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Xing Y, Yang M, Chen X. Fabrication of P and N Co-Doped Carbon Dots for Fe 3+ Detection in Serum and Lysosomal Tracking in Living Cells. BIOSENSORS 2023; 13:230. [PMID: 36831996 PMCID: PMC9954533 DOI: 10.3390/bios13020230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Doping with heteroatoms allows the retention of the general characteristics of carbon dots while allowing their physicochemical and photochemical properties to be effectively modulated. In this work, we report the preparation of ultrastable P and N co-doped carbon dots (PNCDs) that can be used for the highly selective detection of Fe3+ and the tracking of lysosomes in living cells. Fluorescent PNCDs were facilely prepared via a hydrothermal treatment of ethylenediamine and phytic acid, and they exhibited a high quantum yield of 22.0%. The strong coordination interaction between the phosphorus groups of PNCDs and Fe3+ rendered them efficient probes for use in selective Fe3+ detection, with a detection limit of 0.39 μM, and we demonstrated their practicability by accurately detecting the Fe3+ contents in bio-samples. At the same time, PNCDs exhibited high lysosomal location specificity in different cell lines due to surface lipophilic amino groups, and real-time tracking of the lysosome morphology in HeLa cells was achieved. The present work suggests that the fabrication of heteroatom-doped CDs might be an effective strategy to provide promising tools for cytology, such as organelle tracking.
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Affiliation(s)
- Yanzhi Xing
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Mei Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, China
| | - Xuwei Chen
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
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2
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Nagarajan R, Kamaraj E, Kim CH, Lee KH. Novel bis naphthalene-2-ol based colorimetric chemosensor for the detection of Fe2+ in physiological pH and its DFT calculation studies. TALANTA OPEN 2022. [DOI: 10.1016/j.talo.2022.100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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3
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Yeh CCG, Mokkawes T, Bradley J, Le Brun NE, de Visser S. Second coordination sphere effects on the mechanistic pathways for dioxygen activation by a ferritin: involvement of a Tyr radical and the identification of a cation binding site. Chembiochem 2022; 23:e202200257. [PMID: 35510795 PMCID: PMC9401865 DOI: 10.1002/cbic.202200257] [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: 05/04/2022] [Revised: 05/05/2022] [Indexed: 11/09/2022]
Abstract
Ferritins are ubiquitous diiron enzymes involved in iron(II) detoxification and oxidative stress responses and can act as metabolic iron stores. The overall reaction mechanisms of ferritin enzymes are still unclear, particularly concerning the role of the conserved, near catalytic center Tyr residue. Thus, we carried out a computational study of a ferritin using a large cluster model of well over 300 atoms including its first- and second-coordination sphere. The calculations reveal important insight into the structure and reactivity of ferritins. Specifically, the active site Tyr residue delivers a proton and electron in the catalytic cycle prior to iron(II) oxidation. In addition, the calculations highlight a likely cation binding site at Asp65, which through long-range electrostatic interactions, influences the electronic configuration and charge distributions of the metal center. The results are consistent with experimental observations but reveal novel detail of early mechanistic steps that lead to an unusual mixed-valent iron(III)-iron(II) center.
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Affiliation(s)
- Chieh-Chih George Yeh
- The University of Manchester, Department of Chemical Engineering, Oxford Road, Manchester, UNITED KINGDOM
| | - Thirakorn Mokkawes
- The University of Manchester, Department of Chemical Engineering, Manchester, UNITED KINGDOM
| | - Justin Bradley
- University of East Anglia, School of Chemistry, UNITED KINGDOM
| | - Nick E Le Brun
- University of East Anglia, School of Chemistry, UNITED KINGDOM
| | - Samuel de Visser
- The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN, Manchester, UNITED KINGDOM
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4
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Mukherjee G, Satpathy JK, Bagha UK, Mubarak MQE, Sastri CV, de Visser SP. Inspiration from Nature: Influence of Engineered Ligand Scaffolds and Auxiliary Factors on the Reactivity of Biomimetic Oxidants. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01993] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Gourab Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Jagnyesh K. Satpathy
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Umesh K. Bagha
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - M. Qadri E. Mubarak
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Fakulti Sains dan Teknologi, Universiti Sains Islam Malaysia, Bandar Baru Nilai, 71800 Nilai, Negeri Sembilan Malaysia
| | - Chivukula V. Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Sam P. de Visser
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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Negative catalysis / non-Bell-Evans-Polanyi reactivity by metalloenzymes: Examples from mononuclear heme and non-heme iron oxygenases. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.213914] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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6
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Xue X, Gao M, Rao H, Luo M, Wang H, An P, Feng T, Lu X, Xue Z, Liu X. Photothermal and colorimetric dual mode detection of nanomolar ferric ions in environmental sample based on in situ generation of prussian blue nanoparticles. Anal Chim Acta 2020; 1105:197-207. [DOI: 10.1016/j.aca.2020.01.049] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/28/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022]
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7
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Lv P, Xu Y, Liu Z, Li G, Ye B. Carbon dots doped lanthanide coordination polymers as dual-function fluorescent probe for ratio sensing Fe2+/3+ and ascorbic acid. Microchem J 2020. [DOI: 10.1016/j.microc.2019.104255] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mehmood R, Qi HW, Steeves AH, Kulik HJ. The Protein’s Role in Substrate Positioning and Reactivity for Biosynthetic Enzyme Complexes: The Case of SyrB2/SyrB1. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00865] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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9
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Chaturvedi SS, Ramanan R, Waheed SO, Ainsley J, Evison M, Ames JM, Schofield CJ, Karabencheva-Christova TG, Christov CZ. Conformational Dynamics Underlies Different Functions of Human KDM7 Histone Demethylases. Chemistry 2019; 25:5422-5426. [PMID: 30817054 DOI: 10.1002/chem.201900492] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/26/2019] [Indexed: 11/11/2022]
Abstract
The human KDM7 subfamily histone H3 Nϵ-methyl lysine demethylases PHF8 (KDM7B) and KIAA1718 (KDM7A) have different substrate selectivities and are linked to genetic diseases and cancer. We describe experimentally based computational studies revealing that flexibility of the region linking the PHD finger and JmjC domains in PHF8 and KIAA1718 regulates interdomain interactions, the nature of correlated motions, and ultimately H3 binding and demethylation site selectivity. F279S an X-linked mental retardation mutation in PHF8 is involved in correlated motions with the iron ligands and second sphere residues. The calculations reveal key roles of a flexible protein environment in productive formation of enzyme-substrate complexes and suggest targeting the flexible KDM7 linker region is of interest from a medicinal chemistry perspective.
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Affiliation(s)
- Shobhit S Chaturvedi
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Rajeev Ramanan
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Jon Ainsley
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 BST, UK
| | - Martin Evison
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 BST, UK
| | - Jennifer M Ames
- Centre for Research in Biosciences, University of West of England, Coldharbour Lane, Bristol, BS16 1QY, UK
| | | | - Tatyana G Karabencheva-Christova
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 BST, UK
| | - Christo Z Christov
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 BST, UK
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Xu K, Hirao H. Revisiting the catalytic mechanism of Mo-Cu carbon monoxide dehydrogenase using QM/MM and DFT calculations. Phys Chem Chem Phys 2018; 20:18938-18948. [PMID: 29744484 DOI: 10.1039/c8cp00858b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Previous density functional theory (DFT) studies have shown that the release of the produced carbon dioxide (CO2) from an active-site cluster is a thermodynamically or kinetically difficult step in the enzymatic carbon monoxide (CO) oxidation catalyzed by Mo-Cu carbon monoxide dehydrogenase (Mo-Cu CODH). To better understand the effect of the protein environment on this difficult CO2 release step as well as other reaction steps, we applied hybrid quantum mechanics and molecular mechanics (QM/MM) calculations to the Mo-Cu CODH enzyme. The results show that in the first step, the equatorial Mo[double bond, length as m-dash]O group in the active-site cluster attacks the nearby CO molecule bound to the Cu site. Afterward, a stable thiocarbonate intermediate is formed in which the CO2 molecule is embedded and the copper-S(μ-sulfido) bond is broken. A free CO2 molecule, i.e., the final product, is then released from the active-site cluster, not directly from the thiocarbonate intermediate but via a previously formed intermediate that also contains CO2 but retains the Cu-S(μ-sulfido) bond. In contrast to the previous DFT results, the calculated barrier for this process was low in our QM/MM calculations. An additional QM/MM analysis of the barrier height showed that the effect of the protein environment on this barrier lowering is not very large. We found that the reason for the low barrier obtained by QM/MM is that the barrier for CO2 release is already not high at the DFT level. These results allow us to conclude that the CO oxidation reaction passes through the formation of a thiocarbonate intermediate, and that the subsequent CO2 release is kinetically not difficult. Nevertheless, the protein environment has an important role to play in making the latter process thermodynamically favored. No low-barrier pathway for the product release could be obtained for the reaction of n-butylisocyanide, which is consistent with the experimental fact that n-butylisocyanide inhibits Mo-Cu CODH.
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Affiliation(s)
- Kai Xu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
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Abdizadeh H, Atilgan AR, Atilgan C, Dedeoglu B. Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins. Metallomics 2018; 9:1513-1533. [PMID: 28967944 DOI: 10.1039/c7mt00216e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
With the advances in three-dimensional structure determination techniques, high quality structures of the iron transport proteins transferrin and the bacterial ferric binding protein (FbpA) have been deposited in the past decade. These are proteins of relatively large size, and developments in hardware and software have only recently made it possible to study their dynamics using standard computational resources. We review computational techniques towards understanding the equilibrium and kinetic properties of iron transport proteins under different environmental conditions. At the level of detail that requires quantum chemical treatments, the octahedral geometry around iron has been scrutinized and it has been established that the iron coordinating tyrosines are in an unusual deprotonated state. At the atomistic level, both the N-lobe and the full bilobal structure of transferrin have been studied under varying conditions of pH, ionic strength and binding of other metal ions by molecular dynamics (MD) simulations. These studies have allowed questions to be answered, among others, on the function of second shell residues in iron release, the role of synergistic anions in preparing the active site for iron binding, and the differences between the kinetics of the N- and the C-lobe. MD simulations on FbpA have led to the detailed observation of the binding kinetics of phosphate to the apo form, and to the conformational preferences of the holo form under conditions mimicking the environmental niches provided by the periplasmic space. To study the dynamics of these proteins with their receptors, one must resort to coarse-grained methodologies, since these systems are prohibitively large for atomistic simulations. A study of the complex of human transferrin (hTf) with its pathogenic receptor by such methods has revealed a potential mechanistic explanation for the defense mechanism that arises in evolutionary warfare. Meanwhile, the motions in the transferrin receptor bound hTf have been shown to disfavor apo hTf dissociation, explaining why the two proteins remain in complex during the recycling process from the endosome to the cell surface. Open problems and possible technological applications related to metal ion binding-release in iron transport proteins that may be handled by hybrid use of quantum mechanical, MD and coarse-grained approaches are discussed.
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Affiliation(s)
- H Abdizadeh
- Faculty of Engineering and Natural Sciences, Sabancı University, Orhanlı 34956, Tuzla, Istanbul, Turkey.
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12
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Shangguan J, Huang J, He D, He X, Wang K, Ye R, Yang X, Qing T, Tang J. Highly Fe3+-Selective Fluorescent Nanoprobe Based on Ultrabright N/P Codoped Carbon Dots and Its Application in Biological Samples. Anal Chem 2017. [DOI: 10.1021/acs.analchem.7b01053] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jingfang Shangguan
- State Key Laboratory
of Chemo/Biosensing and Chemometrics, College of Biology, College
of Chemistry and Chemical Engineering, and Key Laboratory for Bio-Nanotechnology
and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Jin Huang
- State Key Laboratory
of Chemo/Biosensing and Chemometrics, College of Biology, College
of Chemistry and Chemical Engineering, and Key Laboratory for Bio-Nanotechnology
and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Dinggeng He
- State Key Laboratory
of Chemo/Biosensing and Chemometrics, College of Biology, College
of Chemistry and Chemical Engineering, and Key Laboratory for Bio-Nanotechnology
and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Xiaoxiao He
- State Key Laboratory
of Chemo/Biosensing and Chemometrics, College of Biology, College
of Chemistry and Chemical Engineering, and Key Laboratory for Bio-Nanotechnology
and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Kemin Wang
- State Key Laboratory
of Chemo/Biosensing and Chemometrics, College of Biology, College
of Chemistry and Chemical Engineering, and Key Laboratory for Bio-Nanotechnology
and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Runzhi Ye
- State Key Laboratory
of Chemo/Biosensing and Chemometrics, College of Biology, College
of Chemistry and Chemical Engineering, and Key Laboratory for Bio-Nanotechnology
and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Xue Yang
- State Key Laboratory
of Chemo/Biosensing and Chemometrics, College of Biology, College
of Chemistry and Chemical Engineering, and Key Laboratory for Bio-Nanotechnology
and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Taiping Qing
- State Key Laboratory
of Chemo/Biosensing and Chemometrics, College of Biology, College
of Chemistry and Chemical Engineering, and Key Laboratory for Bio-Nanotechnology
and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Jinlu Tang
- State Key Laboratory
of Chemo/Biosensing and Chemometrics, College of Biology, College
of Chemistry and Chemical Engineering, and Key Laboratory for Bio-Nanotechnology
and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
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13
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Celebrating Ed Solomon. J Biol Inorg Chem 2016. [DOI: 10.1007/s00775-016-1383-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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