fixation, maximal and actual efficiency of PSII, chlorophyll synthesis, as well as the stimulation of the accumulation of violaxanthin cycle components and increase in non-photochemical quenching were the strongest in cFedef+Cad plants, otherwise these parameters changed parallel to the iron deficiency of leaves. Tendency of changes in thylakoid composition were similar under Cad treatments and strong iron deficiency: particularly PSI and LHCII decreased. Therefore, the development of the photosynthetic apparatus under Cd stress was mainly influenced by the Cd-induced strong iron deficiency, while leaf growth was affected primarily by the presence of Cd.
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Affiliation(s)
- Eva Sárvári
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary.
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8
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Fagioni M, D’Amici GM, Timperio AM, Zolla L. Proteomic Analysis of Multiprotein Complexes in the Thylakoid Membrane upon Cadmium Treatment. J Proteome Res 2008; 8:310-26. [DOI: 10.1021/pr800507x] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marco Fagioni
- Department of Environmental Sciences, Tuscia University, Viterbo, Italy
| | | | | | - Lello Zolla
- Department of Environmental Sciences, Tuscia University, Viterbo, Italy
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9
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Leal SS, Teixeira M, Gomes CM. Studies on the degradation pathway of iron-sulfur centers during unfolding of a hyperstable ferredoxin: cluster dissociation, iron release and protein stability. J Biol Inorg Chem 2004; 9:987-96. [PMID: 15578277 DOI: 10.1007/s00775-004-0599-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Accepted: 09/05/2004] [Indexed: 11/28/2022]
Abstract
The ferredoxin from the thermoacidophile Acidianus ambivalens is a representative of the archaeal family of di-cluster [3Fe-4S][4Fe-4S] ferredoxins. Previous studies have shown that these ferredoxins are intrinsically very stable and led to the suggestion that upon protein unfolding the iron-sulfur clusters degraded via linear three-iron sulfur center species, with 610 and 520 nm absorption bands, resembling those observed in purple aconitase. In this work, a kinetic and spectroscopic investigation on the alkaline chemical denaturation of the protein was performed in an attempt to elucidate the degradation pathway of the iron-sulfur centers in respect to protein unfolding events. For this purpose we investigated cluster dissociation, iron release and protein unfolding by complementary biophysical techniques. We found that shortly after initial protein unfolding, iron release proceeds monophasically at a rate comparable to that of cluster degradation, and that no typical EPR features of linear three-iron sulfur centers are observed. Further, it was observed that EDTA prevents formation of the transient bands and that sulfide significantly enhances its intensity and lifetime, even after protein unfolding. Altogether, our data suggest that iron sulfides, which are formed from the release of iron and sulfide resulting from cluster degradation during protein unfolding in alkaline conditions, are in fact responsible for the observed intermediate spectral species, thus disproving the hypothesis suggesting the presence of a linear three-iron center intermediate. Kinetic studies monitored by visible, fluorescence and UV second-derivative spectroscopies have elicited that upon initial perturbation of the tertiary structure the iron-sulfur centers start decomposing and that the presence of EDTA accelerates the process. Also, the presence of EDTA lowers the observed melting temperature in thermal ramp experiments and the midpoint denaturant concentration in equilibrium chemical unfolding experiments, further suggesting that the clusters also play a structural role in the maintenance of the conformation of the folded state.
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Affiliation(s)
- Sónia S Leal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República, 2784-505, Oeiras, Portugal
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10
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Johnson KA, Brereton PS, Verhagen MF, Calzolai L, La Mar GN, Adams MW, Amster IJ. A gallium-substituted cubane-type cluster in Pyrococcus furiosus ferredoxin. J Am Chem Soc 2001; 123:7935-6. [PMID: 11493079 DOI: 10.1021/ja0160795] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K A Johnson
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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11
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Bera AK, Grinberg A, Bernhardt R. A step toward understanding the folding mechanism of bovine adrenodoxin. Arch Biochem Biophys 1999; 361:315-22. [PMID: 9882462 DOI: 10.1006/abbi.1998.1005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The iron-sulfur clusters of iron-sulfur proteins are not only essential for the structure and function but they also seem to play an important role in the folding process of these proteins. So far, no data on reversible unfolding/refolding of iron-sulfur proteins under aerobic conditions have been reported. We found appropriate conditions, which might also be applicable for other iron-sulfur proteins, for reversible unfolding/refolding of bovine adrenodoxin (Adx) that prevent cluster decomposition during the unfolding process. The unfolding/refolding studies have been performed under aerobic conditions using fluorescence measurements (with mutant Y82W of Adx, providing a sensitive internal probe), absorption, and circular dichroism (CD) spectroscopy as well as activity measurements. Without protecting reagent, adrenodoxin becomes an apoprotein upon denaturation which is an irreversible process with respect to cluster rebinding. However, reversibility of unfolding/refolding can be observed after protein denaturation in the presence of dithiothreitol (DTT). Upon removal of the denaturant, we regained 65, 63, and 64% refolding from CD, fluorescence, and activity measurements, respectively. In the case of thermal denaturation, the percentage of refolding is about 60% according to CD measurements. DTT appears to stabilize the [2Fe-2S] cluster and prevents its decomposition during aerobic unfolding, providing thereby the means of correct refolding of the protein.
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Affiliation(s)
- A K Bera
- Fachbereich 12 Pharmazie und Umwelttechnologie, Fachrichtung 12.4 Biochemie, Universität des Saarlandes, Im Stadtwald, Saarbrücken, Germany
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12
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Sticht H, Rösch P. The structure of iron-sulfur proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1998; 70:95-136. [PMID: 9785959 DOI: 10.1016/s0079-6107(98)00027-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ferredoxins are a group of iron-sulfur proteins for which a wealth of structural and mutational data have recently become available. Previously unknown structures of ferredoxins which are adapted to halophilic, acidophilic or hyperthermophilic environments and new cysteine patterns for cluster ligation and non-cysteine cluster ligation have been described. Site-directed mutagenesis experiments have given insight into factors that influence the geometry, stability, redox potential, electronic properties and electron-transfer reactivity of iron-sulfur clusters.
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Affiliation(s)
- H Sticht
- Lehrstuhl für Struktur und Chemie der Biopolymere, Universität Bayreuth, Germany.
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13
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Vo E, Wang HC, Germanas JP. Preparation and Characterization of [2Ga-2S] Anabaena 7120 Ferredoxin, the First Gallium−Sulfur Cluster-Containing Protein. J Am Chem Soc 1997. [DOI: 10.1021/ja961330f] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Evanly Vo
- Contribution from the Department of Chemistry, University of Houston, Houston, Texas 77204-5641
| | - Harry C. Wang
- Contribution from the Department of Chemistry, University of Houston, Houston, Texas 77204-5641
| | - Juris P. Germanas
- Contribution from the Department of Chemistry, University of Houston, Houston, Texas 77204-5641
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