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Huang XL. Unveiling the role of inorganic nanoparticles in Earth's biochemical evolution through electron transfer dynamics. iScience 2024; 27:109555. [PMID: 38638571 PMCID: PMC11024932 DOI: 10.1016/j.isci.2024.109555] [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] [Indexed: 04/20/2024] Open
Abstract
This article explores the intricate interplay between inorganic nanoparticles and Earth's biochemical history, with a focus on their electron transfer properties. It reveals how iron oxide and sulfide nanoparticles, as examples of inorganic nanoparticles, exhibit oxidoreductase activity similar to proteins. Termed "life fossil oxidoreductases," these inorganic enzymes influence redox reactions, detoxification processes, and nutrient cycling in early Earth environments. By emphasizing the structural configuration of nanoparticles and their electron conformation, including oxygen defects and metal vacancies, especially electron hopping, the article provides a foundation for understanding inorganic enzyme mechanisms. This approach, rooted in physics, underscores that life's origin and evolution are governed by electron transfer principles within the framework of chemical equilibrium. Today, these nanoparticles serve as vital biocatalysts in natural ecosystems, participating in critical reactions for ecosystem health. The research highlights their enduring impact on Earth's history, shaping ecosystems and interacting with protein metal centers through shared electron transfer dynamics, offering insights into early life processes and adaptations.
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Affiliation(s)
- Xiao-Lan Huang
- Center for Clean Water Technology, School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-6044, USA
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Huang XL, Harmer JR, Schenk G, Southam G. Inorganic Fe-O and Fe-S oxidoreductases: paradigms for prebiotic chemistry and the evolution of enzymatic activity in biology. Front Chem 2024; 12:1349020. [PMID: 38389729 PMCID: PMC10881703 DOI: 10.3389/fchem.2024.1349020] [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: 12/04/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Oxidoreductases play crucial roles in electron transfer during biological redox reactions. These reactions are not exclusive to protein-based biocatalysts; nano-size (<100 nm), fine-grained inorganic colloids, such as iron oxides and sulfides, also participate. These nanocolloids exhibit intrinsic redox activity and possess direct electron transfer capacities comparable to their biological counterparts. The unique metal ion architecture of these nanocolloids, including electron configurations, coordination environment, electron conductivity, and the ability to promote spontaneous electron hopping, contributes to their transfer capabilities. Nano-size inorganic colloids are believed to be among the earliest 'oxidoreductases' to have 'evolved' on early Earth, playing critical roles in biological systems. Representing a distinct type of biocatalysts alongside metalloproteins, these nanoparticles offer an early alternative to protein-based oxidoreductase activity. While the roles of inorganic nano-sized catalysts in current Earth ecosystems are intuitively significant, they remain poorly understood and underestimated. Their contribution to chemical reactions and biogeochemical cycles likely helped shape and maintain the balance of our planet's ecosystems. However, their potential applications in biomedical, agricultural, and environmental protection sectors have not been fully explored or exploited. This review examines the structure, properties, and mechanisms of such catalysts from a material's evolutionary standpoint, aiming to raise awareness of their potential to provide innovative solutions to some of Earth's sustainability challenges.
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Affiliation(s)
- Xiao-Lan Huang
- NYS Center for Clean Water Technology, School of Marine and Atmospheric Sciences, Stony Brook, NY, United States
| | - Jeffrey R Harmer
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Gerhard Schenk
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Gordon Southam
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
- School of the Environment, The University of Queensland, Brisbane, QLD, Australia
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Cazacu N, Chilom CG, Iftimie S, Bălășoiu M, Ladygina VP, Stolyar SV, Orelovich OL, Kovalev YS, Rogachev AV. Biogenic Ferrihydrite Nanoparticles Produced by Klebsiella oxytoca: Characterization, Physicochemical Properties and Bovine Serum Albumin Interactions. NANOMATERIALS 2022; 12:nano12020249. [PMID: 35055266 PMCID: PMC8778533 DOI: 10.3390/nano12020249] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 12/20/2022]
Abstract
The synthesis of nanoparticles inside microorganisms is an economical alternative to chemical and physical methods of nanoparticle synthesis. In this study, ferrihydrite nanoparticles synthesized by Klebsiella oxytoca bacterium in special conditions were characterized by scanning electron microscopy (SEM), energy-dispersive X-ray analysis (EDS), small-angle X-ray (SAXS), UV-Vis spectroscopy, fluorescence, fluorescence resonance energy transfer (FRET), and molecular docking. The morphology and the structure of the particles were characterized by means of SEM and SAXS. The elemental content was determined by means of the EDS method. The absorption properties of the ferrihydrite nanoparticles were investigated by UV-Vis spectroscopy. The binding mechanism of the biogenic ferrihydrite nanoparticles to Bovine Serum Albumin (BSA) protein, studied by fluorescence, showed a static and weak process, combined with FRET. Protein denaturation by temperature and urea in the presence of the ferrihydrite nanoparticles demonstrated their influence on the unfolding process. The AutoDock Vina and UCSF Chimera programs were used to predict the optimal binding site of the ferrihydrite to BSA and to find the location of the hydrophobic cavities in the sub-domain IIA of the BSA structure.
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Affiliation(s)
- Nicoleta Cazacu
- Department of Electricity, Solid State and Biophysics, Faculty of Physics, University of Bucharest, RO-077125 Măgurele, Romania; (N.C.); (S.I.)
| | - Claudia G. Chilom
- Department of Electricity, Solid State and Biophysics, Faculty of Physics, University of Bucharest, RO-077125 Măgurele, Romania; (N.C.); (S.I.)
- Correspondence:
| | - Sorina Iftimie
- Department of Electricity, Solid State and Biophysics, Faculty of Physics, University of Bucharest, RO-077125 Măgurele, Romania; (N.C.); (S.I.)
| | - Maria Bălășoiu
- Department of Nuclear Physics, “Horia Hulubei” National Institute of Physics and Nuclear Engineering, RO-077125 Măgurele, Romania;
- Joint Institute for Nuclear Research, 141980 Dubna, Russia; (O.L.O.); (Y.S.K.); (A.V.R.)
- Moscow Institute of Physics and Technology, 141701 Dolgoprudniy, Russia
| | - Valentina P. Ladygina
- Federal Research Center KSC, Siberian Branch, Russian Academy of Sciences, 660036 Krasnoyarsk, Russia; (V.P.L.); (S.V.S.)
| | - Sergey V. Stolyar
- Federal Research Center KSC, Siberian Branch, Russian Academy of Sciences, 660036 Krasnoyarsk, Russia; (V.P.L.); (S.V.S.)
- Physics Department, School of Engineering Physics and Radio Electronics, Siberian Federal University, 660041 Krasnoyarsk, Russia
- Kirensky Institute of Physics, Siberian Branch, Russian Academy of Sciences, 660036 Krasnoyarsk, Russia
| | - Oleg L. Orelovich
- Joint Institute for Nuclear Research, 141980 Dubna, Russia; (O.L.O.); (Y.S.K.); (A.V.R.)
| | - Yuriy S. Kovalev
- Joint Institute for Nuclear Research, 141980 Dubna, Russia; (O.L.O.); (Y.S.K.); (A.V.R.)
| | - Andrey V. Rogachev
- Joint Institute for Nuclear Research, 141980 Dubna, Russia; (O.L.O.); (Y.S.K.); (A.V.R.)
- Moscow Institute of Physics and Technology, 141701 Dolgoprudniy, Russia
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Chilom CG, Sandu N, Iftimie S, Bălăşoiu M, Rogachev A, Orelovich O, Stolyar S. Interactions of Chemically Synthesized Ferrihydrite Nanoparticles with Human Serum Transferrin: Insights from Fluorescence Spectroscopic Studies. Int J Mol Sci 2021; 22:ijms22137034. [PMID: 34210014 PMCID: PMC8268179 DOI: 10.3390/ijms22137034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/26/2021] [Accepted: 06/26/2021] [Indexed: 01/21/2023] Open
Abstract
Human serum transferrin (HST) is a glycoprotein involved in iron transport that may be a candidate for functionalized nanoparticles to bind and target cancer cells. In this study, the effects of the simple and doped with cobalt (Co) and copper (Cu) ferrihydrite nanoparticles (Fh-NPs, Cu-Fh-NPs, and Co-Fh-NPs) were studied by spectroscopic and molecular approaches. Fluorescence spectroscopy revealed a static quenching mechanism for all three types of Fh-NPs. All Fh-NPs interacted with HST with low affinity, and the binding was driven by hydrogen bonding and van der Waals forces for simple Fh-NPs and by hydrophobic interactions for Cu-Fh-NPs and Co-Fh-NPs binding, respectively. Of all samples, simple Fh-NPs bound the most to the HST binding site. Fluorescence resonance energy transfer (FRET) allowed the efficient determination of the energy transfer between HST and NPs and the distance at which the transfer takes place and confirmed the mechanism of quenching. The denaturation of the HST is an endothermic process, both in the case of apo HST and HST in the presence of the three types of Fh-NPs. Molecular docking studies revealed that Fh binds with a low affinity to HST (Ka = 9.17 × 103 M−1) in accord with the fluorescence results, where the interaction between simple Fh-NPs and HST was described by a binding constant of 9.54 × 103 M−1.
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Affiliation(s)
- Claudia G. Chilom
- Department of Electricity, Solid Physics and Biophysics, Faculty of Physics, University of Bucharest, Str Atomistilor 405, CP MG 11, RO-077125 Măgurele, Romania; (N.S.); (S.I.)
- Correspondence:
| | - Nicoleta Sandu
- Department of Electricity, Solid Physics and Biophysics, Faculty of Physics, University of Bucharest, Str Atomistilor 405, CP MG 11, RO-077125 Măgurele, Romania; (N.S.); (S.I.)
| | - Sorina Iftimie
- Department of Electricity, Solid Physics and Biophysics, Faculty of Physics, University of Bucharest, Str Atomistilor 405, CP MG 11, RO-077125 Măgurele, Romania; (N.S.); (S.I.)
| | - Maria Bălăşoiu
- Joint Institute for Nuclear Research, Joliot-Curie No. 6, 141980 Dubna, Russia; (M.B.); (A.R.); (O.O.)
- Horia Hulubei National Institute for R&D in Physics and Nuclear Engineering, RO-077125 Măgurele, Romania
- Moscow Institute of Physics and Technology, Institutskiy Per. No. 9, 141701 Dolgoprudniy, Russia
| | - Andrey Rogachev
- Joint Institute for Nuclear Research, Joliot-Curie No. 6, 141980 Dubna, Russia; (M.B.); (A.R.); (O.O.)
- Moscow Institute of Physics and Technology, Institutskiy Per. No. 9, 141701 Dolgoprudniy, Russia
| | - Oleg Orelovich
- Joint Institute for Nuclear Research, Joliot-Curie No. 6, 141980 Dubna, Russia; (M.B.); (A.R.); (O.O.)
| | - Sergey Stolyar
- Krasnoyarsk Science Center of the Siberian, Branch of the Russian Academy of Sciences, Akademgorodok St. No. 50, 660036 Krasnoyarsk, Russia;
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Chilom CG, Bălan A, Sandu N, Bălăşoiu M, Stolyar S, Orelovich O. Exploring the Conformation and Thermal Stability of Human Serum Albumin Corona of Ferrihydrite Nanoparticles. Int J Mol Sci 2020; 21:ijms21249734. [PMID: 33419335 PMCID: PMC7766795 DOI: 10.3390/ijms21249734] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/13/2020] [Accepted: 12/17/2020] [Indexed: 12/16/2022] Open
Abstract
In the last few years, a great amount of attention has been given to nanoparticles research due to their physicochemical properties that allow their use in analytical instruments or in promising imaging applications on biological systems. The use of ferrihydrite nanoparticles (Fh-NPs) in practical applications implies a particular control of their magnetic properties, stability, biocompatibility, interaction with the surface of the target, and low toxicity. In this study, the formation and organization of human serum albumin (HSA) molecules around the simple Fh-NPs and Fh-NPs doped with Co and Cu were examined by Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM) in terms of morphology and particle size. The topology of all Fh-NPs shows an organized area of HSA around each type of Fh-NP. Molecular docking studies were used in order to determine the probable location of the ferrihydrite in the HSA structure. The thermal stability of these nanohybrids was further investigated by fluorimetry, using 214-Trp residue from HSA as a spectral sensor. The denaturation temperature (Tm) was determined, and stabilization of the HSA structure in the presence of Fh-NPs was discussed. This study could be a starting point for the development of different applications targeting the structure and stability of Fh-NPs complexes with proteins.
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Affiliation(s)
- Claudia G. Chilom
- Faculty of Physics, University of Bucharest, Str Atomiștilor 405, CP MG 11, RO-077125 Bucharest, Romania; (A.B.); (N.S.)
- Correspondence:
| | - Adriana Bălan
- Faculty of Physics, University of Bucharest, Str Atomiștilor 405, CP MG 11, RO-077125 Bucharest, Romania; (A.B.); (N.S.)
| | - Nicoleta Sandu
- Faculty of Physics, University of Bucharest, Str Atomiștilor 405, CP MG 11, RO-077125 Bucharest, Romania; (A.B.); (N.S.)
| | - Maria Bălăşoiu
- Joint Institute for Nuclear Research, Joliot-Curie No.6, 141980 Dubna, Russia; (M.B.); (O.O.)
- Moscow Institute of Physics and Technology, Institutskiy Per. No. 9, 141701 Dolgoprudniy, Russia
- Horia Hulubei National Institute of Physics and Nuclear Engineering, RO-077125 Măgurele, Romania
| | - Sergey Stolyar
- Krasnoyarsk Scientific Center, Federal Research Center KSC SB RAS, Akademgorodok St. No. 50, 660036 Krasnoyarsk, Russia;
| | - Oleg Orelovich
- Joint Institute for Nuclear Research, Joliot-Curie No.6, 141980 Dubna, Russia; (M.B.); (O.O.)
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The interaction of a thiosemicarbazone derived from R - (+) - limonene with lipid membranes. Chem Phys Lipids 2020; 234:105018. [PMID: 33232725 DOI: 10.1016/j.chemphyslip.2020.105018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 11/21/2022]
Abstract
As a potential drug, 2-nitrobenzaldehyde-thiosemicarbazone (2-TSC), a thiosemicarbazone derived from the terpene R-(+)-limonene, was studied through calorimetric and spectroscopic techniques. Differential Scanning Calorimetry (DSC) data showed that 2-TSC causes structural changes in a 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DMPC) membrane, strongly decreasing the cooperativity of the bilayer gel-fluid thermal transition. Optical absorption spectroscopy showed that 2-TSC is more soluble in ethanol and lipids than in water medium, and that the drug displays different structures in the different environments. Though 2-TSC displays no fluorescence, time resolved fluorescence showed that the drug is an effective quencher of the fluorescent probe 6-dodecanoyl-2-dimethylaminonaphthalene (Laurdan). As it is well accepted that Laurdan is positioned into the bilayer close to the membrane surface, that is possibly the localization of 2-TSC in a bilayer. Electron spin resonance (ESR) of the probe 1-palmitoyl-2-stearoyl-(14-doxyl)-sn-glycero-3-phosphocholine (14-PCSL) revealed that 2-TSC is inserted into the hydrocarbon part of the bilayer, fluidizing the lipid bilayer gel phase and rigidifying or organizing the bilayer fluid phase. Similar effects are found for other lipophilic molecules, including cholesterol. These results are useful to improve the understanding of the processes that govern the interaction of thiosemicarbazones with cell membranes, related to the activity of the drugs and their cytotoxicity.
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Ferrihydrite nanoparticles insights: Structural characterization, lactate dehydrogenase binding and virtual screening assay. Int J Biol Macromol 2020; 164:3559-3567. [PMID: 32890566 DOI: 10.1016/j.ijbiomac.2020.08.242] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/31/2020] [Accepted: 08/30/2020] [Indexed: 12/18/2022]
Abstract
The binding between the enzyme lactate dehydrogenase (LDH) and ferrihydrite nanoparticles (Fh-NPs) was investigated by means of small-angle neutron scattering (SANS), Fourier-transform infrared (FTIR) spectroscopy, fluorescence and Förster resonance energy transfer (FRET) and molecular docking. Fh-NPs - LDH compounds of dimensions under 100 nm are formed. The conformational changes and the mechanism of interaction between LDH and Fh-NPs simple and doped with Cu and Co, and the effect of these NPs on the thermal denaturation of LDH were monitored. The quenching mechanism is static, the binding occurring with moderate affinity, being mainly driven by hydrogen bonding and van der Waals forces. FRET occurs at a minimal distance of 2.55 nm. Thermal denaturation of LDH in the presence of simple and doped Fh-NPs shows that the thermodynamic parameters of protein unfolding are significantly changed with temperature. The denaturation temperature of LDH shifts to higher values in the presence of all Fh-NPs, than in the case of simple LDH. The docking approach estimates the energy corresponding to the best fit of the ferrihydrite in the LDH binding site near Trp. These results have direct implications on the uses of the complex of LDH with Fh-NPs in various biochemical, biological, or clinical applications.
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