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Dar F, Cohen SR, Mitrea DM, Phillips AH, Nagy G, Leite WC, Stanley CB, Choi JM, Kriwacki RW, Pappu RV. Biomolecular condensates form spatially inhomogeneous network fluids. Nat Commun 2024; 15:3413. [PMID: 38649740 PMCID: PMC11035652 DOI: 10.1038/s41467-024-47602-z] [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: 10/07/2023] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
The functions of biomolecular condensates are thought to be influenced by their material properties, and these will be determined by the internal organization of molecules within condensates. However, structural characterizations of condensates are challenging, and rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that are formed by macromolecules from nucleolar granular components (GCs). We show that these minimal facsimiles of GCs form condensates that are network fluids featuring spatial inhomogeneities across different length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights suggest that condensates formed by multivalent proteins share features with network fluids formed by systems such as patchy or hairy colloids.
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Affiliation(s)
- Furqan Dar
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Samuel R Cohen
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Diana M Mitrea
- Dewpoint Therapeutics Inc., 451 D Street, Boston, MA, 02210, USA
| | - Aaron H Phillips
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Gergely Nagy
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wellington C Leite
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Jeong-Mo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea.
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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2
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Snoj J, Lapenta F, Jerala R. Preorganized cyclic modules facilitate the self-assembly of protein nanostructures. Chem Sci 2024; 15:3673-3686. [PMID: 38455016 PMCID: PMC10915844 DOI: 10.1039/d3sc06658d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/15/2024] [Indexed: 03/09/2024] Open
Abstract
The rational design of supramolecular assemblies aims to generate complex systems based on the simple information encoded in the chemical structure. Programmable molecules such as nucleic acids and polypeptides are particularly suitable for designing diverse assemblies and shapes not found in nature. Here, we describe a strategy for assembling modular architectures based on structurally and covalently preorganized subunits. Cyclization through spontaneous self-splicing of split intein and coiled-coil dimer-based interactions of polypeptide chains provide structural constraints, facilitating the desired assembly. We demonstrate the implementation of a strategy based on the preorganization of the subunits by designing a two-chain coiled-coil protein origami (CCPO) assembly that adopts a tetrahedral topology only when one or both subunit chains are covalently cyclized. Employing this strategy, we further design a 109 kDa trimeric CCPO assembly comprising 24 CC-forming segments. In this case, intein cyclization was crucial for the assembly of a concave octahedral scaffold, a newly designed protein fold. The study highlights the importance of preorganization of building modules to facilitate the self-assembly of higher-order supramolecular structures.
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Affiliation(s)
- Jaka Snoj
- Department of Synthetic Biology and Immunology, National Institute of Chemistry Hajdrihova 19 SI-1000 Ljubljana Slovenia
- Interdisciplinary Doctoral Program in Biomedicine, University of Ljubljana Kongresni trg 12 SI-1000 Ljubljana Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry Hajdrihova 19 SI-1000 Ljubljana Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry Hajdrihova 19 SI-1000 Ljubljana Slovenia
- EN-FIST Centre of Excellence Trg OF 13 SI-1000 Ljubljana Slovenia
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3
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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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4
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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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5
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Jeon J, Lee KZ, Zhang X, Jaeger J, Kim E, Li J, Belaygorod L, Arif B, Genin GM, Foston MB, Zayed MA, Zhang F. Genetically Engineered Protein-Based Bioadhesives with Programmable Material Properties. ACS APPLIED MATERIALS & INTERFACES 2023:10.1021/acsami.3c12919. [PMID: 38039085 PMCID: PMC11421886 DOI: 10.1021/acsami.3c12919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2023]
Abstract
Silk-amyloid-mussel foot protein (SAM) hydrogels made from recombinant fusion proteins containing β-amyloid peptide, spider silk domain, and mussel foot protein (Mfp) are attractive bioadhesives as they display a unique combination of tunability, biocompatibility, bioabsorbability, strong cohesion, and underwater adhesion to a wide range of biological surfaces. To design tunable SAM hydrogels for tailored surgical repair applications, an understanding of the relationships between protein sequence and hydrogel properties is imperative. Here, we fabricated SAM hydrogels using fusion proteins of varying lengths of silk-amyloid repeats and Mfps to characterize their structure and properties. We found that increasing silk-amyloid repeats enhanced the hydrogel's β-sheet content (r = 0.74), leading to higher cohesive strength and toughness. Additionally, increasing the Mfp length beyond the half-length of the full Mfp sequence (1/2 Mfp) decreased the β-sheet content (r = -0.47), but increased hydrogel surface adhesion. Among different variants, the hydrogel made of 16xKLV-2Mfp displayed a high ultimate strength of 3.0 ± 0.3 MPa, an ultimate strain of 664 ± 119%, and an attractive underwater adhesivity of 416 ± 20 kPa to porcine skin. Collectively, the sequence-structure-property relationships learned from this study will be useful to guide the design of future protein adhesives with tunable characteristics for tailored surgical applications.
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Affiliation(s)
- Juya Jeon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - Kok Zhi Lee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - Xiaolu Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - John Jaeger
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - Eugene Kim
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - Jingyao Li
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - Larisa Belaygorod
- Department of Surgery, Section of Vascular Surgery, Washington University of Medicine in St. Louis, Saint Louis, Missouri 63110, United States
| | - Batool Arif
- Department of Surgery, Section of Vascular Surgery, Washington University of Medicine in St. Louis, Saint Louis, Missouri 63110, United States
| | - Guy M. Genin
- NSF Science and Technology Center for Engineering MechanoBiology, Department of Mechanical Engineering & Materials Science, Institute of Materials Science and Engineering, and Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - Marcus B. Foston
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - Mohamed A. Zayed
- Department of Surgery, Section of Vascular Surgery, Department of Radiology, Division of Molecular Cell Biology, and Division of Molecular Cell Biology, Washington University of Medicine in St. Louis, Saint Louis, Missouri 63110, United States; Veterans Affairs St. Louis Health Care System, St. Louis, Missouri 63106, United States
| | - Fuzhong Zhang
- Department of Energy, Environmental & Chemical Engineering, Institute of Materials Science and Engineering, and Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
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6
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Lee KZ, Jeon J, Jiang B, Subramani SV, Li J, Zhang F. Protein-Based Hydrogels and Their Biomedical Applications. Molecules 2023; 28:4988. [PMID: 37446650 DOI: 10.3390/molecules28134988] [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: 05/26/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Hydrogels made from proteins are attractive materials for diverse medical applications, as they are biocompatible, biodegradable, and amenable to chemical and biological modifications. Recent advances in protein engineering, synthetic biology, and material science have enabled the fine-tuning of protein sequences, hydrogel structures, and hydrogel mechanical properties, allowing for a broad range of biomedical applications using protein hydrogels. This article reviews recent progresses on protein hydrogels with special focus on those made of microbially produced proteins. We discuss different hydrogel formation strategies and their associated hydrogel properties. We also review various biomedical applications, categorized by the origin of protein sequences. Lastly, current challenges and future opportunities in engineering protein-based hydrogels are discussed. We hope this review will inspire new ideas in material innovation, leading to advanced protein hydrogels with desirable properties for a wide range of biomedical applications.
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Affiliation(s)
- Kok Zhi Lee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MI 63130, USA
| | - Juya Jeon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MI 63130, USA
| | - Bojing Jiang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MI 63130, USA
| | - Shri Venkatesh Subramani
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MI 63130, USA
| | - Jingyao Li
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MI 63130, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MI 63130, USA
- Institute of Materials Science and Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MI 63130, USA
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Saint Louis, MI 63130, USA
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7
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Li J, Jiang B, Chang X, Yu H, Han Y, Zhang F. Bi-terminal fusion of intrinsically-disordered mussel foot protein fragments boosts mechanical strength for protein fibers. Nat Commun 2023; 14:2127. [PMID: 37059716 PMCID: PMC10104820 DOI: 10.1038/s41467-023-37563-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/22/2023] [Indexed: 04/16/2023] Open
Abstract
Microbially-synthesized protein-based materials are attractive replacements for petroleum-derived synthetic polymers. However, the high molecular weight, high repetitiveness, and highly-biased amino acid composition of high-performance protein-based materials have restricted their production and widespread use. Here we present a general strategy for enhancing both strength and toughness of low-molecular-weight protein-based materials by fusing intrinsically-disordered mussel foot protein fragments to their termini, thereby promoting end-to-end protein-protein interactions. We demonstrate that fibers of a ~60 kDa bi-terminally fused amyloid-silk protein exhibit ultimate tensile strength up to 481 ± 31 MPa and toughness of 179 ± 39 MJ*m-3, while achieving a high titer of 8.0 ± 0.70 g/L by bioreactor production. We show that bi-terminal fusion of Mfp5 fragments significantly enhances the alignment of β-nanocrystals, and intermolecular interactions are promoted by cation-π and π-π interactions between terminal fragments. Our approach highlights the advantage of self-interacting intrinsically-disordered proteins in enhancing material mechanical properties and can be applied to a wide range of protein-based materials.
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Affiliation(s)
- Jingyao Li
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
| | - Bojing Jiang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
| | - Xinyuan Chang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
| | - Han Yu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
| | - Yichao Han
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA.
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA.
- Institute of Materials Science & Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA.
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Jeon J, Subramani SV, Lee KZ, Jiang B, Zhang F. Microbial Synthesis of High-Molecular-Weight, Highly Repetitive Protein Polymers. Int J Mol Sci 2023; 24:6416. [PMID: 37047388 PMCID: PMC10094428 DOI: 10.3390/ijms24076416] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023] Open
Abstract
High molecular weight (MW), highly repetitive protein polymers are attractive candidates to replace petroleum-derived materials as these protein-based materials (PBMs) are renewable, biodegradable, and have outstanding mechanical properties. However, their high MW and highly repetitive sequence features make them difficult to synthesize in fast-growing microbial cells in sufficient amounts for real applications. To overcome this challenge, various methods were developed to synthesize repetitive PBMs. Here, we review recent strategies in the construction of repetitive genes, expression of repetitive proteins from circular mRNAs, and synthesis of repetitive proteins by ligation and protein polymerization. We discuss the advantages and limitations of each method and highlight future directions that will lead to scalable production of highly repetitive PBMs for a wide range of applications.
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Affiliation(s)
- Juya Jeon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.J.); (S.V.S.); (K.Z.L.); (B.J.)
| | - Shri Venkatesh Subramani
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.J.); (S.V.S.); (K.Z.L.); (B.J.)
| | - Kok Zhi Lee
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.J.); (S.V.S.); (K.Z.L.); (B.J.)
| | - Bojing Jiang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.J.); (S.V.S.); (K.Z.L.); (B.J.)
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.J.); (S.V.S.); (K.Z.L.); (B.J.)
- Institute of Materials Science and Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO 63130, USA
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9
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Zhao L, Ma Z, Wang Q, Hu M, Zhang J, Chen L, Shi G, Ding Z. Engineering the Thermostability of Sucrose Synthase by Reshaping the Subunit Interaction Contributes to Efficient UDP-Glucose Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3832-3841. [PMID: 36795895 DOI: 10.1021/acs.jafc.2c08642] [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: 06/18/2023]
Abstract
The restricted availability of UDP-glucose, an essential precursor that targets oligo/polysaccharide and glycoside synthesis, makes its practical application difficult. Sucrose synthase (Susy), which catalyzes one-step UDP-glucose synthesis, is a promising candidate. However, due to poor thermostability of Susy, mesophilic conditions are required for synthesis, which slow down the process, limit productivity, and prevent scaled and efficient UDP-glucose preparation. Here, we obtained an engineered thermostable Susy (mutant M4) from Nitrosospira multiformis through automated prediction and greedy accumulation of beneficial mutations. The mutant improved the T1/2 value at 55 °C by 27-fold, resulting in UDP-glucose synthesis at 37 g/L/h of space-time yield that met industrial biotransformation standards. Furthermore, global interaction between mutant M4 subunits was reconstructed by newly formed interfaces according to molecular dynamics simulations, with residue Trp162 playing an important role in strengthening the interface interaction. This work enabled effective, time-saving UDP-glucose production and paved the way for rational thermostability engineering of oligomeric enzymes.
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Affiliation(s)
- Liting Zhao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Zhongbao Ma
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Qiong Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Manfeng Hu
- School of Science, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Jingxiang Zhang
- School of Science, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Lei Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Guiyang Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Zhongyang Ding
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
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10
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Bhullar AS, Zhang L, Burns N, Cheng X, Guo P. Voltage controlled shutter regulates channel size and motion direction of protein aperture as durable nano-electric rectifier-----An opinion in biomimetic nanoaperture. Biomaterials 2022; 291:121863. [PMID: 36356474 PMCID: PMC9766157 DOI: 10.1016/j.biomaterials.2022.121863] [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: 05/05/2022] [Revised: 09/30/2022] [Accepted: 10/15/2022] [Indexed: 11/09/2022]
Abstract
In optical devices such as camera or microscope, an aperture is used to regulate light intensity for imaging. Here we report the discovery and construction of a durable bio-aperture at nanometerscale that can regulate current at the pico-ampere scale. The nano-aperture is made of 12 identical protein subunits that form a 3.6-nm channel with a shutter and "one-way traffic" property. This shutter responds to electrical potential differences across the aperture and can be turned off for double stranded DNA translocation. This voltage enables directional control, and three-step regulation for opening and closing. The nano-aperture was constructed in vitro and purified into homogeneity. The aperture was stable at pH2-12, and a temperature of -85C-60C. When an electrical potential was held, three reproducible discrete steps of current flowing through the channel were recorded. Each step reduced 32% of the channel dimension evident by the reduction of the measured current flowing through the aperture. The current change is due to the change of the resistance of aperture size. The transition between these three distinct steps and the direction of the current was controlled via the polarity of the voltage applied across the aperture. When the C-terminal of the aperture was fused to an antigen, the antibody and antigen interaction resulted in a 32% reduction of the channel size. This phenomenon was used for disease diagnosis since the incubation of the antigen-nano-aperture with a specific cancer antibody resulted in a change of 32% of current. The purified truncated cone-shape aperture automatically self-assembled efficiently into a sheet of the tetragonal array via head-to-tail self-interaction. The nano-aperture discovery with a controllable shutter, discrete-step current regulation, formation of tetragonal sheet, and one-way current traffic provides a nanoscale electrical circuit rectifier for nanodevices and disease diagnosis.
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Affiliation(s)
- Abhjeet S Bhullar
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; And Comprehensive Cancer Center. The Ohio State University, Columbus, OH, 43210, USA; Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Long Zhang
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; And Comprehensive Cancer Center. The Ohio State University, Columbus, OH, 43210, USA
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; And Comprehensive Cancer Center. The Ohio State University, Columbus, OH, 43210, USA
| | - Xiaolin Cheng
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA; College of Pharmacy, Translational Data Analytics Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; And Comprehensive Cancer Center. The Ohio State University, Columbus, OH, 43210, USA; Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA; College of Pharmacy, Translational Data Analytics Institute, The Ohio State University, Columbus, OH, 43210, USA.
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11
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Hartline CJ, Zhang R, Zhang F. Transient Antibiotic Tolerance Triggered by Nutrient Shifts From Gluconeogenic Carbon Sources to Fatty Acid. Front Microbiol 2022; 13:854272. [PMID: 35359720 PMCID: PMC8963472 DOI: 10.3389/fmicb.2022.854272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/22/2022] [Indexed: 12/04/2022] Open
Abstract
Nutrient shifts from glycolytic-to-gluconeogenic carbon sources can create large sub-populations of extremely antibiotic tolerant bacteria, called persisters. Positive feedback in Escherichia coli central metabolism was believed to play a key role in the formation of persister cells. To examine whether positive feedback in nutrient transport can also support high persistence to β-lactams, we performed nutrient shifts for E. coli from gluconeogenic carbon sources to fatty acid (FA). We observed tri-phasic antibiotic killing kinetics characterized by a transient period of high antibiotic tolerance, followed by rapid killing then a slower persister-killing phase. The duration of transient tolerance (3-44 h) varies with pre-shift carbon source and correlates strongly with the time needed to accumulate the FA degradation enzyme FadD after the shift. Additionally, FadD accumulation time and thus transient tolerance time can be reduced by induction of the glyoxylate bypass prior to switching, highlighting that two interacting feedback loops simultaneously control the length of transient tolerance. Our results demonstrate that nutrient switches along with positive feedback are not sufficient to trigger persistence in a majority of the population but instead triggers only a temporary tolerance. Additionally, our results demonstrate that the pre-shift metabolic state determines the duration of transient tolerance and that supplying glyoxylate can facilitate antibiotic killing of bacteria.
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Affiliation(s)
- Christopher J. Hartline
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, United States
| | - Ruixue Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, United States
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, United States
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO, United States
- Institute of Materials Science and Engineering, Washington University in St. Louis, Saint Louis, MO, United States
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12
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Artificial protein assemblies with well-defined supramolecular protein nanostructures. Biochem Soc Trans 2021; 49:2821-2830. [PMID: 34812854 DOI: 10.1042/bst20210808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022]
Abstract
Nature uses a wide range of well-defined biomolecular assemblies in diverse cellular processes, where proteins are major building blocks for these supramolecular assemblies. Inspired by their natural counterparts, artificial protein-based assemblies have attracted strong interest as new bio-nanostructures, and strategies to construct ordered protein assemblies have been rapidly expanding. In this review, we provide an overview of very recent studies in the field of artificial protein assemblies, with the particular aim of introducing major assembly methods and unique features of these assemblies. Computational de novo designs were used to build various assemblies with artificial protein building blocks, which are unrelated to natural proteins. Small chemical ligands and metal ions have also been extensively used for strong and bio-orthogonal protein linking. Here, in addition to protein assemblies with well-defined sizes, protein oligomeric and array structures with rather undefined sizes (but with definite repeat protein assembly units) also will be discussed in the context of well-defined protein nanostructures. Lastly, we will introduce multiple examples showing how protein assemblies can be effectively used in various fields such as therapeutics and vaccine development. We believe that structures and functions of artificial protein assemblies will be continuously evolved, particularly according to specific application goals.
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13
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Kim E, Jeon J, Zhu Y, Hoppe ED, Jun YS, Genin GM, Zhang F. A Biosynthetic Hybrid Spidroin-Amyloid-Mussel Foot Protein for Underwater Adhesion on Diverse Surfaces. ACS APPLIED MATERIALS & INTERFACES 2021; 13:48457-48468. [PMID: 34633172 PMCID: PMC10041942 DOI: 10.1021/acsami.1c14182] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Strong underwater adhesives are attractive materials for biomedical healing and underwater repair, but their success in applications has been limited, owing to challenges with underwater setting and with balancing surface adhesion and cohesion. Here, we applied synthetic biology approaches to overcome these challenges through design and synthesis of a novel hybrid protein consisting of the zipper-forming domains of an amyloid protein, flexible spider silk sequences, and a dihydroxyphenylalanine (DOPA)-containing mussel foot protein (Mfp). This partially structured, hybrid protein can self-assemble into a semi-crystalline hydrogel that exhibits high strength and toughness as well as strong underwater adhesion to a variety of surfaces, including difficult-to-adhere plastics, tendon, and skin. The hydrogel allows selective debonding by oxidation or iron-chelating treatments. Both the material design and the biosynthetic approach explored in this study will inspire future work for a wide range of hybrid protein-based materials with tunable properties and broad applications.
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Affiliation(s)
- Eugene Kim
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
| | - Juya Jeon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
| | - Yaguang Zhu
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
| | - Ethan D. Hoppe
- NSF Science and Technology Center for Engineering MechanoBiology, Department of Mechanical Engineering & Materials Science, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
| | - Young-Shin Jun
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
- Institute of Materials Science and Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
| | - Guy M. Genin
- NSF Science and Technology Center for Engineering MechanoBiology, Department of Mechanical Engineering & Materials Science, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
- Institute of Materials Science and Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
| | - Fuzhong Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
- Institute of Materials Science and Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
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14
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Amyloids as Building Blocks for Macroscopic Functional Materials: Designs, Applications and Challenges. Int J Mol Sci 2021; 22:ijms221910698. [PMID: 34639037 PMCID: PMC8508955 DOI: 10.3390/ijms221910698] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/29/2021] [Accepted: 09/29/2021] [Indexed: 12/25/2022] Open
Abstract
Amyloids are self-assembled protein aggregates that take cross-β fibrillar morphology. Although some amyloid proteins are best known for their association with Alzheimer’s and Parkinson’s disease, many other amyloids are found across diverse organisms, from bacteria to humans, and they play vital functional roles. The rigidity, chemical stability, high aspect ratio, and sequence programmability of amyloid fibrils have made them attractive candidates for functional materials with applications in environmental sciences, material engineering, and translational medicines. This review focuses on recent advances in fabricating various types of macroscopic functional amyloid materials. We discuss different design strategies for the fabrication of amyloid hydrogels, high-strength materials, composite materials, responsive materials, extracellular matrix mimics, conductive materials, and catalytic materials.
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15
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Mahynski NA, Shen VK. Symmetry-derived structure directing agents for two-dimensional crystals of arbitrary colloids. SOFT MATTER 2021; 17:7853-7866. [PMID: 34382053 PMCID: PMC9793339 DOI: 10.1039/d1sm00875g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We derive properties of self-assembling rings which can template the organization of an arbitrary colloid into any periodic symmetry in two Euclidean dimensions. By viewing this as a tiling problem, we illustrate how the shape and chemical patterning of these rings are derivable, and are explicitly reflected by the symmetry group's orbifold symbol. We performed molecular dynamics simulations to observe their self-assembly and found 5 different characteristics which could be easily rationalized on the basis of this symbol. These include systems which undergo chiral phase separation, are addressably complex, exhibit self-limiting growth into clusters, form ordered "rods" in only one-dimension akin to a smectic phase, and those from symmetry groups which are pluripotent and allow one to select rings which exhibit different behaviors. We discuss how the curvature of the ring's edges plays an integral role in achieving correct self-assembly, and illustrate how to obtain these shapes. This provides a method for patterning colloidal systems at interfaces without explicitly programming this information onto the colloid itself.
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Affiliation(s)
- Nathan A Mahynski
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8320, USA.
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16
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Bowen CH, Sargent CJ, Wang A, Zhu Y, Chang X, Li J, Mu X, Galazka JM, Jun YS, Keten S, Zhang F. Microbial production of megadalton titin yields fibers with advantageous mechanical properties. Nat Commun 2021; 12:5182. [PMID: 34462443 PMCID: PMC8405620 DOI: 10.1038/s41467-021-25360-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 08/05/2021] [Indexed: 02/07/2023] Open
Abstract
Manmade high-performance polymers are typically non-biodegradable and derived from petroleum feedstock through energy intensive processes involving toxic solvents and byproducts. While engineered microbes have been used for renewable production of many small molecules, direct microbial synthesis of high-performance polymeric materials remains a major challenge. Here we engineer microbial production of megadalton muscle titin polymers yielding high-performance fibers that not only recapture highly desirable properties of natural titin (i.e., high damping capacity and mechanical recovery) but also exhibit high strength, toughness, and damping energy - outperforming many synthetic and natural polymers. Structural analyses and molecular modeling suggest these properties derive from unique inter-chain crystallization of folded immunoglobulin-like domains that resists inter-chain slippage while permitting intra-chain unfolding. These fibers have potential applications in areas from biomedicine to textiles, and the developed approach, coupled with the structure-function insights, promises to accelerate further innovation in microbial production of high-performance materials.
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Affiliation(s)
- Christopher H Bowen
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Cameron J Sargent
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Ao Wang
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, USA
| | - Yaguang Zhu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Xinyuan Chang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Jingyao Li
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Xinyue Mu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Jonathan M Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Young-Shin Jun
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA.
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA.
- Institute of Materials Science & Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA.
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17
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A nanobody toolbox targeting dimeric coiled-coil modules for functionalization of designed protein origami structures. Proc Natl Acad Sci U S A 2021; 118:2021899118. [PMID: 33893235 PMCID: PMC8092592 DOI: 10.1073/pnas.2021899118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Coiled-coil (CC) dimers are widely used in protein design because of their modularity and well-understood sequence-structure relationship. In CC protein origami design, a polypeptide chain is assembled from a defined sequence of CC building segments that determine the self-assembly of protein cages into polyhedral shapes, such as the tetrahedron, triangular prism, or four-sided pyramid. However, a targeted functionalization of the CC modules could significantly expand the versatility of protein origami scaffolds. Here, we describe a panel of single-chain camelid antibodies (nanobodies) directed against different CC modules of a de novo designed protein origami tetrahedron. We show that these nanobodies are able to recognize the same CC modules in different polyhedral contexts, such as isolated CC dimers, tetrahedra, triangular prisms, or trigonal bipyramids, thereby extending the ability to functionalize polyhedra with nanobodies in a desired stoichiometry. Crystal structures of five nanobody-CC complexes in combination with small-angle X-ray scattering show binding interactions between nanobodies and CC dimers forming the edges of a tetrahedron with the nanobody entering the tetrahedral cavity. Furthermore, we identified a pair of allosteric nanobodies in which the binding to the distant epitopes on the antiparallel homodimeric APH CC is coupled via a strong positive cooperativity. A toolbox of well-characterized nanobodies specific for CC modules provides a unique tool to target defined sites in the designed protein structures, thus opening numerous opportunities for the functionalization of CC protein origami polyhedra or CC-based bionanomaterials.
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18
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Sarkar D, Harms H, Galleano I, Sheikh ZP, Pless SA. Ion channel engineering using protein trans-splicing. Methods Enzymol 2021; 654:19-48. [PMID: 34120713 DOI: 10.1016/bs.mie.2021.01.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Conventional site-directed mutagenesis and genetic code expansion approaches have been instrumental in providing detailed functional and pharmacological insight into membrane proteins such as ion channels. Recently, this has increasingly been complemented by semi-synthetic strategies, in which part of the protein is generated synthetically. This means a vast range of chemical modifications, including non-canonical amino acids (ncAA), backbone modifications, chemical handles, fluorescent or spectroscopic labels and any combination of these can be incorporated. Among these approaches, protein trans-splicing (PTS) is particularly promising for protein reconstitution in live cells. It relies on one or more split inteins, which can spontaneously and covalently link flanking peptide or protein sequences. Here, we describe the use of PTS and its variant tandem PTS (tPTS) in semi-synthesis of ion channels in Xenopus laevis oocytes to incorporate ncAAs, post-translational modifications or metabolically stable mimics thereof. This strategy has the potential to expand the type and number of modifications in ion channel research.
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Affiliation(s)
- Debayan Sarkar
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Hendrik Harms
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Iacopo Galleano
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Zeshan Pervez Sheikh
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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19
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Božič Abram S, Gradišar H, Aupič J, Round AR, Jerala R. Triangular in Vivo Self-Assembling Coiled-Coil Protein Origami. ACS Chem Biol 2021; 16:310-315. [PMID: 33476117 PMCID: PMC7901019 DOI: 10.1021/acschembio.0c00812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Coiled-coil protein
origami (CCPO) polyhedra are designed self-assembling
nanostructures constructed from coiled coil (CC)-forming modules connected
into a single chain. For testing new CCPO building modules, simpler
polyhedra could be used that should maintain most features relevant
to larger scaffolds. We show the design and characterization of nanoscale
single-chain triangles, composed of six concatenated parallel CC dimer-forming
segments connected by flexible linker peptides. The polypeptides self-assembled
in bacteria in agreement with the design, and the shape of the polypeptides
was confirmed with small-angle X-ray scattering. Fusion with split-fluorescent
protein domains was used as a functional assay in bacteria, based
on the discrimination between the correctly folded and misfolded nanoscale
triangles comprising correct, mismatched, or truncated modules. This
strategy was used to evaluate the optimal size of linkers between
CC segments which comprised eight amino acid residues.
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Affiliation(s)
- Sabina Božič Abram
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Helena Gradišar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, 1000 Ljubljana, Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Adam R. Round
- EMBL Grenoble outstation, 38042 Grenoble, France
- School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, United Kingdom
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, 1000 Ljubljana, Slovenia
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20
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Lapenta F, Aupič J, Vezzoli M, Strmšek Ž, Da Vela S, Svergun DI, Carazo JM, Melero R, Jerala R. Self-assembly and regulation of protein cages from pre-organised coiled-coil modules. Nat Commun 2021; 12:939. [PMID: 33574245 PMCID: PMC7878516 DOI: 10.1038/s41467-021-21184-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/13/2021] [Indexed: 11/09/2022] Open
Abstract
Coiled-coil protein origami (CCPO) is a modular strategy for the de novo design of polypeptide nanostructures. CCPO folds are defined by the sequential order of concatenated orthogonal coiled-coil (CC) dimer-forming peptides, where a single-chain protein is programmed to fold into a polyhedral cage. Self-assembly of CC-based nanostructures from several chains, similarly as in DNA nanotechnology, could facilitate the design of more complex assemblies and the introduction of functionalities. Here, we show the design of a de novo triangular bipyramid fold comprising 18 CC-forming segments and define the strategy for the two-chain self-assembly of the bipyramidal cage from asymmetric and pseudo-symmetric pre-organised structural modules. In addition, by introducing a protease cleavage site and masking the interfacial CC-forming segments in the two-chain bipyramidal cage, we devise a proteolysis-mediated conformational switch. This strategy could be extended to other modular protein folds, facilitating the construction of dynamic multi-chain CC-based complexes. Coiled-coil protein origami is a strategy for the de novo design of polypeptide nanostructures based on coiled-coil dimer forming peptides, where a single chain protein folds into a polyhedral cage. Here, the authors design a single-chain triangular bipyramid and also demonstrate that the bipyramid can be self-assembled as a heterodimeric complex, comprising pre-defined subunits.
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Affiliation(s)
- Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Marco Vezzoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | | | - Roberto Melero
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Ljubljana, Slovenia.
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21
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Han S, Kim YN, Jo G, Kim YE, Kim HM, Choi JM, Jung Y. Multivalent-Interaction-Driven Assembly of Discrete, Flexible, and Asymmetric Supramolecular Protein Nano-Prisms. Angew Chem Int Ed Engl 2020; 59:23244-23251. [PMID: 32856385 DOI: 10.1002/anie.202010054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Indexed: 12/25/2022]
Abstract
Current approaches to design monodisperse protein assemblies require rigid, tight, and symmetric interactions between oligomeric protein units. Herein, we introduce a new multivalent-interaction-driven assembly strategy that allows flexible, spaced, and asymmetric assembly between protein oligomers. We discovered that two polygonal protein oligomers (ranging from triangle to hexagon) dominantly form a discrete and stable two-layered protein prism nanostructure via multivalent interactions between fused binding pairs. We demonstrated that protein nano-prisms with long flexible peptide linkers (over 80 amino acids) between protein oligomer layers could be discretely formed. Oligomers with different structures could also be monodispersely assembled into two-layered but asymmetric protein nano-prisms. Furthermore, producing higher-order architectures with multiple oligomer layers, for example, 3-layered nano-prisms or nanotubes, was also feasible.
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Affiliation(s)
- Suyeong Han
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Yu-Na Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Gyunghee Jo
- Biomedical Science and Engineering Interdisciplinary Program, KAIST, Daejeon, 34141, Korea
| | - Young Eun Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Ho Min Kim
- Graduate School of Medical Science & Engineering, KAIST, Daejeon, 34141, Korea.,Center for Biomolecular & Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Korea
| | - Jeong-Mo Choi
- Natural Science Research Institute, KAIST, Daejeon, 34141, Korea.,Department of Chemistry, Busan National University, Busan, 46241, Korea
| | - Yongwon Jung
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
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22
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Han S, Kim Y, Jo G, Kim YE, Kim HM, Choi J, Jung Y. Multivalent‐Interaction‐Driven Assembly of Discrete, Flexible, and Asymmetric Supramolecular Protein Nano‐Prisms. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Suyeong Han
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Korea
| | - Yu‐na Kim
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Korea
| | - Gyunghee Jo
- Biomedical Science and Engineering Interdisciplinary Program KAIST Daejeon 34141 Korea
| | - Young Eun Kim
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Korea
| | - Ho Min Kim
- Graduate School of Medical Science & Engineering KAIST Daejeon 34141 Korea
- Center for Biomolecular & Cellular Structure Institute for Basic Science (IBS) Daejeon 34126 Korea
| | - Jeong‐Mo Choi
- Natural Science Research Institute KAIST Daejeon 34141 Korea
- Department of Chemistry Busan National University Busan 46241 Korea
| | - Yongwon Jung
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Korea
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23
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Jiang L, Kirshenbaum K. A modular approach for organizing dimeric coiled coils on peptoid oligomer scaffolds. Org Biomol Chem 2020; 18:2312-2320. [PMID: 32159574 DOI: 10.1039/d0ob00453g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a general approach to promote the folding of synthetic oligopeptides capable of forming homodimeric coiled coil assemblies. By pre-organizing the peptides on macrocyclic oligomer scaffolds, the stability of the coiled coils is enhanced with an observed increase in the melting temperature of 30 °C to 40 °C. Molecular dynamics simulations substantiate the hypothesis that the enhanced stability is established by constraining motion at the peptide termini and by pre-organizing intramolecular helix-helix contacts. We demonstrate the modularity of this approach by using a family of peptoid scaffolds to promote the folding of a dimeric coiled coil. Importantly, this strategy for templating coiled coils allows preservation of native amino acid sequences. Comparing a macrocyclic peptoid scaffold to its linear counterparts indicates that both types of assemblies are effective for organizing stable coiled coils. These results will guide future designs of coiled coil peptides for biomedical applications and as building blocks for more complex supramolecular assemblies.
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Affiliation(s)
- Linhai Jiang
- Chemistry Department, New York University, New York, NY 10003, USA.
| | - Kent Kirshenbaum
- Chemistry Department, New York University, New York, NY 10003, USA.
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24
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Díaz S, Insua I, Bhak G, Montenegro J. Sequence Decoding of 1D to 2D Self‐Assembling Cyclic Peptides. Chemistry 2020; 26:14765-14770. [DOI: 10.1002/chem.202003265] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/09/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Sandra Díaz
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela Santiago de Compostela 15782 Spain
| | - Ignacio Insua
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela Santiago de Compostela 15782 Spain
| | - Ghibom Bhak
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela Santiago de Compostela 15782 Spain
| | - Javier Montenegro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela Santiago de Compostela 15782 Spain
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25
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Arrabito G, Ferrara V, Bonasera A, Pignataro B. Artificial Biosystems by Printing Biology. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1907691. [PMID: 32511894 DOI: 10.1002/smll.201907691] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 05/09/2020] [Indexed: 05/09/2023]
Abstract
The continuous progress of printing technologies over the past 20 years has fueled the development of a plethora of applications in materials sciences, flexible electronics, and biotechnologies. More recently, printing methodologies have started up to explore the world of Artificial Biology, offering new paradigms in the direct assembly of Artificial Biosystems (small condensates, compartments, networks, tissues, and organs) by mimicking the result of the evolution of living systems and also by redesigning natural biological systems, taking inspiration from them. This recent progress is reported in terms of a new field here defined as Printing Biology, resulting from the intersection between the field of printing and the bottom up Synthetic Biology. Printing Biology explores new approaches for the reconfigurable assembly of designed life-like or life-inspired structures. This work presents this emerging field, highlighting its main features, i.e., printing methodologies (from 2D to 3D), molecular ink properties, deposition mechanisms, and finally the applications and future challenges. Printing Biology is expected to show a growing impact on the development of biotechnology and life-inspired fabrication.
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Affiliation(s)
- Giuseppe Arrabito
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, Building 17, Palermo, 90128, Italy
| | - Vittorio Ferrara
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, Building 17, Palermo, 90128, Italy
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria, 6, Catania, 95125, Italy
| | - Aurelio Bonasera
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, Building 17, Palermo, 90128, Italy
| | - Bruno Pignataro
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, Building 17, Palermo, 90128, Italy
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26
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Lapenta F, Jerala R. Design of novel protein building modules and modular architectures. Curr Opin Struct Biol 2020; 63:90-96. [PMID: 32505942 DOI: 10.1016/j.sbi.2020.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/31/2022]
Abstract
Nature uses only a limited number of protein topologies and while several folds have evolved independently over time, there are clearly many possible topologies that have not been explored by evolution. With recent advances of protein design concepts, computational modeling tools, high resolution and high-throughput experimental methods it is now possible to design new protein architectures. The collection of building blocks and design principles widened both in size and complexity, offering an expanded toolset for building new modular folds and functional protein structures. Here we review and discuss recent achievements of protein design, focusing in particular on the use and prospects of modular approaches for assembling new protein folds.
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Affiliation(s)
- Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia; EN-FIST Centre of Excellence, Ljubljana, Slovenia.
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Abstract
Proteins are versatile macromolecules with diverse structure, charge, and function. They are ideal building blocks for biomaterials for drug delivery, biosensing, or tissue engineering applications. Simultaneously, the need to develop green alternatives to chemical processes has led to renewed interest in multienzyme biocatalytic routes to fine, specialty, and commodity chemicals. Therefore, a method to reliably assemble protein complexes using protein-protein interactions would facilitate the rapid production of new materials. Here we show a method for modular assembly of protein materials using a supercharged protein as a scaffolding "hub" onto which target proteins bearing oppositely charged domains have been self-assembled. The physical properties of the material can be tuned through blending and heating and disassembly triggered using changes in pH or salt concentration. The system can be extended to the synthesis of living materials. Our modular method can be used to reliably direct the self-assembly of proteins using small charged tag domains that can be easily encoded in a fusion protein.
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Affiliation(s)
- James A. J. Arpino
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Karen Marie Polizzi
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
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28
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Zhou W, Šmidlehner T, Jerala R. Synthetic biology principles for the design of protein with novel structures and functions. FEBS Lett 2020; 594:2199-2212. [PMID: 32324903 DOI: 10.1002/1873-3468.13796] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/29/2020] [Accepted: 04/03/2020] [Indexed: 12/14/2022]
Abstract
Nature provides a large number of functional proteins that evolved during billions of years of evolution. The diversity of natural proteins encompasses versatile functions and more than a thousand different folds, which, however, represents only a tiny fraction of all possible folds and polypeptide sequences. Recent advances in the rational design of proteins demonstrate that it is possible to design de novo protein folds unseen in nature. Novel protein topologies have been designed based on similar principles as natural proteins using advanced computational modelling or modular construction principles, such as oligomerization domains. Designed proteins exhibit several interesting features such as extreme stability, designability of 3D topologies and folding pathways. Moreover, designed protein assemblies can implement symmetry similar to the viral capsids, while, on the other hand, single-chain pseudosymmetric designs can address each position independently. Recently, the design is expanding towards the introduction of new functions into designed proteins, and we may soon be able to design molecular machines.
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Affiliation(s)
- Weijun Zhou
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tamara Šmidlehner
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
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29
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Khoo KK, Galleano I, Gasparri F, Wieneke R, Harms H, Poulsen MH, Chua HC, Wulf M, Tampé R, Pless SA. Chemical modification of proteins by insertion of synthetic peptides using tandem protein trans-splicing. Nat Commun 2020; 11:2284. [PMID: 32385250 PMCID: PMC7210297 DOI: 10.1038/s41467-020-16208-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/20/2020] [Indexed: 12/20/2022] Open
Abstract
Manipulation of proteins by chemical modification is a powerful way to decipher their function. However, most ribosome-dependent and semi-synthetic methods have limitations in the number and type of modifications that can be introduced, especially in live cells. Here, we present an approach to incorporate single or multiple post-translational modifications or non-canonical amino acids into proteins expressed in eukaryotic cells. We insert synthetic peptides into GFP, NaV1.5 and P2X2 receptors via tandem protein trans-splicing using two orthogonal split intein pairs and validate our approach by investigating protein function. We anticipate the approach will overcome some drawbacks of existing protein enigineering methods.
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Affiliation(s)
- K K Khoo
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - I Galleano
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - F Gasparri
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - R Wieneke
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Strasse 9, 60438, Frankfurt/Main, Germany
| | - H Harms
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - M H Poulsen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - H C Chua
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - M Wulf
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - R Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Strasse 9, 60438, Frankfurt/Main, Germany
| | - S A Pless
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark.
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Pinto F, Thornton EL, Wang B. An expanded library of orthogonal split inteins enables modular multi-peptide assemblies. Nat Commun 2020; 11:1529. [PMID: 32251274 PMCID: PMC7090010 DOI: 10.1038/s41467-020-15272-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/26/2020] [Indexed: 01/03/2023] Open
Abstract
Inteins are protein segments capable of joining adjacent residues via a peptide bond. In this process known as protein splicing, the intein itself is not present in the final sequence, thus achieving scarless peptide ligation. Here, we assess the splicing activity of 34 inteins (both uncharacterized and known) using a rapid split fluorescent reporter characterization platform, and establish a library of 15 mutually orthogonal split inteins for in vivo applications, 10 of which can be simultaneously used in vitro. We show that orthogonal split inteins can be coupled to multiple split transcription factors to implement complex logic circuits in living organisms, and that they can also be used for the in vitro seamless assembly of large repetitive proteins with biotechnological relevance. Our work demonstrates the versatility and vast potential of an expanded library of orthogonal split inteins for their use in the fields of synthetic biology and protein engineering.
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Affiliation(s)
- Filipe Pinto
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Ella Lucille Thornton
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK.
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31
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Affiliation(s)
- Ignacio Insua
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - Javier Montenegro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain
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