1
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Naudé M, Faller P, Lebrun V. A Closer Look at Type I Left-Handed β-Helices Provides a Better Understanding in Their Sequence-Structure Relationship: Toward Their Rational Design. Proteins 2024. [PMID: 38980225 DOI: 10.1002/prot.26726] [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: 01/29/2024] [Revised: 04/17/2024] [Accepted: 06/20/2024] [Indexed: 07/10/2024]
Abstract
Understanding the sequence-structure relationship in protein is of fundamental interest, but has practical applications such as the rational design of peptides and proteins. This relationship in the Type I left-handed β-helix containing proteins is updated and revisited in this study. Analyzing the available experimental structures in the Protein Data Bank, we could describe, further in detail, the structural features that are important for the stability of this fold, as well as its nucleation and termination. This study is meant to complete previous work, as it provides a separate analysis of the N-terminal and C-terminal rungs of the helix. Particular sequence motifs of these rungs are described along with the structural element they form.
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Affiliation(s)
- Maxime Naudé
- Institute of Chemistry of Strasbourg (UMR 7177), University of Strasbourg-CNRS, Strasbourg, France
| | - Peter Faller
- Institute of Chemistry of Strasbourg (UMR 7177), University of Strasbourg-CNRS, Strasbourg, France
| | - Vincent Lebrun
- Institute of Chemistry of Strasbourg (UMR 7177), University of Strasbourg-CNRS, Strasbourg, France
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2
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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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3
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Liu B, Fang R, Li W, Wu X, Liu T, Lin M, Sun J, Chen X. Fast Catalyst-Free Synthesis of Stereoselective Polypeptides via Hierarchical Chiral Assembly. J Am Chem Soc 2024. [PMID: 38858162 DOI: 10.1021/jacs.4c03281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Understanding how life's essential homochiral biopolymers arose from racemic precursors is a challenging quest. Herein, we present a groundbreaking approach involving hierarchical chiral assembly-driven stereoselective ring-opening polymerization of ε-benzyloxycarbonyl-l/d-lysine N-carboxyanhydrides assisted by ultrasonication in an aqueous medium. This method enabled a narrow dispersity within a few minutes and the achievement of high molecular weight for polypeptides, employing a living polymerization mechanism. The polymerization of l and d enantiomers yielded predominantly right- and left-handed superhelical assemblies in a one-pot preparation, respectively. Notably, stereoselective polypeptide segments were efficiently prepared through hierarchical assembly-driven polymerization of racemic monomers in the absence of a catalyst. This research offers an innovative strategy for the convenient preparations of stereoenriched polypeptides and, more importantly, sheds light on the plausible emergence of homochiral peptides in the origin of life.
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Affiliation(s)
- Borui Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
| | - Rui Fang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
| | - Wenlong Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
| | - Xiaoyu Wu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
| | - Tianli Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
| | - Min Lin
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
| | - Jing Sun
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
| | - Xuesi Chen
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022 Changchun, China
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4
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Liu X, Guo Z, Wang J, Shen W, Jia Z, Jia S, Li L, Wang J, Wang L, Li J, Sun Y, Chen Y, Zhang M, Bai J, Wang L, Li X. Thiolation-Based Protein-Protein Hydrogels for Improved Wound Healing. Adv Healthc Mater 2024; 13:e2303824. [PMID: 38303578 DOI: 10.1002/adhm.202303824] [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: 11/02/2023] [Revised: 01/28/2024] [Indexed: 02/03/2024]
Abstract
The limitations of protein-based hydrogels, including their insufficient mechanical properties and restricted biological functions, arise from the highly specific functions of proteins as natural building blocks. A potential solution to overcome these shortcomings is the development of protein-protein hydrogels, which integrate structural and functional proteins. In this study, a protein-protein hydrogel formed by crosslinking bovine serum albumin (BSA) and a genetically engineered intrinsically disordered collagen-like protein (CLP) through Ag─S bonding is introduced. The approach involves thiolating lysine residues of BSA and crosslinking CLP with Ag+ ions, utilizing thiolation of BSA and the free-cysteines of CLP. The resulting protein-protein hydrogels exhibit exceptional properties, including notable plasticity, inherent self-healing capabilities, and gel-sol transition in response to redox conditions. In comparison to standalone BSA hydrogels, these protein-protein hydrogels demonstrate enhanced cellular viability, and improved cellular migration. In vivo experiments provide conclusive evidence of accelerated wound healing, observed not only in murine models with streptozotocin (Step)-induced diabetes but also in zebrafish models subjected to UV-burn injuries. Detailed mechanistic insights, combined with assessments of proinflammatory cytokines and the expression of epidermal differentiation-related proteins, robustly validate the protein-protein hydrogel's effectiveness in promoting wound repair.
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Affiliation(s)
- Xing Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Institute of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, P .R. China
| | - Zhao Guo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Institute of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, P .R. China
| | - Jie Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Institute of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, P .R. China
| | - Wenting Shen
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Science, Shandong Normal University, Jinan, 250014, P. R. China
| | - Zhenzhen Jia
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Science, Shandong Normal University, Jinan, 250014, P. R. China
| | - Shuang Jia
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Institute of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, P .R. China
| | - Limiao Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Institute of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, P .R. China
| | - Jieqi Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Institute of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, P .R. China
| | - Liping Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Institute of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, P .R. China
| | - Jiaqi Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Institute of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, P .R. China
| | - Yinan Sun
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Institute of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, P .R. China
| | - Yufang Chen
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Institute of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, P .R. China
| | - Min Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Institute of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, P .R. China
| | - Jia Bai
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Institute of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, P .R. China
| | - Liyao Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Institute of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, P .R. China
| | - Xinyu Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Institute of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, P .R. China
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5
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Xu Z, Yu X, Gao F, Zang M, Huang L, Liu W, Xu J, Yu S, Wang T, Sun H, Liu J. Fighting bacteria with bacteria: A biocompatible living hydrogel patch for combating bacterial infections and promoting wound healing. Acta Biomater 2024; 181:176-187. [PMID: 38719158 DOI: 10.1016/j.actbio.2024.04.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/28/2024] [Accepted: 04/30/2024] [Indexed: 05/23/2024]
Abstract
Bacterial infections are among the most critical global health challenges that seriously threaten the security of human. To address this issue, a biocompatible engineered living hydrogel patch was developed by co-embedding engineered photothermal bacteria (EM), photosensitizer (porphyrin) and reactive oxygen species amplifier (laccase) in a protein hydrogel. Remarkably, the genetice engineered bacteria can express melanin granules in vivo and this allows them to exhibit photothermal response upon being exposed to NIR-II laser (1064 nm) irradiation. Besides, electrostatically adhered tetramethylpyridinium porphyrin (TMPyP) on the bacterial surface and encapsulated laccase (Lac) in protein gel can generate highly toxic singlet oxygen (1O2) and hydroxyl radical (·OH) in the presence of visible light and lignin, respectively. Interestingly, the engineered bacteria hydrogel patch (EMTL@Gel) was successfully applied in synergistic photothermal, photodynamic and chemodynamic therapy, in which it was able to efficiently treat bacterial infection in mouse wounds and enhance wound healing. This work demonstrates the concept of "fighting bacteria with bacteria" combining bacterial engineering and material engineering into an engineered living hydrogel path that can synergistically boost the therapeutic outcome. STATEMENT OF SIGNIFICANCE: Genetically engineered bacteria produce melanin granules in vivo, exhibiting remarkable photothermal properties. These bacteria, along with a photosensitizer (TMPyP) and a reactive oxygen species amplifier (laccase), are incorporated into a biocompatible protein hydrogel patch. Under visible light, the patch generates toxic singlet oxygen (1O2) and hydroxyl radical (·OH), demonstrates outstanding synergistic effects in photothermal, photodynamic, and chemodynamic therapy, effectively treating bacterial infections and promoting wound healing in mice.
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Affiliation(s)
- Zhengwei Xu
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, PR China
| | - Xiaoxuan Yu
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, PR China
| | - Fan Gao
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, PR China
| | - Mingsong Zang
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, PR China
| | - Liwei Huang
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, PR China
| | - Wang Liu
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, PR China
| | - Jiayun Xu
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, PR China
| | - Shuangjiang Yu
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, PR China
| | - Tingting Wang
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, PR China.
| | - Hongcheng Sun
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, PR China.
| | - Junqiu Liu
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, PR China.
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6
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Szyszka TN, Andreas MP, Lie F, Miller LM, Adamson LSR, Fatehi F, Twarock R, Draper BE, Jarrold MF, Giessen TW, Lau YH. Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages. Proc Natl Acad Sci U S A 2024; 121:e2321260121. [PMID: 38722807 PMCID: PMC11098114 DOI: 10.1073/pnas.2321260121] [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: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 05/18/2024] Open
Abstract
Protein capsids are a widespread form of compartmentalization in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximizes the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of unique symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryoelectron microscopy, we determine the structures of a precedented 60-mer icosahedral assembly and an unexpected 36-mer tetrahedron that features significant geometric rearrangements around a new interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple-point mutation to various amino acids and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent a unique example of tetrahedral geometry when surveying all characterized encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in the protein sequence.
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Affiliation(s)
- Taylor N. Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW2006, Australia
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI48109
| | - Felicia Lie
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
| | - Lohra M. Miller
- Chemistry Department, Indiana University, Bloomington, IN47405
| | | | - Farzad Fatehi
- Department of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, YorkYO10 5DD, United Kingdom
| | - Reidun Twarock
- Department of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, YorkYO10 5DD, United Kingdom
- Department of Biology, University of York, YorkYO10 5DD, United Kingdom
| | | | | | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI48109
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW2006, Australia
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7
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Mo X, Zhang Z, Song J, Wang Y, Yu Z. Self-assembly of peptides in living cells for disease theranostics. J Mater Chem B 2024; 12:4289-4306. [PMID: 38595070 DOI: 10.1039/d4tb00365a] [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: 04/11/2024]
Abstract
The past few decades have witnessed substantial progress in biomedical materials for addressing health concerns and improving disease therapeutic and diagnostic efficacy. Conventional biomedical materials are typically created through an ex vivo approach and are usually utilized under physiological environments via transfer from preparative media. This transfer potentially gives rise to challenges for the efficient preservation of the bioactivity and implementation of theranostic goals on site. To overcome these issues, the in situ synthesis of biomedical materials on site has attracted great attention in the past few years. Peptides, which exhibit remarkable biocompability and reliable noncovalent interactions, can be tailored via tunable assembly to precisely create biomedical materials. In this review, we summarize the progress in the self-assembly of peptides in living cells for disease diagnosis and therapy. After a brief introduction to the basic design principles of peptide assembly systems in living cells, the applications of peptide assemblies for bioimaging and disease treatment are highlighted. The challenges in the field of peptide self-assembly in living cells and the prospects for novel peptide assembly systems towards next-generation biomaterials are also discussed, which will hopefully help elucidate the great potential of peptide assembly in living cells for future healthcare applications.
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Affiliation(s)
- Xiaowei Mo
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, 94 Weijin Road, Tianjin 300071, China.
| | - Zeyu Zhang
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, 94 Weijin Road, Tianjin 300071, China.
| | - Jinyan Song
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, 94 Weijin Road, Tianjin 300071, China.
| | - Yushi Wang
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, 94 Weijin Road, Tianjin 300071, China.
| | - Zhilin Yu
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, 94 Weijin Road, Tianjin 300071, China.
- Haihe Laboratory of Synthetic Biology, 21 West 15th Avenue, Tianjin 300308, China
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8
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Jeon H, Han AR, Oh S, Park JG, Namkoong M, Bang KM, Kim HM, Kim NK, Hwang KY, Hur K, Lee BJ, Heo J, Kim S, Song HK, Cho H, Lee IG. Polymorphic Self-Assembly with Procedural Flexibility for Monodisperse Quaternary Protein Structures of DegQ Enzymes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308837. [PMID: 38351715 DOI: 10.1002/adma.202308837] [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: 08/30/2023] [Revised: 02/08/2024] [Indexed: 02/29/2024]
Abstract
As large molecular tertiary structures, some proteins can act as small robots that find, bind, and chaperone target protein clients, showing the potential to serve as smart building blocks in self-assembly fields. Instead of using such intrinsic functions, most self-assembly methodologies for proteins aim for de novo-designed structures with accurate geometric assemblies, which can limit procedural flexibility. Here, a strategy enabling polymorphic clustering of quaternary proteins, exhibiting simplicity and flexibility of self-assembling paths for proteins in forming monodisperse quaternary cage particles is presented. It is proposed that the enzyme protomer DegQ, previously solved at low resolution, may potentially be usable as a threefold symmetric building block, which can form polyhedral cages incorporated by the chaperone action of DegQ in the presence of protein clients. To obtain highly monodisperse cage particles, soft, and hence, less resistive client proteins, which can program the inherent chaperone activity of DegQ to efficient formations of polymorphic cages, depending on the size of clients are utilized. By reconstructing the atomic resolution cryogenic electron microscopy DegQ structures using obtained 12- and 24-meric clusters, the polymorphic clustering of DegQ enzymes is validated in terms of soft and rigid domains, which will provide effective routes for protein self-assemblies with procedural flexibility.
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Affiliation(s)
- Hanul Jeon
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Ah-Reum Han
- Center for Biomolecular and Cellular Structure, Life Science Cluster, Institute for Basic Science (IBS), 55, Expo-ro, Daejeon, 34126, Republic of Korea
| | - Sangmin Oh
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Jin-Gyeong Park
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Myeong Namkoong
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Kyeong-Mi Bang
- Advanced Analysis Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- Department of Life Science, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Life Science Cluster, Institute for Basic Science (IBS), 55, Expo-ro, Daejeon, 34126, Republic of Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291, Daehak-ro, Daejeon, 34126, Republic of Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Kahyun Hur
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Science, Seoul National University, 599, Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- College of Pharmacy, Ajou University, 206, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Jeongyun Heo
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Sehoon Kim
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Hyun Kyu Song
- Department of Life Science, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Hyesung Cho
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - In-Gyun Lee
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
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9
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Solomonov A, Kozell A, Shimanovich U. Designing Multifunctional Biomaterials via Protein Self-Assembly. Angew Chem Int Ed Engl 2024; 63:e202318365. [PMID: 38206201 DOI: 10.1002/anie.202318365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Protein self-assembly is a fundamental biological process where proteins spontaneously organize into complex and functional structures without external direction. This process is crucial for the formation of various biological functionalities. However, when protein self-assembly fails, it can trigger the development of multiple disorders, thus making understanding this phenomenon extremely important. Up until recently, protein self-assembly has been solely linked either to biological function or malfunction; however, in the past decade or two it has also been found to hold promising potential as an alternative route for fabricating materials for biomedical applications. It is therefore necessary and timely to summarize the key aspects of protein self-assembly: how the protein structure and self-assembly conditions (chemical environments, kinetics, and the physicochemical characteristics of protein complexes) can be utilized to design biomaterials. This minireview focuses on the basic concepts of forming supramolecular structures, and the existing routes for modifications. We then compare the applicability of different approaches, including compartmentalization and self-assembly monitoring. Finally, based on the cutting-edge progress made during the last years, we summarize the current knowledge about tailoring a final function by introducing changes in self-assembly and link it to biomaterials' performance.
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Affiliation(s)
- Aleksei Solomonov
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 234 Herzl st., Rehovot, 76100, Israel
| | - Anna Kozell
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 234 Herzl st., Rehovot, 76100, Israel
| | - Ulyana Shimanovich
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 234 Herzl st., Rehovot, 76100, Israel
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10
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Inaba H, Shisaka Y, Ariyasu S, Sakakibara E, Ueda G, Aiba Y, Shimizu N, Sugimoto H, Shoji O. Heme-substituted protein assembly bridged by synthetic porphyrin: achieving controlled configuration while maintaining rotational freedom. RSC Adv 2024; 14:8829-8836. [PMID: 38495978 PMCID: PMC10941265 DOI: 10.1039/d4ra01042f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 03/04/2024] [Indexed: 03/19/2024] Open
Abstract
The use of biological host-guest interactions, specifically the binding of hemoprotein to heme, has attracted significant research interest in the design of artificial protein assemblies. However, because of the inherent flexibility of the propionic acid group of heme, it is difficult to control the positioning and orientation of the protein unit and to construct well-ordered structures. Herein, we report a heme-substituted protein dimer composed of the native hemoprotein HasA, which accommodates a tetraphenylporphyrin bearing an additional metal coordination site. The specific binding of the tetraphenylporphyrin with an additional metal coordination site that protrudes in a fixed direction confines the configuration of the dimer structure to a defined bent form. The small-angle X-ray scattering profile shows the dimer structure with a bent form and suggests dynamic rotational behavior while keeping its bent-core structure, resembling a bevel gear. This unique dimer structure demonstrates that the design of heme-substituted protein assemblies can be expanded to protein assemblies while maintaining the rotational freedom of the individual protein units.
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Affiliation(s)
- Hiroaki Inaba
- Department of Chemistry, School of Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-0802 Japan
| | - Yuma Shisaka
- Department of Chemistry, School of Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-0802 Japan
| | - Shinya Ariyasu
- Department of Chemistry, School of Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-0802 Japan
| | - Erika Sakakibara
- Department of Chemistry, School of Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-0802 Japan
| | - Garyo Ueda
- Department of Chemistry, School of Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-0802 Japan
| | - Yuichiro Aiba
- Department of Chemistry, School of Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-0802 Japan
| | - Nobutaka Shimizu
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) 1-1 Oho Tsukuba Ibaraki 305-0801 Japan
- RIKEN SPring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
| | | | - Osami Shoji
- Department of Chemistry, School of Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-0802 Japan
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11
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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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12
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Flood R, Mockler NM, Thureau A, Malinska M, Crowley PB. Supramolecular Synthons in Protein-Ligand Frameworks. CRYSTAL GROWTH & DESIGN 2024; 24:2149-2156. [PMID: 38463617 PMCID: PMC10921380 DOI: 10.1021/acs.cgd.3c01480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 03/12/2024]
Abstract
Supramolecular synthons, defined as reproducible intermolecular structural units, have greatly aided small molecule crystal engineering. In this paper, we propose that supramolecular synthons guide ligand-mediated protein crystallization. The protein RSL and the macrocycle sulfonato-calix[8]arene cocrystallize in at least four ways. One of these cocrystals is a highly porous cube comprising protein nodes connected by calixarene dimers. We show that mutating an aspartic acid to an asparagine results in two new cubic assemblies that depend also on the crystallization method. One of the new cubic arrangements is mediated by calixarene trimers and has a ∼30% increased cell volume relative to the original crystal with calixarene dimers. Crystals of the sulfonato-calix[8]arene sodium salt were obtained from buffered conditions similar to those used to grow the protein-calix[8]arene cocrystals. X-ray analysis reveals a coordination polymer of the anionic calix[8]arene and sodium cation in which the macrocycle is arranged as staggered stacks of the pleated loop conformation. Remarkably, the calixarene packing arrangement is the same in the simple salt as in the protein cocrystal. With the pleated loop conformation, the calixarene presents an extended surface for binding other calixarenes (oligomerization) as well as binding to a protein patch (biomolecular complexation). Small-angle X-ray scattering data suggest pH-dependent calixarene assembly in solution. Therefore, the calix[8]arene-calix[8]arene structural unit may be regarded as a supramolecular synthon that directs at least two types of protein assembly, suggesting applications in protein crystal engineering.
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Affiliation(s)
- Ronan
J. Flood
- SSPC,
Science Foundation Ireland Research Centre for Pharmaceuticals, School
of Biological and Chemical Sciences, University
of Galway, University
Road, Galway H91 TK33, Ireland
| | - Niamh M. Mockler
- SSPC,
Science Foundation Ireland Research Centre for Pharmaceuticals, School
of Biological and Chemical Sciences, University
of Galway, University
Road, Galway H91 TK33, Ireland
| | - Aurélien Thureau
- Synchrotron
SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, Cedex, Gif-sur-Yvette 91192, France
| | - Maura Malinska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Peter B. Crowley
- SSPC,
Science Foundation Ireland Research Centre for Pharmaceuticals, School
of Biological and Chemical Sciences, University
of Galway, University
Road, Galway H91 TK33, Ireland
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13
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Nguyen HK, Minato T, Teramoto T, Ogo S, Kakuta Y, Yoon KS. Disassembly and reassembly of the non-conventional thermophilic C-phycocyanin. J Biosci Bioeng 2024; 137:179-186. [PMID: 38238241 DOI: 10.1016/j.jbiosc.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 03/03/2024]
Abstract
C-phycocyanin (CPC), which contains open-chain tetrapyrroles, is a major light-harvesting red-fluorescent protein with an important role in aquatic photosynthesis. Recently, we reported a non-conventional CPC from Thermoleptolyngbya sp. O-77 (CPCO77) that contains two different structures, i.e., a hexameric structure and a non-conventional octameric structure. However, the assembly and disassembly mechanisms of the non-conventional octameric form of CPC remain unclear. To understand this assembly mechanism, we performed an in vitro experiment to study the disassembly and reassembly behaviors of CPC using isolated CPC subunits. The dissociation of the CPCO77 subunit was performed using a Phenyl-Sepharose column in 20 mM potassium phosphate buffer (pH 6.0) containing 7.0 M urea. For the first time, crystals of isolated CPC subunits were obtained and analyzed after separation. After the removal of urea from the purified α and β subunits, we performed an in vitro reassembly experiment for CPC and analyzed the reconstructed CPC using spectrophotometric and X-ray crystal structure analyses. The crystal structure of the reassembled CPC was nearly identical to that of the original CPCO77. The findings of this study indicate that the octameric CPCO77 is a naturally occurring form in the thermophilic cyanobacterium Thermoleptolyngbya sp. O-77.
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Affiliation(s)
- Hung Khac Nguyen
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takuo Minato
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; International Institute for Carbon-Neutral Energy Research (WPI-I(2)CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; Department of Applied Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Takamasa Teramoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Seiji Ogo
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; International Institute for Carbon-Neutral Energy Research (WPI-I(2)CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshimitsu Kakuta
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; Laboratory of Structural Biology, Graduate School of System Life Sciences, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ki-Seok Yoon
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; International Institute for Carbon-Neutral Energy Research (WPI-I(2)CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.
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14
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Bosch-Camós L, Martínez-Torró C, López-Laguna H, Lascorz J, Argilaguet J, Villaverde A, Rodríguez F, Vázquez E. Nanoparticle-Based Secretory Granules Induce a Specific and Long-Lasting Immune Response through Prolonged Antigen Release. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:435. [PMID: 38470766 DOI: 10.3390/nano14050435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024]
Abstract
Developing prolonged antigen delivery systems that mimic long-term exposure to pathogens appears as a promising but still poorly explored approach to reach durable immunities. In this study, we have used a simple technology by which His-tagged proteins can be assembled, assisted by divalent cations, as supramolecular complexes with progressive complexity, namely protein-only nanoparticles and microparticles. Microparticles produced out of nanoparticles are biomimetics of secretory granules from the mammalian hormonal system. Upon subcutaneous administration, they slowly disintegrate, acting as an endocrine-like secretory system and rendering the building block nanoparticles progressively bioavailable. The performance of such materials, previously validated for drug delivery in oncology, has been tested here regarding the potential for time-prolonged antigen release. This has been completed by taking, as a building block, a nanostructured version of p30, a main structural immunogen from the African swine fever virus (ASFV). By challenging the system in both mice and pigs, we have observed unusually potent pro-inflammatory activity in porcine macrophages, and long-lasting humoral and cellular responses in vivo, which might overcome the need for an adjuvant. The robustness of both innate and adaptive responses tag, for the first time, these dynamic depot materials as a novel and valuable instrument with transversal applicability in immune stimulation and vaccinology.
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Affiliation(s)
- Laia Bosch-Camós
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain
| | - Carlos Martínez-Torró
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN, ISCIII), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Hèctor López-Laguna
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN, ISCIII), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jara Lascorz
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN, ISCIII), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jordi Argilaguet
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain
| | - Antonio Villaverde
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN, ISCIII), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Fernando Rodríguez
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain
| | - Esther Vázquez
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN, ISCIII), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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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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Zaorska E, Malinska M. Cucurbit[7]uril-mediated Histidine Dimerization: Exploring the Structure and Binding Mechanism. Chemistry 2024; 30:e202302250. [PMID: 38055216 DOI: 10.1002/chem.202302250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/07/2023]
Abstract
Cucurbit[7,8]urils are known to form inclusion complexes with hydrophobic amino acids such as Trp, Tyr, Phe, and Met, as well as peptides containing these residues at the N-terminus. Despite their widespread use in protein purification, the affinity of histidine (His) for cucurbit[7,8]urils has not been extensively explored. In this study, X-ray diffraction experiments were conducted to investigate the binding of two histidine moieties to the cucurbit[7]uril (CB7) cavity, resulting in a network of π-π and hydrogen bonds. This assembly was found to induce a His pKa shift of ΔpKa=-4. Histidine weakly bound to CB7 or CB8; however, isothermal titration calorimetry revealed micromolar equilibrium dissociation constant values for CB7 and CB8 when bound to dipeptides containing His at the C-terminus. Conversely, dipeptides with His at the N-terminus exhibited millimolar values. Additionally, the His-Gly-Gly tripeptide formed a 2 : 1 complex with CB7. These findings suggest the potential use of histidine and histidine-containing tags in conjunction with CB7 for various biological applications.
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Affiliation(s)
- Ewelina Zaorska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Maura Malinska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
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17
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Guo XY, Yi L, Yang J, An HW, Yang ZX, Wang H. Self-assembly of peptide nanomaterials at biointerfaces: molecular design and biomedical applications. Chem Commun (Camb) 2024; 60:2009-2021. [PMID: 38275083 DOI: 10.1039/d3cc05811e] [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: 01/27/2024]
Abstract
Self-assembly is an important strategy for constructing ordered structures and complex functions in nature. Based on this, people can imitate nature and artificially construct functional materials with novel structures through the supermolecular self-assembly pathway of biological interfaces. Among the many assembly units, peptide molecular self-assembly has received widespread attention in recent years. In this review, we introduce the interactions (hydrophobic interaction, hydrogen bond, and electrostatic interaction) between peptide nanomaterials and biological interfaces, summarizing the latest advancements in multifunctional self-assembling peptide materials. We systematically demonstrate the assembly mechanisms of peptides at biological interfaces, such as proteins and cell membranes, while highlighting their application potential and challenges in fields like drug delivery, antibacterial strategies, and cancer therapy.
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Affiliation(s)
- Xin-Yuan Guo
- College of Chemistry, Huazhong Agricultural University, Shizishan 1, Hongshan District, Wuhan, 430070, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China.
| | - Li Yi
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China.
| | - Jia Yang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China.
| | - Hong-Wei An
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China.
| | - Zi-Xin Yang
- College of Chemistry, Huazhong Agricultural University, Shizishan 1, Hongshan District, Wuhan, 430070, China
| | - Hao Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China.
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18
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Szyszka TN, Andreas MP, Lie F, Miller LM, Adamson LSR, Fatehi F, Twarock R, Draper BE, Jarrold MF, Giessen TW, Lau YH. Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579038. [PMID: 38370832 PMCID: PMC10871247 DOI: 10.1101/2024.02.05.579038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Protein capsids are a widespread form of compartmentalisation in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximises the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of novel symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryo-EM, we determine the structures of a precedented 60-mer icosahedral assembly and an unprecedented 36-mer tetrahedron that features significant geometric rearrangements around a novel interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple point mutation to various amino acids, and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent the first example of tetrahedral geometry across all characterised encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in protein sequence.
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Affiliation(s)
- Taylor N Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Felicia Lie
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Lohra M Miller
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Lachlan S R Adamson
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Farzad Fatehi
- Department of Mathematics, University of York, York, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Reidun Twarock
- Department of Mathematics, University of York, York, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - Benjamin E Draper
- Megadalton Solutions Inc., 3750 E Bluebird Ln, Bloomington, IN 47401, USA
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
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19
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Fu C, Wang Z, Zhou X, Hu B, Li C, Yang P. Protein-based bioactive coatings: from nanoarchitectonics to applications. Chem Soc Rev 2024; 53:1514-1551. [PMID: 38167899 DOI: 10.1039/d3cs00786c] [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: 01/05/2024]
Abstract
Protein-based bioactive coatings have emerged as a versatile and promising strategy for enhancing the performance and biocompatibility of diverse biomedical materials and devices. Through surface modification, these coatings confer novel biofunctional attributes, rendering the material highly bioactive. Their widespread adoption across various domains in recent years underscores their importance. This review systematically elucidates the behavior of protein-based bioactive coatings in organisms and expounds on their underlying mechanisms. Furthermore, it highlights notable advancements in artificial synthesis methodologies and their functional applications in vitro. A focal point is the delineation of assembly strategies employed in crafting protein-based bioactive coatings, which provides a guide for their expansion and sustained implementation. Finally, the current trends, challenges, and future directions of protein-based bioactive coatings are discussed.
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Affiliation(s)
- Chengyu Fu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Zhengge Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Xingyu Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Bowen Hu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Chen Li
- School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Eastern HuaLan Avenue, Xinxiang, Henan 453003, China
| | - Peng Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
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20
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Ibrahim IH. Metalloproteins and metalloproteomics in health and disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:123-176. [PMID: 38960472 DOI: 10.1016/bs.apcsb.2023.12.013] [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: 07/05/2024]
Abstract
Metalloproteins represents more than one third of human proteome, with huge variation in physiological functions and pathological implications, depending on the metal/metals involved and tissue context. Their functions range from catalysis, bioenergetics, redox, to DNA repair, cell proliferation, signaling, transport of vital elements, and immunity. The human metalloproteomic studies revealed that many families of metalloproteins along with individual metalloproteins are dysregulated under several clinical conditions. Also, several sorts of interaction between redox- active or redox- inert metalloproteins are observed in health and disease. Metalloproteins profiling shows distinct alterations in neurodegenerative diseases, cancer, inflammation, infection, diabetes mellitus, among other diseases. This makes metalloproteins -either individually or as families- a promising target for several therapeutic approaches. Inhibitors and activators of metalloenzymes, metal chelators, along with artificial metalloproteins could be versatile in diagnosis and treatment of several diseases, in addition to other biomedical and industrial applications.
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Affiliation(s)
- Iman Hassan Ibrahim
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt.
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21
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Guo Y, Zhai X, Li N, Zan X. Recent Progress in Protein-Polyphenol Assemblies for Biomedical Applications. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:2005-2014. [PMID: 38227800 DOI: 10.1021/acs.langmuir.3c03244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Nowadays, natural materials as smart building blocks for assembling functional materials have aroused extensive interest in the scientific community. Proteins and polyphenols are typical natural building blocks that are widely used. On the one hand, proteins are one of the most versatile classes of biomolecules, serving as catalysts, signaling molecules, transporters, receptors, scaffolds that maintain the integrity of cell and tissue, and more. On the other hand, the facile adhesion of naturally abundant polyphenols with other substances and their potential biomedical applications have been highly attractive for functional biomaterials fabrication. Additionally, there are a variety of interactions between the proteins and polyphenols, mainly hydrogen bonding, hydrophobic, and ionic interactions. These reversible dynamic interactions enable proteins and polyphenols to form stable protein-polyphenol assemblies and maintain their inherent structures and biological activities in the assemblies. Therefore, protein-polyphenol assemblies can be applied to design a variety of advanced functional materials for biomedical applications. Herein, recent progress in protein-polyphenol particles, capsules, coatings, and hydrogels is summarized, the preparation and application of these assemblies are introduced in detail, and the future of the field is prospected.
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Affiliation(s)
- Yan Guo
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, 317000, China
- Hunan Provincial Key Laboratory of Advanced Materials for New Energy Storage and Conversion, School of Materials Science and Engineering, Hunan University of Science and Technology, Hunan 411201, China
| | - Xinyue Zhai
- Hunan Provincial Key Laboratory of Advanced Materials for New Energy Storage and Conversion, School of Materials Science and Engineering, Hunan University of Science and Technology, Hunan 411201, China
| | - Na Li
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou Key Laboratory of Perioperative Medicine, Wenzhou 325001, China
| | - Xingjie Zan
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, 317000, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou Key Laboratory of Perioperative Medicine, Wenzhou 325001, China
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22
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Zhao F, Frandsen M, Capodaglio S, Sleiman HF. DNA-Mediated Peptide Assembly into Protein Mimics. J Am Chem Soc 2024; 146:1946-1956. [PMID: 38226787 DOI: 10.1021/jacs.3c08984] [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: 01/17/2024]
Abstract
The design of new protein structures is challenging due to their vast sequence space and the complexity of protein folding. Here, we report a new modular DNA-templated strategy to construct protein mimics. We achieve the spatial control of multiple peptide units by conjugation with DNA and hybridization to a branched DNA trimer template followed by covalent stapling of the preorganized peptides into a single unit. A library of protein mimics with different lengths, sequences, and heptad registers has been efficiently constructed. DNA-templated protein mimics show an α-helix or coiled-coil motif formation even when they are constructed from weakly interacting peptide units. Their attached DNA handles can be used to exert dynamic control over the protein mimics' secondary and tertiary structures. This modular strategy will facilitate the development of DNA-encoded protein libraries for the rapid discovery of new therapeutics, enzymes, and antibody mimics.
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Affiliation(s)
- Fangzhou Zhao
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Martin Frandsen
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, Aarhus 8000, Denmark
| | - Sabrina Capodaglio
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma I-43124, Italy
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
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23
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Kavčič L, Kežar A, Koritnik N, Žnidarič MT, Klobučar T, Vičič Ž, Merzel F, Holden E, Benesch JLP, Podobnik M. From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y. Commun Chem 2024; 7:14. [PMID: 38233506 PMCID: PMC10794713 DOI: 10.1038/s42004-024-01100-x] [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: 09/20/2023] [Accepted: 01/05/2024] [Indexed: 01/19/2024] Open
Abstract
The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid nanoparticles. However, the potential of CPs of the wide-spread flexuous filamentous plant viruses remains to be explored. Here, we show that we can control the shape, size, RNA encapsidation ability, symmetry, stability and surface functionalization of nanoparticles through structure-based design of CP from potato virus Y (PVY). We provide high-resolution insight into CP-based self-assemblies, ranging from large polymorphic or monomorphic filaments to smaller annular, cubic or spherical particles. Furthermore, we show that we can prevent CP self-assembly in bacteria by fusion with a cleavable protein, enabling controlled nanoparticle formation in vitro. Understanding the remarkable structural diversity of PVY CP not only provides possibilities for the production of biodegradable nanoparticles, but may also advance future studies of CP's polymorphism in a biological context.
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Affiliation(s)
- Luka Kavčič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Chemical Sciences', Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Andreja Kežar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Neža Koritnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Biomedicine', Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Tajda Klobučar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Biosciences', Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Žiga Vičič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, Ljubljana, Slovenia
| | - Ellie Holden
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia.
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24
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Wang Y, Rencus-Lazar S, Zhou H, Yin Y, Jiang X, Cai K, Gazit E, Ji W. Bioinspired Amino Acid Based Materials in Bionanotechnology: From Minimalistic Building Blocks and Assembly Mechanism to Applications. ACS NANO 2024; 18:1257-1288. [PMID: 38157317 DOI: 10.1021/acsnano.3c08183] [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: 01/03/2024]
Abstract
Inspired by natural hierarchical self-assembly of proteins and peptides, amino acids, as the basic building units, have been shown to self-assemble to form highly ordered structures through supramolecular interactions. The fabrication of functional biomaterials comprised of extremely simple biomolecules has gained increasing interest due to the advantages of biocompatibility, easy functionalization, and structural modularity. In particular, amino acid based assemblies have shown attractive physical characteristics for various bionanotechnology applications. Herein, we propose a review paper to summarize the design strategies as well as research advances of amino acid based supramolecular assemblies as smart functional materials. We first briefly introduce bioinspired reductionist design strategies and assembly mechanism for amino acid based molecular assembly materials through noncovalent interactions in condensed states, including self-assembly, metal ion mediated coordination assembly, and coassembly. In the following part, we provide an overview of the properties and functions of amino acid based materials toward applications in nanotechnology and biomedicine. Finally, we give an overview of the remaining challenges and future perspectives on the fabrication of amino acid based supramolecular biomaterials with desired properties. We believe that this review will promote the prosperous development of innovative bioinspired functional materials formed by minimalistic building blocks.
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Affiliation(s)
- Yuehui Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, People's Republic of China
| | - Sigal Rencus-Lazar
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Haoran Zhou
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, People's Republic of China
| | - Yuanyuan Yin
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Stomatological Hospital of Chongqing Medical University, Chongqing 401147, People's Republic of China
| | - Xuemei Jiang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, People's Republic of China
| | - Kaiyong Cai
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, People's Republic of China
| | - Ehud Gazit
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Wei Ji
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, People's Republic of China
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25
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Guo J, Duan Y, Jia Y, Zhao Z, Gao X, Liu P, Li F, Chen H, Ye Y, Liu Y, Zhao M, Tang Z, Liu Y. Biomimetic chiral hydrogen-bonded organic-inorganic frameworks. Nat Commun 2024; 15:139. [PMID: 38167785 PMCID: PMC10762213 DOI: 10.1038/s41467-023-43700-6] [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: 05/31/2023] [Accepted: 11/16/2023] [Indexed: 01/05/2024] Open
Abstract
Assembly ubiquitously occurs in nature and gives birth to numerous functional biomaterials and sophisticated organisms. In this work, chiral hydrogen-bonded organic-inorganic frameworks (HOIFs) are synthesized via biomimicking the self-assembly process from amino acids to proteins. Enjoying the homohelical configurations analogous to α-helix, the HOIFs exhibit remarkable chiroptical activity including the chiral fluorescence (glum = 1.7 × 10-3) that is untouched among the previously reported hydrogen-bonded frameworks. Benefitting from the dynamic feature of hydrogen bonding, HOIFs enable enantio-discrimination of chiral aliphatic substrates with imperceivable steric discrepancy based on fluorescent change. Moreover, the disassembled HOIFs after recognition applications are capable of being facilely regenerated and self-purified via aprotic solvent-induced reassembly, leading to at least three consecutive cycles without losing the enantioselectivity. The underlying mechanism of chirality bias is decoded by the experimental isothermal titration calorimetry together with theoretic simulation.
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Affiliation(s)
- Jun Guo
- State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry, Tiangong University, 300387, Tianjin, P. R. China.
| | - Yulong Duan
- State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry, Tiangong University, 300387, Tianjin, P. R. China
| | - Yunling Jia
- School of Materials Science and Engineering, Tiangong University, 300387, Tianjin, P. R. China
| | - Zelong Zhao
- State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry, Tiangong University, 300387, Tianjin, P. R. China
| | - Xiaoqing Gao
- Wenzhou Key Laboratory of Biomaterials and Engineering, Wenzhou Institute, University of Chinese Academy of Sciences, 325000, Wenzhou, P. R. China
| | - Pai Liu
- School of Materials Science and Engineering, Tiangong University, 300387, Tianjin, P. R. China
| | - Fangfang Li
- State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry, Tiangong University, 300387, Tianjin, P. R. China
| | - Hongli Chen
- School of Materials Science and Engineering, Tiangong University, 300387, Tianjin, P. R. China
| | - Yutong Ye
- School of Materials Science and Engineering, Tiangong University, 300387, Tianjin, P. R. China
| | - Yujiao Liu
- State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry, Tiangong University, 300387, Tianjin, P. R. China
| | - Meiting Zhao
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, Institute of Molecular Aggregation Science, Tianjin University, 300072, Tianjin, P. R. China.
| | - Zhiyong Tang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 100190, Beijing, P. R. China.
| | - Yi Liu
- State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry, Tiangong University, 300387, Tianjin, P. R. China.
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26
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Wu J, Zhou L, Peng H, Wang Z, Wang Z, Keasling JD, Liu S, Zhou G, Ding S, Wang Q, Wang X, Chen X, Lang Y, Xia M, Guan X, Dong M, Zhou J, Chen J. A General and Convenient Peptide Self-Assembling Mechanism for Developing Supramolecular Versatile Nanomaterials Based on The Biosynthetic Hybrid Amyloid-Resilin Protein. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2304364. [PMID: 37885340 DOI: 10.1002/adma.202304364] [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: 05/10/2023] [Revised: 10/17/2023] [Indexed: 10/28/2023]
Abstract
Self-assembling peptides are valuable building blocks to fabricate supramolecular biomaterials, which have broad applications from biomedicine to biotechnology. However, limited choices to induce different globular proteins into hydrogels hinder these designs. Here, an easy-to-implement and tunable self-assembling strategy, which employs Ure2 amyloidogenic peptide, are described to induce any target proteins to assemble into supramolecular hydrogels alone or in combination with notable compositional control. Furthermore, the collective effect of nanoscale interactions among amyloid nanofibrils and partially disordered elastomeric polypeptides are investigated. This led to many useful macroscopic material properties simultaneously emerging from one pure protein material, i.e. strong adhesion to any substrates under wet conditions, rapidly self--assembling into robust and porous hydrogels, adaptation to remodeling processes, strongly promoting cell adhesion, proliferation and differentiation. Moreover, he demonstrated this supramolecular material's robust performance in vitro and vivo for tissue engineering, cosmetic and hemostasis applications and exhibited superior performance compared to corresponding commercial counterparts. To the best of his knowledge, few pure protein-based materials could meet such seemingly mutually exclusive properties simultaneously. Such versatility renders this novel supramolecular nanomaterial as next-generation functional protein-based materials, and he demonstrated the sequence level modulation of structural order and disorder as an untapped principle to design new proteins.
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Affiliation(s)
- Junjun Wu
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Lin Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Hu Peng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhaojun Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhaoshi Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jay D Keasling
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California Berkeley, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Center for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Shike Liu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Guanghong Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Shijie Ding
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Qiong Wang
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Xuejian Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xinxiu Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yifei Lang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Mo Xia
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xin Guan
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Mingsheng Dong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
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27
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Chen Z, Wu T, Yu S, Li M, Fan X, Huo YX. Self-assembly systems to troubleshoot metabolic engineering challenges. Trends Biotechnol 2024; 42:43-60. [PMID: 37451946 DOI: 10.1016/j.tibtech.2023.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Enzyme self-assembly is a technology in which enzyme units can aggregate into ordered macromolecules, assisted by scaffolds. In metabolic engineering, self-assembly strategies have been explored for aggregating multiple enzymes in the same pathway to improve sequential catalytic efficiency, which in turn enables high-level production. The performance of the scaffolds is critical to the formation of an efficient and stable assembly system. This review comprehensively analyzes these scaffolds by exploring how they assemble, and it illustrates how to apply self-assembly strategies for different modules in metabolic engineering. Functional modifications to scaffolds will further promote efficient strategies for production.
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Affiliation(s)
- Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Tong Wu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Min Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Xuanhe Fan
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China.
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28
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Abe T, Sanada N, Takeuchi K, Okazawa A, Hiraoka S. Assembly of Six Types of Heteroleptic Pd 2L 4 Cages under Kinetic Control. J Am Chem Soc 2023; 145:28061-28074. [PMID: 38096127 PMCID: PMC10755705 DOI: 10.1021/jacs.3c09359] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/20/2023] [Accepted: 12/01/2023] [Indexed: 12/28/2023]
Abstract
Heteroleptic assemblies composed of several kinds of building blocks have been seen in nature. It is still unclear how natural systems design and create such complicated assemblies selectively. Past efforts on multicomponent self-assembly of artificial metal-organic cages have mainly focused on finding a suitable combination of building blocks to lead to a single multicomponent self-assembly as the thermodynamically most stable product. Here, we present another approach to selectively produce multicomponent Pd(II)-based self-assemblies under kinetic control based on the selective ligand exchanges of weak Pd-L coordination bonds retaining the original orientation of the metal centers in a kinetically stabilized cyclic structure and on local reversibility given in certain areas of the energy landscape in the presence of the assist molecule that facilitates error correction of coordination bonds. The kinetic approach enabled us to build all six types of Pd2L4 cages and heteroleptic tetranuclear cages composed of three kinds of ditopic ligands. Although the cage complexes thus obtained are metastable, they are stable for 1 month or more at room temperature.
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Affiliation(s)
- Tsukasa Abe
- Department
of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Naoki Sanada
- Department
of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Keisuke Takeuchi
- Department
of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Atsushi Okazawa
- Department
of Electrical Engineering and Bioscience, Waseda University, Tokyo 169-8555, Japan
| | - Shuichi Hiraoka
- Department
of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
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29
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Rahban M, Ahmad F, Piatyszek MA, Haertlé T, Saso L, Saboury AA. Stabilization challenges and aggregation in protein-based therapeutics in the pharmaceutical industry. RSC Adv 2023; 13:35947-35963. [PMID: 38090079 PMCID: PMC10711991 DOI: 10.1039/d3ra06476j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/30/2023] [Indexed: 04/26/2024] Open
Abstract
Protein-based therapeutics have revolutionized the pharmaceutical industry and become vital components in the development of future therapeutics. They offer several advantages over traditional small molecule drugs, including high affinity, potency and specificity, while demonstrating low toxicity and minimal adverse effects. However, the development and manufacturing processes of protein-based therapeutics presents challenges related to protein folding, purification, stability and immunogenicity that should be addressed. These proteins, like other biological molecules, are prone to chemical and physical instabilities. The stability of protein-based drugs throughout the entire manufacturing, storage and delivery process is essential. The occurrence of structural instability resulting from misfolding, unfolding, and modifications, as well as aggregation, poses a significant risk to the efficacy of these drugs, overshadowing their promising attributes. Gaining insight into structural alterations caused by aggregation and their impact on immunogenicity is vital for the advancement and refinement of protein therapeutics. Hence, in this review, we have discussed some features of protein aggregation during production, formulation and storage as well as stabilization strategies in protein engineering and computational methods to prevent aggregation.
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Affiliation(s)
- Mahdie Rahban
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences Kerman Iran
| | - Faizan Ahmad
- Department of Biochemistry, School of Chemical & Life Sciences, Jamia Hamdard New Delhi-110062 India
| | | | | | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", Sapienza University Rome Italy
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran Tehran 1417614335 Iran +9821 66404680 +9821 66956984
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Wang Q, Wang Y, Jian X, Wang N, Li C, Liu H. Site-specific crosslinking and assembly of tetrameric β-glucuronidase improve glycyrrhizin hydrolysis. Biotechnol Bioeng 2023; 120:3570-3584. [PMID: 37707439 DOI: 10.1002/bit.28556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/24/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023]
Abstract
In this study, eight nonconserved residues with exposed surfaces and flexible conformations of the homotetrameric PGUS (β-glucuronidase from Aspergillus oryzae Li-3) were identified. Single-point mutation into cysteine enabled the thiol-maleimide reaction and site-specific protein assembly using a two-arm polyethylene glycol (PEG)-maleimide crosslinker (Mal2 ). The Mal2 (1k) (with 1 kDa PEG spacer)-crosslinked PGUS assemblies showed low crosslinking efficiency and unimproved thermostability except for G194C-Mal2 (1k). To improve the crosslinking efficiency, a lengthened crosslinker Mal2 (2k) (with 2 kDa PEG spacer) was used to produce PGUS assembly and a highly improved thermostability was achieved with a half-life of 47.2-169.2 min at 70°C, which is 1.04-3.74 times that of wild type PGUS. It is found that the thermostability of PGUS assembly was closely associated with the formation of inter-tetramer assembly and intratetramer crosslinking, rather than the PEGylation of the enzyme. Therefore, the four-arm PEG-maleimide crosslinker Mal4 (2k) (with 2 kDa PEG spacer) was employed to simultaneously increase the inter-tetramer assembly and intratetramer crosslinking, and the resulting PGUS assemblies showed further improved thermostabilities compared with Mal2 (2k)-crosslinked assemblies. Finally, the application of PGUS assemblies with significantly improved thermostability to the bioconversion of GL proved that the PGUS assembly is a strong catalyst for glycyrrhizin (GL) hydrolysis in industrial applications.
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Affiliation(s)
- Qibin Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, P.R. China
| | - Yingying Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, P.R. China
| | - Xing Jian
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, P.R. China
| | - Ning Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, P.R. China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, P.R. China
- Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, P.R. China
- Center for Synthetic & Systems Biology, Tsinghua University, Beijing, P.R. China
| | - Hu Liu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, P.R. China
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Chen X, Zhang T, Liu H, Zang J, Lv C, Du M, Zhao G. Shape-Anisotropic Assembly of Protein Nanocages with Identical Building Blocks by Designed Intermolecular π-π Interactions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2305398. [PMID: 37870198 PMCID: PMC10724428 DOI: 10.1002/advs.202305398] [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: 08/04/2023] [Revised: 09/12/2023] [Indexed: 10/24/2023]
Abstract
Protein lattices that shift the structure and shape anisotropy in response to environmental cues are closely coupled to potential functionality. However, to design and construct shape-anisotropic protein arrays from the same building blocks in response to different external stimuli remains challenging. Here, by a combination of the multiple, symmetric interaction sites on the outer surface of protein nanocages and the tunable features of phenylalanine-phenylalanine interactions, a protein engineering approach is reported to construct a variety of superstructures with shape anisotropy, including 3D cubic, 2D hexagonal layered, and 1D rod-like crystalline protein nanocage arrays by using one single protein building block. Notably, the assembly of these crystalline protein arrays is reversible, which can be tuned by external stimuli (pH and ionic strength). The anisotropic morphologies of the fabricated macroscopic crystals can be correlated with the Å-to-nm scale protein arrangement details by crystallographic elucidation. These results enhance the understanding of the freedom offered by an object's symmetry and inter-object π-π stacking interactions for protein building blocks to assemble into direction- and shape-anisotropic biomaterials.
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Affiliation(s)
- Xuemin Chen
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Tuo Zhang
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Hanxiong Liu
- School of Food Science and TechnologyNational Engineering Research Center of SeafoodDalian Polytechnic UniversityDalian116034China
| | - Jiachen Zang
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Chenyan Lv
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Ming Du
- School of Food Science and TechnologyNational Engineering Research Center of SeafoodDalian Polytechnic UniversityDalian116034China
| | - Guanghua Zhao
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
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32
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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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Schmid SY, Lachowski K, Chiang HT, Pozzo L, De Yoreo J, Zhang S. Mechanisms of Biomolecular Self-Assembly Investigated Through In Situ Observations of Structures and Dynamics. Angew Chem Int Ed Engl 2023; 62:e202309725. [PMID: 37702227 DOI: 10.1002/anie.202309725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Indexed: 09/14/2023]
Abstract
Biomolecular self-assembly of hierarchical materials is a precise and adaptable bottom-up approach to synthesizing across scales with considerable energy, health, environment, sustainability, and information technology applications. To achieve desired functions in biomaterials, it is essential to directly observe assembly dynamics and structural evolutions that reflect the underlying energy landscape and the assembly mechanism. This review will summarize the current understanding of biomolecular assembly mechanisms based on in situ characterization and discuss the broader significance and achievements of newly gained insights. In addition, we will also introduce how emerging deep learning/machine learning-based approaches, multiparametric characterization, and high-throughput methods can boost the development of biomolecular self-assembly. The objective of this review is to accelerate the development of in situ characterization approaches for biomolecular self-assembly and to inspire the next generation of biomimetic materials.
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Affiliation(s)
- Sakshi Yadav Schmid
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kacper Lachowski
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
| | - Huat Thart Chiang
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
| | - Lilo Pozzo
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Jim De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Shuai Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
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Pham TT, Abe S, Date K, Hirata K, Suzuki T, Ueno T. Displaying a Protein Cage on a Protein Crystal by In-Cell Crystal Engineering. NANO LETTERS 2023; 23:10118-10125. [PMID: 37955329 DOI: 10.1021/acs.nanolett.3c02117] [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: 11/14/2023]
Abstract
The development of solid biomaterials has rapidly progressed in recent years in applications in bionanotechnology. The immobilization of proteins, such as enzymes, within protein crystals is being used to develop solid catalysts and functionalized materials. However, an efficient method for encapsulating protein assemblies has not yet been established. This work presents a novel approach to displaying protein cages onto a crystalline protein scaffold using in-cell protein crystal engineering. The polyhedra crystal (PhC) scaffold, which displays a ferritin cage, was produced by coexpression of polyhedrin monomer (PhM) and H1-ferritin (H1-Fr) monomer in Escherichia coli. The H1-tag is derived from the H1-helix of PhM. Our technique represents a unique strategy for immobilizing protein assemblies onto in-cell protein crystals and is expected to contribute to various applications in bionanotechnology.
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Affiliation(s)
- Thuc Toan Pham
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
| | - Koki Date
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
| | - Kunio Hirata
- SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun 679-5148, Hyogo, Japan
| | - Taiga Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
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Aftahy K, Arrasate P, Bashkirov PV, Kuzmin PI, Maurizot V, Huc I, Frolov VA. Molecular Sensing and Manipulation of Protein Oligomerization in Membrane Nanotubes with Bolaamphiphilic Foldamers. J Am Chem Soc 2023; 145:25150-25159. [PMID: 37948300 PMCID: PMC10682987 DOI: 10.1021/jacs.3c05753] [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: 06/03/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023]
Abstract
Adaptive and reversible self-assembly of supramolecular protein structures is a fundamental characteristic of dynamic living matter. However, the quantitative detection and assessment of the emergence of mesoscale protein complexes from small and dynamic oligomeric precursors remains highly challenging. Here, we present a novel approach utilizing a short membrane nanotube (sNT) pulled from a planar membrane reservoir as nanotemplates for molecular reconstruction, manipulation, and sensing of protein oligomerization and self-assembly at the mesoscale. The sNT reports changes in membrane shape and rigidity caused by membrane-bound proteins as variations of the ionic conductivity of the sNT lumen. To confine oligomerization to the sNT, we have designed and synthesized rigid oligoamide foldamer tapes (ROFTs). Charged ROFTs incorporate into the planar and sNT membranes, mediate protein binding to the membranes, and, driven by the luminal electric field, shuttle the bound proteins between the sNT and planar membranes. Using Annexin-V (AnV) as a prototype, we show that the sNT detects AnV oligomers shuttled into the nanotube by ROFTs. Accumulation of AnV on the sNT induces its self-assembly into a curved lattice, restricting the sNT geometry and inhibiting the material uptake from the reservoir during the sNT extension, leading to the sNT fission. By comparing the spontaneous and ROFT-mediated entry of AnV into the sNT, we reveal how intricate membrane curvature sensing by small AnV oligomers controls the lattice self-assembly. These results establish sNT-ROFT as a powerful tool for molecular reconstruction and functional analyses of protein oligomerization and self-assembly, with broad application to various membrane processes.
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Affiliation(s)
- Kathrin Aftahy
- Department
of Pharmacy, Ludwig-Maximilians-Universität
München, Munich 81377, Germany
| | - Pedro Arrasate
- Biofisika
Institute (CSIC, UPV/EHU), University of
the Basque Country, Leioa 48940, Spain
- Department
of Biochemistry and Molecular Biology, University
of the Basque Country, Leioa 48940, Spain
| | - Pavel V. Bashkirov
- Research
Institute for Systems Biology and Medicine, Moscow 117246, Russia
| | - Petr I. Kuzmin
- A.N.
Frumkin Institute of Physical Chemistry and Electrochemistry, Moscow 119071, Russia
| | - Victor Maurizot
- Univ. Bordeaux,
CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Pessac 33600, France
| | - Ivan Huc
- Department
of Pharmacy, Ludwig-Maximilians-Universität
München, Munich 81377, Germany
| | - Vadim A. Frolov
- Biofisika
Institute (CSIC, UPV/EHU), University of
the Basque Country, Leioa 48940, Spain
- Department
of Biochemistry and Molecular Biology, University
of the Basque Country, Leioa 48940, Spain
- Ikerbasque,
Basque Foundation for Science, Bilbao 48009, Spain
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Arnaouteli S, Bamford NC, Brandani GB, Morris RJ, Schor M, Carrington JT, Hobley L, van Aalten DMF, Stanley-Wall NR, MacPhee CE. Lateral interactions govern self-assembly of the bacterial biofilm matrix protein BslA. Proc Natl Acad Sci U S A 2023; 120:e2312022120. [PMID: 37903266 PMCID: PMC7615278 DOI: 10.1073/pnas.2312022120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/11/2023] [Indexed: 11/01/2023] Open
Abstract
The soil bacterium Bacillus subtilis is a model organism to investigate the formation of biofilms, the predominant form of microbial life. The secreted protein BslA self-assembles at the surface of the biofilm to give the B. subtilis biofilm its characteristic hydrophobicity. To understand the mechanism of BslA self-assembly at interfaces, here we built a molecular model based on the previous BslA crystal structure and the crystal structure of the BslA paralogue YweA that we determined. Our analysis revealed two conserved protein-protein interaction interfaces supporting BslA self-assembly into an infinite 2-dimensional lattice that fits previously determined transmission microscopy images. Molecular dynamics simulations and in vitro protein assays further support our model of BslA elastic film formation, while mutagenesis experiments highlight the importance of the identified interactions for biofilm structure. Based on this knowledge, YweA was engineered to form more stable elastic films and rescue biofilm structure in bslA deficient strains. These findings shed light on protein film assembly and will inform the development of BslA technologies which range from surface coatings to emulsions in fast-moving consumer goods.
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Affiliation(s)
- Sofia Arnaouteli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, DundeeDD5 4EH, United Kingdom
| | - Natalie C. Bamford
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, DundeeDD5 4EH, United Kingdom
| | - Giovanni B. Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto606 8501, Japan
| | - Ryan J. Morris
- National Biofilms Innovation Centre, School of Physics & Astronomy, University of Edinburgh, EdinburghEH9 3FD, United Kingdom
| | - Marieke Schor
- UB Education, Content & Support, Maastricht University, Maastricht6211 LK, Netherlands
| | - Jamie T. Carrington
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Laura Hobley
- School of Biosciences, University of Nottingham, NottinghamNG7 2RD, United Kingdom
| | - Daan M. F. van Aalten
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, DundeeDD5 4EH, United Kingdom
- Department of Molecular Biology and Genetics, University of Aarhus, Aarhus8000, Denmark
| | - Nicola R. Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, DundeeDD5 4EH, United Kingdom
| | - Cait E. MacPhee
- National Biofilms Innovation Centre, School of Physics & Astronomy, University of Edinburgh, EdinburghEH9 3FD, United Kingdom
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Zhang C, Chen X, Liu B, Zang J, Zhang T, Zhao G. Preparation and Unique Three-Dimensional Self-Assembly Property of Starfish Ferritin. Foods 2023; 12:3903. [PMID: 37959022 PMCID: PMC10647799 DOI: 10.3390/foods12213903] [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: 10/09/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
The structure and assembly properties of ferritin derived from aquatic products remain to be explored. Constructing diverse three-dimensional (3D) protein architectures with the same building blocks has important implications for nutrient delivery, medicine and materials science. Herein, ferritin from Asterias forbesii (AfFer) was prepared, and its crystal structure was resolved at 1.91 Å for the first time. Notably, different from the crystal structure of other reported ferritin, AfFer exhibited a BCT lattice arrangement in its crystals. Bioinspired by the crystal structure of AfFer, we described an effective approach for manufacturing 3D porous, crystalline nanoarchitectures by redesigning the shared protein interface involved in different 3D protein arrays. Based on this strategy, two 3D superlattices of body-centered tetragonal and simple cubicwere constructed with ferritin molecules as the building blocks. This study provided a potentially generalizable strategy for constructing different 3D protein-based crystalline biomaterials with the same building blocks.
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Affiliation(s)
| | | | | | | | | | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; (C.Z.); (X.C.); (B.L.); (J.Z.); (T.Z.)
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Abstract
Drawing inspiration from allosteric proteins, a zigzag-shaped π-conjugation was structurally engineered into a tweezer-like ionophore having multiple disparate binding sites. When a soft metal ion binds to the central tridentate ligand motif, the rigid backbone folds, bringing two macrocyclic arms into close proximity. Stabilized by a coordinating anion, the tweezer-like conformation of the resulting metalloligand recruits a hard cation to form a sandwich-like complex with a remarkably enhanced binding affinity and selectivity.
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Affiliation(s)
- Suk-Il Kang
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Hyun Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Sungryul Bae
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Dongwhan Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
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Gomes MC, Pinho AR, Custódio C, Mano JF. Self-Assembly of Platelet Lysates Proteins into Microparticles by Unnatural Disulfide Bonds for Bottom-Up Tissue Engineering. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2304659. [PMID: 37354139 DOI: 10.1002/adma.202304659] [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: 05/17/2023] [Revised: 06/15/2023] [Indexed: 06/26/2023]
Abstract
There is a demand to design microparticles holding surface topography while presenting inherent bioactive cues for applications in the biomedical and biotechnological fields. Using the pool of proteins present in human-derived platelet lysates (PLs), the production of protein-based microparticles via a simple and cost-effective method is reported, exploring the prone redox behavior of cysteine (Cy-SH) amino acid residues. The forced formation of new intermolecular disulfide bonds results in the precipitation of the proteins as spherical, pompom-like microparticles with adjustable sizes (15-50 µm in diameter) and surface topography consisting of grooves and ridges. These PL microparticles exhibit extraordinary cytocompatibility, allowing cell-guided microaggregates to form, while also working as injectable systems for cell support. Early studies also suggest that the surface topography provided by these PL microparticles can support osteogenic behavior. Consequently, these PL microparticles may find use to create live tissues via bottom-up procedures or injectable tissue-defect fillers, particularly for bone regeneration, with the prospect of working under xeno-free conditions.
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Affiliation(s)
- Maria C Gomes
- Department of Chemistry CICECO-Aveiro Institute of Materials University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Ana Rita Pinho
- Department of Chemistry CICECO-Aveiro Institute of Materials University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Catarina Custódio
- Department of Chemistry CICECO-Aveiro Institute of Materials University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - João F Mano
- Department of Chemistry CICECO-Aveiro Institute of Materials University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
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40
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Das A, K V, S SD, Mahendran KR. Synthetic α-Helical Nanopore Reactor for Chemical Sensing. JACS AU 2023; 3:2467-2477. [PMID: 37772177 PMCID: PMC10523496 DOI: 10.1021/jacsau.3c00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 09/30/2023]
Abstract
The use of nanopores for the single-molecule sensing of folded proteins and biomacromolecules has recently gained attention. Here, we introduce a simplified synthetic α-helical transmembrane pore, pPorA, as a nanoreactor and sensor that exhibits functional versatility comparable to that of engineered protein and DNA nanopores. The pore, built from the assembly of synthetic 40-amino-acid-long peptides, is designed to contain cysteine residues within the lumen and at the pore terminus for site-specific chemical modification probed using single-channel electrical recordings. The reaction of the pore with differently charged activated thiol reagents was studied, wherein positively charged reagents electrophoretically driven into the pore resulted in pore blocking in discrete steps upon covalent bond formation. The asymmetric blockage patterns resulting from cis and trans-side addition of reagents reveal the pore orientation in the lipid membrane. Furthermore, activated PEG thiols covalently blocked the pores over a longer duration in a charge-independent manner, establishing the large diameter and orientation of the formed pores. While the covalent binding of thiol reagents caused a drop in the pore conductance, cationic cyclic octasaccharides produced time-resolved translocation events, confirming the structural flexibility and tunability of the pores. The ability of the pore to accommodate large analytes and the considerable current amplitude variation following bond formation events are promising for developing platforms to resolve multistep chemical reactions at the single-molecule level for applications in synthetic nanobiotechnology.
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Affiliation(s)
- Anjali
Devi Das
- Membrane Biology Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India 695014
| | - Vidhu K
- Membrane Biology Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India 695014
| | - Smitha Devi S
- Membrane Biology Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India 695014
| | - Kozhinjampara R Mahendran
- Membrane Biology Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India 695014
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41
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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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42
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Nicolau I, Hădade ND, Matache M, Funeriu DP. Synthetic Approaches of Epoxysuccinate Chemical Probes. Chembiochem 2023; 24:e202300157. [PMID: 37096389 DOI: 10.1002/cbic.202300157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 04/26/2023]
Abstract
Synthetic chemical probes are powerful tools for investigating biological processes. They are particularly useful for proteomic studies such as activity-based protein profiling (ABPP). These chemical methods initially used mimics of natural substrates. As the techniques gained prominence, more and more elaborate chemical probes with increased specificity towards given enzyme/protein families and amenability to various reaction conditions were used. Among the chemical probes, peptidyl-epoxysuccinates represent one of the first types of compounds used to investigate the activity of the cysteine protease papain-like family of enzymes. Structurally derived from the natural substrate, a wide body of inhibitors and activity- or affinity-based probes bearing the electrophilic oxirane unit for covalent labeling of active enzymes now exists. Herein, we review the literature regarding the synthetic approaches to epoxysuccinate-based chemical probes together with their reported applications, from biological chemistry and inhibition studies to supramolecular chemistry and the formation of protein arrays.
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Affiliation(s)
- Ioana Nicolau
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
| | - Niculina D Hădade
- Babes-Bolyai University, Faculty of Chemistry and Chemical Engineering, Supramolecular and Organometallic Chemistry Centre, 11 Arany Janos Street, 400028, Cluj-Napoca, Romania
| | - Mihaela Matache
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
| | - Daniel P Funeriu
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
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43
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Fan X, Li K, Liu S, Wang T, Ma Y, Li Z, He C. Protein Nanotubes Assembled from Imidazole-Grafted Horseradish Peroxidase Nanogels. ACS Macro Lett 2023; 12:1031-1036. [PMID: 37433040 DOI: 10.1021/acsmacrolett.3c00198] [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: 07/13/2023]
Abstract
Protein assembly, a common phenomenon in nature, plays an important role in the evolution of life. Inspired by nature, assembling protein monomers into delicate nanostructures has emerged as an attractive research area. However, sophisticated protein assemblies usually need complicated designs or templates. In this work, we successfully fabricated protein nanotubes in a facile way by coordination interactions between imidazole-grafted horseradish peroxidase (HRP) nanogels (iHNs) and Cu2+. The iHNs were synthesized by polymerization on the surface of HRP by employing vinyl imidazole as a comonomer. By direct addition of Cu2+ into iHN solution, protein tubes were therefore formed. The size of the protein tubes could be adjusted by changing the added Cu2+ amount, and the mechanism behind the formation of protein nanotubes was elucidated. Furthermore, a highly sensitive H2O2 detection system was established based on the protein tubes. This work provides a facile method to construct diverse sophisticated functional protein nanomaterials.
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Affiliation(s)
- Xiaotong Fan
- Department of Materials Science and Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117576, Singapore
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Singapore
| | - Ke Li
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology, and Research (A*STAR), 2 Fusionopolis Way, Innovis, Singapore 138634, Singapore
| | - Siqi Liu
- Department of Materials Science and Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117576, Singapore
| | - Tingting Wang
- Department of Materials Science and Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117576, Singapore
| | - Yedong Ma
- Department of Materials Science and Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117576, Singapore
| | - Zibiao Li
- Department of Materials Science and Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117576, Singapore
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Singapore
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology, and Research (A*STAR), 2 Fusionopolis Way, Innovis, Singapore 138634, Singapore
| | - Chaobin He
- Department of Materials Science and Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117576, Singapore
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology, and Research (A*STAR), 2 Fusionopolis Way, Innovis, Singapore 138634, Singapore
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44
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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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45
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Nie J, Sun Y, Cheng X, Wen G, Liu X, Cheng M, Zhao J, Li W. Plant Protein-Peptide Supramolecular Polymers with Reliable Tissue Adhesion for Surgical Sealing. Adv Healthc Mater 2023; 12:e2203301. [PMID: 36960795 DOI: 10.1002/adhm.202203301] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/08/2023] [Indexed: 03/25/2023]
Abstract
The fusion of protein science and peptide science opens up new frontiers in creating innovative biomaterials. Herein, a new kind of adhesive soft materials based on a natural occurring plant protein and short peptides via a simple co-assembly route are explored. The hydrophobic zein is supercharged by sodium dodecyl sulfate to form a stable protein colloid, which is intended to interact with charge-complementary short peptides via multivalent ionic and hydrogen bonds, forming adhesive materials at macroscopic level. The adhesion performance of the resulting soft materials can be fine-manipulated by customizing the peptide sequences. The adhesive materials can resist over 78 cmH2 O of bursting pressure, which is high enough to meet the sealing requirements of dural defect. Dural sealing and repairing capability of the protein-peptide biomaterials are further identified in rat and rabbit models. In vitro and in vivo assays demonstrate that the protein-peptide adhesive shows excellent anti-swelling property, low cell cytotoxicity, hemocompatibility, and inflammation response. In particular, the protein-peptide supramolecular biomaterials can in vivo dissociate and degrade within two weeks, which can well match with the time-window of the dural repairing. This work underscores the versatility and availability of the supramolecular toolbox in the easy-to-implement fabrication of protein-peptide biomaterials.
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Affiliation(s)
- Junlian Nie
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun, 130012, P. R. China
| | - Yingchuan Sun
- Department of Orthopedics, The Second Hospital of Jilin University, 218 Ziqiang Street, Nanguan District, Changchun, Jilin Province, 130014, P. R. China
| | - Xueliang Cheng
- Department of Orthopedics, The Second Hospital of Jilin University, 218 Ziqiang Street, Nanguan District, Changchun, Jilin Province, 130014, P. R. China
| | - Guang Wen
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun, 130012, P. R. China
| | - Xiaohuan Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun, 130012, P. R. China
| | - Meng Cheng
- Department of Orthopedics, The Second Hospital of Jilin University, 218 Ziqiang Street, Nanguan District, Changchun, Jilin Province, 130014, P. R. China
| | - Jianwu Zhao
- Department of Orthopedics, The Second Hospital of Jilin University, 218 Ziqiang Street, Nanguan District, Changchun, Jilin Province, 130014, P. R. China
| | - Wen Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun, 130012, P. R. China
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46
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Mallik BB, Stanislaw J, Alawathurage TM, Khmelinskaia A. De Novo Design of Polyhedral Protein Assemblies: Before and After the AI Revolution. Chembiochem 2023; 24:e202300117. [PMID: 37014094 DOI: 10.1002/cbic.202300117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023]
Abstract
Self-assembling polyhedral protein biomaterials have gained attention as engineering targets owing to their naturally evolved sophisticated functions, ranging from protecting macromolecules from the environment to spatially controlling biochemical reactions. Precise computational design of de novo protein polyhedra is possible through two main types of approaches: methods from first principles, using physical and geometrical rules, and more recent data-driven methods based on artificial intelligence (AI), including deep learning (DL). Here, we retrospect first principle- and AI-based approaches for designing finite polyhedral protein assemblies, as well as advances in the structure prediction of such assemblies. We further highlight the possible applications of these materials and explore how the presented approaches can be combined to overcome current challenges and to advance the design of functional protein-based biomaterials.
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Affiliation(s)
- Bhoomika Basu Mallik
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Jenna Stanislaw
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Tharindu Madhusankha Alawathurage
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Alena Khmelinskaia
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
- Current address: Department of Chemistry, Ludwig Maximillian University, 80539, Munich, Germany
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47
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Dowling QM, Park YJ, Gerstenmaier N, Yang EC, Wargacki A, Hsia Y, Fries CN, Ravichandran R, Walkey C, Burrell A, Veesler D, Baker D, King NP. Hierarchical design of pseudosymmetric protein nanoparticles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545393. [PMID: 37398374 PMCID: PMC10312784 DOI: 10.1101/2023.06.16.545393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Discrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions 1-3. Despite remarkable recent progress in accurately designing new self-assembling proteins, the size and complexity of these assemblies has been limited by a reliance on strict symmetry 4,5. Inspired by the pseudosymmetry observed in bacterial microcompartments and viral capsids, we developed a hierarchical computational method for designing large pseudosymmetric self-assembling protein nanomaterials. We computationally designed pseudosymmetric heterooligomeric components and used them to create discrete, cage-like protein assemblies with icosahedral symmetry containing 240, 540, and 960 subunits. At 49, 71, and 96 nm diameter, these nanoparticles are the largest bounded computationally designed protein assemblies generated to date. More broadly, by moving beyond strict symmetry, our work represents an important step towards the accurate design of arbitrary self-assembling nanoscale protein objects.
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Affiliation(s)
- Quinton M Dowling
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Neil Gerstenmaier
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Erin C Yang
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Adam Wargacki
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Yang Hsia
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Chelsea N Fries
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Carl Walkey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Anika Burrell
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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48
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Li Z, Hu C, Chen H, Meng F, Mir B, Hu X, Yang J, Zhang H. Rational design of a self-assembly promoting fusion domain enhances high molecular weight levan synthesis by levansucrase SacB. Int J Biol Macromol 2023:125442. [PMID: 37330087 DOI: 10.1016/j.ijbiomac.2023.125442] [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: 03/29/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023]
Abstract
The catalytic product of levansucrase from Bacillus subtilis (SacB) is mainly composed of 10 % high molecular weight levan (HMW, ~2000 kDa) and 90 % low molecular weight levan (LMW, ~7000 Da). In order to achieve efficient production of food hydrocolloid, high molecular weight levan (HMW), with the help of molecular dynamics simulation software, a protein self-assembly element, Dex-GBD, was found and fused with the C-terminus of SacB to construct a novel fusion enzyme, SacB-GBD. The product distribution of SacB-GBD was reversed compared with SacB, and the proportion of HMW in the total polysaccharide was significantly increased to >95 %. We then confirmed that the self-assembly was responsible for the reversal of the SacB-GBD product distribution by the simultaneous modulation of SacB-GBD particle size and product distribution by SDS. The hydrophobic effect may be the main driver of self-assembly as analyzed by molecular simulations and hydrophobicity determination. Our study provides an enzyme source for the industrial production of HMW and provides a new theoretical basis for guiding the molecular modification of levansucrase towards the size of the catalytic product.
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Affiliation(s)
- Zhiwei Li
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Chao Hu
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Huiyong Chen
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Fanping Meng
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Baiza Mir
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Xueqin Hu
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Jingwen Yang
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China.
| | - Hongbin Zhang
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China.
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49
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Le Ouay B, Minami R, Boruah PK, Kunitomo R, Ohtsubo Y, Torikai K, Ohtani R, Sicard C, Ohba M. Water-Soluble Ionic Metal-Organic Polyhedra as a Versatile Platform for Enzyme Bio-immobilization. J Am Chem Soc 2023. [PMID: 37192338 DOI: 10.1021/jacs.2c13798] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Metal-organic polyhedra (MOPs) can act as elementary structural units for the design of modular porous materials; however, their association with biological systems remains greatly restricted by their typically low stabilities and solubilities in water. Herein, we describe the preparation of novel MOPs bearing either anionic or cationic groups and exhibiting a high affinity for proteins. Simple mixing of the protein bovine serum albumin (BSA) and ionic MOP aqueous solutions resulted in the spontaneous formation of MOP-protein assemblies, in a colloidal state or as solid precipitates depending on the initial mixing ratio. The versatility of the method was further illustrated using two enzymes, catalase and cytochrome c, with different sizes and isoelectric points (pI's) below and above 7. This mode of assembly led to the high retention of catalytic activity and enabled recyclability. Furthermore, the co-immobilization of cytochrome c with highly charged MOPs resulted in a substantial 44-fold increase of its catalytic activity.
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Affiliation(s)
- Benjamin Le Ouay
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ryosuke Minami
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Purna K Boruah
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Rin Kunitomo
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yuta Ohtsubo
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kohei Torikai
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Faculty of Chemistry, National University of Uzbekistan Named after Mirzo Ulugbek, 4 University Street, Tashkent 100174, Uzbekistan
| | - Ryo Ohtani
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Clémence Sicard
- Institut Lavoisier de Versailles, UVSQ, CNRS, Université Paris-Saclay, 45 Avenue des États-Unis, Bâtiment Lavoisier, Versailles 78035, France
- Institut Universitaire de France (IUF), 103 Boulevard St Michel, Paris 75005, France
| | - Masaaki Ohba
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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Ramberg KO, Crowley PB. Cage versus Sheet: Probing the Determinants of Protein - Cucurbit[7]uril Crystalline Architectures. J Struct Biol 2023; 215:107969. [PMID: 37137399 DOI: 10.1016/j.jsb.2023.107969] [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: 02/28/2023] [Revised: 04/22/2023] [Accepted: 04/25/2023] [Indexed: 05/05/2023]
Abstract
The donut-shaped cucurbit[n]urils (Qn) are a class of rigid macrocyclic receptor with protein recognition capabilities. Qn encapsulation of amino acid side chains can enable protein assembly. Recently, cucurbit[7]uril (Q7) has been applied as a molecular glue for organizing protein building blocks into crystalline architectures. Q7 co-crystallization with dimethylated Ralstonia solanacearum lectin (RSL*) has yielded novel crystalline architectures. Co-crystallization of RSL* and Q7 yields either cage- or sheet-like architectures which may be modulated via protein engineering. However, questions remain as to the factors dictating the formation of one architecture over another (cage versus sheet). Here, we make use of an engineered RSL*-Q7 system which co-crystallizes as the cage or sheet assembly with easily-distinguished crystal morphologies. Using this model system, we probe how the crystallization conditions dictate which crystalline architecture is adopted. Protein-ligand ratios and the sodium concentration were identified as key determinants for the growth of the cage versus sheet assemblies.
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Affiliation(s)
- Kiefer O Ramberg
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway, H91 TK33, Ireland
| | - Peter B Crowley
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway, H91 TK33, Ireland.
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