1
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Wang W, Xi H, Fu D, Ma D, Gong W, Zhao Y, Li X, Wu L, Guo Y, Zhao G, Wang H. Growth Process of Fe-O Nanoclusters with Different Sizes Biosynthesized by Protein Nanocages. J Am Chem Soc 2024; 146:11657-11668. [PMID: 38641862 DOI: 10.1021/jacs.3c13830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
All protein-directed syntheses of metal nanoclusters (NCs) and nanoparticles (NPs) have attracted considerable attention because protein scaffolds provide a unique metal coordination environment and can adjust the shape and morphology of NCs and NPs. However, the detailed formation mechanisms of NCs or NPs directed by protein templates remain unclear. In this study, by taking advantage of the ferritin nanocage as a biotemplate to monitor the growth of Fe-O NCs as a function of time, we synthesized a series of iron NCs with different sizes and shapes and subsequently solved their corresponding three-dimensional atomic-scale structures by X-ray protein crystallography and cryo-electron microscopy. The time-dependent structure analyses revealed the growth process of these Fe-O NCs with the 4-fold channel of ferritin as nucleation sites. To our knowledge, the newly biosynthesized Fe35O23Glu12 represents the largest Fe-O NCs with a definite atomic structure. This study contributes to our understanding of the formation mechanism of iron NCs and provides an effective method for metal NC synthesis.
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Affiliation(s)
- Wenming Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of the Education Ministry, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
| | - Hongfang Xi
- Key Laboratory of Chemical Biology and Molecular Engineering of the Education Ministry, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
| | - Dan Fu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Danyang Ma
- Key Laboratory of Chemical Biology and Molecular Engineering of the Education Ministry, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
| | - Wenjun Gong
- Key Laboratory of Chemical Biology and Molecular Engineering of the Education Ministry, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
| | - Yaqin Zhao
- Key Laboratory of Chemical Biology and Molecular Engineering of the Education Ministry, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
| | - Xiaomei Li
- Shanxi Provincial Key Laboratory of Protein Structure Determination, Shanxi Academy of Advanced Research and Innovation, Taiyuan 030012, China
| | - Lijie Wu
- IHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Hongfei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of the Education Ministry, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
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2
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Maity B, Kameyama S, Tian J, Pham TT, Abe S, Chatani E, Murata K, Ueno T. Fusion of amyloid beta with ferritin yields an isolated oligomeric beta-sheet-rich aggregate inside the ferritin cage. Biomater Sci 2024; 12:2408-2417. [PMID: 38511491 DOI: 10.1039/d4bm00173g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Alzheimer's disease is a severe brain condition caused by the formation of amyloid plaques composed of amyloid beta (Aβ) peptides. These peptides form oligomers, protofibrils, and fibrils before deposition into amyloid plaques. Among these intermediates, Aβ oligomers (AβOs) were found to be the most toxic and therefore an appealing target for drug development and understanding their role in the disease. However, precise isolation and characterization of AβOs have proven challenging because AβOs tend to aggregate and form heterogeneous mixtures in solution. As a solution, we genetically fused the Aβ peptide with a ferritin monomer. Such fusion allowed the encapsulation of precisely 24 Aβ peptides inside the 24-mer ferritin cage. Using high-speed atomic force microscopy (HS-AFM), we disassembled ferritin and directly visualized the Aβ core enclosed within the cage. The thioflavin-T assay (ThT) and attenuated total reflection infrared spectroscopy (ATR-IR) revealed the presence of a β-sheet structure in the encapsulated oligomeric aggregate. Gallic acid, an amyloid inhibitor, can inhibit the fluorescence of ThT bound AβOs. Our approach represents a significant advancement in the isolation and characterization of β-sheet rich AβOs and is expected to be useful for future studies of other disordered peptides such as α-synuclein and tau.
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Affiliation(s)
- Basudev Maity
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
| | - Shiori Kameyama
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
| | - Jiaxin Tian
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
| | - Thuc Toan Pham
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
| | - Eri Chatani
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute for Natural Sciences, Okazaki, Aichi, 444-8585, Japan
- National Institute for Physiological Sciences (NIPS), National Institute for Natural Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
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3
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Singh SK, Siegler N, Pandey H, Yanir N, Popov M, Goldstein-Levitin A, Sadan M, Debs G, Zarivach R, Frank GA, Kass I, Sindelar CV, Zalk R, Gheber L. Noncanonical interaction with microtubules via the N-terminal nonmotor domain is critical for the functions of a bidirectional kinesin. SCIENCE ADVANCES 2024; 10:eadi1367. [PMID: 38324691 PMCID: PMC10849588 DOI: 10.1126/sciadv.adi1367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024]
Abstract
Several kinesin-5 motors (kinesin-5s) exhibit bidirectional motility. The mechanism of such motility remains unknown. Bidirectional kinesin-5s share a long N-terminal nonmotor domain (NTnmd), absent in exclusively plus-end-directed kinesins. Here, we combined in vivo, in vitro, and cryo-electron microscopy (cryo-EM) studies to examine the impact of NTnmd mutations on the motor functions of the bidirectional kinesin-5, Cin8. We found that NTnmd deletion mutants exhibited cell viability and spindle localization defects. Using cryo-EM, we examined the structure of a microtubule (MT)-bound motor domain of Cin8, containing part of its NTnmd. Modeling and molecular dynamic simulations based on the cryo-EM map suggested that the NTnmd of Cin8 interacts with the C-terminal tail of β-tubulin. In vitro experiments on subtilisin-treated MTs confirmed this notion. Last, we showed that NTnmd mutants are defective in plus-end-directed motility in single-molecule and antiparallel MT sliding assays. These findings demonstrate that the NTnmd, common to bidirectional kinesin-5s, is critical for their bidirectional motility and intracellular functions.
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Affiliation(s)
- Sudhir K. Singh
- 1Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Nurit Siegler
- 1Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Himanshu Pandey
- 1Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Neta Yanir
- 1Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Mary Popov
- 1Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | | | - Mayan Sadan
- 1Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Garrett Debs
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Gabriel A. Frank
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Itamar Kass
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Charles V. Sindelar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Ran Zalk
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Larisa Gheber
- 1Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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4
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Huang Y, Zhang X, Mao R, Li D, Luo F, Wang L, Chen Y, Lu J, Ge X, Liu Y, Yang X, Fan Y, Zhang X, Wang K. Nucleation Domains in Biomineralization: Biomolecular Sequence and Conformational Features. Inorg Chem 2024; 63:689-705. [PMID: 38146716 DOI: 10.1021/acs.inorgchem.3c03576] [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: 12/27/2023]
Abstract
Biomolecules play a vital role in the regulation of biomineralization. However, the characteristics of practical nucleation domains are still sketchy. Herein, the effects of the representative biomolecular sequence and conformations on calcium phosphate (Ca-P) nucleation and mineralization are investigated. The results of computer simulations and experiments prove that the line in the arrangement of dual acidic/essential amino acids with a single interval (Bc (Basic) -N (Neutral) -Bc-N-Ac (Acidic)- NN-Ac-N) is most conducive to the nucleation. 2α-helix conformation can best induce Ca-P ion cluster formation and nucleation. "Ac- × × × -Bc" sequences with α-helix are found to be the features of efficient nucleation domains, in which process, molecular recognition plays a non-negligible role. It further indicates that the sequence determines the potential of nucleation/mineralization of biomolecules, and conformation determines the ability of that during functional execution. The findings will guide the synthesis of biomimetic mineralized materials with improved performance for bone repair.
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Affiliation(s)
- Yawen Huang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Xinyue Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Ruiqi Mao
- College of Materials Science and Engineering, Sichuan University, Chengdu 610064, China
| | - Dongxuan Li
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Fengxiong Luo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Ling Wang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Yafang Chen
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Jian Lu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Xiang Ge
- Key Laboratory of Mechanism Theory and Equipment Design of Ministry of Education, School of Mechanical Engineering, Tianjin University, Tianjin 300354, China
| | - Yue Liu
- Key Laboratory for Industrial Ceramics of Jiangxi Province, Pingxiang University, Pingxiang 337055 China
| | - Xusheng Yang
- Department of Industrial and Systems Engineering, Research Institute for Advanced Manufacturing, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, China
| | - Yujiang Fan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Xingdong Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
- Research Center for Material Genome Engineering, Sichuan University, Chengdu 610064, China
| | - Kefeng Wang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
- Research Center for Material Genome Engineering, Sichuan University, Chengdu 610064, China
- Provincial Engineering Research Center for Biomaterials Genome of Sichuan, Chengdu 610064, China
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5
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Sharaby Y, Gilboa Y, Alfiya Y, Sabach S, Cheruti U, Friedler E. Whole campus wastewater surveillance of SARS-CoV-2 for COVID-19 outbreak management. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2023; 87:910-923. [PMID: 36853770 DOI: 10.2166/wst.2023.030] [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
In this long-term study (eight months), a wastewater-based epidemiology program was initiated as a decision support tool for the detection and containment of COVID-19 spread in the Technion campus. The on-campus students' accommodations (∼3,300 residents) were divided into housing clusters and monitored through wastewater SARS-CoV-2 surveillance in 10 manholes. Results were used to create a 'traffic-light' scheme allowing the Technion's COVID-19 task force to track COVID-19 spatiotemporal spread on the campus, and consequently, contain it before high morbidity levels develop. Of the 523 sewage samples analysed, 87.4% were negative for SARS-CoV-2 while 11.5% were positive, corroborating morbidity information the COVID-19 task force had. For 7.6% of the SARS-CoV-2 positive samples, the task force had no information about positive resident/s. In these events, new cases were identified after the relevant residents were clinically surge tested for COVID-19. Hence, in these instances, wastewater surveillance provided early warning helping to secure the health of the campus residents by minimising COVID-19 spread. The inflammation biomarker ferritin levels in SARS-CoV-2 positive sewage samples were significantly higher than in negative ones. This may indicate that in the future, ferritin (and other biomarkers) concentrations in wastewater could serve as indicators of infectious and inflammatory disease outbreaks.
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Affiliation(s)
- Y Sharaby
- Faculty of Civil & Environmental Engineering, Technion-Israel Institute of Technology, Haifa, Israel E-mail: ; Current address: Department of Biology & Environment, University of Haifa, Oranim, Tivon, Israel
| | - Y Gilboa
- Faculty of Civil & Environmental Engineering, Technion-Israel Institute of Technology, Haifa, Israel E-mail:
| | - Y Alfiya
- Faculty of Civil & Environmental Engineering, Technion-Israel Institute of Technology, Haifa, Israel E-mail:
| | - S Sabach
- Faculty of Civil & Environmental Engineering, Technion-Israel Institute of Technology, Haifa, Israel E-mail:
| | - U Cheruti
- Faculty of Civil & Environmental Engineering, Technion-Israel Institute of Technology, Haifa, Israel E-mail:
| | - Eran Friedler
- Faculty of Civil & Environmental Engineering, Technion-Israel Institute of Technology, Haifa, Israel E-mail:
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6
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Kadamannil NN, Heo JM, Jang D, Zalk R, Kolusheva S, Zarivach R, Frank GA, Kim JM, Jelinek R. High-Resolution Cryo-Electron Microscopy Reveals the Unique Striated Hollow Structure of Photocatalytic Macrocyclic Polydiacetylene Nanotubes. J Am Chem Soc 2022; 144:17889-17896. [PMID: 36126329 DOI: 10.1021/jacs.2c06710] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-resolution structures are crucial for understanding the functional properties of nanomaterials. We applied single-particle cryo-electron microscopy (cryo-EM), a method traditionally used for structure determination of biological macromolecules, to obtain high-resolution structures of synthetic non-biological filaments formed by photopolymerization of macrocyclic diacetylene (MDA) amphiphilic monomers. Tomographic analysis showed that the MDA monomers self-assemble into hollow nanotubes upon dispersion in water. Single-particle analysis revealed tubes consisting of six pairs of covalently bonded filaments held together by hydrophobic interactions, where each filament is composed of macrocyclic rings stacked in parallel "chair" conformations. The hollow MDA nanotube structures we found may account for the efficient scavenging of amphiphilic pollutants in water and subsequent photodegradation of the guest species.
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Affiliation(s)
| | - Jung-Moo Heo
- Department of Chemical Engineering, Hanyang University, Seoul 04763, Korea
| | - Daewoong Jang
- Department of Chemical Engineering, Hanyang University, Seoul 04763, Korea
| | - Ran Zalk
- Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Sofiya Kolusheva
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Raz Zarivach
- Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Gabriel A Frank
- Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Jong-Man Kim
- Department of Chemical Engineering, Hanyang University, Seoul 04763, Korea
| | - Raz Jelinek
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
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7
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Atomic Details of Biomineralization Proteins Inspiring Protein Design and Reengineering for Functional Biominerals. CHEMISTRY 2022. [DOI: 10.3390/chemistry4030059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biominerals are extraordinary materials that provide organisms with a variety of functions to support life. The synthesis of biominerals and organization at the macroscopic level is a consequence of the interactions of these materials with proteins. The association of biominerals and proteins is very ancient and has sparked a wealth of research across biological, medical and material sciences. Calcium carbonate, hydroxyapatite, and silica represent widespread natural biominerals. The atomic details of the interface between macromolecules and these biominerals is very intriguing from a chemical perspective, considering the association of chemical entities that are structurally different. With this review I provide an overview of the available structural studies of biomineralization proteins, explored from the Protein Data Bank (wwPDB) archive and scientific literature, and of how these studies are inspiring the design and engineering of proteins able to synthesize novel biominerals. The progression of this review from classical template proteins to silica polymerization seeks to benefit researchers involved in various interdisciplinary aspects of a biomineralization project, who need background information and a quick update on advances in the field. Lessons learned from structural studies are exemplary and will guide new projects for the imaging of new hybrid biomineral/protein superstructures at the atomic level.
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8
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Eldar A, Amos I, Shkolnisky Y. ASOCEM: Automatic Segmentation Of Contaminations in cryo-EM. J Struct Biol 2022; 214:107871. [DOI: 10.1016/j.jsb.2022.107871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/10/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022]
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9
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Pohl A, Young SAE, Schmitz TC, Farhadi D, Zarivach R, Faivre D, Blank KG. Magnetite-binding proteins from the magnetotactic bacterium Desulfamplus magnetovallimortis BW-1. NANOSCALE 2021; 13:20396-20400. [PMID: 34860229 DOI: 10.1039/d1nr04870h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Magnetite-binding proteins are in high demand for the functionalization of magnetic nanoparticles. Binding analysis of six previously uncharacterized proteins from the magnetotactic Deltaproteobacterium Desulfamplus magnetovallimortis BW-1 identified two new magnetite-binding proteins (Mad10, Mad11). These proteins can be utilized as affinity tags for the immobilization of recombinant fusion proteins to magnetite.
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Affiliation(s)
- Anna Pohl
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476 Potsdam, Germany.
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Sarah A E Young
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476 Potsdam, Germany.
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Tara C Schmitz
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Daniel Farhadi
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Raz Zarivach
- Department of Life Sciences, The National Institute for Biotechnology in the Negev and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Damien Faivre
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476 Potsdam, Germany.
- Aix-Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul lez Durance, France
| | - Kerstin G Blank
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476 Potsdam, Germany.
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10
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Hoelzgen F, Zalk R, Alcalay R, Cohen-Schwartz S, Garau G, Shahar A, Mazor O, Frank GA. Neutralization of the anthrax toxin by antibody-mediated stapling of its membrane-penetrating loop. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1197-1205. [PMID: 34473089 DOI: 10.1107/s2059798321007816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/30/2021] [Indexed: 12/15/2022]
Abstract
Anthrax infection is associated with severe illness and high mortality. Protective antigen (PA) is the central component of the anthrax toxin, which is one of two major virulence factors of Bacillus anthracis, the causative agent of anthrax disease. Upon endocytosis, PA opens a pore in the membranes of endosomes, through which the cytotoxic enzymes of the toxin are extruded. The PA pore is formed by a cooperative conformational change in which the membrane-penetrating loops of PA associate, forming a hydrophobic rim that pierces the membrane. Due to its crucial role in anthrax progression, PA is an important target for monoclonal antibody-based therapy. cAb29 is a highly effective neutralizing antibody against PA. Here, the cryo-EM structure of PA in complex with the Fab portion of cAb29 was determined. It was found that cAb29 neutralizes the toxin by clamping the membrane-penetrating loop of PA to the static surface-exposed loop of the D3 domain of the same subunit, thereby preventing pore formation. These results provide the structural basis for the antibody-based neutralization of PA and bring into focus the membrane-penetrating loop of PA as a target for the development of better anti-anthrax vaccines.
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Affiliation(s)
- F Hoelzgen
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - R Zalk
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - R Alcalay
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - S Cohen-Schwartz
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - G Garau
- Biostructures Lab, IIT@NEST - Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56124 Pisa, Italy
| | - A Shahar
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - O Mazor
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - G A Frank
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
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11
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SAMase of Bacteriophage T3 Inactivates Escherichia coli's Methionine S-Adenosyltransferase by Forming Heteropolymers. mBio 2021; 12:e0124221. [PMID: 34340545 PMCID: PMC8406200 DOI: 10.1128/mbio.01242-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
S-Adenosylmethionine lyase (SAMase) of bacteriophage T3 degrades the intracellular SAM pools of the host Escherichia coli cells, thereby inactivating a crucial metabolite involved in a plethora of cellular functions, including DNA methylation. SAMase is the first viral protein expressed upon infection, and its activity prevents methylation of the T3 genome. Maintenance of the phage genome in a fully unmethylated state has a profound effect on the infection strategy. It allows T3 to shift from a lytic infection under normal growth conditions to a transient lysogenic infection under glucose starvation. Using single-particle cryoelectron microscopy (cryo-EM) and biochemical assays, we demonstrate that SAMase performs its function by not only degrading SAM but also by interacting with and efficiently inhibiting the host's methionine S-adenosyltransferase (MAT), the enzyme that produces SAM. Specifically, SAMase triggers open-ended head-to-tail assembly of E. coli MAT into an unusual linear filamentous structure in which adjacent MAT tetramers are joined by two SAMase dimers. Molecular dynamics simulations together with normal mode analyses suggest that the entrapment of MAT tetramers within filaments leads to an allosteric inhibition of MAT activity due to a shift to low-frequency, high-amplitude active-site-deforming modes. The amplification of uncorrelated motions between active-site residues weakens MAT's substrate binding affinity, providing a possible explanation for the observed loss of function. We propose that the dual function of SAMase as an enzyme that degrades SAM and as an inhibitor of MAT activity has emerged to achieve an efficient depletion of the intracellular SAM pools. IMPORTANCE Self-assembly of enzymes into filamentous structures in response to specific metabolic cues has recently emerged as a widespread strategy of metabolic regulation. In many instances, filamentation of metabolic enzymes occurs in response to starvation and leads to functional inactivation. Here, we report that bacteriophage T3 modulates the metabolism of the host E. coli cells by recruiting a similar strategy: silencing a central metabolic enzyme by subjecting it to phage-mediated polymerization. This observation points to an intriguing possibility that virus-induced polymerization of the host metabolic enzymes is a common mechanism implemented by viruses to metabolically reprogram and subdue infected cells.
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