1
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Ji W, Hu Y, Wang X, Zhao J, He Y, Zhu Z, Rao J. Biomimetic protein structural transitions regulate activation and inhibition of the broad-spectrum bactericidal activity of cationic nanoparticles. Acta Biomater 2024:S1742-7061(24)00261-7. [PMID: 38750919 DOI: 10.1016/j.actbio.2024.05.022] [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: 02/13/2024] [Revised: 05/01/2024] [Accepted: 05/09/2024] [Indexed: 06/02/2024]
Abstract
The development of cationic polymers as alternative materials to antibiotics necessitates addressing the challenge of balancing their antimicrobial activity and toxicity. Here we propose a precise switching strategy inspired by biomimetic voltage-gated ion channels, enabling controlled activation and inhibition of cationic antimicrobial functions through protein conformational transitions in diverse physiological environments. Following thermodynamic studies on the specific recognition between mannose end groups on polycations and concanavalin A (ConA), we synthesized a type of ConA-polycation nanoparticle. The nanoparticle was inhibited under neutral conditions, with cationic moieties shielded by ConA's β-sheet. This shielding suppresses their antimicrobial activity, thereby ensuring satisfactory biocompatibility. In mildly acidic environments, however, the transition of a portion of ConA to an α-helix conformation exposed cations at the particle periphery, activating antibacterial functionality. Compared to inhibited nanoparticles, those in the activated state exhibited a 32-256 times reduction in the minimum bactericidal concentration against bacteria and fungi (2-16 µg/mL). In a murine acute pulmonary infection model, intravenous administration of inhibited nanoparticles effectively reduced bacterial counts by 4-log within 12 h. The biomimetic design, regulating cationic antimicrobial functionality through the alteration in protein secondary structure, significantly retards bacterial resistance development, holding great promise for intelligent antimicrobial materials. STATEMENT OF SIGNIFICANCE: Cationic antimicrobial polymers exhibit advantages distinct from antibiotics due to their lower propensity for resistance development. However, the presence of cationic moieties also poses a threat to healthy cells and tissues, significantly constraining their potential for clinical applications. To address this challenge, we propose a biomimetic strategy that mimics voltage-gated ion channels to activate the antimicrobial functionality of cations selectively in bacterial environments through the conformational transitions of proteins between β-sheets and α-helices. In healthy tissues, the antimicrobial functionality is inhibited, ensuring satisfactory biocompatibility. Antimicrobial cationic materials capable of intelligent switching between an activated state and an inhibited state in response to environmental changes offer an effective strategy to prevent the development of resistance and mitigate potential side effects.
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Affiliation(s)
- Wenke Ji
- Hubei Key Laboratory of Material Chemistry and Service Failure, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, PR China
| | - Yongjin Hu
- Hubei Key Laboratory of Material Chemistry and Service Failure, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, PR China
| | - Xiao Wang
- Hubei Key Laboratory of Material Chemistry and Service Failure, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, PR China
| | - Jinghua Zhao
- Hubei Key Laboratory of Material Chemistry and Service Failure, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, PR China
| | - Yan He
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, PR China
| | - Zhiyuan Zhu
- Taizhou Research Institute, Southern University of Science and Technology, Taizhou, Zhejiang, 318001, PR China
| | - Jingyi Rao
- Hubei Key Laboratory of Material Chemistry and Service Failure, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, PR China.
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2
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Lu Q, Xu Y, Poppleton E, Zhou K, Sulc P, Stephanopoulos N, Ke Y. DNA-Nanostructure-Guided Assembly of Proteins into Programmable Shapes. NANO LETTERS 2024; 24:1703-1709. [PMID: 38278134 PMCID: PMC10853956 DOI: 10.1021/acs.nanolett.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
The development of methods to synthesize artificial protein complexes with precisely controlled configurations will enable diverse biological and medical applications. Using DNA to link proteins provides programmability that can be difficult to achieve with other methods. Here, we use DNA origami as an "assembler" to guide the linking of protein-DNA conjugates using a series of oligonucleotide hybridization and displacement operations. We constructed several isomeric protein nanostructures, including a dimer, two types of trimer structures, and three types of tetramer assemblies, on a DNA origami platform by using a C3-symmetric building block composed of a protein trimer modified with DNA handles. Our approach expands the scope for the precise assembly of protein-based nanostructures and will enable the formulation of functional protein complexes with stoichiometric and geometric control.
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Affiliation(s)
- Qinyi Lu
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Yang Xu
- Biodesign
Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Erik Poppleton
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Kun Zhou
- Department
of Biomedical Engineering, Georgia Institute
of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Petr Sulc
- Biodesign
Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Nicholas Stephanopoulos
- Biodesign
Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yonggang Ke
- Department
of Biomedical Engineering, Georgia Institute
of Technology and Emory University, Atlanta, Georgia 30322, United States
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3
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Li Z, Wang S, Nattermann U, Bera AK, Borst AJ, Yaman MY, Bick MJ, Yang EC, Sheffler W, Lee B, Seifert S, Hura GL, Nguyen H, Kang A, Dalal R, Lubner JM, Hsia Y, Haddox H, Courbet A, Dowling Q, Miranda M, Favor A, Etemadi A, Edman NI, Yang W, Weidle C, Sankaran B, Negahdari B, Ross MB, Ginger DS, Baker D. Accurate computational design of three-dimensional protein crystals. NATURE MATERIALS 2023; 22:1556-1563. [PMID: 37845322 DOI: 10.1038/s41563-023-01683-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 09/07/2023] [Indexed: 10/18/2023]
Abstract
Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing arrangements and space group preferences being largely unpredictable. Programming protein crystallization through precisely engineered side-chain-side-chain interactions across protein-protein interfaces is an outstanding challenge. Here we develop a general computational approach for designing three-dimensional protein crystals with prespecified lattice architectures at atomic accuracy that hierarchically constrains the overall number of degrees of freedom of the system. We design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into >100 µm three-dimensional crystals. The structures of these crystals are nearly identical to the computational design models, closely corresponding in both overall architecture and the specific protein-protein interactions. The dimensions of the crystal unit cell can be systematically redesigned while retaining the space group symmetry and overall architecture, and the crystals are extremely porous and highly stable. Our approach enables the computational design of protein crystals with high accuracy, and the designed protein crystals, which have both structural and assembly information encoded in their primary sequences, provide a powerful platform for biological materials engineering.
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Affiliation(s)
- Zhe Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Shunzhi Wang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Una Nattermann
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure & Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Andrew J Borst
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Muammer Y Yaman
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Erin C Yang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure & Design, University of Washington, Seattle, WA, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Byeongdu Lee
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA
| | - Soenke Seifert
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Radhika Dalal
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Joshua M Lubner
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Yang Hsia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hugh Haddox
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alexis Courbet
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- HHMI, University of Washington, Seattle, WA, USA
| | - Quinton Dowling
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Marcos Miranda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Andrew Favor
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
| | - Ali Etemadi
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Natasha I Edman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Wei Yang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Connor Weidle
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Babak Negahdari
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Michael B Ross
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, USA
| | - David S Ginger
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- HHMI, University of Washington, Seattle, WA, USA.
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4
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Han K, Zhang Z, Tezcan FA. Spatially Patterned, Porous Protein Crystals as Multifunctional Materials. J Am Chem Soc 2023; 145:19932-19944. [PMID: 37642457 DOI: 10.1021/jacs.3c06348] [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] [Indexed: 08/31/2023]
Abstract
While the primary use of protein crystals has historically been in crystallographic structure determination, they have recently emerged as promising materials with many advantageous properties such as high porosity, biocompatibility, stability, structural and functional versatility, and genetic/chemical tailorability. Here, we report that the utility of protein crystals as functional materials can be further augmented through their spatial patterning and control of their morphologies. To this end, we took advantage of the chemically and kinetically controllable nature of ferritin self-assembly and constructed core-shell crystals with chemically distinct domains, tunable structural patterns, and morphologies. The spatial organization within ferritin crystals enabled the generation of patterned, multi-enzyme frameworks with cooperative catalytic behavior. We further exploited the differential growth kinetics of ferritin crystal facets to assemble Janus-type architectures with an anisotropic arrangement of chemically distinct domains. These examples represent a step toward using protein crystals as reaction vessels for complex multi-step reactions and broadening their utility as functional, solid-state materials. Our results demonstrate that morphology control and spatial patterning, which are key concepts in materials science and nanotechnology, can also be applied for engineering protein crystals.
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Affiliation(s)
- Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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5
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Li L, Li Z, Wang Z, Chen S, Liu R, Xu X, Zhang Z, Ye L, Ding Y, Luo Q, Cao S, Zhang L, Imberty A, Chen G. Spatiotemporal Landscape for the Sophisticated Transformation of Protein Assemblies Defined by Multiple Supramolecular Interactions. ACS NANO 2023; 17:15001-15011. [PMID: 37459282 DOI: 10.1021/acsnano.3c04029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Precise protein assemblies not only constitute a series of living machineries but also provide an advanced class of biomaterials. Previously, we developed the inducing ligand strategy to generate various fixed protein assemblies, without the formation of noncovalent interactions between proteins. Here, we demonstrated that controlling the symmetry and number of supramolecular interactions introduced on protein surfaces could direct the formation of unspecific interactions between proteins and induce various nanoscale assemblies, including coiling nanowires, nanotubes, and nanosheets, without manipulation of the protein's native surfaces. More importantly, these nanoscale assemblies could spontaneously evolve into more ordered architectures, crystals. We further showed that the transformation from the introduced supramolecular interactions to the interactions formed between proteins was crucial for pathway selection and outcomes of evolution. These findings reveal a transformation mechanism of protein self-assembly that has not been exploited before and may provide an approach to generate complex and transformable biomacromolecular self-assemblies.
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Affiliation(s)
- Long Li
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Zhen Li
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Ziying Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shuyu Chen
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi'an Jiaotong University, Xi'an 710049, China
| | - Rongying Liu
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Xuyang Xu
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Zhi Zhang
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Linfei Ye
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Yu Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
- Key Laboratory of Emergency and Trauma, Ministry of Education, College of Emergency and Trauma, Hainan Medical University, Haikou 571199, China
| | - Sheng Cao
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi'an Jiaotong University, Xi'an 710049, China
| | - Anne Imberty
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble 38000, France
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Multiscale Research Institute for Complex Systems, Fudan University, Shanghai 200433, China
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6
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van Hengel CDN, van Adrichem KE, Jansen TLC. Simulation of two-dimensional infrared Raman spectroscopy with application to proteins. J Chem Phys 2023; 158:064106. [PMID: 36792507 DOI: 10.1063/5.0138958] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Two-dimensional infrared Raman spectroscopy is a powerful technique for studying the structure and interaction in molecular and biological systems. Here, we present a new implementation of the simulation of the two-dimensional infrared Raman signals. The implementation builds on the numerical integration of the Schrödinger equation approach. It combines the prediction of dynamics from molecular dynamics with a map-based approach for obtaining Hamiltonian trajectories and response function calculations. The new implementation is tested on the amide-I region for two proteins, where one is dominated by α-helices and the other by β-sheets. We find that the predicted spectra agree well with experimental observations. We further find that the two-dimensional infrared Raman spectra at least of the studied proteins are much less sensitive to the laser polarization used compared to conventional two-dimensional infrared experiments. The present implementation and findings pave the way for future applications for the interpretation of two-dimensional infrared Raman spectra.
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Affiliation(s)
- Carleen D N van Hengel
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kim E van Adrichem
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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7
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Cerofolini L, Ramberg KO, Padilla LC, Antonik P, Ravera E, Luchinat C, Fragai M, Crowley PB. Solid-state NMR - a complementary technique for protein framework characterization. Chem Commun (Camb) 2023; 59:776-779. [PMID: 36546612 DOI: 10.1039/d2cc05725e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein frameworks are an emerging class of biomaterial with medical and technological applications. Frameworks are studied mainly by X-ray diffraction or scattering techniques. Complementary strategies are required. Here, we report solid-state NMR analyses of a microcrystalline protein-macrocycle framework and the rehydrated freeze-dried protein. This methodology may aid the characterization of low-crystallinity frameworks.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy. .,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Kiefer O Ramberg
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland.
| | - Luis C Padilla
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy. .,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Paweł Antonik
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland.
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy. .,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, Sesto Fiorentino 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy. .,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, Sesto Fiorentino 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy. .,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, Sesto Fiorentino 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Peter B Crowley
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland.
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8
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Winegar PH, Figg CA, Teplensky MH, Ramani N, Mirkin CA. Modular Nucleic Acid Scaffolds for Synthesizing Monodisperse and Sequence-Encoded Antibody Oligomers. Chem 2022; 8:3018-3030. [PMID: 36405374 PMCID: PMC9674055 DOI: 10.1016/j.chempr.2022.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Synthesizing protein oligomers that contain exact numbers of multiple different proteins in defined architectures is challenging. DNA-DNA interactions can be used to program protein assembly into oligomers; however, existing methods require changes to DNA design to achieve different numbers and oligomeric sequences of proteins. Herein, we develop a modular DNA scaffold that uses only six synthetic oligonucleotides to organize proteins into defined oligomers. As a proof-of-concept, model proteins (antibodies) are oligomerized into dimers and trimers, where antibody function is retained. Illustrating the modularity of this technique, dimer and trimer building blocks are then assembled into pentamers containing three different antibodies in an exact stoichiometry and oligomeric sequence. In sum, this report describes a generalizable method for organizing proteins into monodisperse, sequence-encoded oligomers using DNA. This advance will enable studies into how oligomeric protein sequences affect material properties in areas spanning pharmaceutical development, cascade catalysis, synthetic photosynthesis, and membrane transport.
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Affiliation(s)
- Peter H. Winegar
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- These authors contributed equally
| | - C. Adrian Figg
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- These authors contributed equally
| | - Michelle H. Teplensky
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Namrata Ramani
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Chad A. Mirkin
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Lead contact
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9
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Kong Y, Du Q, Li J, Xing H. Engineering bacterial surface interactions using DNA as a programmable material. Chem Commun (Camb) 2022; 58:3086-3100. [PMID: 35077527 DOI: 10.1039/d1cc06138k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The diverse surface interactions and functions of a bacterium play an important role in cell signaling, host infection, and colony formation. To understand and synthetically control the biological functions of individual cells as well as the whole community, there is growing attention on the development of chemical and biological tools that can integrate artificial functional motifs onto the bacterial surface to replace the native interactions, enabling a variety of applications in biosynthesis, environmental protection, and human health. Among all these functional motifs, DNA emerges as a powerful tool that can precisely control bacterial interactions at the bio-interface due to its programmability and biorecognition properties. Compared with conventional chemical and genetic approaches, the sequence-specific Watson-Crick interaction enables almost unlimited programmability in DNA nanostructures, realizing one base-pair spatial control and bio-responsive properties. This highlight aims to provide an overview on this emerging research topic of DNA-engineered bacterial interactions from the aspect of synthetic chemists. We start with the introduction of native bacterial surface ligands and established synthetic approaches to install artificial ligands, including direct modification, metabolic engineering, and genetic engineering. A brief overview of DNA nanotechnology, reported DNA-bacteria conjugation chemistries, and several examples of DNA-engineered bacteria are included in this highlight. The future perspectives and challenges in this field are also discussed, including the development of dynamic bacterial surface chemistry, assembly of programmable multicellular community, and realization of bacteria-based theranostic agents and synthetic microbiota as long-term goals.
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Affiliation(s)
- Yuhan Kong
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Qi Du
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Juan Li
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
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10
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Yan XY, Guo QY, Liu XY, Wang Y, Wang J, Su Z, Huang J, Bian F, Lin H, Huang M, Lin Z, Liu T, Liu Y, Cheng SZD. Superlattice Engineering with Chemically Precise Molecular Building Blocks. J Am Chem Soc 2021; 143:21613-21621. [PMID: 34913335 DOI: 10.1021/jacs.1c09831] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Correlating nanoscale building blocks with mesoscale superlattices, mimicking metal alloys, a rational engineering strategy becomes critical to generate designed periodicity with emergent properties. For molecule-based superlattices, nevertheless, nonrigid molecular features and multistep self-assembly make the molecule-to-superlattice correlation less straightforward. In addition, single component systems possess intrinsically limited volume asymmetry of self-assembled spherical motifs (also known as "mesoatoms"), further hampering novel superlattices' emergence. In the current work, we demonstrate that properly designed molecular systems could generate a spectrum of unconventional superlattices. Four categories of giant molecules are presented. We systematically explore the lattice-forming principles in unary and binary systems, unveiling how molecular stoichiometry, topology, and size differences impact the mesoatoms and further toward their superlattices. The presence of novel superlattices helps to correlate with Frank-Kasper phases previously discovered in soft matter. We envision the present work offers new insights about how complex superlattices could be rationally fabricated by scalable-preparation and easy-to-process materials.
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Affiliation(s)
- Xiao-Yun Yan
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China.,Department of Polymer Science, School of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio 44325-3909, United States
| | - Qing-Yun Guo
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China.,Department of Polymer Science, School of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio 44325-3909, United States
| | - Xian-You Liu
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yicong Wang
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Jing Wang
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Zebin Su
- Department of Polymer Science, School of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio 44325-3909, United States
| | - Jiahao Huang
- Department of Polymer Science, School of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio 44325-3909, United States
| | - Fenggang Bian
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204, China
| | - Haixin Lin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen 361005, China.,Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Mingjun Huang
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China.,Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Zhiwei Lin
- Department of Polymer Science, School of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio 44325-3909, United States
| | - Tong Liu
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China.,Department of Polymer Science, School of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio 44325-3909, United States
| | - Yuchu Liu
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China.,Department of Polymer Science, School of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio 44325-3909, United States
| | - Stephen Z D Cheng
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China.,Department of Polymer Science, School of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio 44325-3909, United States
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11
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Kojima M, Abe S, Ueno T. Engineering of protein crystals for use as solid biomaterials. Biomater Sci 2021; 10:354-367. [PMID: 34928275 DOI: 10.1039/d1bm01752g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein crystals have attracted a great deal of attention as solid biomaterials because they have porous structures created by regular assemblies of proteins. The lattice structures of protein crystals are controlled by designing molecular interfacial interactions via covalent bonds and non-covalent bonds. Protein crystals have been functionalized as templates to immobilize foreign molecules such as metal nanoparticles, metal complexes, and proteins. These hybrid crystals are used as functional materials for catalytic reactions and structural analysis. Furthermore, in-cell protein crystals have been studied extensively, providing progress in rapid protein crystallization and crystallography. This review highlights recent advances in crystal engineering for protein crystallization and generation of solid functional materials both in vitro and within cells.
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Affiliation(s)
- Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
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12
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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13
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Encoding hierarchical assembly pathways of proteins with DNA. Proc Natl Acad Sci U S A 2021; 118:2106808118. [PMID: 34593642 DOI: 10.1073/pnas.2106808118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2021] [Indexed: 11/18/2022] Open
Abstract
The structural and functional diversity of materials in nature depends on the controlled assembly of discrete building blocks into complex architectures via specific, multistep, hierarchical assembly pathways. Achieving similar complexity in synthetic materials through hierarchical assembly is challenging due to difficulties with defining multiple recognition areas on synthetic building blocks and controlling the sequence through which those recognition sites direct assembly. Here, we show that we can exploit the chemical anisotropy of proteins and the programmability of DNA ligands to deliberately control the hierarchical assembly of protein-DNA materials. Through DNA sequence design, we introduce orthogonal DNA interactions with disparate interaction strengths ("strong" and "weak") onto specific geometric regions of a model protein, stable protein 1 (Sp1). We show that the spatial encoding of DNA ligands leads to highly directional assembly via strong interactions and that, by design, the first stage of assembly increases the multivalency of weak DNA-DNA interactions that give rise to an emergent second stage of assembly. Furthermore, we demonstrate that judicious DNA design not only directs assembly along a given pathway but can also direct distinct structural outcomes from a single pathway. This combination of protein surface and DNA sequence design allows us to encode the structural and chemical information necessary into building blocks to program their multistep hierarchical assembly. Our findings represent a strategy for controlling the hierarchical assembly of proteins to realize a diverse set of protein-DNA materials by design.
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