1
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Zhou W, Li Y, Partridge BE, Mirkin CA. Engineering Anisotropy into Organized Nanoscale Matter. Chem Rev 2024. [PMID: 39315621 DOI: 10.1021/acs.chemrev.4c00299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Programming the organization of discrete building blocks into periodic and quasi-periodic arrays is challenging. Methods for organizing materials are particularly important at the nanoscale, where the time required for organization processes is practically manageable in experiments, and the resulting structures are of interest for applications spanning catalysis, optics, and plasmonics. While the assembly of isotropic nanoscale objects has been extensively studied and described by empirical design rules, recent synthetic advances have allowed anisotropy to be programmed into macroscopic assemblies made from nanoscale building blocks, opening new opportunities to engineer periodic materials and even quasicrystals with unnatural properties. In this review, we define guidelines for leveraging anisotropy of individual building blocks to direct the organization of nanoscale matter. First, the nature and spatial distribution of local interactions are considered and three design rules that guide particle organization are derived. Subsequently, recent examples from the literature are examined in the context of these design rules. Within the discussion of each rule, we delineate the examples according to the dimensionality (0D-3D) of the building blocks. Finally, we use geometric considerations to propose a general inverse design-based construction strategy that will enable the engineering of colloidal crystals with unprecedented structural control.
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Affiliation(s)
- Wenjie Zhou
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Yuanwei Li
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Benjamin E Partridge
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Chad A Mirkin
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
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2
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Shi C, Zorman M, Zhao X, Salmeron MB, Pfaendtner J, Liu XY, Zhang S, De Yoreo JJ. Two-dimensional silk. SCIENCE ADVANCES 2024; 10:eado4142. [PMID: 39292781 PMCID: PMC11409968 DOI: 10.1126/sciadv.ado4142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 08/12/2024] [Indexed: 09/20/2024]
Abstract
Despite the promise of silk-based devices, the inherent disorder of native silk limits performance. Here, we report highly ordered two-dimensional silk fibroin (SF) films grown epitaxially on van der Waals (vdW) substrates. Using atomic force microscopy, nano-Fourier transform infrared spectroscopy, and molecular dynamics, we show that the films consist of lamellae of SF molecules that exhibit the same secondary structure as the nanocrystallites of native silk. Increasing the SF concentration results in multilayers that grow either by direct assembly of SF molecules into the lamellae or, at high concentrations, along a two-step pathway beginning with a disordered monolayer that then crystallizes. Scanning Kelvin probe measurements show that these films substantially alter the surface potential; thus, they provide a platform for silk-based electronics on vdW solids.
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Affiliation(s)
- Chenyang Shi
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Marlo Zorman
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA 98195, USA
| | - Xiao Zhao
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Miquel B Salmeron
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA
| | - Jim Pfaendtner
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Xiang Yang Liu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Shuai Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA
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3
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Torkelson K, Pfaendtner J. Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations. Biomacromolecules 2024. [PMID: 39292171 DOI: 10.1021/acs.biomac.4c00527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Peptoids are a class of sequence-defined biomimetic polymers with peptide-like backbones and side chains located on backbone nitrogens rather than alpha carbons. These materials demonstrate a strong ability for precise control of single-chain structure, multiunit self-assembly, and macromolecular assembly through careful tuning of sequence due to the diversity of available side chains, although the driving forces behind these assemblies are often not understood. Prior experimental work has shown that linked 15mer peptoids can mimic the protein helical hairpin structure by leveraging the chirality-inducing nature of bulky side chains and hydrophobicity, but there are still gaps in our understanding of the relationship between sequence, stability, and particular secondary or tertiary structure. We present a molecular dynamics (MD) study on the folding behavior of these polymers into hairpins, discussing the differences in structure from sequences with various characteristics in water and acetonitrile, and then compare the handedness preference of common helical motifs between solvents.
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Affiliation(s)
- Kaylyn Torkelson
- University of Washington, Chemical Engineering, Box 351750, Seattle, Washington 98195-1750, United States
| | - Jim Pfaendtner
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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4
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Jian T, Wang M, Hettige J, Li Y, Wang L, Gao R, Yang W, Zheng R, Zhong S, Baer MD, Noy A, De Yoreo JJ, Cai J, Chen CL. Self-Assembling and Pore-Forming Peptoids as Antimicrobial Biomaterials. ACS NANO 2024; 18:23077-23089. [PMID: 39146502 DOI: 10.1021/acsnano.4c05250] [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: 08/17/2024]
Abstract
Bacterial infections have been a serious threat to mankind throughout history. Natural antimicrobial peptides (AMPs) and their membrane disruption mechanism have generated immense interest in the design and development of synthetic mimetics that could overcome the intrinsic drawbacks of AMPs, such as their susceptibility to proteolytic degradation and low bioavailability. Herein, by exploiting the self-assembly and pore-forming capabilities of sequence-defined peptoids, we discovered a family of low-molecular weight peptoid antibiotics that exhibit excellent broad-spectrum activity and high selectivity toward a panel of clinically significant Gram-positive and Gram-negative bacterial strains, including vancomycin-resistant Enterococcus faecalis (VREF), methicillin-resistant Staphylococcus aureus (MRSA), methicillin-resistant Staphylococcus epidermidis (MRSE), Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Tuning the peptoid side chain chemistry and structure enabled us to tune the efficacy of antimicrobial activity. Mechanistic studies using transmission electron microscopy (TEM), bacterial membrane depolarization and lysis, and time-kill kinetics assays along with molecular dynamics simulations reveal that these peptoids kill both Gram-positive and Gram-negative bacteria through a membrane disruption mechanism. These robust and biocompatible peptoid-based antibiotics can provide a valuable tool for combating emerging drug resistance.
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Affiliation(s)
- Tengyue Jian
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Minghui Wang
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Jeevapani Hettige
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yuhao Li
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Lei Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, China
| | - Ruixuan Gao
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Wenchao Yang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Renyu Zheng
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Shengliang Zhong
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, China
| | - Marcel D Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Aleksandr Noy
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- School of Natural Sciences, University of California, Merced, Merced, California 95343, United States
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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5
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Jin H, Wu P, Liu Z, Sun Z, Feng W, Ding Y, Cao H, Lin Z, Lin S. Robust Multifunctional Ultrathin 2 Nanometer Organic Nanofibers. ACS NANO 2024. [PMID: 39094189 DOI: 10.1021/acsnano.4c08229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Ultrathin organic nanofibers (UTONFs) represent an emerging class of nanomaterials as they carry a set of favorable attributes, including ultrahigh specific surface area, lightweight, and mechanical flexibility, over inorganic counterparts, for use in biomedicine and nanotechnology. However, precise synthesis of uniform UTONFs (diameter ≤ 2 nm) with tailored functionalities remained challenging. Herein, we report robust multifunctional UTONFs using hydrophobic interaction-driven self-assembly of amphiphilic alternating peptoids containing hydrophobic photoresponsive azobenzene and hydrophilic hydroxyl moieties periodically arranged along the peptoid backbone. Notably, the as-crafted UTONFs are approximately 2 nm in diameter and tens of micrometers in length (an aspect ratio, AR, of ∼10000), exemplifying the UTONFs with the smallest diameter yielded via self-assembly. Intriguingly, UTONFs were disassembled into short-segmented nanofibers and controllably reassembled into UTONFs, resembling "step-growth polymerization". Photoisomerization of azobenzene moieties leads to reversible transformation between UTONFs and spherical micelles. Such meticulously engineered UTONFs demonstrate potential for catalysis, bioimaging, and antibacterial therapeutics. Our study highlights the significance of the rational design of amphiphiles containing alternating hydrophobic and hydrophilic moieties in constructing otherwise unattainable extremely thin UTONFs with ultrahigh AR and stimuli-responsive functionalities for energy and bionanotechnology.
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Affiliation(s)
- Haibao Jin
- Shanghai Key Laboratory of Advanced Polymeric Materials, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Pengchao Wu
- Shanghai Key Laboratory of Advanced Polymeric Materials, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhenghui Liu
- Shanghai Key Laboratory of Advanced Polymeric Materials, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zichao Sun
- Shanghai Key Laboratory of Advanced Polymeric Materials, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Weisheng Feng
- Shanghai Key Laboratory of Advanced Polymeric Materials, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yanhuai Ding
- School of Mechanical Engineering and Mechanics, Xiangtan University, Xiangtan 411105, Hunan, China
| | - Huiliang Cao
- Shanghai Key Laboratory of Advanced Polymeric Materials, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhiqun Lin
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Shaoliang Lin
- Shanghai Key Laboratory of Advanced Polymeric Materials, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
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6
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Heinz S, Gemmer L, Janka O, Gallei M. Ferrocene-Modified Polyacrylonitrile-Containing Block Copolymers as Preceramic Materials. Polymers (Basel) 2024; 16:2142. [PMID: 39125169 PMCID: PMC11314306 DOI: 10.3390/polym16152142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/18/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
In the pursuit of fabricating functional ceramic nanostructures, the design of preceramic functional polymers has garnered significant interest. With their easily adaptable chemical composition, molecular structure, and processing versatility, these polymers hold immense potential in this field. Our study succeeded in focusing on synthesizing ferrocene-containing block copolymers (BCPs) based on polyacrylonitrile (PAN). The synthesis is accomplished via different poly(acrylonitrile-block-methacrylate)s via atom transfer radical polymerization (ATRP) and activators regenerated by electron transfer ATRP (ARGET ATRP) for the PAN macroinitiators. The molecular weights of the BCPs range from 44 to 82 kDa with dispersities between 1.19 and 1.5 as determined by SEC measurements. The volume fraction of the PMMA block ranges from 0.16 to 0.75 as determined by NMR. The post-modification of the BCPs using 3-ferrocenyl propylamine has led to the creation of redox-responsive preceramic polymers. The thermal stabilization of the polymer film has resulted in stabilized morphologies based on the oxidative PAN chemistry. The final pyrolysis of the sacrificial block segment and conversion of the metallopolymer has led to the formation of a porous carbon network with an iron oxide functionalized surface, investigated by scanning electron microscopy (SEM), energy dispersive X-ray mapping (EDX), and powder X-ray diffraction (PXRD). These findings could have significant implications in various applications, demonstrating the practical value of our research in convenient ceramic material design.
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Affiliation(s)
- Sebastian Heinz
- Polymer Chemistry, Campus C4 2, Saarland University, 66123 Saarbrücken, Germany; (S.H.); (L.G.)
| | - Lea Gemmer
- Polymer Chemistry, Campus C4 2, Saarland University, 66123 Saarbrücken, Germany; (S.H.); (L.G.)
| | - Oliver Janka
- Inorganic Solid State Chemistry, Campus C4 1, Saarland University, 66123 Saarbrücken, Germany;
| | - Markus Gallei
- Polymer Chemistry, Campus C4 2, Saarland University, 66123 Saarbrücken, Germany; (S.H.); (L.G.)
- Saarene, Campus C4 2, Saarland Center for Energy Materials and Sustainability, 66123 Saarbrücken, Germany
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7
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Qin J, Wang Y, Wang T, Wang N, Xu W, Cheng L, Yu W, Yan X, Gao L, Zheng B, Wu B. Anion-Coordination Foldamer-Based Polymer Network: from Molecular Spring to Elastomer. Angew Chem Int Ed Engl 2024; 63:e202400989. [PMID: 38623921 DOI: 10.1002/anie.202400989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/25/2024] [Accepted: 04/15/2024] [Indexed: 04/17/2024]
Abstract
Foldamer is a scaled-down version of coil spring, which can absorb and release energy by conformational change. Here, polymer networks with high density of molecular springs were developed by employing anion-coordination-based foldamers as the monomer. The coiling of the foldamer is controlled by oligo(urea) ligands coordinating to chloride ions; subsequently, the folding and unfolding of foldamer conformations endow the polymer network with excellent energy dissipation and toughness. The mechanical performance of the corresponding polymer networks shows a dramatic increase from P-L2UCl (non-folding), to P-L4UCl (a full turn), and then to P-L6UCl (1.5 turns), in terms of strength (2.62 MPa; 14.26 MPa; 22.93 MPa), elongation at break (70 %; 325 %; 352 %), Young's modulus (2.69 MPa; 63.61 MPa; 141.50 MPa), and toughness (1.12 MJ/m3; 21.39 MJ/m3; 49.62 MJ/m3), respectively, which is also better than those without anion centers and the non-foldamer based counterparts. Moreover, P-L6UCl shows enhanced strength and toughness than most of the molecular-spring based polymer networks. Thus, an effective strategy for designing high-performance anion-coordination-based materials is presented.
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Affiliation(s)
- Jiangping Qin
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, P. R. China
| | - Yongming Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
| | - Tian Wang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, P. R. China
| | - Na Wang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, P. R. China
| | - Wenhua Xu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, P. R. China
| | - Lin Cheng
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
| | - Wei Yu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
| | - Xuzhou Yan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
| | - Lingyan Gao
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, P. R. China
| | - Bo Zheng
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, P. R. China
| | - Biao Wu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, P. R. China
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 100081, Beijing, P. R. China
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8
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Shao L, Hu D, Zheng SL, Trinh TKH, Zhou W, Wang H, Zong Y, Li C, Chen CL. Hierarchical Self-Assembly of Multidimensional Functional Materials from Sequence-Defined Peptoids. Angew Chem Int Ed Engl 2024; 63:e202403263. [PMID: 38657031 DOI: 10.1002/anie.202403263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
Hierarchical self-assembly represents a powerful strategy for the fabrication of functional materials across various length scales. However, achieving precise formation of functional hierarchical assemblies remains a significant challenge and requires a profound understanding of molecular assembly interactions. In this study, we present a molecular-level understanding of the hierarchical assembly of sequence-defined peptoids into multidimensional functional materials, including twisted nanotube bundles serving as a highly efficient artificial light harvesting system. By employing synchrotron-based powder X-ray diffraction and analyzing single crystal structures of model compounds, we elucidated the molecular packing and mechanisms underlying the assembly of peptoids into multidimensional nanostructures. Our findings demonstrate that incorporating aromatic functional groups, such as tetraphenyl ethylene (TPE), at the termini of assembling peptoid sequences promotes the formation of twisted bundles of nanotubes and nanosheets, thus enabling the creation of a highly efficient artificial light harvesting system. This research exemplifies the potential of leveraging sequence-defined synthetic polymers to translate microscopic molecular structures into macroscopic assemblies. It holds promise for the development of functional materials with precisely controlled hierarchical structures and designed functions.
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Affiliation(s)
- Li Shao
- Department of Materials Science and Engineering, Zhejiang Sci-Tech University, Hangzhou, 310018, China
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Dehong Hu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Shao-Liang Zheng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thi Kim Hoang Trinh
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Wenhao Zhou
- Department of Materials Science, University of Washington, Seattle, WA 98195, USA
| | - Haoyu Wang
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Yanxu Zong
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Materials Science and Engineering, Binghamton University, Binghamton, NY 13902, USA
| | - Changning Li
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
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9
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Redondo-Gómez C, Parreira P, Martins MCL, Azevedo HS. Peptide-based self-assembled monolayers (SAMs): what peptides can do for SAMs and vice versa. Chem Soc Rev 2024; 53:3714-3773. [PMID: 38456490 DOI: 10.1039/d3cs00921a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Self-assembled monolayers (SAMs) represent highly ordered molecular materials with versatile biochemical features and multidisciplinary applications. Research on SAMs has made much progress since the early begginings of Au substrates and alkanethiols, and numerous examples of peptide-displaying SAMs can be found in the literature. Peptides, presenting increasing structural complexity, stimuli-responsiveness, and biological relevance, represent versatile functional components in SAMs-based platforms. This review examines the major findings and progress made on the use of peptide building blocks displayed as part of SAMs with specific functions, such as selective cell adhesion, migration and differentiation, biomolecular binding, advanced biosensing, molecular electronics, antimicrobial, osteointegrative and antifouling surfaces, among others. Peptide selection and design, functionalisation strategies, as well as structural and functional characteristics from selected examples are discussed. Additionally, advanced fabrication methods for dynamic peptide spatiotemporal presentation are presented, as well as a number of characterisation techniques. All together, these features and approaches enable the preparation and use of increasingly complex peptide-based SAMs to mimic and study biological processes, and provide convergent platforms for high throughput screening discovery and validation of promising therapeutics and technologies.
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Affiliation(s)
- Carlos Redondo-Gómez
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal.
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - Paula Parreira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal.
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - M Cristina L Martins
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal.
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 4050-313 Porto, Portugal
| | - Helena S Azevedo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal.
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
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10
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Zheng R, Zhao M, Du JS, Sudarshan TR, Zhou Y, Paravastu AK, De Yoreo JJ, Ferguson AL, Chen CL. Assembly of short amphiphilic peptoids into nanohelices with controllable supramolecular chirality. Nat Commun 2024; 15:3264. [PMID: 38627405 PMCID: PMC11021492 DOI: 10.1038/s41467-024-46839-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024] Open
Abstract
A long-standing challenge in bioinspired materials is to design and synthesize synthetic materials that mimic the sophisticated structures and functions of natural biomaterials, such as helical protein assemblies that are important in biological systems. Herein, we report the formation of a series of nanohelices from a type of well-developed protein-mimetics called peptoids. We demonstrate that nanohelix structures and supramolecular chirality can be well-controlled through the side-chain chemistry. Specifically, the ionic effects on peptoids from varying the polar side-chain groups result in the formation of either single helical fiber or hierarchically stacked helical bundles. We also demonstrate that the supramolecular chirality of assembled peptoid helices can be controlled by modifying assembling peptoids with a single chiral amino acid side chain. Computational simulations and theoretical modeling predict that minimizing exposure of hydrophobic domains within a twisted helical form presents the most thermodynamically favorable packing of these amphiphilic peptoids and suggests a key role for both polar and hydrophobic domains on nanohelix formation. Our findings establish a platform to design and synthesize chiral functional materials using sequence-defined synthetic polymers.
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Affiliation(s)
- Renyu Zheng
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Mingfei Zhao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Jingshan S Du
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Tarunya Rao Sudarshan
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Yicheng Zhou
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- Department of Materials Science, University of Washington, Seattle, WA, 98195, USA
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Chun-Long Chen
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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11
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Qi X, Pfaendtner J. High-Throughput Computational Screening of Solid-Binding Peptides. J Chem Theory Comput 2024; 20:2959-2968. [PMID: 38499981 DOI: 10.1021/acs.jctc.3c01286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Inspired by biomineralization, a naturally occurring, protein-facilitated process, solid-binding peptides (SBPs) have gained much attention for their potential to fabricate various shaped nanocrystals and hierarchical nanostructures. The advantage of SBPs over other traditionally used synthetic polymers or short ligands is their tunable interaction with the solid material surface via carefully programmed sequence and being solution-dependent simultaneously. However, designing a sequence with targeted binding affinity or selectivity often involves intensive processes such as phage display, and only a limited number of sequences can be identified. Other computational efforts have also been introduced, but the validation process remains prohibitively expensive once a suitable sequence has been identified. In this paper, we present a new model to rapidly estimate the binding free energy of any given sequence to a solid surface. We show how the overall binding of a polypeptide can be estimated from the free energy contribution of each residue based on the statistics of the thermodynamically stable structure ensemble. We validated our model using five silica-binding peptides of different binding affinities and lengths and showed that the model is accurate and robust across a wider range of chemistries and binding strengths. The computational cost of this method can be as low as 3% of the commonly used enhanced sampling scheme for similar studies and has a great potential to be used in high-throughput algorithms to obtain larger training data sets for machine learning SBP screening.
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Affiliation(s)
- Xin Qi
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03784, United States
| | - Jim Pfaendtner
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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12
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Heble AY, Chen CL. Access to Advanced Functional Materials through Postmodification of Biomimetic Assemblies via Click Chemistry. Biomacromolecules 2024; 25:1391-1407. [PMID: 38422548 DOI: 10.1021/acs.biomac.3c01454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The design, synthesis, and fabrication of functional nanomaterials with specific properties remain a long-standing goal for many scientific fields. The self-assembly of sequence-defined biomimetic synthetic polymers presents a fundamental strategy to explore the chemical space beyond biological systems to create advanced nanomaterials. Moreover, subsequent chemical modification of existing nanostructures is a unique approach for accessing increasingly complex nanostructures and introducing functionalities. Of these modifications, covalent conjugation chemistries, such as the click reactions, have been the cornerstone for chemists and materials scientists. Herein, we highlight some recent advances that have successfully employed click chemistries for the postmodification of assembled one-dimensional (1D) and two-dimensional (2D) nanostructures to achieve applications in molecular recognition, mineralization, and optoelectronics. Specifically, biomimetic nanomaterials assembled from sequence-defined macromolecules such as peptides and peptoids are described.
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Affiliation(s)
- Annie Y Heble
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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13
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Du S, Sun S, Ju Z, Wang W, Su K, Qiu F, Yu X, Xu G, Yuan D. Hierarchical Self-Assembly of Capsule-Shaped Zirconium Coordination Cages with Quaternary Structure. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308445. [PMID: 38229156 PMCID: PMC10953209 DOI: 10.1002/advs.202308445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/07/2024] [Indexed: 01/18/2024]
Abstract
Biological macromolecules exhibit emergent functions through hierarchical self-assembly, a concept that is extended to design artificial supramolecular assemblies. Here, the first example of breaking the common parallel arrangement of capsule-shaped zirconium coordination cages is reported by constructing the hierarchical porous framework ZrR-1. ZrR-1 adopts a quaternary structure resembling protein and contains 12-connected chloride clusters, representing the highest connectivity for zirconium-based cages reported thus far. Compared to the parallel framework ZrR-2, ZrR-1 demonstrated enhanced stability in acidic aqueous solutions and a tenfold increase in BET surface area (879 m2 g-1 ). ZrR-1 also exhibits excellent proton conductivity, reaching 1.31 × 10-2 S·cm-1 at 353 K and 98% relative humidity, with a low activation energy of 0.143 eV. This finding provides insights into controlling the hierarchical self-assembly of metal-organic cages to discover superstructures with emergent properties.
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Affiliation(s)
- Shunfu Du
- State Key Laboratory of Structural ChemistryFujian Provincial Key Laboratory of Materials and Techniques toward Hydrogen EnergyFujian Institute of Research on the Structure of MatterThe Chinese Academy of SciencesFuzhouFujian350108P. R. China
- University of the Chinese Academy of SciencesBeijing100049P. R. China
| | - Shihao Sun
- State Key Laboratory of Structural ChemistryFujian Provincial Key Laboratory of Materials and Techniques toward Hydrogen EnergyFujian Institute of Research on the Structure of MatterThe Chinese Academy of SciencesFuzhouFujian350108P. R. China
| | - Zhanfeng Ju
- State Key Laboratory of Structural ChemistryFujian Provincial Key Laboratory of Materials and Techniques toward Hydrogen EnergyFujian Institute of Research on the Structure of MatterThe Chinese Academy of SciencesFuzhouFujian350108P. R. China
- University of the Chinese Academy of SciencesBeijing100049P. R. China
| | - Wenjing Wang
- State Key Laboratory of Structural ChemistryFujian Provincial Key Laboratory of Materials and Techniques toward Hydrogen EnergyFujian Institute of Research on the Structure of MatterThe Chinese Academy of SciencesFuzhouFujian350108P. R. China
- University of the Chinese Academy of SciencesBeijing100049P. R. China
| | - Kongzhao Su
- State Key Laboratory of Structural ChemistryFujian Provincial Key Laboratory of Materials and Techniques toward Hydrogen EnergyFujian Institute of Research on the Structure of MatterThe Chinese Academy of SciencesFuzhouFujian350108P. R. China
- University of the Chinese Academy of SciencesBeijing100049P. R. China
| | - Fenglei Qiu
- State Key Laboratory of Structural ChemistryFujian Provincial Key Laboratory of Materials and Techniques toward Hydrogen EnergyFujian Institute of Research on the Structure of MatterThe Chinese Academy of SciencesFuzhouFujian350108P. R. China
- College of ChemistryFuzhou UniversityFuzhou350108P. R. China
| | - Xuying Yu
- State Key Laboratory of Structural ChemistryFujian Provincial Key Laboratory of Materials and Techniques toward Hydrogen EnergyFujian Institute of Research on the Structure of MatterThe Chinese Academy of SciencesFuzhouFujian350108P. R. China
- University of the Chinese Academy of SciencesBeijing100049P. R. China
| | - Gang Xu
- State Key Laboratory of Structural ChemistryFujian Provincial Key Laboratory of Materials and Techniques toward Hydrogen EnergyFujian Institute of Research on the Structure of MatterThe Chinese Academy of SciencesFuzhouFujian350108P. R. China
- University of the Chinese Academy of SciencesBeijing100049P. R. China
| | - Daqiang Yuan
- State Key Laboratory of Structural ChemistryFujian Provincial Key Laboratory of Materials and Techniques toward Hydrogen EnergyFujian Institute of Research on the Structure of MatterThe Chinese Academy of SciencesFuzhouFujian350108P. R. China
- University of the Chinese Academy of SciencesBeijing100049P. R. China
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14
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Tarasovetc EV, Sissoko GB, Mukhina AS, Maiorov A, Ataullakhanov FI, Cheeseman IM, Grishchuk EL. Molecular density-accelerated binding-site maturation underlies CENP-T-dependent kinetochore assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.25.581584. [PMID: 38464265 PMCID: PMC10925139 DOI: 10.1101/2024.02.25.581584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Formation of macromolecular cellular structures relies on recruitment of multiple proteins, requiring the precisely controlled pairwise binding interactions. At human kinetochores, our recent work found that the high molecular density environment enables strong bonding between the Ndc80 complex and its two binding sites at the CENP-T receptor. However, the mechanistic basis for this unusual density-dependent facilitation remains unknown. Here, using quantitative single-molecule approaches, we reveal two distinct mechanisms that drive preferential recruitment of the Ndc80 complex to higher-order structures of CENP-T, as opposed to CENP-T monomers. First, the Ndc80 binding sites within the disordered tail of the CENP-T mature over time, leading to a stronger grip on the Spc24/25 heads of the Ndc80 complexes. Second, the maturation of Ndc80 binding sites is accelerated when CENP-T molecules are clustered in close proximity. The rates of the clustering-induced maturation are remarkably different for two binding sites within CENP-T, correlating with different interfaces formed by the corresponding CENP-T sequences as they wrap around the Spc24/25 heads. The differential clustering-dependent regulation of these sites is preserved in dividing human cells, suggesting a distinct regulatory entry point to control kinetochore-microtubule interactions. The tunable acceleration of slowly maturing binding sites by a high molecular-density environment may represent a fundamental physicochemical mechanism to assist the assembly of mitotic kinetochores and other macromolecular structures.
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Affiliation(s)
- Ekaterina V. Tarasovetc
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA
| | - Gunter B. Sissoko
- Whitehead Institute for Biomedical Research; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - Anna S. Mukhina
- Department of Physics, Lomonosov Moscow State University; Moscow, 119991, Russia
| | - Aleksandr Maiorov
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA
| | - Fazoil I. Ataullakhanov
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences; Moscow, 119991, Russia
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology; Moscow, 117198, Russia
- Moscow Institute of Physics and Technology; 141701, Dolgoprudny, Russia
| | - Iain M. Cheeseman
- Whitehead Institute for Biomedical Research; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - Ekaterina L. Grishchuk
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA
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15
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Son S, Song WJ. Programming interchangeable and reversible heterooligomeric protein self-assembly using a bifunctional ligand. Chem Sci 2024; 15:2975-2983. [PMID: 38404387 PMCID: PMC10882485 DOI: 10.1039/d3sc05448a] [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: 10/13/2023] [Accepted: 01/10/2024] [Indexed: 02/27/2024] Open
Abstract
Protein design for self-assembly allows us to explore the emergence of protein-protein interfaces through various chemical interactions. Heterooligomers, unlike homooligomers, inherently offer a comprehensive range of structural and functional variations. Besides, the macromolecular repertoire and their applications would significantly expand if protein components could be easily interchangeable. This study demonstrates that a rationally designed bifunctional linker containing an enzyme inhibitor and maleimide can guide the formation of diverse protein heterooligomers in an easily applicable and exchangeable manner without extensive sequence optimizations. As proof of concept, we selected four structurally and functionally unrelated proteins, carbonic anhydrase, aldolase, acetyltransferase, and encapsulin, as building block proteins. The combinations of two proteins with the bifunctional linker yielded four two-component heterooligomers with discrete sizes, shapes, and enzyme activities. Besides, the overall size and formation kinetics of the heterooligomers alter upon adding metal chelators, acidic buffer components, and reducing agents, showing the reversibility and tunability in the protein self-assembly. Given that the functional groups of both the linker and protein components are readily interchangeable, our work broadens the scope of protein-assembled architectures and their potential applications as functional biomaterials.
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Affiliation(s)
- Soyeun Son
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
| | - Woon Ju Song
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
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16
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Cai Y, Qi X, Boese J, Zhao Y, Hellner B, Chun J, Mundy CJ, Baneyx F. Towards predictive control of reversible nanoparticle assembly with solid-binding proteins. SOFT MATTER 2024; 20:1935-1942. [PMID: 38323470 DOI: 10.1039/d4sm00094c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Although a broad range of ligand-functionalized nanoparticles and physico-chemical triggers have been exploited to create stimuli-responsive colloidal systems, little attention has been paid to the reversible assembly of unmodified nanoparticles with non-covalently bound proteins. Previously, we reported that a derivative of green fluorescent protein engineered with oppositely located silica-binding peptides mediates the repeated assembly and disassembly of 10-nm silica nanoparticles when pH is toggled between 7.5 and 8.5. We captured the subtle interplay between interparticle electrostatic repulsion and their protein-mediated short-range attraction with a multiscale model energetically benchmarked to collective system behavior captured by scattering experiments. Here, we show that both solution conditions (pH and ionic strength) and protein engineering (sequence and position of engineered silica-binding peptides) provide pathways for reversible control over growth and fragmentation, leading to clusters ranging in size from 25 nm protein-coated particles to micrometer-size aggregate. We further find that the higher electrolyte environment associated with successive cycles of base addition eventually eliminates reversibility. Our model accurately predicts these multiple length scales phenomena. The underpinning concepts provide design principles for the dynamic control of other protein- and particle-based nanocomposites.
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Affiliation(s)
- Yifeng Cai
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
| | - Xin Qi
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
| | - Julia Boese
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
| | - Yundi Zhao
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
| | - Brittney Hellner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
| | - Jaehun Chun
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
- Levich Institute and Department of Chemical Engineering, CUNY City College of New York, New York, New York 10031, USA
| | - Christopher J Mundy
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - François Baneyx
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
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17
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Min J, Rong X, Zhang J, Su R, Wang Y, Qi W. Computational Design of Peptide Assemblies. J Chem Theory Comput 2024; 20:532-550. [PMID: 38206800 DOI: 10.1021/acs.jctc.3c01054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
With the ongoing development of peptide self-assembling materials, there is growing interest in exploring novel functional peptide sequences. From short peptides to long polypeptides, as the functionality increases, the sequence space is also expanding exponentially. Consequently, attempting to explore all functional sequences comprehensively through experience and experiments alone has become impractical. By utilizing computational methods, especially artificial intelligence enhanced molecular dynamics (MD) simulation and de novo peptide design, there has been a significant expansion in the exploration of sequence space. Through these methods, a variety of supramolecular functional materials, including fibers, two-dimensional arrays, nanocages, etc., have been designed by meticulously controlling the inter- and intramolecular interactions. In this review, we first provide a brief overview of the current main computational methods and then focus on the computational design methods for various self-assembled peptide materials. Additionally, we introduce some representative protein self-assemblies to offer guidance for the design of self-assembling peptides.
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Affiliation(s)
- Jiwei Min
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Xi Rong
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Jiaxing Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
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18
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Yang L, Wang Y, Zhang W, Ma G. New Insight into the Structural Nature of Diphenylalanine Nanotube through Comparison with Amyloid Assemblies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1046-1057. [PMID: 38153333 DOI: 10.1021/acs.langmuir.3c03270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Diphenylalanine (FF) nanotubes are a star material in the field of peptide self-assembly and have demonstrated numerous intriguing applications. Due to its resemblance to amyloid assembly, the FF nanotube is widely regarded as a simplified mimic of amyloids. Yet, whether FF nanotube truly possesses amyloid structure remains an open question. To better understand the structural nature of FF nanotube, we herein performed a comparative structural investigation between FF nanotube and typical amyloid systems by Aβ1-40, Aβ1-42, Aβ16-22, Aβ13-23, α-synuclein, and lysozyme using Fourier transform infrared spectroscopy. Through this comparative investigation, we obtained clear evidence to support that the FF nanotube does not possess a β-sheet structure, a key structural characteristic of amyloid assembly, thus revealing the non-amyloid structural nature of the FF nanotube. At last, in light of our new finding, we further discussed the unique self-assembly behaviors of FF during nanotube formation and the implications of our work for FF nanotube related applications.
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Affiliation(s)
- Lujuan Yang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, State Key Laboratory of New Pharmaceutical Preparations and Excipients, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
| | - Yao Wang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, State Key Laboratory of New Pharmaceutical Preparations and Excipients, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
| | - Wenkai Zhang
- Department of Physics, Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Gang Ma
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, State Key Laboratory of New Pharmaceutical Preparations and Excipients, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
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19
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Li Q, Liu J, Wan H, Zhang M. Inherent molecular characteristics and effect of garlic polysaccharides on dough micro- and mesoscopic properties. Food Chem X 2023; 19:100757. [PMID: 37408954 PMCID: PMC10319188 DOI: 10.1016/j.fochx.2023.100757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023] Open
Abstract
Directional control of the process of doughs with nutrition fortification is challenging. Thus, this study aimed to develop non-starch polysaccharides that can modify the quality of flour products. Polysaccharides were extracted from three different garlic cultivars, evaluated for physicochemical properties and used to enrich doughs for microstructure and mesoscopic characteristics analysis. We assessed the moisture distribution, texture characteristics, thermodynamic properties, dynamic viscoelastic properties, protein structure, microstructure and molecular interaction of the doughs and demonstrated a relatively high molecular weight, lower steric hindrance of molecular chains and higher cross-linking ability with the dough network in the supernatant polysaccharide from Yunnan single-clove-garlic (SGSOS) fraction. These features of SGSOS fraction improved the rheological, thermodynamic, texture characteristics, and water distribution of doughs. These findings provide information on the use of garlic polysaccharides during the processing and manufacturing of foods to enhance their processing adaptability and qualities.
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Affiliation(s)
- Qian Li
- Tianjin Agricultural University, Tianjin 300392, PR China
- China-Russia Agricultural Processing Joint Laboratory, Tianjin Agricultural University, Tianjin 300392, PR China
- State Key Laboratory of Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Jiaming Liu
- Tianjin Agricultural University, Tianjin 300392, PR China
- Tianjin Guangyuan Livestock and Poultry Breeding CO., LTD, Tianjin 301800, PR China
| | - Huiqi Wan
- Tianjin Agricultural University, Tianjin 300392, PR China
| | - Min Zhang
- Tianjin Agricultural University, Tianjin 300392, PR China
- China-Russia Agricultural Processing Joint Laboratory, Tianjin Agricultural University, Tianjin 300392, PR China
- State Key Laboratory of Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, PR China
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20
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Heil CM, Patil A, Vanthournout B, Singla S, Bleuel M, Song JJ, Hu Z, Gianneschi NC, Shawkey MD, Sinha SK, Jayaraman A, Dhinojwala A. Mechanism of structural colors in binary mixtures of nanoparticle-based supraballs. SCIENCE ADVANCES 2023; 9:eadf2859. [PMID: 37235651 DOI: 10.1126/sciadv.adf2859] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/20/2023] [Indexed: 05/28/2023]
Abstract
Inspired by structural colors in avian species, various synthetic strategies have been developed to produce noniridescent, saturated colors using nanoparticle assemblies. Nanoparticle mixtures varying in particle chemistry and size have additional emergent properties that affect the color produced. For complex multicomponent systems, understanding the assembled structure and a robust optical modeling tool can empower scientists to identify structure-color relationships and fabricate designer materials with tailored color. Here, we demonstrate how we can reconstruct the assembled structure from small-angle scattering measurements using the computational reverse-engineering analysis for scattering experiments method and use the reconstructed structure in finite-difference time-domain calculations to predict color. We successfully, quantitatively predict experimentally observed color in mixtures containing strongly absorbing nanoparticles and demonstrate the influence of a single layer of segregated nanoparticles on color produced. The versatile computational approach that we present is useful for engineering synthetic materials with desired colors without laborious trial-and-error experiments.
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Affiliation(s)
- Christian M Heil
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716, USA
| | - Anvay Patil
- School of Polymer Science and Polymer Engineering, The University of Akron, 170 University Ave., Akron, OH 44325, USA
| | - Bram Vanthournout
- Evolution and Optics of Nanostructures Group, Department of Biology, Ghent University, Ledeganckstraat 35, Ghent 9000, Belgium
| | - Saranshu Singla
- School of Polymer Science and Polymer Engineering, The University of Akron, 170 University Ave., Akron, OH 44325, USA
| | - Markus Bleuel
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20878, USA
- Department of Materials Science and Engineering, University of Maryland, 4418 Stadium Dr., College Park, MD 20742, USA
| | - Jing-Jin Song
- Department of Materials Science & Engineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Ziying Hu
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Nathan C Gianneschi
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Department of Biomedical Engineering, Department of Pharmacology, International Institute of Nanotechnology, Simpson-Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, Evanston, IL 60208, USA
| | - Matthew D Shawkey
- Evolution and Optics of Nanostructures Group, Department of Biology, Ghent University, Ledeganckstraat 35, Ghent 9000, Belgium
| | - Sunil K Sinha
- Department of Physics, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716, USA
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, DE 19716, USA
| | - Ali Dhinojwala
- School of Polymer Science and Polymer Engineering, The University of Akron, 170 University Ave., Akron, OH 44325, USA
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21
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Zhao M, Zhang S, Zheng R, Alamdari S, Mundy CJ, Pfaendtner J, Pozzo LD, Chen CL, De Yoreo JJ, Ferguson AL. Computational and Experimental Determination of the Properties, Structure, and Stability of Peptoid Nanosheets and Nanotubes. Biomacromolecules 2023. [PMID: 37141445 DOI: 10.1021/acs.biomac.3c00107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Peptoids (N-substituted glycines) are a group of highly controllable peptidomimetic polymers. Amphiphilic diblock peptoids have been engineered to assemble crystalline nanospheres, nanofibrils, nanosheets, and nanotubes with biochemical, biomedical, and bioengineering applications. The mechanical properties of peptoid nanoaggregates and their relationship to the emergent self-assembled morphologies have been relatively unexplored and are critical for the rational design of peptoid nanomaterials. In this work, we consider a family of amphiphilic diblock peptoids consisting of a prototypical tube-former (Nbrpm6Nc6, a NH2-capped hydrophobic block of six N-((4-bromophenyl)methyl)glycine residues conjugated to a polar NH3(CH2)5CO tail), a prototypical sheet-former (Nbrpe6Nc6, where the hydrophobic block comprises six N-((4-bromophenyl)ethyl)glycine residues), and an intermediate sequence that forms mixed structures ((NbrpeNbrpm)3Nc6). We combine all-atom molecular dynamics simulations and atomic force microscopy to determine the mechanical properties of the self-assembled 2D crystalline nanosheets and relate these properties to the observed self-assembled morphologies. We find good agreement between our computational predictions and experimental measurements of Young's modulus of crystalline nanosheets. A computational analysis of the bending modulus along the two axes of the planar crystalline nanosheets reveals bending to be more favorable along the axis in which the peptoids stack by interdigitation of the side chains compared to that in which they form columnar crystals with π-stacked side chains. We construct molecular models of nanotubes of the Nbrpm6Nc6 tube-forming peptoid and predict a stability optimum in good agreement with experimental measurements. A theoretical model of nanotube stability suggests that this optimum is a free energy minimum corresponding to a "Goldilocks" tube radius at which capillary wave fluctuations in the tube wall are minimized.
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Affiliation(s)
- Mingfei Zhao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Shuai Zhang
- Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Renyu Zheng
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Sarah Alamdari
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Christopher J Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Lilo D Pozzo
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - James J De Yoreo
- Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
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22
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Heil C, Ma Y, Bharti B, Jayaraman A. Computational Reverse-Engineering Analysis for Scattering Experiments for Form Factor and Structure Factor Determination (" P( q) and S( q) CREASE"). JACS AU 2023; 3:889-904. [PMID: 37006757 PMCID: PMC10052275 DOI: 10.1021/jacsau.2c00697] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 05/11/2023]
Abstract
In this paper, we present an open-source machine learning (ML)-accelerated computational method to analyze small-angle scattering profiles [I(q) vs q] from concentrated macromolecular solutions to simultaneously obtain the form factor P(q) (e.g., dimensions of a micelle) and the structure factor S(q) (e.g., spatial arrangement of the micelles) without relying on analytical models. This method builds on our recent work on Computational Reverse-Engineering Analysis for Scattering Experiments (CREASE) that has either been applied to obtain P(q) from dilute macromolecular solutions (where S(q) ∼1) or to obtain S(q) from concentrated particle solutions when P(q) is known (e.g., sphere form factor). This paper's newly developed CREASE that calculates P(q) and S(q), termed as "P(q) and S(q) CREASE", is validated by taking as input I(q) vs q from in silico structures of known polydisperse core(A)-shell(B) micelles in solutions at varying concentrations and micelle-micelle aggregation. We demonstrate how "P(q) and S(q) CREASE" performs if given two or three of the relevant scattering profiles-I total(q), I A(q), and I B(q)-as inputs; this demonstration is meant to guide experimentalists who may choose to do small-angle X-ray scattering (for total scattering from the micelles) and/or small-angle neutron scattering with appropriate contrast matching to get scattering solely from one or the other component (A or B). After validation of "P(q) and S(q) CREASE" on in silico structures, we present our results analyzing small-angle neutron scattering profiles from a solution of core-shell type surfactant-coated nanoparticles with varying extents of aggregation.
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Affiliation(s)
- Christian
M. Heil
- Department
of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, Delaware 19716, United States
| | - Yingzhen Ma
- Cain
Department of Chemical Engineering, Louisiana
State University, 3307 Patrick F. Taylor Hall, Baton Rouge, Louisiana 70803, United States
| | - Bhuvnesh Bharti
- Cain
Department of Chemical Engineering, Louisiana
State University, 3307 Patrick F. Taylor Hall, Baton Rouge, Louisiana 70803, United States
| | - Arthi Jayaraman
- Department
of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, Delaware 19716, United States
- Department
of Materials Science and Engineering, University
of Delaware, 201 DuPont
Hall, Newark, Delaware 19716, United States
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23
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Li Q, Wang Y, Zhang G, Su R, Qi W. Biomimetic mineralization based on self-assembling peptides. Chem Soc Rev 2023; 52:1549-1590. [PMID: 36602188 DOI: 10.1039/d2cs00725h] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Biomimetic science has attracted great interest in the fields of chemistry, biology, materials science, and energy. Biomimetic mineralization is the process of synthesizing inorganic minerals under the control of organic molecules or biomolecules under mild conditions. Peptides are the motifs that constitute proteins, and can self-assemble into various hierarchical structures and show a high affinity for inorganic substances. Therefore, peptides can be used as building blocks for the synthesis of functional biomimetic materials. With the participation of peptides, the morphology, size, and composition of mineralized materials can be controlled precisely. Peptides not only provide well-defined templates for the nucleation and growth of inorganic nanomaterials but also have the potential to confer inorganic nanomaterials with high catalytic efficiency, selectivity, and biotherapeutic functions. In this review, we systematically summarize research progress in the formation mechanism, nanostructural manipulation, and applications of peptide-templated mineralized materials. These can further inspire researchers to design structurally complex and functionalized biomimetic materials with great promising applications.
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Affiliation(s)
- Qing Li
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Gong Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou Industrial Park, Suzhou 215123, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China.,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China.,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
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