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Arad E, Jelinek R. Catalytic physiological amyloids. Methods Enzymol 2024; 697:77-112. [PMID: 38816136 DOI: 10.1016/bs.mie.2024.01.014] [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] [Indexed: 06/01/2024]
Abstract
Amyloid fibrils have been identified in many protein systems, mostly linked to progression and cytotoxicity in neurodegenerative diseases and other pathologies, but have also been observed in normal physiological systems. A growing body of work has shown that amyloid fibrils can catalyze chemical reactions. Most studies have focused on catalysis by de-novo synthetic amyloid-like peptides; however, recent studies reveal that physiological, native amyloids are catalytic as well. Here, we discuss methodologies and major experimental aspects pertaining to physiological catalytic amyloids. We highlight analyzes of kinetic parameters related to the catalytic activities of amyloid fibrils, structure-function considerations, characterization of the catalytic active sites, and deciphering of catalytic mechanisms.
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Affiliation(s)
- Elad Arad
- Ilse Katz Institute for Nanoscale Science and Technology and the Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel; Department of Chemical Engineering, Columbia University in the City of New York, New York, NY, United States.
| | - Raz Jelinek
- Ilse Katz Institute for Nanoscale Science and Technology and the Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
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Arad E, Pedersen KB, Malka O, Mambram Kunnath S, Golan N, Aibinder P, Schiøtt B, Rapaport H, Landau M, Jelinek R. Staphylococcus aureus functional amyloids catalyze degradation of β-lactam antibiotics. Nat Commun 2023; 14:8198. [PMID: 38081813 PMCID: PMC10713593 DOI: 10.1038/s41467-023-43624-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Antibiotic resistance of bacteria is considered one of the most alarming developments in modern medicine. While varied pathways for bacteria acquiring antibiotic resistance have been identified, there still are open questions concerning the mechanisms underlying resistance. Here, we show that alpha phenol-soluble modulins (PSMαs), functional bacterial amyloids secreted by Staphylococcus aureus, catalyze hydrolysis of β-lactams, a prominent class of antibiotic compounds. Specifically, we show that PSMα2 and, particularly, PSMα3 catalyze hydrolysis of the amide-like bond of the four membered β-lactam ring of nitrocefin, an antibiotic β-lactam surrogate. Examination of the catalytic activities of several PSMα3 variants allowed mapping of the active sites on the amyloid fibrils' surface, specifically underscoring the key roles of the cross-α fibril organization, and the combined electrostatic and nucleophilic functions of the lysine arrays. Molecular dynamics simulations further illuminate the structural features of β-lactam association upon the fibril surface. Complementary experimental data underscore the generality of the functional amyloid-mediated catalytic phenomenon, demonstrating hydrolysis of clinically employed β-lactams by PSMα3 fibrils, and illustrating antibiotic degradation in actual S. aureus biofilms and live bacteria environments. Overall, this study unveils functional amyloids as catalytic agents inducing degradation of β-lactam antibiotics, underlying possible antibiotic resistance mechanisms associated with bacterial biofilms.
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Affiliation(s)
- Elad Arad
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Kasper B Pedersen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Orit Malka
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Sisira Mambram Kunnath
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Nimrod Golan
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Polina Aibinder
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Hanna Rapaport
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
- Centre for Structural Systems Biology (CSSB), and European Molecular Biology Laboratory (EMBL), Hamburg, 22607, Germany
| | - Raz Jelinek
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel.
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel.
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Abstract
Enzymes fold into three-dimensional structures to distribute amino acid residues for catalysis, which inspired the supramolecular approach to construct enzyme-mimicking catalysts. A key concern in the development of supramolecular strategies is the ability to confine and orient functional groups to form enzyme-like active sites in artificial materials. This review introduces the design principles and construction of supramolecular nanomaterials exhibiting catalytic functions of heme-dependent enzymes, a large class of metalloproteins, which rely on a heme cofactor and spatially configured residues to catalyze diverse reactions via a complex multistep mechanism. We focus on the structure-activity relationship of the supramolecular catalysts and their applications in materials synthesis/degradation, biosensing, and therapeutics. The heme-free catalysts that catalyze reactions achieved by hemeproteins are also briefly discussed. Towards the end of the review, we discuss the outlook on the challenges related to catalyst design and future prospective, including the development of structure-resolving techniques and design concepts, with the aim of creating enzyme-mimicking materials that possess catalytic power rivaling that of natural enzymes..
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Affiliation(s)
- Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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Roy S, Chatterjee A, Bal S, Das D. Cross β Amyloid Nanotubes Demonstrate Promiscuous Catalysis in a Chemical Reaction Network via Co‐option. Angew Chem Int Ed Engl 2022; 61:e202210972. [DOI: 10.1002/anie.202210972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Soumili Roy
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Ayan Chatterjee
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Subhajit Bal
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
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Arad E, Jelinek R. Catalytic amyloids. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Chatterjee A, Ghosh S, Ghosh C, Das D. Fluorescent Microswimmers Based on Cross-β Amyloid Nanotubes and Divergent Cascade Networks. Angew Chem Int Ed Engl 2022; 61:e202201547. [PMID: 35578748 DOI: 10.1002/anie.202201547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Indexed: 12/21/2022]
Abstract
Shaped through millions of years of evolution, the spatial localization of multiple enzymes in living cells employs extensive cascade reactions to enable highly coordinated multimodal functions. Herein, by utilizing a complex divergent cascade, we exploit the catalytic potential as well as templating abilities of streamlined cross-β amyloid nanotubes to yield two orthogonal roles simultaneously. The short peptide based paracrystalline nanotube surfaces demonstrated the generation of fluorescence signals within entangled networks loaded with alcohol dehydrogenase (ADH). The nanotubular morphologies were further used to generate cascade-driven microscopic motility through surface entrapment of sarcosine oxidase (SOX) and catalase (Cat). Moreover, a divergent cascade network was initiated by upstream catalysis of the substrate molecules through the surface mutation of catalytic moieties. Notably, the resultant downstream products led to the generation of motile fluorescent microswimmers by utilizing the two sets of orthogonal properties and, thus, mimicked the complex cascade-mediated functionalities of extant biology.
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Affiliation(s)
- Ayan Chatterjee
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, West Bengal, 741246, India
| | - Souvik Ghosh
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, West Bengal, 741246, India
| | - Chandranath Ghosh
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, West Bengal, 741246, India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, West Bengal, 741246, India
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Fluorescent Microswimmers Based on Cross‐β Amyloid Nanotubes and Divergent Cascade Networks. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Pal S, Reja A, Bal S, Tikader B, Das D. Emergence of a Promiscuous Peroxidase Under Non-Equilibrium Conditions. Angew Chem Int Ed Engl 2022; 61:e202111857. [PMID: 34767668 DOI: 10.1002/anie.202111857] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Indexed: 11/07/2022]
Abstract
Herein, we report the substrate induced generation of a transient catalytic microenvironment from a single amino acid functionalized fatty acid in presence of a cofactor hemin. The catalytic state accessed under non-equilibrium conditions showed acceleration of peroxidase activity resulting in degradation of the substrate and subsequently led to disassembly. Equilibrated systems could not access the three-dimensional microphases and showed substantially lower catalytic activity. Further, the assembled state showed latent catalytic function (promiscuity) to hydrolyze a precursor to yield the same substrate. Consequently, the assembly demonstrated protometabolism by exploiting the peroxidase-hydrolase cascade to augment the lifetime and the mechanical properties of the catalytic state.
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Affiliation(s)
- Sumit Pal
- Department of Chemical Sciences &, Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Antara Reja
- Department of Chemical Sciences &, Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Subhajit Bal
- Department of Chemical Sciences &, Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Baishakhi Tikader
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Dibyendu Das
- Department of Chemical Sciences &, Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
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Pal S, Reja A, Bal S, Tikader B, Das D. Emergence of a Promiscuous Peroxidase Under Non‐Equilibrium Conditions**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sumit Pal
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Antara Reja
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Subhajit Bal
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Baishakhi Tikader
- Department of Chemistry Indian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
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Liu S, Du P, Sun H, Yu HY, Wang ZG. Bioinspired Supramolecular Catalysts from Designed Self-Assembly of DNA or Peptides. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03753] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Siyuan Liu
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
- College of Chemistry and Materials Science, Anhui Normal University, 189 Jiuhua Nanlu, Wuhu, Anhui 241002, China
| | - Peidong Du
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
| | - Hao Sun
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
| | - Hai-Yin Yu
- College of Chemistry and Materials Science, Anhui Normal University, 189 Jiuhua Nanlu, Wuhu, Anhui 241002, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
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