1
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Sendker FL, Lo YK, Heimerl T, Bohn S, Persson LJ, Mais CN, Sadowska W, Paczia N, Nußbaum E, Del Carmen Sánchez Olmos M, Forchhammer K, Schindler D, Erb TJ, Benesch JLP, Marklund EG, Bange G, Schuller JM, Hochberg GKA. Emergence of fractal geometries in the evolution of a metabolic enzyme. Nature 2024; 628:894-900. [PMID: 38600380 PMCID: PMC11041685 DOI: 10.1038/s41586-024-07287-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
Fractals are patterns that are self-similar across multiple length-scales1. Macroscopic fractals are common in nature2-4; however, so far, molecular assembly into fractals is restricted to synthetic systems5-12. Here we report the discovery of a natural protein, citrate synthase from the cyanobacterium Synechococcus elongatus, which self-assembles into Sierpiński triangles. Using cryo-electron microscopy, we reveal how the fractal assembles from a hexameric building block. Although different stimuli modulate the formation of fractal complexes and these complexes can regulate the enzymatic activity of citrate synthase in vitro, the fractal may not serve a physiological function in vivo. We use ancestral sequence reconstruction to retrace how the citrate synthase fractal evolved from non-fractal precursors, and the results suggest it may have emerged as a harmless evolutionary accident. Our findings expand the space of possible protein complexes and demonstrate that intricate and regulatable assemblies can evolve in a single substitution.
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Affiliation(s)
- Franziska L Sendker
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Yat Kei Lo
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Stefan Bohn
- Cryo-EM Platform and Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany
| | - Louise J Persson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | - Wiktoria Sadowska
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Nicole Paczia
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Eva Nußbaum
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Tübingen, Germany
| | | | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Tübingen, Germany
| | - Daniel Schindler
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- MaxGENESYS Biofoundry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J Erb
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Max Planck Fellow Group Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan M Schuller
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany.
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany.
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Wang J, Jiang Z, Liu W, Wu Z, Miao R, Fu F, Yin JF, Chen B, Dong Q, Zhao H, Li K, Wang G, Liu D, Yin P, Li Y, Chen M, Wang P. The Marriage of Sierpiński Triangles and Platonic Polyhedra. Angew Chem Int Ed Engl 2023; 62:e202214237. [PMID: 36323638 DOI: 10.1002/anie.202214237] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Fractal structures with self-similarity are of fundamental importance in the fields of aesthetic, chemistry and mathematics. Here, by taking advantage of constructs the rational geometry-directed precursor design, we report the construction of two fascinating Platonic solids, the Sierpiński tetrahedron ST-T and the Sierpiński octahedron ST-O, in which each possesses a fractal Sierpiński triangle on their independent faces. These two discrete complexes are formed in near-quantitative yield from the multi-component self-assembly of truncated Sierpiński triangular kernel L1 with tribenzotriquinacene-based hexatopic and anthracene-based tetratopic terpyridine ligands (L3 and L4 ) in the presence of metal ions, respectively. The enhanced stabilities of the 3D discrete structures were investigated by gradient tandem mass spectrometry (gMS2 ). This work provides new constructs for the imitation of complex virus assemblies and for the molecular encapsulation of giant guest molecules.
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Affiliation(s)
- Jun Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, 510006, Guangzhou, China
| | - Zhilong Jiang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, 510006, Guangzhou, China
| | - Weiya Liu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, 510006, Guangzhou, China
| | - Zihao Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, 510006, Guangzhou, China
| | - Rui Miao
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, 510006, Guangzhou, China
| | - Fan Fu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, 510006, Guangzhou, China
| | - Jia-Fu Yin
- South China Advanced Institute for Soft Matter Science and Technology & State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, 510640, Guangzhou, China
| | - Bangtang Chen
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, 510006, Guangzhou, China
| | - Qiangqiang Dong
- College of Chemistry and Chemical Engineering, Central South University, 410083, Changsha, China
| | - He Zhao
- College of Chemistry and Chemical Engineering, Central South University, 410083, Changsha, China
| | - Kaixiu Li
- College of Chemistry and Chemical Engineering, Central South University, 410083, Changsha, China
| | - Guotao Wang
- College of Chemistry and Chemical Engineering, Central South University, 410083, Changsha, China
| | - Die Liu
- College of Chemistry and Chemical Engineering, Central South University, 410083, Changsha, China
| | - Panchao Yin
- South China Advanced Institute for Soft Matter Science and Technology & State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, 510640, Guangzhou, China
| | - Yiming Li
- College of Chemistry and Chemical Engineering, Central South University, 410083, Changsha, China
| | - Mingzhao Chen
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, 510006, Guangzhou, China
| | - Pingshan Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, 510006, Guangzhou, China.,College of Chemistry and Chemical Engineering, Central South University, 410083, Changsha, China
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3
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Duan Q, An J, Mao H, Liang D, Li H, Wang S, Huang C. Review about the Application of Fractal Theory in the Research of Packaging Materials. MATERIALS 2021; 14:ma14040860. [PMID: 33670233 PMCID: PMC7916937 DOI: 10.3390/ma14040860] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 11/24/2022]
Abstract
The work is intended to summarize the recent progress in the work of fractal theory in packaging material to provide important insights into applied research on fractal in packaging materials. The fractal analysis methods employed for inorganic materials such as metal alloys and ceramics, polymers, and their composites are reviewed from the aspects of fractal feature extraction and fractal dimension calculation methods. Through the fractal dimension of packaging materials and the fractal in their preparation process, the relationship between the fractal characteristic parameters and the properties of packaging materials is discussed. The fractal analysis method can qualitatively and quantitatively characterize the fractal characteristics, microstructure, and properties of a large number of various types of packaging materials. The method of using fractal theory to probe the preparation and properties of packaging materials is universal; the relationship between the properties of packaging materials and fractal dimension will be a critical trend of fractal theory in the research on properties of packaging materials.
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Affiliation(s)
- Qingshan Duan
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China; (Q.D.); (J.A.); (D.L.); (H.L.); (S.W.)
- Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, Nanning 530004, China
| | - Jiejie An
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China; (Q.D.); (J.A.); (D.L.); (H.L.); (S.W.)
- Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, Nanning 530004, China
| | - Hanling Mao
- School of Mechanical Engineering, Guangxi University, Nanning 530004, China;
| | - Dongwu Liang
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China; (Q.D.); (J.A.); (D.L.); (H.L.); (S.W.)
- Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, Nanning 530004, China
| | - Hao Li
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China; (Q.D.); (J.A.); (D.L.); (H.L.); (S.W.)
- Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, Nanning 530004, China
| | - Shuangfei Wang
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China; (Q.D.); (J.A.); (D.L.); (H.L.); (S.W.)
- Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, Nanning 530004, China
| | - Chongxing Huang
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China; (Q.D.); (J.A.); (D.L.); (H.L.); (S.W.)
- Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, Nanning 530004, China
- Correspondence:
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4
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Chen M, Cao JN, Li S, Liu D, Wang J, Zhao H, Wang G, Wu T, Jiang Z, Wang P. Customized self-assembled molecules: rim adjustable coronal polygons with multiple-folds symmetry. Org Chem Front 2021. [DOI: 10.1039/d1qo01316e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three desired discrete metallomacrocyclic wreaths with four-, five- and six-fold symmetry were successfully realized in a controlled fashion.
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Affiliation(s)
- Mingzhao Chen
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education; Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Jia-nan Cao
- Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Suqing Li
- Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Die Liu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education; Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Jun Wang
- Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - He Zhao
- Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Guotao Wang
- Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Tun Wu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education; Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Zhilong Jiang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education; Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Pingshan Wang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education; Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
- Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
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5
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Wang J, Zhao H, Chen M, Jiang Z, Wang F, Wang G, Li K, Zhang Z, Liu D, Jiang Z, Wang P. Construction of Macromolecular Pinwheels Using Predesigned Metalloligands. J Am Chem Soc 2020; 142:21691-21701. [PMID: 33206521 DOI: 10.1021/jacs.0c08020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Developing a methodology to build target structures is one of the major themes of synthetic chemistry. However, it has proven to be immensely challenging to achieve multilevel elaborate molecular architectures in a predictable way. Herein, we describe the self-assembly of a series of pinwheel-shaped starlike supramolecules through three rationally preorganized metalloligands L1-L3. The key octa-uncomplexed terpyridine (tpy) metalloligand L3, synthesized with an 8-fold Suzuki coupling reaction to metal-containing complexes, has four different types of terpyridines connected with three ⟨tpy-Ru2+-tpy⟩ units, making this the most subunits known so far for a preorganized module. Based on the principle of geometric complementation and the high "density of coordination sites", these metalloligands were assembled with Zn2+ ions to form a pinwheel-shaped star trigon P1, pentagram P2, and hexagram P3 with precisely controlled shapes in nearly quantitative yields. With molecular weights ranging from 16756 to 56053 Da and diameters of 6.7-13.6 nm, the structural composition, shape, and rigidity of these pinwheel-shaped architectures have been fully characterized by 1D and 2D (NMR), electrospray ionization mass spectrometry, traveling-wave ion mobility mass spectrometry, and transmission electron microscopy.
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Affiliation(s)
- Jun Wang
- Department of Organic and Polymer Chemistry; Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - He Zhao
- Department of Organic and Polymer Chemistry; Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Mingzhao Chen
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education; Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Zhiyuan Jiang
- Department of Organic and Polymer Chemistry; Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Feng Wang
- Department of Organic and Polymer Chemistry; Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Guotao Wang
- Department of Organic and Polymer Chemistry; Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Kaixiu Li
- Department of Organic and Polymer Chemistry; Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Zhe Zhang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education; Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Die Liu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education; Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Zhilong Jiang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education; Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Pingshan Wang
- Department of Organic and Polymer Chemistry; Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China.,Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education; Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
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