Hydrolysis of Phosphate Esters Catalyzed by ...

Support information

Hydrolysis of Phosphate Esters Catalyzed by Inorganic Iron Oxide Nanoparticles Acting as Biocatalysts

By Xiao-Lan Huang*. Independent researcher, Cincinnati, OH, 45243 USA

SI-Figure 1. The di-nuclear iron center in rat purple acid phosphatase (a) Stereoview of the di-nuclear iron center in rat purple acid phosphatase. The bound sulfate ion at the active-site is also shown. In red part of the Fo−Fc difference electron density map, contoured at 3.5σ, indicative of a μ-(hydr)oxo bridge and a bound solvent molecule at the di-iron center. This map was calculated before any solvent ligand had been included in the model.

(b). A view of the di-iron center and the active-site of rat purple acid phosphatase as seen in the crystals. Dotted lines indicate hydrogen-bonds or coordination bonds.

Ylva Lindqvist, Eva Johansson, Helena Kaija, Pirkko Vihko, Gunter Schneider Three-dimensional structure of a mammalian purple acid phosphatase at 2.2 Å resolution with a μ-(hydr)oxo bridged di-iron center Journal of Molecular Biology, 291 (1), 1999, 135–147 doi.org/10.1006/jmbi.1999.2962

SI-Figure 2. Proposed reaction mechanism for PAP-catalyzed hydrolysis.

Gerhard Schenk, Nataša Mitić, Graeme R. Hanson, Peter Comba Purple acid phosphatase: A journey into the function and mechanism of a colorful enzyme Coordination Chemistry Reviews, 257 (2), 2013, 473–482, http://dx.doi.org/10.1016/j.ccr.2012.03.020

PAP and the substrate interact to form a pre-catalytic complex; subsequently, the substrate is rearranged to coordinate directly to at least one of the metal ions in the active site (a–c). Nucleophilic attack by either the μ-hydroxide (as shown) or a noncoordinating hydroxide in the second coordination sphere is followed by the release of the leaving group, and the active site is returned to its resting state by the exchange of the bound phosphate group by two water molecules (d–h). Where available crystallographic snapshots of relevant active site structures are also shown. (a) rkbPAP–sulfate complex; (b) rat PAP–sulfate complex; (c) pig PAP–phosphate complex; (d) sweet potato PAP–phosphate complex; (e) rkbPAP–phosphate complex; (h) rkbPAP.

Structural model compounds for the oxidized uteroferrin– phosphato complex Fe2(tbpo)(O2PO(OH))2]ClO4 · CH3OH · 8.5H2O contain μalkoxo-bis(μ-hydrogenphosphato)diiron(III) core, with the Fe⋯Fe distance 3.42 A

Structural model compounds for the oxidized uteroferrin–arsenato complex [Fe2(mtbpo)(O2As(CH3)2)(Cl)2(CH3OH)](ClO4)2 · 4CH3OH contain a (μ-alkoxo)(μ-dimethylarsinato)diiron(III) core; The Fe⋯Fe distance is 3.54 A.

Structural model compound for the oxidized form of PAP from beef spleen. [Fe2(tbpo)(O2P(OPh)2)(Cl)2(CH3OH)](ClO4)2 · 3CH3OH is the first binuclear iron(III) complex with a terminally coordinated phosphato ligand, The metal–metal separation is 3.7A

SI-Figure 3. PAPs mimics (Adapted from the Figure 3, 4, and 5, Roberto Than, Arnold A. Feldmann, Bernt Krebs Structural and functional studies on model compounds of purple acid phosphatases and catechol oxidases, Coordination Chemistry Reviews, Volume 182, Issue 1, 1999, 211–241, https://doi.org/10.1016/S0010-8545(98)00234-3)

SI-Figure 4. Schematic diagram of the catalysis process of G6P hydrolysis in the presence of the tetrahedral anions in the aged inorganic iron solutions. E is the aged inorganic iron species; A is the active binding sites on the aged iron species. S is G6P and I is tetrahedral anions. ES and EI are the two intermediates. Xiaolan Huang, Jia-Zhong Zhang Hydrolysis of glucose-6-phosphate in aged, acid-forced hydrolysed nanomolar inorganic iron solutions—an inorganic biocatalyst? RSC Advances, 2012, 2, 199-208

DOI: 10.1039/C1RA00353D

SI-Figure 5. The Structure of Ferrihydrite Nanocrystalline Material The basic structural motif of the Ferrihydrit, which is closely related to the Baker-Figgis d-Keggin cluster, consists of 13 iron atoms and 40 oxygens . The central tetrahedrally coordinated Fe is connected by m4-oxo bridges to 12 peripheral octahedrally coordinated Fe atoms arranged in edge-sharing groups of three. The 2- to 6-nm ferrihydrite nanoparticles can then be described as a three-dimensional packing of these clusters with adjacent clusters connected by a common pair of edge-shared octahedra, forming μ4-oxo bridges from the three μ2-OH groups cis to each of the μ4-oxo centers in the bare cluster. This arrangement creates a cubane-like moiety corresponding to four edge-shared Fe octahedra. Marc Michel, Lars Ehm, Sytle M. Antao, Peter L. Lee, Peter J. Chupas, Gang Liu, Daniel R. Strongin, Martin A. A. Schoonen, Brian L. Phillips, John B. Paris

Science 2007: 316 (5832): 1726-1729 http://dx.doi.org/10.1126/science.1142525

SI-Figure 6. Aqueous formation and manipulation of the iron-oxo Keggin ion

Omid Sadeghi, Lev N. Zakharov, May Nyma Science, 2015; 347, 1359-1362 http://dx.doi.org/10.1126/science.aaa4620

The iron Keggin ion.

Views of the iron Keggin ion in different structures. (Left) Magnetite, (FeIItet)(FeIIIoct)2O4 emphasizing the εKeggin isomer building unit (red polyhedra). The four trimers of edge-sharing octahedra are likewise connected together by edge-sharing. (Middle) Bi6-α-[FeO4Fe12O12(OH)12(O2C(CCl3)12]17–, Bi6Fe13L12. In the α-isomer, the four trimers are linked together by corner-sharing. (Right) A view of ferrihydrite, structure determined from pair distribution function. The red polyhedra emphasize the δ-Fe13 building block. In the δ-isomer, three of the trimers are edge-sharing, and the fourth is corner-linked.

SI- Figure 7. The structure of ferric iron (Fe3+) dimers in aqueous solutions using extended X-ray absorption fine structure (EXAFS) spectroscopy. The results indicated that a Fe–Fe distance at ∼3.6A were confirmed in the 0.2 M ferric nitrate solutions at pH 1.28–1.81, strongly indicating that the dimers take the μ-oxo form.

Mengqiang Zhu, Brendan W. Puls, Cathrine Frandsen, James D. Kubicki, Hengzhong Zhang, and Glenn A. Waychunas In Situ Structural Characterization of Ferric Iron Dimers in Aqueous Solutions: Identification of μ-Oxo Species Inorg. Chem., 2013, 52 (12), pp 6788–6797

http://dx.doi.org/10.1021/ic302053w

SI-Figure 8. Structures of iron monomers (a, b) and dimers (c, d, e) sampled at the ends of MD simulations a–e correspond to the MD systems 1–5 in Table 1: red, O; green, Fe; gray, H; blue, Cl. Hengzhong Zhang; Glenn A. Waychunas; Jillian F. Banfield

Molecular Dynamics Simulation Study of the Early Stages of Nucleation of Iron Oxyhydroxide Nanoparticles in Aqueous Solutions. J. Phys. Chem. B 2015, 119, 10630-10642. DOI: 10.1021/acs.jpcb.5b03801

Copyright © 2015 American Chemical Society

SI- Figure 9. V2O5 nanowires with an intrinsic peroxidase-like activity A) Single layer from the V2O5 structure. In the V2O5 nanowires these layers are stacked along [001], and wires extend along the [100] direction. A view of the exposed (110) planes shows a great similarity with the V-HPO active sites. B) Proposed mechanism for the formation of ABTS with the formation of a vanadium peroxo complex intermediate and oxidation attack of ABTS and release of the product (ABTS*+). As hydrogen peroxide is a two-electron oxidant, another molecule of ABTS is required for regeneration of the V2O5 nanowires leading to the formation of a new product (ABTS*)

André R, Natálio F, Humanes M, Leppin J, Heinze K, Wever R, Schröder HC, Müller WEG, and Tremel W. V2O5 nanowires with an intrinsic peroxidase-like activity Advanced Functional Materials,, 21, 2011, 501-509; DOI: 10.1002/adfm.20100130

SI-Figure 10. Schematic diagram showing the molecular details of the mechanism of V2O5 nanozyme’s activity The formation of peroxido species 1 was confirmed by Raman spectroscopic studies

Vernekar AA, Sinha D, Srivastava S, Paramasivam PU, D'Silva P, and Mugesh G An antioxidant nanozyme that uncovers the cytoprotective potential of vanadia nanowires Nature Communications 5, Article number: 5301 (2014) doi:10.1038/ncomms6301

SI- Figure 11. Architecture of the active site in HRP and comparison with the histidine-modified Fe3O4 nanozyme (A) Protein structure of HRP (PDB entry 1HCH); (B) architecture of active site in HRP; (C) H bond between histidine residual and H2O2 in the initial state of catalysis of HRP; (D) enhancement of Fe3O4 nanozyme activity by histidine modification.

Fan K., Wang H., Xi J., Liu Q., Meng X., Duan D., Gao L., and Yan X. Optimization of Fe3O4 nanozyme activity via single amino acid modification mimicking an enzyme active site Chemical Communications, 2017, 53: 424-427 DOI: 10.1039/C6CC08542C

.

Surface functionalization of 2 nm MoO3 nanoparticles with ligand containing dopamine as anchor group and TPP as mitochondria targeting agent

SI-Figure 12. Molybdenum Trioxide Nanoparticles with Intrinsic Sulfite Oxidase Activity

Ruben Ragg; Filipe Natalio; Muhammad Nawaz Tahir; Henning Janssen; Anubha Kashyap; Dennis Strand; Susanne Strand; Wolfgang Tremel Molybdenum Trioxide Nanoparticles with Intrinsic Sulfite Oxidase Activity ACS Nano 2014, 8, 5182-5189 DOI: 10.1021/nn501235j .

Concentration dependence and steadystate kinetics of MoO3-TPP nanoparticles. (a) Concentration dependence of the sulfite oxidase activity of functionalized MoO3-TPP nanoparticles (blue diamonds) and bulk MoO3 (orange diamonds) in the presence of constant concentrations of SO32– (0.66 mM) and potassium ferricyanide (0.33 mM). A 4fold activity difference between nanoscale and bulk MoO3 indicates the importance of a higher surface area for attaining higher catalytic efficiencies. (b) Variation of the SO32– concentration (0.03–1.65 mM) while keeping the MoO3TPP nanoparticle (0.025 mg/mL) and ferricyanide (0.33 μM) concentrations constant. (c) Proposed catalytic sulfite oxidase mechanism for MoO3 nanoparticles.

SI-Figure 13. A comparison of the active site of methane monooxygenase with the Fe 2O2 building block of Fe(OH)2, a precipitate highly prone to oxidation to green rust or fougerite (~[FeIIFeIII(OH)4]+[OH]−) . Wolfgang Nitschke, Shawn E. McGlynn, E. James Milner-White, Michael J. Russell On the antiquity of metalloenzymes and their substrates in bioenergetics Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1827 (8–9), 2013, 871–881 http://dx.doi.org/10.1016/j.bbabio.2013.02.008