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Liutkus M, Sasselli IR, Rojas AL, Cortajarena AL. Diverse crystalline protein scaffolds through metal-dependent polymorphism. Protein Sci 2024; 33:e4971. [PMID: 38591647 PMCID: PMC11002994 DOI: 10.1002/pro.4971] [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: 07/26/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 04/10/2024]
Abstract
As protein crystals are increasingly finding diverse applications as scaffolds, controlled crystal polymorphism presents a facile strategy to form crystalline assemblies with controllable porosity with minimal to no protein engineering. Polymorphs of consensus tetratricopeptide repeat proteins with varying porosity were obtained through co-crystallization with metal salts, exploiting the innate metal ion geometric requirements. A single structurally exposed negative amino acid cluster was responsible for metal coordination, despite the abundance of negatively charged residues. Density functional theory calculations showed that while most of the crystals were the most thermodynamically stable assemblies, some were kinetically trapped states. Thus, crystalline porosity diversity is achieved and controlled with metal coordination, opening a new scope in the application of proteins as biocompatible protein-metal-organic frameworks (POFs). In addition, metal-dependent polymorphic crystals allow direct comparison of metal coordination preferences.
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Affiliation(s)
- Mantas Liutkus
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology AllianceSan SebastianSpain
| | - Ivan R. Sasselli
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology AllianceSan SebastianSpain
- Present address:
Centro de Física de Materiales (CFM)CSIC‐UPV/EHUSan SebastiánSpain
| | - Adriana L. Rojas
- Centre for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceBilbaoSpain
| | - Aitziber L. Cortajarena
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology AllianceSan SebastianSpain
- IkerbasqueBasque Foundation for ScienceBilbaoSpain
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2
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Bio template route for fabrication of a hybrid material composed of hierarchical boehmite, layered double hydroxides (Mg-Al) and porous carbon on a steel fiber for solid phase microextraction of agrochemicals. Mikrochim Acta 2019; 186:678. [PMID: 31515633 DOI: 10.1007/s00604-019-3782-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/24/2019] [Indexed: 10/26/2022]
Abstract
Nanosheets of a porous layered double hydroxide were directionally arranged on boehmite nanowires and porous carbon and used as a coating for solid-phase microextraction (SPME) method. Porous carbon tubes were prepared from goat grass and then coated with layered double hydroxide nanosheets and boehmite nanowires. The nanomaterial was placed on a stainless-steel wire which then was used for the extraction of fifteen agrochemicals from aqueous sample solutions. The extraction temperature, extraction time, ionic strength, stirring rate, and desorption temperature and time were optimized. Following thermal desorption of the agrochemicals in the injector of the gas chromatograph, they were quantified by GC/MS. Under optimum conditions, the repeatability for one fiber, expressed as relative standard deviation, was between 2.9 and 11.1%. The detection limits for the agrochemicals are between 2-29 ng L-1. The method is simple, fast, and inexpensive (in terms of equipment). The fiber is thermally stable, and the relative recoveries from spiked samples are better compared to conventional methods of extraction. Graphical abstract Schematic illustration of the preparation of three-dimensional hierarchical boehmite/ layered double hydroxides/ porous carbon (Boeh/LDH/pC) SPME fibers and application for the extraction of fifteen agrochemicals from aqueous sample solutions following quantification by GC/MS.
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3
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Ye F, Huang Y, Li J, Ma Y, Xie C, Liu Z, Deng X, Wan J, Xue T, Liu W, Zhang M. An unexpected INAD PDZ tandem-mediated plcβ binding in Drosophila photo receptors. eLife 2018; 7:41848. [PMID: 30526850 PMCID: PMC6300352 DOI: 10.7554/elife.41848] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/08/2018] [Indexed: 01/08/2023] Open
Abstract
INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. However, the molecular mechanism that governs the interaction between INAD and NORPA (phospholipase Cβ, PLCβ), a key step for the fast kinetics of the light signaling, is not known. Here, we show that the NORPA C-terminal coiled-coil domain and PDZ-binding motif (CC-PBM) synergistically bind to INAD PDZ45 tandem with an unexpected mode and unprecedented high affinity. Guided by the structure of the INAD-NORPA complex, we discover that INADL is probably a mammalian counterpart of INAD. The INADL PDZ89 tandem specifically binds to PLCβ4 with a mode that is strikingly similar to that of the INAD-NORPA complex, as revealed by the structure of the INADL PDZ89-PLCβ4 CC-PBM complex. Therefore, our study suggests that the highly specific PDZ tandem - PLCβ interactions are an evolutionarily conserved mechanism in PLCβ signaling in the animal kingdom.
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Affiliation(s)
- Fei Ye
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China.,Institute for Advanced Study, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yuxin Huang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jianchao Li
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yuqian Ma
- Hefei National Laboratory for Physical Sciences at Microscale,CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Chensu Xie
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Zexu Liu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiaoying Deng
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jun Wan
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China.,Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Tian Xue
- Hefei National Laboratory for Physical Sciences at Microscale,CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wei Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China.,Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
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4
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Hartje LF, Snow CD. Protein crystal based materials for nanoscale applications in medicine and biotechnology. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2018; 11:e1547. [DOI: 10.1002/wnan.1547] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/28/2018] [Accepted: 10/12/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Luke F. Hartje
- Department of Biochemistry and Molecular Biology Colorado State University Fort Collins Colorado
| | - Christopher D. Snow
- Department of Chemical and Biological Engineering Colorado State University Fort Collins Colorado
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5
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Yamada KD, Kunishima N, Matsuura Y, Nakai K, Naitow H, Fukasawa Y, Tomii K. Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids. Acta Crystallogr D Struct Biol 2017; 73:757-766. [PMID: 28876239 PMCID: PMC5586248 DOI: 10.1107/s2059798317010932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 07/25/2017] [Indexed: 11/13/2023] Open
Abstract
An alternative rational approach to improve protein crystals by using single-site mutation of surface residues is proposed based on the results of a statistical analysis using a compiled data set of 918 independent crystal structures, thereby reflecting not only the entropic effect but also other effects upon protein crystallization. This analysis reveals a clear difference in the crystal-packing propensity of amino acids depending on the secondary-structural class. To verify this result, a systematic crystallization experiment was performed with the biotin carboxyl carrier protein from Pyrococcus horikoshii OT3 (PhBCCP). Six single-site mutations were examined: Ala138 on the surface of a β-sheet was mutated to Ile, Tyr, Arg, Gln, Val and Lys. In agreement with prediction, it was observed that the two mutants (A138I and A138Y) harbouring the residues with the highest crystal-packing propensities for β-sheet at position 138 provided better crystallization scores relative to those of other constructs, including the wild type, and that the crystal-packing propensity for β-sheet provided the best correlation with the ratio of obtaining crystals. Two new crystal forms of these mutants were obtained that diffracted to high resolution, generating novel packing interfaces with the mutated residues (Ile/Tyr). The mutations introduced did not affect the overall structures, indicating that a β-sheet can accommodate a successful mutation if it is carefully selected so as to avoid intramolecular steric hindrance. A significant negative correlation between the ratio of obtaining amorphous precipitate and the crystal-packing propensity was also found.
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Affiliation(s)
- Kazunori D. Yamada
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Naoki Kunishima
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshinori Matsuura
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Koshiro Nakai
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hisashi Naitow
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshinori Fukasawa
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Kentaro Tomii
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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6
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Freeman A. Protein-Mediated Biotemplating on the Nanoscale. Biomimetics (Basel) 2017; 2:E14. [PMID: 31105177 PMCID: PMC6352702 DOI: 10.3390/biomimetics2030014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/18/2017] [Accepted: 08/01/2017] [Indexed: 12/26/2022] Open
Abstract
Purified proteins offer a homogeneous population of biological nanoparticles, equipped in many cases with specific binding sites enabling the directed self-assembly of envisaged one-, two- or three-dimensional arrays. These arrays may serve as nanoscale biotemplates for the preparation of novel functional composite materials, which exhibit potential applications, especially in the fields of nanoelectronics and optical devices. This review provides an overview of the field of protein-mediated biotemplating, focussing on achievements made throughout the past decade. It is comprised of seven sections designed according to the size and configuration of the protein-made biotemplate. Each section describes the design and size of the biotemplate, the resulting hybrid structures, the fabrication methodology, the analytical tools employed for the structural analysis of the hybrids obtained, and, finally, their claimed/intended applications and a feasibility demonstration (whenever available). In conclusion, a short assessment of the overall status of the achievements already made vs. the future challenges of this field is provided.
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Affiliation(s)
- Amihay Freeman
- Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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7
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Yan EK, Cao HL, Zhang CY, Lu QQ, Ye YJ, He J, Huang LJ, Yin DC. Cross-linked protein crystals by glutaraldehyde and their applications. RSC Adv 2015. [DOI: 10.1039/c5ra01722j] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The mechanism of cross-linked protein crystals using glutaraldehyde, and their properties and applications are discussed in detail.
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Affiliation(s)
- Er-Kai Yan
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Hui-Ling Cao
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Chen-Yan Zhang
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Qin-Qin Lu
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Ya-Jing Ye
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Jin He
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Lin-Jun Huang
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Da-Chuan Yin
- Institute for Special Environmental Biophysics
- Key Laboratory for Space Bioscience and Space Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
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8
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Kalyoncu S, Hyun J, Pai JC, Johnson JL, Entzminger K, Jain A, Heaner DP, Morales IA, Truskett TM, Maynard JA, Lieberman RL. Effects of protein engineering and rational mutagenesis on crystal lattice of single chain antibody fragments. Proteins 2014; 82:1884-95. [PMID: 24615866 PMCID: PMC4142072 DOI: 10.1002/prot.24542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/12/2014] [Accepted: 02/20/2014] [Indexed: 11/06/2022]
Abstract
Protein crystallization is dependent upon, and sensitive to, the intermolecular contacts that assist in ordering proteins into a three-dimensional lattice. Here we used protein engineering and mutagenesis to affect the crystallization of single chain antibody fragments (scFvs) that recognize the EE epitope (EYMPME) with high affinity. These hypercrystallizable scFvs are under development to assist difficult proteins, such as membrane proteins, in forming crystals, by acting as crystallization chaperones. Guided by analyses of intermolecular crystal lattice contacts, two second-generation anti-EE scFvs were produced, which bind to proteins with installed EE tags. Surprisingly, although noncomplementarity determining region (CDR) lattice residues from the parent scFv framework remained unchanged through the processes of protein engineering and rational design, crystal lattices of the derivative scFvs differ. Comparison of energy calculations and the experimentally-determined lattice interactions for this basis set provides insight into the complexity of the forces driving crystal lattice choice and demonstrates the availability of multiple well-ordered surface features in our scFvs capable of forming versatile crystal contacts.
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Affiliation(s)
- Sibel Kalyoncu
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332-0400
| | - Jeongmin Hyun
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - Jennifer C. Pai
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - Jennifer L. Johnson
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332-0400
| | - Kevin Entzminger
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - Avni Jain
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - David P. Heaner
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332-0400
| | - Ivan A. Morales
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332-0400
| | - Thomas M. Truskett
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - Jennifer A. Maynard
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - Raquel L. Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332-0400
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9
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Abstract
A protein crystal has been grown, which uniquely, is fully cross-linked by cysteine-mediated disulfide bonds along the c-axis.
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Affiliation(s)
- Esben M. Quistgaard
- Department of Medical Biochemistry and Biophysics
- Karolinska Institutet
- SE-171 77 Stockholm, Sweden
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10
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Cohen-Hadar N, Lagziel-Simis S, Wine Y, Frolow F, Freeman A. Re-structuring protein crystals porosity for biotemplating by chemical modification of lysine residues. Biotechnol Bioeng 2010; 108:1-11. [DOI: 10.1002/bit.22921] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Cao F, Li D. Biotemplate synthesis of monodispersed iron phosphate hollow microspheres. BIOINSPIRATION & BIOMIMETICS 2010; 5:16005. [PMID: 20185860 DOI: 10.1088/1748-3182/5/1/016005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Monodispersed iron phosphate hollow microspheres with a high degree of crystallization were prepared through a facile in situ deposition method using rape pollen grains as a biotemplate. The functional group on the surface of the pollen grains could adsorb Fe(3+), which provided the nucleation sites for growth of iron phosphate nanoparticles. After being sintered at 600 degrees C for 10 h, the pollen grains were removed and iron phosphate hollow microspheres were obtained. A scanning electron microscope and x-ray diffraction were applied to characterize the morphology and crystalline structure of the pollen grains, iron phosphate-coated pollen grains and iron phosphate hollow microspheres. Differential scanning calorimetry and thermogravity analyses were performed to investigate the thermal behavior of the iron phosphate-coated pollen grains during the calcinations. Energy dispersive spectroscopy and Fourier transform infrared spectroscopy were utilized to investigate the interaction between the pollen grains and iron phosphate. The effect of the pollen wall on the surface morphology of these iron phosphate hollow microspheres was also proven in this work.
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Affiliation(s)
- Feng Cao
- College of Materials Science and Engineering, Nanjing University of Technology, Jiangsu, Nanjing, People's Republic of China
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