51
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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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52
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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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53
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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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54
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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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55
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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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56
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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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57
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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: 3] [Impact Index Per Article: 3.0] [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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58
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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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59
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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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60
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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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61
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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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62
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Liu M, Yang M, Wan X, Tang Z, Jiang L, Wang S. From Nanoscopic to Macroscopic Materials by Stimuli-Responsive Nanoparticle Aggregation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2208995. [PMID: 36409139 DOI: 10.1002/adma.202208995] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/09/2022] [Indexed: 05/19/2023]
Abstract
Stimuli-responsive nanoparticle (NP) aggregation plays an increasingly important role in regulating NP assembly into microscopic superstructures, macroscopic 2D, and 3D functional materials. Diverse external stimuli are widely used to adjust the aggregation of responsive NPs, such as light, temperature, pH, electric, and magnetic fields. Many unique structures based on responsive NPs are constructed including disordered aggregates, ordered superlattices, structural droplets, colloidosomes, and bulk solids. In this review, the strategies for NP aggregation by external stimuli, and their recent progress ranging from nanoscale aggregates, microscale superstructures to macroscale bulk materials along the length scales as well as their applications are summarized. The future opportunities and challenges for designing functional materials through NP aggregation at different length scales are also discussed.
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Affiliation(s)
- Mingqian Liu
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Man Yang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Xizi Wan
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Zhiyong Tang
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100049, P. R. China
| | - Lei Jiang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Shutao Wang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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63
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Dzuvor CKO, Shanbhag BK, Shen HH, Haritos VS, He L. An Ultrastable Self-Assembled Antibacterial Nanospears Made of Protein. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2302409. [PMID: 37120846 DOI: 10.1002/adma.202302409] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/21/2023] [Indexed: 06/15/2023]
Abstract
Protein-based nanomaterials have broad applications in the biomedical and bionanotechnological sectors owing to their outstanding properties such as high biocompatibility and biodegradability, structural stability, sophisticated functional versatility, and being environmentally benign. They have gained considerable attention in drug delivery, cancer therapeutics, vaccines, immunotherapies, biosensing, and biocatalysis. However, so far, in the battle against the increasing reports of antibiotic resistance and emerging drug-resistant bacteria, unique nanostructures of this kind are lacking, hindering their potential next-generation antibacterial agents. Here, the discovery of a class of supramolecular nanostructures with well-defined shapes, geometries, or architectures (termed "protein nanospears") based on engineered proteins, exhibiting exceptional broad-spectrum antibacterial activities, is reported. The protein nanospears are engineered via spontaneous cleavage-dependent or precisely tunable self-assembly routes using mild metal salt-ions (Mg2+ , Ca2+ , Na+ ) as a molecular trigger. The nanospears' dimensions collectively range from entire nano- to micrometer scale. The protein nanospears display exceptional thermal and chemical stability yet rapidly disassemble upon exposure to high concentrations of chaotropes (>1 mm sodium dodecyl sulfate (SDS)). Using a combination of biological assays and electron microscopy imaging, it is revealed that the nanospears spontaneously induce rapid and irreparable damage to bacterial morphology via a unique action mechanism provided by their nanostructure and enzymatic action, a feat inaccessible to traditional antibiotics. These protein-based nanospears show promise as a potent tool to combat the growing threats of resistant bacteria, inspiring a new way to engineer other antibacterial protein nanomaterials with diverse structural and dimensional architectures and functional properties.
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Affiliation(s)
- Christian K O Dzuvor
- Department of Chemical and Biological Engineering Monash University Clayton, Victoria, 3800, Australia
| | - Bhuvana K Shanbhag
- Department of Chemical and Biological Engineering Monash University Clayton, Victoria, 3800, Australia
| | - Hsin-Hui Shen
- Department of Chemical and Biological Engineering Monash University Clayton, Victoria, 3800, Australia
| | - Victoria S Haritos
- Department of Chemical and Biological Engineering Monash University Clayton, Victoria, 3800, Australia
| | - Lizhong He
- Department of Chemical and Biological Engineering Monash University Clayton, Victoria, 3800, Australia
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64
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D'Alonzo D, De Fenza M, Pavone V, Lombardi A, Nastri F. Selective Oxidation of Halophenols Catalyzed by an Artificial Miniaturized Peroxidase. Int J Mol Sci 2023; 24:ijms24098058. [PMID: 37175773 PMCID: PMC10178546 DOI: 10.3390/ijms24098058] [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: 03/27/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
The development of artificial enzymes for application in sustainable technologies, such as the transformation of environmental pollutants or biomass, is one of the most challenging goals in metalloenzyme design. In this work, we describe the oxidation of mono-, di-, tri- and penta-halogenated phenols catalyzed by the artificial metalloenzyme Fe-MC6*a. It promoted the dehalogenation of 4-fluorophenol into the corresponding 1,4-benzoquinone, while under the same experimental conditions, 4-chloro, 4-bromo and 4-iodophenol were selectively converted into higher molecular weight compounds. Analysis of the 4-chlorophenol oxidation products clarified that oligomers based on C-O bonds were exclusively formed in this case. All results show that Fe-MC6*a holds intriguing enzymatic properties, as it catalyzes halophenol oxidation with substrate-dependent chemoselectivity.
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Affiliation(s)
- Daniele D'Alonzo
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
| | - Maria De Fenza
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
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65
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Xiao T, Zhou Y. A cavity formation energy formula for hard spheres in simple electrolyte solutions. Phys Chem Chem Phys 2023; 25:13080-13087. [PMID: 37115098 DOI: 10.1039/d3cp00623a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
A formula for cavity formation energy of a hard sphere in restricted primitive electrolyte solutions is derived based on the integral equation theory. Specifically, the contact values of radial distribution functions between the hard sphere and the ionic species, determined analytically from the first-order mean spherical approximation theory, are used to evaluate the cavity formation energy. In the large solute-size limit, the scaling relation of the cavity formation energy further leads to an analytical expression for the surface tension of the electrolyte solution near a curved interface. Our theory is applied to hard spheres immersed in restricted primitive electrolyte solutions, where the good agreement of the cavity formation energy with the hyper-netted chain theory demonstrates the accuracy of our theory.
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Affiliation(s)
- Tiejun Xiao
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, Guiyang 550018, People's Republic of China.
| | - Yun Zhou
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, Guiyang 550018, People's Republic of China.
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66
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Lutz ID, Wang S, Norn C, Courbet A, Borst AJ, Zhao YT, Dosey A, Cao L, Xu J, Leaf EM, Treichel C, Litvicov P, Li Z, Goodson AD, Rivera-Sánchez P, Bratovianu AM, Baek M, King NP, Ruohola-Baker H, Baker D. Top-down design of protein architectures with reinforcement learning. Science 2023; 380:266-273. [PMID: 37079676 DOI: 10.1126/science.adf6591] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 03/21/2023] [Indexed: 04/22/2023]
Abstract
As a result of evolutionary selection, the subunits of naturally occurring protein assemblies often fit together with substantial shape complementarity to generate architectures optimal for function in a manner not achievable by current design approaches. We describe a "top-down" reinforcement learning-based design approach that solves this problem using Monte Carlo tree search to sample protein conformers in the context of an overall architecture and specified functional constraints. Cryo-electron microscopy structures of the designed disk-shaped nanopores and ultracompact icosahedra are very close to the computational models. The icosohedra enable very-high-density display of immunogens and signaling molecules, which potentiates vaccine response and angiogenesis induction. Our approach enables the top-down design of complex protein nanomaterials with desired system properties and demonstrates the power of reinforcement learning in protein design.
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Affiliation(s)
- Isaac D Lutz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, 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
| | - Christoffer Norn
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- BioInnovation Institute, DK2200 Copenhagen N, Denmark
| | - Alexis Courbet
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, 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
| | - Yan Ting Zhao
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Oral Health Sciences, University of Washington, Seattle, WA, USA
| | - Annie Dosey
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Jinwei Xu
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Elizabeth M Leaf
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Catherine Treichel
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Patrisia Litvicov
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Zhe Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alexander D Goodson
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | | | - Minkyung Baek
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Oral Health Sciences, 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
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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67
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Pinto DEP, Šulc P, Sciortino F, Russo J. Design strategies for the self-assembly of polyhedral shells. Proc Natl Acad Sci U S A 2023; 120:e2219458120. [PMID: 37040398 PMCID: PMC10120017 DOI: 10.1073/pnas.2219458120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/16/2023] [Indexed: 04/12/2023] Open
Abstract
The control over the self-assembly of complex structures is a long-standing challenge of material science, especially at the colloidal scale, as the desired assembly pathway is often kinetically derailed by the formation of amorphous aggregates. Here, we investigate in detail the problem of the self-assembly of the three Archimedean shells with five contact points per vertex, i.e., the icosahedron, the snub cube, and the snub dodecahedron. We use patchy particles with five interaction sites (or patches) as model for the building blocks and recast the assembly problem as a Boolean satisfiability problem (SAT) for the patch-patch interactions. This allows us to find effective designs for all targets and to selectively suppress unwanted structures. By tuning the geometrical arrangement and the specific interactions of the patches, we demonstrate that lowering the symmetry of the building blocks reduces the number of competing structures, which in turn can considerably increase the yield of the target structure. These results cement SAT-assembly as an invaluable tool to solve inverse design problems.
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Affiliation(s)
- Diogo E. P. Pinto
- Dipartimento di Fisica, Sapienza Università di Roma, Rome00185, Italy
| | - Petr Šulc
- Life and Medical Sciences (LIMES), University of Bonn, Bonn53121, Germany
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ85281
| | | | - John Russo
- Dipartimento di Fisica, Sapienza Università di Roma, Rome00185, Italy
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68
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Zhou S, Wei Y. Kaleidoscope megamolecules synthesis and application using self-assembly technology. Biotechnol Adv 2023; 65:108147. [PMID: 37023967 DOI: 10.1016/j.biotechadv.2023.108147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 02/20/2023] [Accepted: 04/02/2023] [Indexed: 04/08/2023]
Abstract
The megamolecules with high ordered structures play an important role in chemical biology and biomedical engineering. Self-assembly, a long-discovered but very appealing technique, could induce many reactions between biomacromolecules and organic linking molecules, such as an enzyme domain and its covalent inhibitors. Enzyme and its small-molecule inhibitors have achieved many successes in medical application, which realize the catalysis process and theranostic function. By employing the protein engineering technology, the building blocks of enzyme fusion protein and small molecule linker can be assembled into a novel architecture with the specified organization and conformation. Molecular level recognition of enzyme domain could provide both covalent reaction sites and structural skeleton for the functional fusion protein. In this review, we will discuss the range of tools available to combine functional domains by using the recombinant protein technology, which can assemble them into precisely specified architectures/valences and develop the kaleidoscope megamolecules for catalytic and medical application.
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Affiliation(s)
- Shengwang Zhou
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China.
| | - Yuan Wei
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China
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69
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Bohlin J, Turberfield AJ, Louis AA, Šulc P. Designing the Self-Assembly of Arbitrary Shapes Using Minimal Complexity Building Blocks. ACS NANO 2023; 17:5387-5398. [PMID: 36763807 DOI: 10.1021/acsnano.2c09677] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The design space for self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. We develop a pipeline to explore the design spaces for a set of structures of various sizes and complexities. To understand the implications of the different solutions, we analyze their assembly dynamics using patchy particle simulations and study the influence of the number of distinct building blocks, and the angular and spatial tolerances on their interactions, on the kinetics and yield of the target assembly. We show that the resource-saving solution with a minimum number of distinct blocks can often assemble just as well (or faster) than designs where each building block is unique. We further use our methods to design multifarious structures, where building blocks are shared between different target structures. Finally, we use coarse-grained DNA simulations to investigate the realization of multicomponent shapes using DNA nanostructures as building blocks.
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Affiliation(s)
- Joakim Bohlin
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, U.K
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA
| | - Andrew J Turberfield
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, U.K
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Keble Road, Oxford OX1 3NP, U.K
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA
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70
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Moreaud L, Viollet S, Urvoas A, Valerio-Lepiniec M, Mesneau A, Li de la Sierra-Gallay I, Miller J, Ouldali M, Marcelot C, Balor S, Soldan V, Meriadec C, Artzner F, Dujardin E, Minard P. Design, synthesis, and characterization of protein origami based on self-assembly of a brick and staple artificial protein pair. Proc Natl Acad Sci U S A 2023; 120:e2218428120. [PMID: 36893280 PMCID: PMC10089216 DOI: 10.1073/pnas.2218428120] [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: 10/28/2022] [Accepted: 02/03/2023] [Indexed: 03/11/2023] Open
Abstract
A versatile strategy to create an inducible protein assembly with predefined geometry is demonstrated. The assembly is triggered by a binding protein that staples two identical protein bricks together in a predictable spatial conformation. The brick and staple proteins are designed for mutual directional affinity and engineered by directed evolution from a synthetic modular repeat protein library. As a proof of concept, this article reports on the spontaneous, extremely fast and quantitative self-assembly of two designed alpha-repeat (αRep) brick and staple proteins into macroscopic tubular superhelices at room temperature. Small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM with staining agent and cryoTEM) elucidate the resulting superhelical arrangement that precisely matches the a priori intended 3D assembly. The highly ordered, macroscopic biomolecular construction sustains temperatures as high as 75 °C thanks to the robust αRep building blocks. Since the α-helices of the brick and staple proteins are highly programmable, their design allows encoding the geometry and chemical surfaces of the final supramolecular protein architecture. This work opens routes toward the design and fabrication of multiscale protein origami with arbitrarily programmed shapes and chemical functions.
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Affiliation(s)
- Laureen Moreaud
- Centre d’Elaboration des Matériaux et d’Etudes Structurales, CNRS UPR8011F-31055, Toulouse, France
| | - Sébastien Viollet
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Agathe Urvoas
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Marie Valerio-Lepiniec
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Agnès Mesneau
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Inès Li de la Sierra-Gallay
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Jessalyn Miller
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
- Department of Chemistry, Emory University, Atlanta, GA30322
| | - Malika Ouldali
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Cécile Marcelot
- Centre d’Elaboration des Matériaux et d’Etudes Structurales, CNRS UPR8011F-31055, Toulouse, France
| | - Stéphanie Balor
- Microscopie Electronique Intégrative Toulouse, Centre de Biologie Intégrative, Université de Toulouse, CNRS, 31062, Toulouse, France
| | - Vanessa Soldan
- Microscopie Electronique Intégrative Toulouse, Centre de Biologie Intégrative, Université de Toulouse, CNRS, 31062, Toulouse, France
| | - Cristelle Meriadec
- Institut de Physique de Rennes, CNRS, UMR6251, Université de Rennes 1F-35042, Rennes, France
| | - Franck Artzner
- Institut de Physique de Rennes, CNRS, UMR6251, Université de Rennes 1F-35042, Rennes, France
| | - Erik Dujardin
- Centre d’Elaboration des Matériaux et d’Etudes Structurales, CNRS UPR8011F-31055, Toulouse, France
- Laboratoire Interdisciplinaire Carnot de Bourgogne, CNRS, UMR6303, Université de Bourgogne Franche-Comté21000, Dijon, France
| | - Philippe Minard
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
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71
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Wu Y, Huang J, He H, Wang M, Yin G, Qi L, He X, Wang HH, Wang K. Logic Nanodevice-Mediated Receptor Assembly for Nongenetic Regulation of Cell Behavior in Tumor-like Microenvironment. NANO LETTERS 2023; 23:1801-1809. [PMID: 36826373 DOI: 10.1021/acs.nanolett.2c04657] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The reprogramming of cell signaling and behavior through the artificial control of cell surface receptor oligomerization shows great promise in biomedical research and cell-based therapy. However, it remains challenging to achieve combinatorial recognition in a complicated environment and logical regulation of receptors for desirable cellular behavior. Herein, we develop a logic-gated DNA nanodevice with responsiveness to multiple environmental inputs for logically controlled assembly of heterogeneous receptors to modulate signaling. The "AND" gate nanodevice uses an i-motif and an ATP-binding aptamer as environmental cue-responsive units, which can successfully implement a logic operation to manipulate receptors on the cell surface. In the presence of both protons and ATP, the DNA nanodevice is activated to selectively assemble MET and CD71, which modulate the HGF/MET signaling, resulting in cytoskeletal reorganization to inhibit cancer cell motility in a tumor-like microenvironment. Our strategy would be highly promising for precision therapeutics, including controlled drug release and cancer treatment.
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Affiliation(s)
- Yuchen Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Hui He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Meixia Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Guanyu Yin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Lanlin Qi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Hong-Hui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
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72
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Komar AA. Molecular Peptide Grafting as a Tool to Create Novel Protein Therapeutics. Molecules 2023; 28:2383. [PMID: 36903628 PMCID: PMC10005171 DOI: 10.3390/molecules28052383] [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: 02/11/2023] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
The study of peptides (synthetic or corresponding to discrete regions of proteins) has facilitated the understanding of protein structure-activity relationships. Short peptides can also be used as powerful therapeutic agents. However, the functional activity of many short peptides is usually substantially lower than that of their parental proteins. This is (as a rule) due to their diminished structural organization, stability, and solubility often leading to an enhanced propensity for aggregation. Several approaches have emerged to overcome these limitations, which are aimed at imposing structural constraints into the backbone and/or sidechains of the therapeutic peptides (such as molecular stapling, peptide backbone circularization and molecular grafting), therefore enforcing their biologically active conformation and thus improving their solubility, stability, and functional activity. This review provides a short summary of approaches aimed at enhancing the biological activity of short functional peptides with a particular focus on the peptide grafting approach, whereby a functional peptide is inserted into a scaffold molecule. Intra-backbone insertions of short therapeutic peptides into scaffold proteins have been shown to enhance their activity and render them a more stable and biologically active conformation.
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Affiliation(s)
- Anton A. Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA; ; Tel.: +1-216-687-2516
- Department of Biochemistry and Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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73
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Liu R, Li L, Chen S, Yang Z, Kochovski Z, Mei S, Lu Y, Zhang L, Chen G. Evolution of Protein Assemblies Driven by the Switching of Interplay Mode. ACS NANO 2023; 17:2245-2256. [PMID: 36648413 DOI: 10.1021/acsnano.2c08583] [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: 06/17/2023]
Abstract
A protein assembly with the ability to switch interplay modes of multiple driving forces has been achieved. Although biomolecular systems driven by multiple driving forces have been exploited, work on such a protein assembly capable of switching the interplay modes at nanoscale has been rarely reported so far as a result of their great fabrication challenge. In this work, two sets of driving forces such as ligand-ligand interaction and protein-protein interaction were leveraged to antagonistically underpin the multilayered stackings and trigger the hollow evolution to afford the well-defined hollow rectangular frame of proteins. While these protein frames further collapsed into aggregates, the ligand-ligand interactions were weakened, and the interplay of two sets of driving forces thereby tended to switch into synergistic mode, converting the protein packing mode from porously loose packing to axially dense packing and thus giving rise to a morphological evolution toward a nanosized protein tube. This strategy not only provides a nanoscale understanding on the mechanism underlying the switch of interplay modes in the context of biomacromolecules but also may provide access for diverse sophisticated biomacromolecular nanostructures that are historically inaccessible for conventional self-assembly strategies.
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Affiliation(s)
- Rongying Liu
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Long Li
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Shuyu Chen
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zdravko Kochovski
- Department for Electrochemical Energy Storage, Helmholtz-Zentrum Berlin für Materialien und Energie, 14109 Berlin, Germany
| | - Shilin Mei
- Department for Electrochemical Energy Storage, Helmholtz-Zentrum Berlin für Materialien und Energie, 14109 Berlin, Germany
| | - Yan Lu
- Department for Electrochemical Energy Storage, Helmholtz-Zentrum Berlin für Materialien und Energie, 14109 Berlin, Germany
- Institute of Chemistry, University of Potsdam, 14467 Potsdam, Germany
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200433, China
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74
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Kikuchi K, Date K, Ueno T. Design of a Hierarchical Assembly at a Solid-Liquid Interface Using an Asymmetric Protein Needle. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:2389-2397. [PMID: 36734675 DOI: 10.1021/acs.langmuir.2c03146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Design and control of processes for a hierarchical assembly of proteins remain challenging because it requires consideration of design principles with atomic-level accuracy. Previous studies have adopted symmetry-based strategies to minimize the complexity of protein-protein interactions and this has placed constraints on the structures of the resulting protein assemblies. In the present work, we used an anisotropic-shaped protein needle, gene product 5 (gp5) from bacteriophage T4 with a C-terminal hexahistidine-tag (His-tag) (gp5_CHis), to construct a hierarchical assembly with two distinct protein-protein interaction sites. High-speed atomic force microscopy (HS-AFM) measurements reveal that it forms unique tetrameric clusters through its N-terminal head on a mica surface. The clusters further self-assemble into a monolayer through the C-terminal His-tag. The HS-AFM images and displacement analyses show that the monolayer is a network-like structure rather than a crystalline lattice. Our results expand the toolbox for constructing hierarchical protein assemblies based on structural anisotropy.
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Affiliation(s)
- Kosuke Kikuchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B-55, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Koki Date
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B-55, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B-55, Nagatsuta-cho, 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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75
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A modular platform for the precise assembly of molecular frameworks composed of ion pairs. Chem 2023. [DOI: 10.1016/j.chempr.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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76
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Zhao H, Xu C, Wang T, Liu J. Biomimetic Construction of Artificial Selenoenzymes. Biomimetics (Basel) 2023; 8:biomimetics8010054. [PMID: 36810385 PMCID: PMC9944854 DOI: 10.3390/biomimetics8010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Selenium exists in the form of selenocysteines in selenoproteins and plays a pivotal role in the catalytic process of the antioxidative enzymes. In order to study the structural and functional properties of selenium in selenoproteins, explore the significance of the role of selenium in the fields of biology and chemistry, scientists conducted a series of artificial simulations on selenoproteins. In this review, we sum up the progress and developed strategies in the construction of artificial selenoenzyme. Using different mechanisms from different catalytic angles, selenium-containing catalytic antibodies, semi-synthetic selenonezyme, and the selenium-containing molecularly imprinted enzymes have been constructed. A variety of synthetic selenoenzyme models have been designed and constructed by selecting host molecules such as cyclodextrins, dendrimers, and hyperbranched polymers as the main scaffolds. Then, a variety of selenoprotein assemblies as well as cascade antioxidant nanoenzymes were built by using electrostatic interaction, metal coordination, and host-guest interaction. The unique redox properties of selenoenzyme glutathione peroxidase (GPx) can be reproduced.
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77
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Alberstein RG, Prelesnik JL, Nakouzi E, Zhang S, De Yoreo JJ, Pfaendtner J, Tezcan FA, Mundy CJ. Discrete Orientations of Interfacial Waters Direct Crystallization of Mica-Binding Proteins. J Phys Chem Lett 2023; 14:80-87. [PMID: 36573690 DOI: 10.1021/acs.jpclett.2c02948] [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: 06/17/2023]
Abstract
Understanding the basis of templated molecular assembly on a solid surface requires a fundamental comprehension of both short- and long-range aqueous response to the surface under a variety of solution conditions. Herein we provide a detailed picture of how the molecular-scale response to different mica surfaces yields distinct solvent orientations that produce quasi-static directional potentials onto which macromolecules can adsorb. We connect this directionality to observed (a)symmetric epitaxial alignment of designed proteins onto these surfaces, corroborate our findings with 3D atomic force microscopy experiments, and identify slight differences in surface structure as the origin of this effect. Our work provides a detailed picture of the intrinsic electrolyte response in the vicinity of mineral interfaces, with clear predictions for experiment, and highlights the role of solvent on the predictive assembly of hierarchical materials on mineral surfaces.
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Affiliation(s)
- Robert G Alberstein
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Jesse L Prelesnik
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Elias Nakouzi
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Shuai Zhang
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - James J De Yoreo
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Christopher J Mundy
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
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78
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Pirro F, La Gatta S, Arrigoni F, Famulari A, Maglio O, Del Vecchio P, Chiesa M, De Gioia L, Bertini L, Chino M, Nastri F, Lombardi A. A De Novo-Designed Type 3 Copper Protein Tunes Catechol Substrate Recognition and Reactivity. Angew Chem Int Ed Engl 2023; 62:e202211552. [PMID: 36334012 DOI: 10.1002/anie.202211552] [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: 08/05/2022] [Indexed: 11/07/2022]
Abstract
De novo metalloprotein design is a remarkable approach to shape protein scaffolds toward specific functions. Here, we report the design and characterization of Due Rame 1 (DR1), a de novo designed protein housing a di-copper site and mimicking the Type 3 (T3) copper-containing polyphenol oxidases (PPOs). To achieve this goal, we hierarchically designed the first and the second di-metal coordination spheres to engineer the di-copper site into a simple four-helix bundle scaffold. Spectroscopic, thermodynamic, and functional characterization revealed that DR1 recapitulates the T3 copper site, supporting different copper redox states, and being active in the O2 -dependent oxidation of catechols to o-quinones. Careful design of the residues lining the substrate access site endows DR1 with substrate recognition, as revealed by Hammet analysis and computational studies on substituted catechols. This study represents a premier example in the construction of a functional T3 copper site into a designed four-helix bundle protein.
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Affiliation(s)
- Fabio Pirro
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Salvatore La Gatta
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Antonino Famulari
- Department of Chemistry, University of Torino, Via Giuria 9, 10125, Torino, Italy.,Department of Condensed Matter Physics, University of of Zaragoza, Calle Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy.,Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), Via Pietro Castellino 111, 80131, Napoli, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Mario Chiesa
- Department of Chemistry, University of Torino, Via Giuria 9, 10125, Torino, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Luca Bertini
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
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79
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Ma J, Jin B, Guye KN, Chowdhury ME, Naser NY, Chen CL, De Yoreo JJ, Baneyx F. Controlling Mineralization with Protein-Functionalized Peptoid Nanotubes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207543. [PMID: 36281797 DOI: 10.1002/adma.202207543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Sequence-defined foldamers that self-assemble into well-defined architectures are promising scaffolds to template inorganic mineralization. However, it has been challenging to achieve robust control of nucleation and growth without sequence redesign or extensive experimentation. Here, peptoid nanotubes functionalized with a panel of solid-binding proteins are used to mineralize homogeneously distributed and monodisperse anatase nanocrystals from the water-soluble TiBALDH precursor. Crystallite size is systematically tuned between 1.4 and 4.4 nm by changing protein coverage and the identity and valency of the genetically engineered solid-binding segments. The approach is extended to the synthesis of gold nanoparticles and, using a protein encoding both material-binding specificities, to the fabrication of titania/gold nanocomposites capable of photocatalysis under visible-light illumination. Beyond uncovering critical roles for hierarchical organization and denticity on solid-binding protein mineralization outcomes, the strategy described herein should prove valuable for the fabrication of hierarchical hybrid materials incorporating a broad range of inorganic components.
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Affiliation(s)
- Jinrong Ma
- Molecular Engineering and Science Institute, University of Washington, Seattle, WA, 98115, USA
| | - Biao Jin
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Kathryn N Guye
- Department of Chemistry, University of Washington, Seattle, WA, 98115, USA
| | - Md Emtias Chowdhury
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Nada Y Naser
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98115, USA
| | - Chun-Long Chen
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98115, USA
| | - James J De Yoreo
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98115, USA
| | - François Baneyx
- Molecular Engineering and Science Institute, University of Washington, Seattle, WA, 98115, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98115, USA
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80
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Ji Z, Huo H, Duan L, Wang S. Design of robust malate dehydrogenases by assembly of motifs of halophilic and thermophilic enzyme based on interaction network. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2022.108758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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81
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Shao L, Ma J, Prelesnik JL, Zhou Y, Nguyen M, Zhao M, Jenekhe SA, Kalinin SV, Ferguson AL, Pfaendtner J, Mundy CJ, De Yoreo JJ, Baneyx F, Chen CL. Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction. Chem Rev 2022; 122:17397-17478. [PMID: 36260695 DOI: 10.1021/acs.chemrev.2c00220] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature. Because hierarchy gives rise to unique properties and functions, many have sought inspiration from nature when designing and fabricating hierarchical matter. More and more, however, nature's own high-information content building blocks, proteins, peptides, and peptidomimetics, are being coopted to build hierarchy because the information that determines structure, function, and interfacial interactions can be readily encoded in these versatile macromolecules. Here, we take stock of recent progress in the rational design and characterization of hierarchical materials produced from high-information content blocks with a focus on stimuli-responsive and "smart" architectures. We also review advances in the use of computational simulations and data-driven predictions to shed light on how the side chain chemistry and conformational flexibility of macromolecular blocks drive the emergence of order and the acquisition of hierarchy and also on how ionic, solvent, and surface effects influence the outcomes of assembly. Continued progress in the above areas will ultimately usher in an era where an understanding of designed interactions, surface effects, and solution conditions can be harnessed to achieve predictive materials synthesis across scale and drive emergent phenomena in the self-assembly and reconfiguration of high-information content building blocks.
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Affiliation(s)
- Li Shao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jinrong Ma
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States
| | - Jesse L Prelesnik
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yicheng Zhou
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Mary Nguyen
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mingfei Zhao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Samson A Jenekhe
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Sergei V Kalinin
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Jim Pfaendtner
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Christopher J Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - François Baneyx
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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82
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Nguyen HD, Do LH. Taming glutathione potentiates metallodrug action. Curr Opin Chem Biol 2022; 71:102213. [PMID: 36206677 PMCID: PMC9759795 DOI: 10.1016/j.cbpa.2022.102213] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 01/27/2023]
Abstract
Metallodrugs that are redox sensitive or have labile coordination sites are particularly susceptible to inhibition by glutathione (GSH) and other endogenous thiols. Because GSH is an essential antioxidant, strategies to prevent thiol deactivation must consider their potential effects on normal cellular functions. In this short review, we describe general approaches for taming glutathione in metallodrug therapy and discuss their strengths and limitations. We also offer our perspectives on developing practical solutions that are effective and clinically relevant.
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83
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Winegar PH, Figg CA, Teplensky MH, Ramani N, Mirkin CA. Modular Nucleic Acid Scaffolds for Synthesizing Monodisperse and Sequence-Encoded Antibody Oligomers. Chem 2022; 8:3018-3030. [PMID: 36405374 PMCID: PMC9674055 DOI: 10.1016/j.chempr.2022.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Synthesizing protein oligomers that contain exact numbers of multiple different proteins in defined architectures is challenging. DNA-DNA interactions can be used to program protein assembly into oligomers; however, existing methods require changes to DNA design to achieve different numbers and oligomeric sequences of proteins. Herein, we develop a modular DNA scaffold that uses only six synthetic oligonucleotides to organize proteins into defined oligomers. As a proof-of-concept, model proteins (antibodies) are oligomerized into dimers and trimers, where antibody function is retained. Illustrating the modularity of this technique, dimer and trimer building blocks are then assembled into pentamers containing three different antibodies in an exact stoichiometry and oligomeric sequence. In sum, this report describes a generalizable method for organizing proteins into monodisperse, sequence-encoded oligomers using DNA. This advance will enable studies into how oligomeric protein sequences affect material properties in areas spanning pharmaceutical development, cascade catalysis, synthetic photosynthesis, and membrane transport.
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Affiliation(s)
- Peter H. Winegar
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- These authors contributed equally
| | - C. Adrian Figg
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- These authors contributed equally
| | - Michelle H. Teplensky
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Namrata Ramani
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Chad A. Mirkin
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Lead contact
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84
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Kriebisch BAK, Kriebisch CME, Bergmann AM, Wanzke C, Tena‐Solsona M, Boekhoven J. Tuning the Kinetic Trapping in Chemically Fueled Self‐Assembly**. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202200035] [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)
- Brigitte A. K. Kriebisch
- School of Natural Science Department of Chemistry Technische Universität München Lichtenbergstraße 4 85748 Garching bei München Germany
| | - Christine M. E. Kriebisch
- School of Natural Science Department of Chemistry Technische Universität München Lichtenbergstraße 4 85748 Garching bei München Germany
| | - Alexander M. Bergmann
- School of Natural Science Department of Chemistry Technische Universität München Lichtenbergstraße 4 85748 Garching bei München Germany
| | - Caren Wanzke
- School of Natural Science Department of Chemistry Technische Universität München Lichtenbergstraße 4 85748 Garching bei München Germany
| | - Marta Tena‐Solsona
- School of Natural Science Department of Chemistry Technische Universität München Lichtenbergstraße 4 85748 Garching bei München Germany
| | - Job Boekhoven
- School of Natural Science Department of Chemistry Technische Universität München Lichtenbergstraße 4 85748 Garching bei München Germany
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85
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Wang J, Wicher B, Maurizot V, Huc I. Directing the Self-Assembly of Aromatic Foldamer Helices using Acridine Appendages and Metal Coordination. Chemistry 2022; 28:e202201345. [PMID: 35965255 PMCID: PMC9826129 DOI: 10.1002/chem.202201345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Indexed: 01/11/2023]
Abstract
Folded molecules provide complex interaction interfaces amenable to sophisticated self-assembly motifs. Because of their high conformational stability, aromatic foldamers constitute suitable candidates for the rational elaboration of self-assembled architectures. Several multiturn helical aromatic oligoamides have been synthesized that possess arrays of acridine appendages pointing in one or two directions. The acridine units were shown to direct self-assembly in the solid state via aromatic stacking leading to recurrent helix-helix association patterns under the form of discrete dimers or extended arrays. In the presence of Pd(II), metal coordination of the acridine units overwhelms other forces and generates new metal-mediated multihelical self-assemblies, including macrocycles. These observations demonstrate simple access to different types of foldamer-containing architectures, ranging from discrete objects to 1D and, by extension, 2D and 3D arrays.
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Affiliation(s)
- Jinhua Wang
- CBMN (UMR5248)Univ. Bordeaux – CNRS – IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
| | - Barbara Wicher
- Department of Chemical Technology of DrugsPoznan University of Medical SciencesGrunwaldzka 660-780PoznanPoland
| | - Victor Maurizot
- CBMN (UMR5248)Univ. Bordeaux – CNRS – IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
| | - Ivan Huc
- CBMN (UMR5248)Univ. Bordeaux – CNRS – IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
- Department of PharmacyLudwig-Maximilians-UniversitätButenandtstrasse 5–1381377MünchenGermany
- Cluster of Excellence e-conversion85748GarchingGermany
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86
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Lee J, Yang M, Song WJ. The expanded landscape of metalloproteins by genetic incorporation of noncanonical amino acids. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jaehee Lee
- Department of Chemistry Seoul National University Seoul South Korea
| | - Minwoo Yang
- Department of Chemistry Seoul National University Seoul South Korea
| | - Woon Ju Song
- Department of Chemistry Seoul National University Seoul South Korea
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87
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Choi TS, Tezcan FA. Design of a Flexible, Zn-Selective Protein Scaffold that Displays Anti-Irving-Williams Behavior. J Am Chem Soc 2022; 144:18090-18100. [PMID: 36154053 PMCID: PMC9949983 DOI: 10.1021/jacs.2c08050] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Selective metal binding is a key requirement not only for the functions of natural metalloproteins but also for the potential applications of artificial metalloproteins in heterogeneous environments such as cells and environmental samples. The selection of transition-metal ions through protein design can, in principle, be achieved through the appropriate choice and the precise positioning of amino acids that comprise the primary metal coordination sphere. However, this task is made difficult by the intrinsic flexibility of proteins and the fact that protein design approaches generally lack the sub-Å precision required for the steric selection of metal ions. We recently introduced a flexible/probabilistic protein design strategy (MASCoT) that allows metal ions to search for optimal coordination geometry within a flexible, yet covalently constrained dimer interface. In an earlier proof-of-principle study, we used MASCoT to generate an artificial metalloprotein dimer, (AB)2, which selectively bound CoII and NiII over CuII (as well as other first-row transition-metal ions) through the imposition of a rigid octahedral coordination geometry, thus countering the Irving-Williams trend. In this study, we set out to redesign (AB)2 to examine the applicability of MASCoT to the selective binding of other metal ions. We report here the design and characterization of a new flexible protein dimer, B2, which displays ZnII selectivity over all other tested metal ions including CuII both in vitro and in cellulo. Selective, anti-Irving-Williams ZnII binding by B2 is achieved through the formation of a unique trinuclear Zn coordination motif in which His and Glu residues are rigidly placed in a tetrahedral geometry. These results highlight the utility of protein flexibility in the design and discovery of selective binding motifs.
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88
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Jacobs M, Bansal P, Shukla D, Schroeder CM. Understanding Supramolecular Assembly of Supercharged Proteins. ACS CENTRAL SCIENCE 2022; 8:1350-1361. [PMID: 36188338 PMCID: PMC9523778 DOI: 10.1021/acscentsci.2c00730] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Indexed: 06/16/2023]
Abstract
Ordered supramolecular assemblies have recently been created using electrostatic interactions between oppositely charged proteins. Despite recent progress, the fundamental mechanisms governing the assembly of oppositely supercharged proteins are not fully understood. Here, we use a combination of experiments and computational modeling to systematically study the supramolecular assembly process for a series of oppositely supercharged green fluorescent protein variants. We show that net charge is a sufficient molecular descriptor to predict the interaction fate of oppositely charged proteins under a given set of solution conditions (e.g., ionic strength), but the assembled supramolecular structures critically depend on surface charge distributions. Interestingly, our results show that a large excess of charge is necessary to nucleate assembly and that charged residues not directly involved in interprotein interactions contribute to a substantial fraction (∼30%) of the interaction energy between oppositely charged proteins via long-range electrostatic interactions. Dynamic subunit exchange experiments further show that relatively small, 16-subunit assemblies of oppositely charged proteins have kinetic lifetimes on the order of ∼10-40 min, which is governed by protein composition and solution conditions. Broadly, our results inform how protein supercharging can be used to create different ordered supramolecular assemblies from a single parent protein building block.
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Affiliation(s)
- Michael
I. Jacobs
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Prateek Bansal
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Diwakar Shukla
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Charles M. Schroeder
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Materials Science and Engineering, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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89
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Matsubara S, Okamoto Y, Yoshikawa M, Tsukiji S, Higuchi M. A Peptide Nanocage Constructed by Self-Assembly of Oligoproline Conjugates. Bioconjug Chem 2022; 33:1785-1788. [PMID: 35900377 DOI: 10.1021/acs.bioconjchem.2c00290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cage-like supramolecular assemblies called molecular cages, which possess attractive functions, have been prepared. Although biomolecule-based nanocages are required for biological/medical applications such as drug delivery systems, the majority of nanocages are constructed using aromatic compounds with lower biocompatibility and biodegradability. In this study, the construction of a peptide nanocage consisting of an oligoproline conjugate is demonstrated. The conjugate was easy to prepare and had high biocompatibility. The oligoproline moiety of the conjugate had a rigid, rod-like structure suitable for the backbone of the supramolecular nanocage. The conjugates self-assembled to form peptide nanocages with a huge inner cavity.
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Affiliation(s)
- Shogo Matsubara
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Yui Okamoto
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Masaru Yoshikawa
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan.,Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Masahiro Higuchi
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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90
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An artificial metalloprotein with metal-adaptive coordination sites and Ni-dependent quercetinase activity. J Inorg Biochem 2022; 235:111914. [PMID: 35841720 DOI: 10.1016/j.jinorgbio.2022.111914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 06/20/2022] [Accepted: 07/03/2022] [Indexed: 11/23/2022]
Abstract
Engineering non-native metal active sites into proteins using canonical amino acids offers many advantages but is hampered by significant challenges. The TIM barrel protein, imidazole glycerol phosphate synthase from the hyperthermophilic organism Thermotoga maritima (tHisF), is well-suited for the construction of artificial metalloenzymes by this approach. To this end, we have generated a tHisF variant (tHisFEHH) with a Glu/His/His motif for metal ion coordination. Crystal structures of ZnII:tHisFEHH and NiII:tHisFEHH reveal that both metal ions bind to the engineered histidines. However, the two metals bind at distinct sites with different geometries, demonstrating the adaptability of tHisF. Only ZnII additionally ligates the Glu residue and adopts a tetrahedral geometry. The pseudo-octahedral NiII site comprises the two His and a native Ser residue. NiII:tHisFEHH catalyzes the oxidative cleavage of the flavanols quercetin and myricetin, providing an unprecedented example of an artificial metalloprotein with quercetinase activity.
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91
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Self-assembled asparaginase-based nanoparticles with enhanced anti-cancer efficacy and anticoagulant activity. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.128933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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92
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Kerns S, Biswas A, Minnetian NM, Borovik AS. Artificial Metalloproteins: At the Interface between Biology and Chemistry. JACS AU 2022; 2:1252-1265. [PMID: 35783165 PMCID: PMC9241007 DOI: 10.1021/jacsau.2c00102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 05/22/2023]
Abstract
Artificial metalloproteins (ArMs) have recently gained significant interest due to their potential to address issues in a broad scope of applications, including biocatalysis, biotechnology, protein assembly, and model chemistry. ArMs are assembled by the incorporation of a non-native metallocofactor into a protein scaffold. This can be achieved by a number of methods that apply tools of chemical biology, computational de novo design, and synthetic chemistry. In this Perspective, we highlight select systems in the hope of demonstrating the breadth of ArM design strategies and applications and emphasize how these systems address problems that are otherwise difficult to do so with strictly biochemical or synthetic approaches.
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Affiliation(s)
- Spencer
A. Kerns
- Department of Chemistry, University of California, 1102 Natural
Science II, Irvine, California 92797, United States
| | - Ankita Biswas
- Department of Chemistry, University of California, 1102 Natural
Science II, Irvine, California 92797, United States
| | - Natalie M. Minnetian
- Department of Chemistry, University of California, 1102 Natural
Science II, Irvine, California 92797, United States
| | - A. S. Borovik
- Department of Chemistry, University of California, 1102 Natural
Science II, Irvine, California 92797, United States
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93
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Kakkis A, Golub E, Choi TS, Tezcan FA. Redox- and metal-directed structural diversification in designed metalloprotein assemblies. Chem Commun (Camb) 2022; 58:6958-6961. [PMID: 35642584 DOI: 10.1039/d2cc02440c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we describe a designed protein building block whose self-assembly behaviour is dually gated by the redox state of disulphide bonds and the identity of exogenous metal ions. This protein construct is shown - through extensive structural and biophysical characterization - to access five distinct oligomeric states, exemplifying how the complex interplay between hydrophobic, metal-ligand, and reversible covalent interactions could be harnessed to obtain multiple, responsive protein architectures from a single building block.
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Affiliation(s)
- Albert Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Eyal Golub
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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94
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Han K, Na Y, Zhang L, Tezcan FA. Dynamic, Polymer-Integrated Crystals for Efficient, Reversible Protein Encapsulation. J Am Chem Soc 2022; 144:10139-10144. [PMID: 35666988 DOI: 10.1021/jacs.2c02584] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crystalline materials are increasingly being used as platforms for encapsulating proteins to create stable, functional materials. However, the uptake efficiencies and stimuli-responsiveness of crystalline frameworks are limited by their rigidities. We have recently reported a new form of materials, polymer-integrated crystals (PIX), which combine the structural order of protein crystals with the dynamic, stimuli-responsive properties of synthetic polymers. Here we show that the crystallinity, flexibility, and chemical tunability of PIX can be exploited to encapsulate guest proteins with high loading efficiencies (up to 46% w/w). The electrostatic host-guest interactions enable reversible, pH-controlled uptake/release of guest proteins as well as the mutual stabilization of the host and the guest, thus creating a uniquely synergistic platform toward the development of functional biomaterials and the controlled delivery of biological macromolecules.
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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
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Ling 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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95
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Precision materials: Computational design methods of accurate protein materials. Curr Opin Struct Biol 2022; 74:102367. [DOI: 10.1016/j.sbi.2022.102367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 11/23/2022]
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96
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Maity B, Taher M, Mazumdar S, Ueno T. Artificial metalloenzymes based on protein assembly. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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97
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Li X, Bai Y, Luo Q, Xu J, Chen T, Liu J. Morphological Selectivity of a Protein Self-Assembly System with a Repertoire of Diverse Interaction Modes. ACS Macro Lett 2022; 11:675-679. [PMID: 35570806 DOI: 10.1021/acsmacrolett.2c00154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multiple metal chelating sites were incorporated onto the second mitochondria-derived activator of caspase (SMAC) building blocks. The combination of different binding sites generated a repertoire of diverse binding modes, among which two different microfilament types (small and large) with distinct patterns were selected under thermodynamic control. Furthermore, the two microfilaments exhibited a pronounced secondary assembly trend due to the potential noncovalent interactions on the protein surfaces. Coupled with stereoselectivity, they presented a strong self-recognition effect and underwent two distinct reassembly patterns. That is, the large filaments self-associated in pairs to form "interlocked chain" structures, while the small ones twisted to form protein helical bundles. This work represents one of the few studies of selective self-assembly of self-assembled protein assemblies. Such an idea may provide inspiration for constructing more sophisticated protein architectures in the future.
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Affiliation(s)
- Xiumei Li
- Department of Chemistry, Jinan University, Guangzhou 510632, P. R. China
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, P. R. China
| | - Yushi Bai
- Department of Preventative and Restorative Dental Sciences, School of Dentistry, University of California, San Francisco, California 94143, United States
| | - Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Jiayun Xu
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, P. R. China
| | - Tianfeng Chen
- Department of Chemistry, Jinan University, Guangzhou 510632, P. R. China
| | - Junqiu Liu
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, P. R. China
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98
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Flood R, Ramberg KO, Mengel DB, Guagnini F, Crowley PB. Protein Frameworks with Thiacalixarene and Zinc. CRYSTAL GROWTH & DESIGN 2022; 22:3271-3276. [PMID: 35529063 PMCID: PMC9073927 DOI: 10.1021/acs.cgd.2c00108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/10/2022] [Indexed: 05/15/2023]
Abstract
Controlled protein assembly provides a means to generate biomaterials. Synthetic macrocycles such as the water-soluble sulfonato-calix[n]arenes are useful mediators of protein assembly. Sulfonato-thiacalix[4]arene (tsclx 4 ), with its metal-binding capacity, affords the potential for simultaneous macrocycle- and metal-mediated protein assembly. Here, we describe the tsclx 4 -/Zn-directed assembly of two proteins: cationic α-helical cytochrome c (cyt c) and neutral β-propeller Ralstonia solanacearum lectin (RSL). Two co-crystal forms were obtained with cyt c, each involving multinuclear zinc sites supported by the cone conformation of tsclx 4 . The tsclx 4 /Zn cluster acted as an assembly node via both lysine encapsulation and metal-mediated protein-protein contacts. In the case of RSL, tsclx 4 adopted the 1,2-alternate conformation and supported a dinuclear zinc site with concomitant encapsulation and metal-binding of two histidine side chains. These results, together with the knowledge of thiacalixarene/metal nanoclusters, suggest promising applications for thiacalixarenes in biomaterials and MOF fabrication.
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99
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Yu W, Zhang K, Zhang J, Liang X, Ge X, Ge Z, Wei C, Song W, Xu T, Wu L. Efficient lamellar two‐dimensional proton channels derived from dipole interactions in a polyelectrolyte membrane. AIChE J 2022. [DOI: 10.1002/aic.17731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Weisheng Yu
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science University of Science and Technology of China Hefei China
| | - Kaiyu Zhang
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science University of Science and Technology of China Hefei China
| | - Jianjun Zhang
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science University of Science and Technology of China Hefei China
| | - Xian Liang
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science University of Science and Technology of China Hefei China
| | - Xiaolin Ge
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science University of Science and Technology of China Hefei China
| | - Zijuan Ge
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science University of Science and Technology of China Hefei China
| | - Chengpeng Wei
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science University of Science and Technology of China Hefei China
| | - Wanjie Song
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science University of Science and Technology of China Hefei China
| | - Tongwen Xu
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science University of Science and Technology of China Hefei China
| | - Liang Wu
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science University of Science and Technology of China Hefei China
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100
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Edwardson TGW, Levasseur MD, Tetter S, Steinauer A, Hori M, Hilvert D. Protein Cages: From Fundamentals to Advanced Applications. Chem Rev 2022; 122:9145-9197. [PMID: 35394752 DOI: 10.1021/acs.chemrev.1c00877] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.
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Affiliation(s)
| | | | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Mao Hori
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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