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Wang X, Kang H, Huang K, Guo M, Wu Y, Ying T, Liu Y, Wei D. Antibody Nanotweezer Constructing Bivalent Transistor-Biomolecule Interface with Spatial Tolerance. NANO LETTERS 2024; 24:3914-3921. [PMID: 38513214 DOI: 10.1021/acs.nanolett.3c05140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Establishing a multivalent interface between the biointerface of a living system and electronic device is vital to building intelligent bioelectronic systems. How to achieve multivalent binding with spatial tolerance at the nanoscale remains challenging. Here, we report an antibody nanotweezer that is a self-adaptive bivalent nanobody enabling strong and resilient binding between transistor and envelope proteins at biointerfaces. The antibody nanotweezer is constructed by a DNA framework, where the nanoscale patterning of nanobodies along with their local spatial adaptivity enables simultaneous recognition of target epitopes without binding stress. As such, effective binding affinity increases by 1 order of magnitude compared with monovalent antibody. The antibody nanotweezer operating on transistor offers enhanced signal transduction, which is implemented to detect clinical pathogens, showing ∼100% overall agreement with PCR results. This work provides a perspective of engineering multivalent interfaces between biosystems with solid-state devices, holding great potential for organoid intelligence on a chip.
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Affiliation(s)
- Xuejun Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Hua Kang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Keke Huang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Mingquan Guo
- Shanghai Institute of Phage, Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yanling Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Tianlei Ying
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yunqi Liu
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
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Ji X, Wang N, Wang J, Wang T, Huang X, Hao H. Non-destructive real-time monitoring and investigation of the self-assembly process using fluorescent probes. Chem Sci 2024; 15:3800-3830. [PMID: 38487216 PMCID: PMC10935763 DOI: 10.1039/d3sc06527h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/22/2024] [Indexed: 03/17/2024] Open
Abstract
Self-assembly has been considered as a strategy to construct superstructures with specific functions, which has been widely used in many different fields, such as bionics, catalysis, and pharmacology. A detailed and in-depth analysis of the self-assembly mechanism is beneficial for directionally and accurately regulating the self-assembly process of substances. Fluorescent probes exhibit unique advantages of sensitivity, non-destructiveness, and real-time self-assembly tracking, compared with traditional methods. In this work, the design principle of fluorescent probes with different functions and their applications for the detection of thermodynamic and kinetic parameters during the self-assembly process were systematically reviewed. Their efficiency, limitations and advantages are also discussed. Furthermore, the promising perspectives of fluorescent probes for investigating the self-assembly process are also discussed and suggested.
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Affiliation(s)
- Xiongtao Ji
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
| | - Na Wang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China +86-22-27374971 +86-22-27405754
| | - Jingkang Wang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China +86-22-27374971 +86-22-27405754
| | - Ting Wang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China +86-22-27374971 +86-22-27405754
| | - Xin Huang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China +86-22-27374971 +86-22-27405754
| | - Hongxun Hao
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China +86-22-27374971 +86-22-27405754
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Wang X, Xia B, Hao Z, Kang H, Liu W, Chen Y, Jiang Q, Liu J, Gou J, Dong B, Wee ATS, Liu Y, Wei D. A closed-loop catalytic nanoreactor system on a transistor. SCIENCE ADVANCES 2023; 9:eadj0839. [PMID: 37729411 PMCID: PMC10511191 DOI: 10.1126/sciadv.adj0839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/17/2023] [Indexed: 09/22/2023]
Abstract
Precision chemistry demands miniaturized catalytic systems for sophisticated reactions with well-defined pathways. An ideal solution is to construct a nanoreactor system functioning as a chemistry laboratory to execute a full chemical process with molecular precision. However, existing nanoscale catalytic systems fail to in situ control reaction kinetics in a closed-loop manner, lacking the precision toward ultimate reaction efficiency. We find an inter-electrochemical gating effect when operating DNA framework-constructed enzyme cascade nanoreactors on a transistor, enabling in situ closed-loop reaction monitoring and modulation electrically. Therefore, a comprehensive system is developed, encapsulating nanoreactors, analyzers, and modulators, where the gate potential modulates enzyme activity and switches cascade reaction "ON" or "OFF." Such electric field-effect property enhances catalytic efficiency of enzyme by 343.4-fold and enables sensitive sarcosine assay for prostate cancer diagnoses, with a limit of detection five orders of magnitude lower than methodologies in clinical laboratory. By coupling with solid-state electronics, this work provides a perspective to construct intelligent nano-systems for precision chemistry.
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Affiliation(s)
- Xuejun Wang
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
- Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Binbin Xia
- Institute of Molecular Medicine, Department of Urology, Department of Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhuang Hao
- School of Mechanical Engineering and Automation, Beihang University, Beijing 100191, China
- School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Hua Kang
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
- Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Wentao Liu
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
- Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Yiheng Chen
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
- Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Qunfeng Jiang
- Department of Physics, Fudan University, Shanghai 200433, China
| | - Jingyuan Liu
- Global Clinical Operation, Johnson & Johnson, Shanghai 200233, China
| | - Jian Gou
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Baijun Dong
- Institute of Molecular Medicine, Department of Urology, Department of Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Andrew Thye Shen Wee
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Yunqi Liu
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
- Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
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Narita H, Shima T, Iizuka R, Uemura S. N-terminal region of Drosophila melanogaster Argonaute2 forms amyloid-like aggregates. BMC Biol 2023; 21:78. [PMID: 37072852 PMCID: PMC10114355 DOI: 10.1186/s12915-023-01569-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 03/17/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Argonaute proteins play a central role in RNA silencing by forming protein-small RNA complexes responsible for the silencing process. While most Argonaute proteins have a short N-terminal region, Argonaute2 in Drosophila melanogaster (DmAgo2) harbors a long and unique N-terminal region. Previous in vitro biochemical studies have shown that the loss of this region does not impair the RNA silencing activity of the complex. However, an N-terminal mutant of Drosophila melanogaster has demonstrated abnormal RNA silencing activity. To explore the causes of this discrepancy between in vitro and in vivo studies, we investigated the biophysical properties of the region. The N-terminal region is highly rich in glutamine and glycine residues, which is a well-known property for prion-like domains, a subclass of amyloid-forming peptides. Therefore, the possibility of the N-terminal region functioning as an amyloid was tested. RESULTS Our in silico and biochemical assays demonstrated that the N-terminal region exhibits amyloid-specific properties. The region indeed formed aggregates that were not dissociated even in the presence of sodium dodecyl sulfate. Also, the aggregates enhanced the fluorescence intensity of thioflavin-T, an amyloid detection reagent. The kinetics of the aggregation followed that of typical amyloid formation exhibiting self-propagating activity. Furthermore, we directly visualized the aggregation process of the N-terminal region under fluorescence microscopy and found that the aggregations took fractal or fibril shapes. Together, the results indicate that the N-terminal region can form amyloid-like aggregates. CONCLUSIONS Many other amyloid-forming peptides have been reported to modulate the function of proteins through their aggregation. Therefore, our findings raise the possibility that aggregation of the N-terminal region regulates the RNA silencing activity of DmAgo2.
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Affiliation(s)
- Haruka Narita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Shima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Ryo Iizuka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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Athar M, Patnaik A. Through-Bond-Driven Through-Space Interactions in a Fullerene C 60 Noncovalent Dyad: An Unusual Strong Binding between Spherical and Planar π Electron Clouds and Culmination of Dyadic Fractals. J Phys Chem A 2022; 126:3629-3641. [PMID: 35658511 DOI: 10.1021/acs.jpca.1c10828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrogen-bond-induced π-depletion as a criterion for π-stacking, a configurationally unique noncovalent strategy enabled an unconventional strong binding between the spherical N-fulleropyrrolidine (NFP) and the planar distributions of π electron clouds of three substituted pybates to form noncovalent fulleropyrrolidino-4-(pyrenyl) butanoate dyads of large computed interaction energies, varying between 37.49 and 44.93 kcal/mol. The geometrical distortion/bending of the alkyl tail of pybate in the noncovalent dyad was experimentally corroborated via UV-vis absorption spectroscopy, which translated into spectral broadening along with pronounced shifts in the n-π* transitions of the oxy-substituted pyrene in different solvents, ensuring through-bond interactions. Facile electron transfer through H-bond influenced the dynamic dispersive forces to be active, revealing the supremacy of through-bond over through-space interactions. The analyses of intermolecular forces using an absolutely localized molecular orbital-based energy decomposition analysis (ALMO-EDA) scheme revealed intricate insights into the intermolecular interactions and characteristic charge transfer; the dominance of forward electron transfer (pybate to NFP) over the reverse in offering stabilization was noted. Charge transfer was investigated further from natural bond orbital (NBO) and absolutely localized molecular orbital-based charge-transfer analysis (ALMO-CTA) methods, establishing the supremacy of donor-to-acceptor electron transfer over the reverse (acceptor-to-donor) one. The characteristic self-assembly of the noncovalent dyad in suitable solvents led to the formation of fractal networks via reaction-limited cluster aggregation with a fractal dimension of 2.37. Adoption of constrained molecular dynamics simulations indicated probable wrapping of pybates around NFP, leading to fractal-like assembly.
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Affiliation(s)
- Mohd Athar
- Colloid and Interface Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Archita Patnaik
- Colloid and Interface Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
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Qi X, Zhao Y, Lachowski K, Boese J, Cai Y, Dollar O, Hellner B, Pozzo L, Pfaendtner J, Chun J, Baneyx F, Mundy CJ. Predictive Theoretical Framework for Dynamic Control of Bioinspired Hybrid Nanoparticle Self-Assembly. ACS NANO 2022; 16:1919-1928. [PMID: 35073061 DOI: 10.1021/acsnano.1c04923] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
At-will tailoring of the formation and reconfiguration of hierarchical structures is a key goal of modern nanomaterial design. Bioinspired systems comprising biomacromolecules and inorganic nanoparticles have potential for new functional material structures. Yet, consequential challenges remain because we lack a detailed understanding of the temporal and spatial interplay between participants when it is mediated by fundamental physicochemical interactions over a wide range of scales. Motivated by a system in which silica nanoparticles are reversibly and repeatedly assembled using a homobifunctional solid-binding protein and single-unit pH changes under near-neutral solution conditions, we develop a theoretical framework where interactions at the molecular and macroscopic scales are rigorously coupled based on colloidal theory and atomistic molecular dynamics simulations. We integrate these interactions into a predictive coarse-grained model that captures the pH-dependent reversibility and accurately matches small-angle X-ray scattering experiments at collective scales. The framework lays a foundation to connect microscopic details with the macroscopic behavior of complex bioinspired material systems and to control their behavior through an understanding of both equilibrium and nonequilibrium characteristics.
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Affiliation(s)
- Xin Qi
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Yundi Zhao
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Kacper Lachowski
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States
| | - Julia Boese
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Yifeng Cai
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Orion Dollar
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Brittney Hellner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Lilo Pozzo
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jaehun Chun
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
- Levich Institute and Department of Chemical Engineering, CUNY City College of New York, New York, New York 10031, United States
| | - François Baneyx
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Christopher J Mundy
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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7
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Hamta A, Ashtiani FZ, Karimi M, Moayedfard S. Asymmetric block copolymer membrane fabrication mechanism through self-assembly and non-solvent induced phase separation (SNIPS) process. Sci Rep 2022; 12:771. [PMID: 35031674 PMCID: PMC8760277 DOI: 10.1038/s41598-021-04759-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/30/2021] [Indexed: 01/08/2023] Open
Abstract
In this paper, the concept of the functional mechanism of copolymer membrane formation is explained and analyzed from the theoretical and experimental points of view. To understand the phase inversion process and control the final membrane morphology, styrene-acrylonitrile copolymer (SAN) membrane morphology through the self-assembly phenomena is investigated. Since the analysis of the membrane morphology requires the study of both thermodynamic and kinetic parameters, the effect of different membrane formation conditions is investigated experimentally; In order to perceive the formation mechanism of the extraordinary structure membrane, a thermodynamic hypothesis is also developed based on the hydrophilic coil migration to the membrane surface. This hypothesis is analyzed according to Hansen Solubility Parameters and proved using EDX, SAXS, and contact angle analysis of SAN25. Moreover, the SAN30 membrane is fabricated under different operating conditions to evaluate the possibility of morphological prediction based on the developed hypothesis.
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Affiliation(s)
- Afshin Hamta
- Department of Chemical Engineering, Amirkabir University of Technology, No. 424, Hafez Ave, Tehran, Iran
| | - Farzin Zokaee Ashtiani
- Department of Chemical Engineering, Amirkabir University of Technology, No. 424, Hafez Ave, Tehran, Iran.
| | - Mohammad Karimi
- Department of Textile Engineering, Amirkabir University of Technology, No. 424, Hafez Ave, Tehran, Iran
| | - Sareh Moayedfard
- Department of Chemical Engineering, Amirkabir University of Technology, No. 424, Hafez Ave, Tehran, Iran
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Fu J, Han W, Zhang X, Sun Y, Bhadane R, Wei B, Li L, Yu L, Yang J, Rosenholm JM, Salo-Ahen OMH, Fan T, Zhang B, Swelm W, Al-Ghamdi AA, Xia L, Zhang H, Qiu M, Zhang H, Wang X. Silica Nanoparticles with Virus-Mimetic Spikes Enable Efficient siRNA Delivery In Vitro and In Vivo. RESEARCH 2022. [DOI: 10.34133/research.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Oligonucleotide-based therapy has experienced remarkable development in the past 2 decades, but its broad applications are severely hampered by delivery vectors. Widely used viral vectors and lipid nanovectors are suffering from immune clearance after repeating usage or requiring refrigerated transportation and storage, respectively. In this work, amino-modified virus-mimetic spike silica nanoparticles (NH
2
-SSNs) were fabricated using a 1-pot surfactant-free approach with controlled spike lengths, which were demonstrated with excellent delivery performance and biosafety in nearly all cell types and mice. It indicated that NH
2
-SSNs entered cells by spike-dependent cell membrane docking and dynamin-dependent endocytosis. The positively charged spikes with proper length on the surface can facilitate the efficient encapsulation of RNAs, protect the loaded RNAs from degradation, and trigger an early endosome escape during intracellular trafficking, similarly to the cellular internalization mechanism of virions. Regarding the fantastic properties of NH
2
-SSNs in nucleic acid delivery, it revealed that nanoparticles with solid spikes on the surface would be excellent vehicles for gene therapy, presenting self-evident advantages in storage, transportation, modification, and quality control in large-scale production compared to lipid nanovectors.
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Affiliation(s)
- Jianye Fu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Collaborative Innovation Center for Optoelectronic Science & Technology, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
- Key Laboratory of Marine Chemistry Theory and Technology (Ocean University of China), Ministry of Education, Qingdao 266100, China
- College of Chemistry and Chemical Engineering, China University of Petroleum, Qingdao 266555, China
| | - Wenwei Han
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Marine Chemistry Theory and Technology (Ocean University of China), Ministry of Education, Qingdao 266100, China
| | - Xue Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yutong Sun
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Rajendra Bhadane
- Pharmaceutical Sciences Laboratory, Åbo Akademi University, 20520 Turku, Finland
- Structural Bioinformatics Laboratory, Biochemistry, Åbo Akademi University, 20520 Turku, Finland
| | - Bo Wei
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Li Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Center for Innovation Marine Drug Screening & Evaluation, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- Marine Biomedical Research Institute of Qingdao, Qingdao 266100, China
| | - Liangmin Yu
- Key Laboratory of Marine Chemistry Theory and Technology (Ocean University of China), Ministry of Education, Qingdao 266100, China
| | - Jinbo Yang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Center for Innovation Marine Drug Screening & Evaluation, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- Marine Biomedical Research Institute of Qingdao, Qingdao 266100, China
| | - Jessica M. Rosenholm
- Pharmaceutical Sciences Laboratory, Åbo Akademi University, 20520 Turku, Finland
| | - Outi M. H. Salo-Ahen
- Pharmaceutical Sciences Laboratory, Åbo Akademi University, 20520 Turku, Finland
- Structural Bioinformatics Laboratory, Biochemistry, Åbo Akademi University, 20520 Turku, Finland
| | - Taojian Fan
- Collaborative Innovation Center for Optoelectronic Science & Technology, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Bin Zhang
- Collaborative Innovation Center for Optoelectronic Science & Technology, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wageh Swelm
- Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed A. Al-Ghamdi
- Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Lin Xia
- Hangzhou No. 14 High School, Hangzhou 310000, China
| | - Han Zhang
- Collaborative Innovation Center for Optoelectronic Science & Technology, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Meng Qiu
- Key Laboratory of Marine Chemistry Theory and Technology (Ocean University of China), Ministry of Education, Qingdao 266100, China
| | - Hongbo Zhang
- Pharmaceutical Sciences Laboratory, Åbo Akademi University, 20520 Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Xin Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Center for Innovation Marine Drug Screening & Evaluation, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- Marine Biomedical Research Institute of Qingdao, Qingdao 266100, China
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9
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Liu Y, Cao Y, Zhang X, Lin Y, Li W, Demir B, Searles DJ, Whittaker AK, Zhang A. Thermoresponsive Supramolecular Assemblies from Dendronized Amphiphiles To Form Fluorescent Spheres with Tunable Chirality. ACS NANO 2021; 15:20067-20078. [PMID: 34866390 DOI: 10.1021/acsnano.1c07764] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Balance between self-association of structural units and self-repulsion from crowding-induced steric hindrance accounts for the supramolecular assembly of the amphiphilic entities to form ordered structures, and solvation provides a toolbox to conveniently modulate the assemblies through differential interactions to various structural units. Here we report solvation-modulated supramolecular chiral assembly in aqueous solutions of amphiphilic dendronized tetraphenylethylenes (TPEs) with three-folded dendritic oligoethylene glycols (OEGs) through dipeptide Ala-Gly linkage. These dendronized amphiphiles can form supramolecular spheres with enhanced supramolecular chirality, which is tunable and dependent on solvation. These nanosized spherical aggregates exhibit thermoresponsive behavior, and their cloud point temperatures are dependent on mixed solvent of water and THF. The phase transition temperatures increase with water fractions due to water-driven shifting of OEG moieties from interiors of the aggregates to their peripheries. Furthermore, the thermally induced dehydration and collapse of OEG moieties mediate the reversible aggregation and deaggregation between the spheres, imparting tunable aggregation-induced fluorescent emission (AIE) and supramolecular chirality. Both experimental results and molecular dynamic simulations have highlighted that reversible chirality transformations of the amphiphilic dendronized assemblies mediated by solvation through change solvent quality or thermally dehydration are dependent on the balance between interactions of OEG dendrons with TPE moieties and with the solvent molecules.
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Affiliation(s)
- Yanjun Liu
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, 99 Shangda Road, Mailbox 152, Shanghai 20444, China
| | - Yuexin Cao
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, 99 Shangda Road, Mailbox 152, Shanghai 20444, China
| | - Xiacong Zhang
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, 99 Shangda Road, Mailbox 152, Shanghai 20444, China
| | - Yaodong Lin
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, 99 Shangda Road, Mailbox 152, Shanghai 20444, China
| | - Wen Li
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, 99 Shangda Road, Mailbox 152, Shanghai 20444, China
| | - Baris Demir
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Debra J Searles
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andrew K Whittaker
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Afang Zhang
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, 99 Shangda Road, Mailbox 152, Shanghai 20444, China
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10
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Artificial protein assemblies with well-defined supramolecular protein nanostructures. Biochem Soc Trans 2021; 49:2821-2830. [PMID: 34812854 DOI: 10.1042/bst20210808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022]
Abstract
Nature uses a wide range of well-defined biomolecular assemblies in diverse cellular processes, where proteins are major building blocks for these supramolecular assemblies. Inspired by their natural counterparts, artificial protein-based assemblies have attracted strong interest as new bio-nanostructures, and strategies to construct ordered protein assemblies have been rapidly expanding. In this review, we provide an overview of very recent studies in the field of artificial protein assemblies, with the particular aim of introducing major assembly methods and unique features of these assemblies. Computational de novo designs were used to build various assemblies with artificial protein building blocks, which are unrelated to natural proteins. Small chemical ligands and metal ions have also been extensively used for strong and bio-orthogonal protein linking. Here, in addition to protein assemblies with well-defined sizes, protein oligomeric and array structures with rather undefined sizes (but with definite repeat protein assembly units) also will be discussed in the context of well-defined protein nanostructures. Lastly, we will introduce multiple examples showing how protein assemblies can be effectively used in various fields such as therapeutics and vaccine development. We believe that structures and functions of artificial protein assemblies will be continuously evolved, particularly according to specific application goals.
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11
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Singh A, Khatun S, Pawar N, Gupta AN. Interactive patches over amyloid-β oligomers mediate fractal self-assembly. Phys Rev E 2021; 104:064404. [PMID: 35030868 DOI: 10.1103/physreve.104.064404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 11/18/2021] [Indexed: 06/14/2023]
Abstract
The monomeric units of intrinsically disordered proteins self-assemble into oligomers, protofilaments, and eventually fibrils which may turn into amyloid. The aggregation of these proteins is primarily studied in bulk with no restriction on their degrees of freedom. Herein we experimentally demonstrate that amyloid-β (Aβ) aggregation under diffusion-limited conditions leads to its fractal self-assembly. Confocal microscopy and scanning electron microscopy with energy dispersion x-ray analysis were used to confirm that the fractal self-assemblies were formed from Aβ rather than the salt present in the two supporting media: deionized water and phosphate buffered saline. The results from the molecular docking experiments implicated that electrostatic and hydrophobic patches on the solvent-accessible surface area of the Aβ oligomers mediate the fractal self-assembly. These implications were tested with laser light scattering experiments on the oligomers formed by breaking mature fibrils of Aβ through sonication, which were observed to self-assemble into fractals when sonicated solutions were drop casted. The electrostatic interactions modulate the fractal morphologies with pH of the solution, which leads to a morphological phase transition observed through the variation in their fractal dimension. These transitions provide experimental evidence for the existing theoretical framework in terms of different kinetic models. The higher surface-to-volume ratio of these fractal self-assemblies may have applications in drug delivery, biosensing, and other biomedical applications.
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Affiliation(s)
- Anurag Singh
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India
| | - Suparna Khatun
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India
| | - Nisha Pawar
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India
| | - Amar Nath Gupta
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India
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12
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Sinha NJ, Langenstein MG, Pochan DJ, Kloxin CJ, Saven JG. Peptide Design and Self-assembly into Targeted Nanostructure and Functional Materials. Chem Rev 2021; 121:13915-13935. [PMID: 34709798 DOI: 10.1021/acs.chemrev.1c00712] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptides have been extensively utilized to construct nanomaterials that display targeted structure through hierarchical assembly. The self-assembly of both rationally designed peptides derived from naturally occurring domains in proteins as well as intuitively or computationally designed peptides that form β-sheets and helical secondary structures have been widely successful in constructing nanoscale morphologies with well-defined 1-d, 2-d, and 3-d architectures. In this review, we discuss these successes of peptide self-assembly, especially in the context of designing hierarchical materials. In particular, we emphasize the differences in the level of peptide design as an indicator of complexity within the targeted self-assembled materials and highlight future avenues for scientific and technological advances in this field.
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Affiliation(s)
- Nairiti J Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Matthew G Langenstein
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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13
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Li C, Li R, Xu Z, Li J, Zhang X, Li N, Zhang Y, Shen Z, Tang H, Wang Y. Packing Biomolecules into Sierpiński Triangles with Global Organizational Chirality. J Am Chem Soc 2021; 143:14417-14421. [PMID: 34387475 DOI: 10.1021/jacs.1c05949] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Fractals are found in nature and play important roles in biological functions. However, it is challenging to controllably prepare biomolecule fractals. In this study, a series of Sierpiński triangles with global organizational chirality is successfully constructed by the coassembly of l-tryptophan and 1,3-bi(4-pyridyl)benzene molecules on Ag(111). The chirality is switched when replacing l-tryptophan by d-tryptophan. The fractal structures are characterized by low-temperature scanning tunneling microscopy at the single-molecule level. Density functional theory calculations reveal that intermolecular hydrogen bonds stabilize the Sierpiński triangles.
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Affiliation(s)
- Chao Li
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, Department of Electronics, Peking University, Beijing 100871, China
| | - Ruoning Li
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, Department of Electronics, Peking University, Beijing 100871, China
| | - Zhen Xu
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, Department of Electronics, Peking University, Beijing 100871, China
| | - Jie Li
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, Department of Electronics, Peking University, Beijing 100871, China
| | - Xue Zhang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, Department of Electronics, Peking University, Beijing 100871, China
| | - Na Li
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, Department of Electronics, Peking University, Beijing 100871, China
| | - Yajie Zhang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, Department of Electronics, Peking University, Beijing 100871, China
| | - Ziyong Shen
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, Department of Electronics, Peking University, Beijing 100871, China
| | - Hao Tang
- CEMES-CNRS, Boîte Postale 94347, 31055 Toulouse, France
| | - Yongfeng Wang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, Department of Electronics, Peking University, Beijing 100871, China.,Beijing Academy of Quantum Information Sciences, Beijing 100193, China
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14
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Wang H, Xiong W. Vibrational Sum-Frequency Generation Hyperspectral Microscopy for Molecular Self-Assembled Systems. Annu Rev Phys Chem 2021; 72:279-306. [PMID: 33441031 DOI: 10.1146/annurev-physchem-090519-050510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this review, we discuss the recent developments and applications of vibrational sum-frequency generation (VSFG) microscopy. This hyperspectral imaging technique can resolve systems without inversion symmetry, such as surfaces, interfaces and noncentrosymmetric self-assembled materials, in the spatial, temporal, and spectral domains. We discuss two common VSFG microscopy geometries: wide-field and confocal point-scanning. We then introduce the principle of VSFG and the relationships between hyperspectral imaging with traditional spectroscopy, microscopy, and time-resolved measurements. We further highlight crucial applications of VSFG microscopy in self-assembled monolayers, cellulose in plants, collagen fibers, and lattice self-assembled biomimetic materials. In these systems, VSFG microscopy reveals relationships between physical properties that would otherwise be hidden without being spectrally, spatially, and temporally resolved. Lastly, we discuss the recent development of ultrafast transient VSFG microscopy, which can spatially measure the ultrafast vibrational dynamics of self-assembled materials. The review ends with an outlook on the technical challenges of and scientific potential for VSFG microscopy.
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Affiliation(s)
- Haoyuan Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA; ,
| | - Wei Xiong
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA; , .,Materials Science and Engineering Program, University of California, San Diego, La Jolla, California 92093, USA
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15
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Li Z, Wang Y, Baryshnikov G, Shen S, Zhang M, Zou Q, Ågren H, Zhu L. Lighting up solid states using a rubber. Nat Commun 2021; 12:908. [PMID: 33568677 PMCID: PMC7876014 DOI: 10.1038/s41467-021-21253-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/13/2021] [Indexed: 11/10/2022] Open
Abstract
It is crucial and desirable to develop green and high-efficient strategies to regulate solid-state structures and their related material properties. However, relative to solution, it is more difficult to break and generate chemical bonds in solid states. In this work, a rubbing-induced photoluminescence on the solid states of ortho-pyridinil phenol family was achieved. This rubbing response relied on an accurately designed topochemical tautomerism, where a negative charge, exactly provided by the triboelectric effect of a rubber, can induce a proton transfer in a double H-bonded dimeric structure. This process instantaneously led to a bright-form tautomer that can be stabilized in the solid-state settings, leading to an up to over 450-fold increase of the fluorescent quantum yield of the materials. The property can be repeatedly used due to the reversibility of the tautomerism, enabling encrypted applications. Moreover, a further modification to the structure can be accomplished to achieve different properties, opening up more possibilities for the design of new-generation smart materials. Changes in molecular properties due to stimuli response are critically important for the development of new materials. However, most processes are slow or inefficient in the solid state. Here the authors demonstrate property switching in the solid state using a rubbing-induced tautomerism in multiple hydrogen-bonded donor-acceptor couples.
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Affiliation(s)
- Zhongyu Li
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, China
| | - Yanjie Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, China
| | - Gleb Baryshnikov
- Division of Theoretical Chemistry and Biology School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden.,Tomsk State University, Tomsk, Russia
| | - Shen Shen
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, China
| | - Man Zhang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, China
| | - Qi Zou
- Shanghai Key Laboratory of Materials Protection and Advanced Materials in Electric Power, Shanghai University of Electric Power, Shanghai, China
| | - Hans Ågren
- Tomsk State University, Tomsk, Russia.,Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Liangliang Zhu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, China.
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16
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Abstract
The article deals with dendritic structures resulting from self-organization processes in aqueous solutions of albumin proteins. The methods for obtaining the structures and experimental results are presented. It is shown that dendrites are fractal structures that are symmetric under certain conditions of their formation and can have different characteristics depending on the isothermal dehydration of liquid samples. The fractal dimension of the structures in films of the albumin protein solution has been calculated. Dependences of the fractal dimension on the concentrations of salts and protein in the initial solutions and also on the dehydration temperature have been revealed. It has been shown that as the protein concentration in the solution grows, the salt concentration for the initiation of the dendritic structure formation increases. It has been found that the temperature dependences of the fractal dimension of the structures become smoother with increasing protein concentration in solutions. The relationship between geometric characteristics of dendrites and self-organization parameters during drying is discussed.
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17
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Kim S, Yun J, Yoo H, Kim S, Kim HM, Lee HS. Metal-Mediated Protein Assembly Using a Genetically Incorporated Metal-Chelating Amino Acid. Biomacromolecules 2020; 21:5021-5028. [PMID: 33253537 DOI: 10.1021/acs.biomac.0c01194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many natural proteins function in oligomeric forms, which are critical for their sophisticated functions. The construction of protein assemblies has great potential for biosensors, enzyme catalysis, and biomedical applications. In designing protein assemblies, a critical process is to create protein-protein interaction (PPI) networks at defined sites of a target protein. Although a few methods are available for this purpose, most of them are dependent on existing PPIs of natural proteins to some extent. In this report, a metal-chelating amino acid, 2,2'-bipyridylalanine (BPA), was genetically introduced into defined sites of a monomeric protein and used to form protein oligomers. Depending on the number of BPAs introduced into the protein and the species of metal ions (Ni2+ and Cu2+), dimers or oligomers with different oligomerization patterns were formed by complexation with a metal ion. Oligomer sizes could also be controlled by incorporating two BPAs at different locations with varied angles to the center of the protein. When three BPAs were introduced, the monomeric protein formed a large complex with Ni2+. In addition, when Cu2+ was used for complex formation with the protein containing two BPAs, a linear complex was formed. The method proposed in this report is technically simple and generally applicable to various proteins with interesting functions. Therefore, this method would be useful for the design and construction of functional protein assemblies.
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Affiliation(s)
- Sanggil Kim
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 121-742, Republic of Korea
| | - Jeongwon Yun
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyunjung Yoo
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 121-742, Republic of Korea
| | - Sooin Kim
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 121-742, Republic of Korea
| | - Ho Min Kim
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Biomolecular & Cellular Structure, Institution for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 121-742, Republic of Korea
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18
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Han M, Liu Y, Zhang F, Sun D, Jiang J. Effect of galactose side-chain on the self-assembly of xyloglucan macromolecule. Carbohydr Polym 2020; 246:116577. [DOI: 10.1016/j.carbpol.2020.116577] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/03/2020] [Indexed: 12/13/2022]
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19
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Chao YJ, Wu K, Chang HH, Chien MJ, Chan JCC. Manifold of self-assembly of a de novo designed peptide: amyloid fibrils, peptide bundles, and fractals. RSC Adv 2020; 10:29510-29515. [PMID: 35521097 PMCID: PMC9055936 DOI: 10.1039/d0ra04480f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/02/2020] [Indexed: 12/18/2022] Open
Abstract
We report that a peptide with the sequence of EGAGAAAAGAGE can have different aggregation states, viz., amyloid fibrils, peptide bundles, and fractal assembly under different incubation conditions. The chemical state of the Glu residue played a pivotal regulating role in the aggregation behavior of the peptide. The mechanism of the fractal assembly of this peptide has been unraveled as follows. The peptide fragments adopting the beta-sheet conformation are well dispersed in alkaline solution. In the buffer of sodium bicarbonate, peptide rods are formed with considerable structural rigidity at the C- and N-termini. The peptide rods undergo random trajectory in the solution and form a fractal pattern on a two-dimensional surface via the diffusion-limited aggregation process.
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Affiliation(s)
- Yu-Jo Chao
- Department of Chemistry, National Taiwan University No. 1, Section 4, Roosevelt Road Taipei 10617 Taiwan
| | - Kan Wu
- Department of Chemistry, National Taiwan University No. 1, Section 4, Roosevelt Road Taipei 10617 Taiwan
| | - Hsun-Hui Chang
- Department of Chemistry, National Taiwan University No. 1, Section 4, Roosevelt Road Taipei 10617 Taiwan
| | - Ming-Jou Chien
- Department of Chemistry, National Taiwan University No. 1, Section 4, Roosevelt Road Taipei 10617 Taiwan
| | - Jerry Chun Chung Chan
- Department of Chemistry, National Taiwan University No. 1, Section 4, Roosevelt Road Taipei 10617 Taiwan
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20
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Hansen WA, Khare SD. Recent progress in designing protein-based supramolecular assemblies. Curr Opin Struct Biol 2020; 63:106-114. [PMID: 32569994 DOI: 10.1016/j.sbi.2020.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022]
Abstract
The design of protein-based assemblies is an emerging area in bionanotechnology with wide ranging applications, from vaccines to smart biomaterials. Design approaches have sought to mimic both the topologies of assemblies observed in nature, as well as their functionally relevant properties, such as being responsive to external cues. In the last few years, diverse design approaches have been used to construct assemblies with integer-dimensional (e.g. filaments, layers, lattices and polyhedra) and non-integer-dimensional (fractal) topologies. Supramolecular structures that assemble/disassemble in response to chemical and physical stimuli have also been built. Hybrid protein-DNA assemblies have expanded the set of building blocks used for generating supramolecular architectures. While still far from reproducing the sophistication of natural assemblies, these exciting results represent important steps towards the design of responsive and functional biomaterials built from the bottom up. As the complexity of topologies and diversity of building blocks increases, considerations of both thermodynamics and kinetics of assembly formation will play crucial roles in making the design of protein-based assemblies robust and useful.
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Affiliation(s)
- William A Hansen
- Institute for Quantitative Biomedicine, Rutgers - The State University of New Jersey, NJ, USA
| | - Sagar D Khare
- Institute for Quantitative Biomedicine, Rutgers - The State University of New Jersey, NJ, USA; Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, NJ, USA.
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21
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Liu R, Kochovski Z, Li L, Yin YW, Yang J, Yang G, Tao G, Xu A, Zhang E, Ding HM, Lu Y, Chen G, Jiang M. Fabrication of Pascal-triangle Lattice of Proteins by Inducing Ligand Strategy. Angew Chem Int Ed Engl 2020; 59:9617-9623. [PMID: 32147901 PMCID: PMC7318223 DOI: 10.1002/anie.202000771] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/26/2020] [Indexed: 01/26/2023]
Abstract
A protein Pascal triangle has been constructed as new type of supramolecular architecture by using the inducing ligand strategy that we previously developed for protein assemblies. Although mathematical studies on this famous geometry have a long history, no work on such Pascal triangles fabricated from native proteins has been reported so far due to their structural complexity. In this work, by carefully tuning the specific interactions between the native protein building block WGA and the inducing ligand R‐SL, a 2D Pascal‐triangle lattice with three types of triangular voids has been assembled. Moreover, a 3D crystal structure was obtained based on the 2D Pascal triangles. The distinctive carbohydrate binding sites of WGA and the intralayer as well as interlayer dimerization of RhB was the key to facilitate nanofabrication in solution. This strategy may be applied to prepare and explore various sophisticated assemblies based on native proteins.
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Affiliation(s)
- Rongying Liu
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200433, China
| | - Zdravko Kochovski
- Institute of Electrochemical Energy Storage, Helmholtz-Zentrum Berlin für Materialien und Energie, 14109, Berlin, Germany
| | - Long Li
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200433, China
| | - Yue-Wen Yin
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou, 215006, China
| | - Jing Yang
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200433, China
| | - Guang Yang
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200433, China
| | - Guoqing Tao
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200433, China
| | - Anqiu Xu
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200433, China
| | - Ensong Zhang
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200433, China
| | - Hong-Ming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou, 215006, China
| | - Yan Lu
- Institute of Electrochemical Energy Storage, Helmholtz-Zentrum Berlin für Materialien und Energie, 14109, Berlin, Germany.,Institute of Chemistry, University of Potsdam, 14476, Potsdam, Germany
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200433, China.,Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, 200433, China
| | - Ming Jiang
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200433, China
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22
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Liu R, Kochovski Z, Li L, Yin Y, Yang J, Yang G, Tao G, Xu A, Zhang E, Ding H, Lu Y, Chen G, Jiang M. Fabrication of Pascal‐triangle Lattice of Proteins by Inducing Ligand Strategy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rongying Liu
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular ScienceFudan University Shanghai 200433 China
| | - Zdravko Kochovski
- Institute of Electrochemical Energy StorageHelmholtz-Zentrum Berlin für Materialien und Energie 14109 Berlin Germany
| | - Long Li
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular ScienceFudan University Shanghai 200433 China
| | - Yue‐wen Yin
- Center for Soft Condensed Matter Physics and Interdisciplinary ResearchSchool of Physical Science and TechnologySoochow University Suzhou 215006 China
| | - Jing Yang
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular ScienceFudan University Shanghai 200433 China
| | - Guang Yang
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular ScienceFudan University Shanghai 200433 China
| | - Guoqing Tao
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular ScienceFudan University Shanghai 200433 China
| | - Anqiu Xu
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular ScienceFudan University Shanghai 200433 China
| | - Ensong Zhang
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular ScienceFudan University Shanghai 200433 China
| | - Hong‐ming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary ResearchSchool of Physical Science and TechnologySoochow University Suzhou 215006 China
| | - Yan Lu
- Institute of Electrochemical Energy StorageHelmholtz-Zentrum Berlin für Materialien und Energie 14109 Berlin Germany
- Institute of ChemistryUniversity of Potsdam 14476 Potsdam Germany
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular ScienceFudan University Shanghai 200433 China
- Multiscale Research Institute of Complex SystemsFudan University Shanghai 200433 China
| | - Ming Jiang
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular ScienceFudan University Shanghai 200433 China
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23
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Khatun S, Singh A, Maji S, Maiti TK, Pawar N, Gupta AN. Fractal self-assembly and aggregation of human amylin. SOFT MATTER 2020; 16:3143-3153. [PMID: 32159545 DOI: 10.1039/c9sm02463h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Human amylin is an intrinsically disordered protein believed to have a central role in Type-II diabetes mellitus (T2DM). The formation of intermediate oligomers is a seminal event in the eventual self-assembled fibril structures of amylin. However, the recent experimental investigations have shown the presence of different self-assembled (oligomers, protofilaments, and fibrils) and aggregated structures (amorphous aggregates) of amylin formed during its aggregation. Here, we show that amylin under diffusion-limited conditions leads to fractal self-assembly. The pH and solvent sensitive fractal self-assemblies of amylin were observed using an optical microscope. Confocal microscopy and scanning electron microscopy (SEM) with energy dispersion X-ray analysis (EDAX) were used to confirm the fractal self-assembly of amylin in water and PBS buffer, respectively. The fractal characteristics of the self-assemblies and the aggregates formed during the aggregation of amylin under different pH conditions were investigated using laser light scattering. The hydropathy and the docking study indicated the interactions between the anisotropically distributed hydrophobic residues and polar/ionic residues on the solvent-accessible surface of the protein as the crucial interaction hot-spots for driving the self-assembly and aggregation of human amylin. The simultaneous presence of various self-assemblies of human amylin was observed through different microscopy techniques. The present study may help in designing different fractal-like nanomaterials with potential applications in drug delivery, sensing, and tissue engineering.
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Affiliation(s)
- Suparna Khatun
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology, Kharagpur-721302, India.
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24
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Bolmatov D, Zav'yalov D, Carrillo JM, Katsaras J. Fractal boundaries underpin the 2D melting of biomimetic rafts. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183249. [PMID: 32147353 DOI: 10.1016/j.bbamem.2020.183249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 02/05/2023]
Affiliation(s)
- Dima Bolmatov
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States.
| | | | - Jan-Michael Carrillo
- Center for Nanophase Materials Sciences and Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - John Katsaras
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States.
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Diverse protein assembly driven by metal and chelating amino acids with selectivity and tunability. Nat Commun 2019; 10:5545. [PMID: 31804480 PMCID: PMC6895169 DOI: 10.1038/s41467-019-13491-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 11/08/2019] [Indexed: 01/01/2023] Open
Abstract
Proteins are versatile natural building blocks with highly complex and multifunctional architectures, and self-assembled protein structures have been created by the introduction of covalent, noncovalent, or metal-coordination bonding. Here, we report the robust, selective, and reversible metal coordination properties of unnatural chelating amino acids as the sufficient and dominant driving force for diverse protein self-assembly. Bipyridine-alanine is genetically incorporated into a D3 homohexamer. Depending on the position of the unnatural amino acid, 1-directional, crystalline and noncrystalline 2-directional, combinatory, and hierarchical architectures are effectively created upon the addition of metal ions. The length and shape of the structures is tunable by altering conditions related to thermodynamics and kinetics of metal-coordination and subsequent reactions. The crystalline 1-directional and 2-directional biomaterials retain their native enzymatic activities with increased thermal stability, suggesting that introducing chelating ligands provides a specific chemical basis to synthesize diverse protein-based functional materials while retaining their native structures and functions. Precise manipulation of protein self-assembly in vitro is challenging. Here, the authors developed an approach for driving metal-mediated reversible protein assembly by genetically installing a bipyridine residue into an oligomeric (D3) protein.
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