1
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Fernandez‐Calvo A, Reifs A, Saa L, Cortajarena AL, De Sancho D, Perez‐Jimenez R. The strongest protein binder is surprisingly labile. Protein Sci 2024; 33:e5030. [PMID: 38864696 PMCID: PMC11168069 DOI: 10.1002/pro.5030] [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: 02/18/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024]
Abstract
Bacterial adhesins are cell-surface proteins that anchor to the cell wall of the host. The first stage of infection involves the specific attachment to fibrinogen (Fg), a protein found in human blood. This attachment allows bacteria to colonize tissues causing diseases such as endocarditis. The study of this family of proteins is hence essential to develop new strategies to fight bacterial infections. In the case of the Gram-positive bacterium Staphylococcus aureus, there exists a class of adhesins known as microbial surface components recognizing adhesive matrix molecules (MSCRAMMs). Here, we focus on one of them, the clumping factor A (ClfA), which has been found to bind Fg through the dock-lock-latch mechanism. Interestingly, it has recently been discovered that MSCRAMM proteins employ a catch-bond to withstand forces exceeding 2 nN, making this type of interaction as mechanically strong as a covalent bond. However, it is not known whether this strength is an evolved feature characteristic of the bacterial protein or is typical only of the interaction with its partner. Here, we combine single-molecule force spectroscopy, biophysical binding assays, and molecular simulations to study the intrinsic mechanical strength of ClfA. We find that despite the extremely high forces required to break its interactions with Fg, ClfA is not by itself particularly strong. Integrating the results from both theory and experiments we dissect contributions to the mechanical stability of this protein.
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Affiliation(s)
- Alba Fernandez‐Calvo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA)DerioBizkaiaSpain
| | - Antonio Reifs
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA)DerioBizkaiaSpain
| | - Laura Saa
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA)Donostia‐San SebastiánSpain
| | - Aitziber L. Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA)Donostia‐San SebastiánSpain
- Ikerbasque Foundation for ScienceBilbaoSpain
| | - David De Sancho
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, University of the Basque Country (UPV/EHU)San SebastianSpain
- Donostia International Physics Center (DIPC)San SebastianSpain
| | - Raul Perez‐Jimenez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA)DerioBizkaiaSpain
- Ikerbasque Foundation for ScienceBilbaoSpain
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2
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Reifs A, Fernandez-Calvo A, Alonso-Lerma B, Schönfelder J, Franco D, Ortega-Muñoz M, Casares S, Jimenez-Lopez C, Saa L, Cortajarena AL, De Sancho D, San Sebastian E, Perez-Jimenez R. High-throughput virtual search of small molecules for controlling the mechanical stability of human CD4. J Biol Chem 2024; 300:107133. [PMID: 38432632 PMCID: PMC11065764 DOI: 10.1016/j.jbc.2024.107133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/15/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024] Open
Abstract
Protein mechanical stability determines the function of a myriad of proteins, especially proteins from the extracellular matrix. Failure to maintain protein mechanical stability may result in diseases and disorders such as cancer, cardiomyopathies, or muscular dystrophy. Thus, developing mutation-free approaches to enhance and control the mechanical stability of proteins using pharmacology-based methods may have important implications in drug development and discovery. Here, we present the first approach that employs computational high-throughput virtual screening and molecular docking to search for small molecules in chemical libraries that function as mechano-regulators of the stability of human cluster of differentiation 4, receptor of HIV-1. Using single-molecule force spectroscopy, we prove that these small molecules can increase the mechanical stability of CD4D1D2 domains over 4-fold in addition to modifying the mechanical unfolding pathways. Our experiments demonstrate that chemical libraries are a source of mechanoactive molecules and that drug discovery approaches provide the foundation of a new type of molecular function, that is, mechano-regulation, paving the way toward mechanopharmacology.
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Affiliation(s)
- Antonio Reifs
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio-Bizkaia, Spain
| | - Alba Fernandez-Calvo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio-Bizkaia, Spain
| | - Borja Alonso-Lerma
- Center for Cooperative Research in Nanoscience (CIC nanoGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sabestian, Spain
| | - Jörg Schönfelder
- Center for Cooperative Research in Nanoscience (CIC nanoGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sabestian, Spain
| | | | - Mariano Ortega-Muñoz
- Faculty of Science, Department of Organic Chemistry, University of Granada, Granada, Spain
| | - Salvador Casares
- Faculty of Science, Department of Physical Chemistry, University of Granada, Granada, Spain
| | | | - Laura Saa
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastian, Spain
| | - Aitziber L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastian, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - David De Sancho
- Donostia International Physics Center (DIPC), San Sebastian, Spain; Faculty of Chemistry, Applied Chemistry Department, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Eider San Sebastian
- Faculty of Chemistry, Applied Chemistry Department, University of the Basque Country (UPV/EHU), San Sebastian, Spain.
| | - Raul Perez-Jimenez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio-Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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3
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Teuber A, Caniglia G, Barth H, Kranz C, Mizaikoff B. Thin-Film Waveguide Laser Spectroscopy: A Novel Platform for Bacterial Analysis. Anal Chem 2023; 95:16600-16608. [PMID: 37883708 DOI: 10.1021/acs.analchem.3c02782] [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: 10/28/2023]
Abstract
Bacterial sensing based on quantum cascade laser spectroscopy coupled with diamond or gallium arsenide thin-film waveguides is a novel analytical tool for gaining high-resolution infrared spectroscopic information of planktonic and sessile bacteria, as shown in the present study for Escherichia coli. During observation periods of up to 24 h, diamond and gallium arsenide thin-film waveguide laser spectroscopy was compared to information obtained via conventional Fourier transform infrared spectroscopy. The proliferation behavior of E. coli at those surfaces was complementarily investigated using atomic force microscopy and scanning electron microscopy.
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Affiliation(s)
- Andrea Teuber
- Institute of Analytical and Bioanalytical Chemistry, University of Ulm, 89081 Ulm, Germany
| | - Giada Caniglia
- Institute of Analytical and Bioanalytical Chemistry, University of Ulm, 89081 Ulm, Germany
| | - Holger Barth
- Institute of Experimental and Clinical Pharmacology and Toxicology and Pharmacology of Natural Products, University of Ulm, 89081 Ulm, Germany
| | - Christine Kranz
- Institute of Analytical and Bioanalytical Chemistry, University of Ulm, 89081 Ulm, Germany
| | - Boris Mizaikoff
- Institute of Analytical and Bioanalytical Chemistry, University of Ulm, 89081 Ulm, Germany
- Hahn-Schickard, 89077 Ulm, Germany
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4
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Fulton DA, Dura G, Peters DT. The polymer and materials science of the bacterial fimbriae Caf1. Biomater Sci 2023; 11:7229-7246. [PMID: 37791425 PMCID: PMC10628683 DOI: 10.1039/d3bm01075a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/22/2023] [Indexed: 10/05/2023]
Abstract
Fimbriae are long filamentous polymeric protein structures located upon the surface of bacteria. Often implicated in pathogenicity, the biosynthesis and function of fimbriae has been a productive topic of study for many decades. Evolutionary pressures have ensured that fimbriae possess unique structural and mechanical properties which are advantageous to bacteria. These properties are also difficult to engineer with well-known synthetic and natural fibres, and this has raised an intriguing question: can we exploit the unique properties of bacterial fimbriae in useful ways? Initial work has set out to explore this question by using Capsular antigen fragment 1 (Caf1), a fimbriae expressed naturally by Yersina pestis. These fibres have evolved to 'shield' the bacterium from the immune system of an infected host, and thus are rather bioinert in nature. Caf1 is, however, very amenable to structural mutagenesis which allows the incorporation of useful bioactive functions and the modulation of the fibre's mechanical properties. Its high-yielding recombinant synthesis also ensures plentiful quantities of polymer are available to drive development. These advantageous features make Caf1 an archetype for the development of new polymers and materials based upon bacterial fimbriae. Here, we cover recent advances in this new field, and look to future possibilities of this promising biopolymer.
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Affiliation(s)
- David A Fulton
- Chemistry-School of Natural Science and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.
| | - Gema Dura
- Chemistry-School of Natural Science and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.
- Departamento de Química Inorgánica Orgánica y Bioquímica Universidad de Castilla-La Mancha Facultad de Ciencias y Tecnologías Químicas-IRICAAvda, C. J. Cela, 10, Ciudad Real 13071, Spain
| | - Daniel T Peters
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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5
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Belyaev AV, Fedotova IV. Molecular mechanisms of catch bonds and their implications for platelet hemostasis. Biophys Rev 2023; 15:1233-1256. [PMID: 37974999 PMCID: PMC10643804 DOI: 10.1007/s12551-023-01144-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/07/2023] [Indexed: 11/19/2023] Open
Abstract
Adhesive molecular bonds between blood cells are essential for thrombosis and hemostasis as they provide means for platelet adhesion, aggregation, and signaling in flowing blood. According to the nowadays conventional definition, a "catch" bond is a type of non-covalent bio-molecular bridge, whose dissociation lifetime counter-intuitively increases with applied tensile force. Following recent experimental findings, such receptor-ligand protein bonds are vital to the blood cells involved in the prevention of bleeding (hemostatic response) and infection (immunity). In this review, we examine the up-to-date experimental discoveries and theoretical insights about catch bonds between the blood cells, their biomechanical principles at the molecular level, and their role in platelet thrombosis and hemostasis.
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Affiliation(s)
- Aleksey V. Belyaev
- Faculty of Physics, M.V.Lomonosov Moscow State University, 1, Leninskiye Gory, build.2, Moscow, 119991 Russia
| | - Irina V. Fedotova
- Faculty of Physics, M.V.Lomonosov Moscow State University, 1, Leninskiye Gory, build.2, Moscow, 119991 Russia
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6
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Wang Z, Wang M, Zhao Z, Zheng P. Quantification of carboxylate-bridged di-zinc site stability in protein due ferri by single-molecule force spectroscopy. Protein Sci 2023; 32:e4583. [PMID: 36718829 PMCID: PMC9926469 DOI: 10.1002/pro.4583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/16/2023] [Accepted: 01/27/2023] [Indexed: 02/01/2023]
Abstract
Carboxylate-bridged diiron proteins belong to a protein family involved in different physiological processes. These proteins share the conservative EXXH motif, which provides the carboxylate bridge and is critical for metal binding. Here, we choose de novo-designed single-chain due ferri protein (DFsc), a four-helical protein with two EXXH motifs as a model protein, to study the stability of the carboxylate-bridged di-metal binding site. The mechanical and kinetic properties of the di-Zn site in DFsc were obtained by atomic force microscopy-based single-molecule force spectroscopy. Zn-DFsc showed a considerable rupture force of ~200 pN, while the apo-protein is mechanically labile. In addition, multiple rupture pathways were observed with different probabilities, indicating the importance of the EXXH-based carboxylate-bridged metal site. These results demonstrate carboxylate-bridged di-metal site is mechanically stable and improve our understanding of this important type of metalloprotein.
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Affiliation(s)
- Zhiyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
| | - Mengdie Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
| | - Zhongxin Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
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7
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Rief M, Žoldák G. Single-molecule mechanical studies of chaperones and their clients. BIOPHYSICS REVIEWS 2022; 3:041301. [PMID: 38505517 PMCID: PMC10903372 DOI: 10.1063/5.0098033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/12/2022] [Indexed: 03/21/2024]
Abstract
Single-molecule force spectroscopy provides access to the mechanics of biomolecules. Recently, magnetic and laser optical tweezers were applied in the studies of chaperones and their interaction with protein clients. Various aspects of the chaperone-client interactions can be revealed based on the mechanical probing strategies. First, when a chaperone is probed under load, one can examine the inner workings of the chaperone while it interacts with and works on the client protein. Second, when protein clients are probed under load, the action of chaperones on folding clients can be studied in great detail. Such client folding studies have given direct access to observing actions of chaperones in real-time, like foldase, unfoldase, and holdase activity. In this review, we introduce the various single molecule mechanical techniques and summarize recent single molecule mechanical studies on heat shock proteins, chaperone-mediated folding on the ribosome, SNARE folding, and studies of chaperones involved in the folding of membrane proteins. An outlook on significant future developments is given.
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Affiliation(s)
- Matthias Rief
- Center for Functional Protein Assemblies (CPA), Physik Department, Technische Universität München, Ernst-Otto-Fischer-Str., 8, D-85748 Garching, Germany
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University, Trieda SNP 1, 040 11 Košice, Slovakia
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8
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Gaines MC, Isupov MN, Sivabalasarma S, Haque RU, McLaren M, Mollat CL, Tripp P, Neuhaus A, Gold VAM, Albers SV, Daum B. Electron cryo-microscopy reveals the structure of the archaeal thread filament. Nat Commun 2022; 13:7411. [PMID: 36456543 PMCID: PMC9715654 DOI: 10.1038/s41467-022-34652-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/02/2022] [Indexed: 12/05/2022] Open
Abstract
Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal gene transfer. The model archaeaon Sulfolobus acidocaldarius assembles three filaments of the type-IV pilus superfamily (archaella, archaeal adhesion pili and UV-inducible pili), as well as a so-far uncharacterised fourth filament, named "thread". Here, we report on the cryo-EM structure of the archaeal thread. The filament is highly glycosylated and consists of subunits of the protein Saci_0406, arranged in a head-to-tail manner. Saci_0406 displays structural similarity, but low sequence homology, to bacterial type-I pilins. Thread subunits are interconnected via donor strand complementation, a feature reminiscent of bacterial chaperone-usher pili. However, despite these similarities in overall architecture, archaeal threads appear to have evolved independently and are likely assembled by a distinct mechanism.
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Affiliation(s)
- Matthew C Gaines
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, EX4 4QD, Exeter, UK
| | - Shamphavi Sivabalasarma
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Risat Ul Haque
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK
| | - Clara L Mollat
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Patrick Tripp
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Alexander Neuhaus
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK
| | - Sonja-Verena Albers
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBBS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK.
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK.
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9
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Ding X, Wang Z, Zheng B, Shi S, Deng Y, Yu H, Zheng P. One-step asparaginyl endopeptidase ( OaAEP1)-based protein immobilization for single-molecule force spectroscopy. RSC Chem Biol 2022; 3:1276-1281. [PMID: 36320890 PMCID: PMC9533667 DOI: 10.1039/d2cb00135g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/18/2022] [Indexed: 11/22/2022] Open
Abstract
Enzymatic protein ligation has become the most powerful and widely used method for high-precision atomic force microscopy single-molecule force spectroscopy (AFM-SMFS) study of protein mechanics. However, this methodology typically requires the functionalization of the glass surface with a corresponding peptide sequence/tag for enzymatic recognition and multiple steps are needed. Thus, it is time-consuming and a high level of experience is needed for reliable results. To solve this problem, we simplified the procedure using two strategies both based on asparaginyl endopeptidase (AEP). First, we designed a heterobifunctional peptide-based crosslinker, GL-peptide-propargylglycine, which links to an N 3-functionalized surface via the click reaction. Then, the target protein with a C-terminal NGL sequence can be immobilized via the AEP-mediated ligation. Furthermore, we took advantage of the direct ligation between primary amino in a small molecule and protein with C-terminal NGL by AEP. Thus, the target protein can be immobilized on an amino-functionalized surface via AEP in one step. Both approaches were successfully applied to the AFM-SMFS study of eGFP, showing consistent single-molecule results.
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Affiliation(s)
- Xuan Ding
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University 163 Xianlin Road Nanjing Jiangsu 210023 P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Ziyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Yibing Deng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Hanyang Yu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University 163 Xianlin Road Nanjing Jiangsu 210023 P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
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10
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Wang Z, Zhao Z, Li G, Zheng P. Single-Molecule Force Spectroscopy Reveals the Dynamic HgS Coordination Site in the De Novo-Designed Metalloprotein α 3DIV. J Phys Chem Lett 2022; 13:5372-5378. [PMID: 35678420 DOI: 10.1021/acs.jpclett.2c01316] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The de novo-designed metalloprotein α3DIV binds to mercury via three cysteine residues under dynamic conditions. An unusual trigonal three-coordinate HgS3 site is formed in the protein in basic solution, whereas a linear two-coordinate HgS2 site is formed in acidic solution. Furthermore, it is unknown whether the two coordinated cysteines in the HgS2 site are fixed or not, which may lead to more dynamics. However, the signal for HgS2 sites with different cysteines may be similar or may be averaged and indistinguishable. To circumvent this problem, we adopt a single-molecule approach to study one mercury site at a time. Using atomic force microscopy-based single-molecule force spectroscopy, the protein is unfolded, and the HgS site is ruptured. The results confirm the formation of HgS3 and HgS2 sites at different pH values. Moreover, it is found that any two of the three cysteines in the protein bind to mercury in the HgS2 site.
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Affiliation(s)
- Ziyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P.R. China
| | - Zhongxing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P.R. China
| | - Guoqiang Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P.R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P.R. China
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11
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Chaudhuri D, Banerjee S, Chakraborty S, Chowdhury D, Haldar S. Direct Observation of the Mechanical Role of Bacterial Chaperones in Protein Folding. Biomacromolecules 2022; 23:2951-2967. [PMID: 35678300 DOI: 10.1021/acs.biomac.2c00451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein folding under force is an integral source of generating mechanical energy in various cellular processes, ranging from protein translation to degradation. Although chaperones are well known to interact with proteins under mechanical force, how they respond to force and control cellular energetics remains unknown. To address this question, we introduce a real-time magnetic tweezer technology herein to mimic the physiological force environment on client proteins, keeping the chaperones unperturbed. We studied two structurally distinct client proteins--protein L and talin with seven different chaperones─independently and in combination and proposed a novel mechanical activity of chaperones. We found that chaperones behave differently, while these client proteins are under force, than their previously known functions. For instance, tunnel-associated chaperones (DsbA and trigger factor), otherwise working as holdase without force, assist folding under force. This process generates an additional mechanical energy up to ∼147 zJ to facilitate translation or translocation. However, well-known cytoplasmic foldase chaperones (PDI, thioredoxin, or DnaKJE) do not possess the mechanical folding ability under force. Notably, the transferring chaperones (DnaK, DnaJ, and SecB) act as holdase and slow down the folding process, both in the presence and absence of force, to prevent misfolding of the client proteins. This provides an emerging insight of mechanical roles of chaperones: they can generate or consume energy by shifting the energy landscape of the client proteins toward a folded or an unfolded state, suggesting an evolutionary mechanism to minimize energy consumption in various biological processes.
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Affiliation(s)
- Deep Chaudhuri
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Souradeep Banerjee
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Soham Chakraborty
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Debojyoti Chowdhury
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Shubhasis Haldar
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
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12
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The Power of Touch: Type 4 Pili, the von Willebrand A Domain, and Surface Sensing by Pseudomonas aeruginosa. J Bacteriol 2022; 204:e0008422. [PMID: 35612303 PMCID: PMC9210963 DOI: 10.1128/jb.00084-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Most microbes in the biosphere are attached to surfaces, where they experience mechanical forces due to hydrodynamic flow and cell-to-substratum interactions. These forces likely serve as mechanical cues that influence bacterial physiology and eventually drive environmental adaptation and fitness. Mechanosensors are cellular components capable of sensing a mechanical input and serve as part of a larger system for sensing and transducing mechanical signals. Two cellular components in bacteria that have emerged as candidate mechanosensors are the type IV pili (TFP) and the flagellum. Current models posit that bacteria transmit and convert TFP- and/or flagellum-dependent mechanical force inputs into biochemical signals, including cAMP and c-di-GMP, to drive surface adaptation. Here, we discuss the impact of force-induced changes on the structure and function of two eukaryotic proteins, titin and the human von Willebrand factor (vWF), and these proteins’ relevance to bacteria. Given the wealth of understanding about these eukaryotic mechanosensors, we can use them as a framework to understand the effect of force on Pseudomonas aeruginosa during the early stages of biofilm formation, with a particular emphasis on TFP and the documented surface-sensing mechanosensors PilY1 and FimH. We also discuss the importance of disulfide bonds in mediating force-induced conformational changes, which may modulate mechanosensing and downstream biochemical signaling. We conclude by sharing our perspective on the state of the field and what we deem exciting frontiers in studying bacterial mechanosensing to better understand the mechanisms whereby bacteria transition from a planktonic to a biofilm lifestyle.
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13
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Mora M, Board S, Languin-Cattoën O, Masino L, Stirnemann G, Garcia-Manyes S. A Single-Molecule Strategy to Capture Non-native Intramolecular and Intermolecular Protein Disulfide Bridges. NANO LETTERS 2022; 22:3922-3930. [PMID: 35549281 PMCID: PMC9136921 DOI: 10.1021/acs.nanolett.2c00043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/23/2022] [Indexed: 05/04/2023]
Abstract
Non-native disulfide bonds are dynamic covalent bridges that form post-translationally between two cysteines within the same protein (intramolecular) or with a neighboring protein (intermolecular), frequently due to changes in the cellular redox potential. The reversible formation of non-native disulfides is intimately linked to alterations in protein function; while they can provide a mechanism to protect against cysteine overoxidation, they are also involved in the early stages of protein multimerization, a hallmark of several protein aggregation diseases. Yet their identification using current protein chemistry technology remains challenging, mainly because of their fleeting reactivity. Here, we use single-molecule spectroscopy AFM and molecular dynamics simulations to capture both intra- and intermolecular disulfide bonds in γD-crystallin, a cysteine-rich, structural human lens protein involved in age-related eye cataracts. Our approach showcases the power of mechanical force as a conformational probe in dynamically evolving proteins and presents a platform to detect non-native disulfide bridges with single-molecule resolution.
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Affiliation(s)
- Marc Mora
- Department
of Physics, Randall Centre for Cell and Molecular Biophysics and London
Centre for Nanotechnology, King’s
College London, Strand, WC2R 2LS London, United Kingdom
- Single
Molecule Mechanobiology Laboratory, The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, London United
Kingdom
| | - Stephanie Board
- Department
of Physics, Randall Centre for Cell and Molecular Biophysics and London
Centre for Nanotechnology, King’s
College London, Strand, WC2R 2LS London, United Kingdom
- Single
Molecule Mechanobiology Laboratory, The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, London United
Kingdom
| | - Olivier Languin-Cattoën
- CNRS
Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Diderot,
Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Laura Masino
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, 1 Midland Road London, NW1 1AT, United Kingdom
| | - Guillaume Stirnemann
- CNRS
Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Diderot,
Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sergi Garcia-Manyes
- Department
of Physics, Randall Centre for Cell and Molecular Biophysics and London
Centre for Nanotechnology, King’s
College London, Strand, WC2R 2LS London, United Kingdom
- Single
Molecule Mechanobiology Laboratory, The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, London United
Kingdom
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14
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Peters DT, Reifs A, Alonso-Caballero A, Madkour A, Waller H, Kenny B, Perez-Jimenez R, Lakey JH. Unraveling the molecular determinants of the anti-phagocytic protein cloak of plague bacteria. PLoS Pathog 2022; 18:e1010447. [PMID: 35358289 PMCID: PMC9004762 DOI: 10.1371/journal.ppat.1010447] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 04/12/2022] [Accepted: 03/16/2022] [Indexed: 12/03/2022] Open
Abstract
The pathogenic bacterium Yersina pestis is protected from macrophage engulfment by a capsule like antigen, F1, formed of long polymers of the monomer protein, Caf1. However, despite the importance of this pathogen, the mechanism of protection was not understood. Here we demonstrate how F1 protects the bacteria from phagocytosis. First, we show that Escherichia coli expressing F1 showed greatly reduced adherence to macrophages. Furthermore, the few cells that did adhere remained on the macrophage surface and were not engulfed. We then inserted, by mutation, an “RGDS” integrin binding motif into Caf1. This did not change the number of cells adhering to macrophages but increased the fraction of adherent cells that were engulfed. Therefore, F1 protects in two separate ways, reducing cell adhesion, possibly by acting as a polymer brush, and hiding innate receptor binding sites needed for engulfment. F1 is very robust and we show that E. coli expressing weakened mutant polymers are engulfed like the RGDS mutant. This suggests that innate attachment sites on the native cell surface are exposed if F1 is weakened. Single-molecule force spectroscopy (SMFS) experiments revealed that wild-type F1 displays a very high mechanical stability of 400 pN. However, the mechanical resistance of the destabilised mutants, that were fully engulfed, was only 20% weaker. By only marginally exceeding the mechanical force applied to the Caf1 polymer during phagocytosis it may be that the exceptional tensile strength evolved to resist the forces applied at this stage of engulfment. Macrophages, a type of white blood cell, form an important element of our immune defence. They interrogate other cells’ surfaces for molecular clues and ingest those presenting a threat in a process known as phagocytosis. Not surprisingly, pathogenic bacteria have developed ways to evade this fate. The plague bacterium, Yersinia pestis, produces the long polymeric F1 coat protein which enables it to avoid ingestion, but the mechanism was unclear. We show that equipping Escherichia coli cells with an F1 coat protected them from phagocytosis by two separate mechanisms, reducing contact with the macrophage surface and hiding the signals that tell the macrophages they are targets. F1 is also a very stable protein polymer and using single molecule force spectroscopy we showed it also has a very high resistance to pulling forces. Surprisingly, mutations which reduced this by only 20% caused adherent bacteria to be fully ingested, indicating that cells are subject to significant forces prior to recognition and ingestion. Thus, F1 has evolved three notable properties (i) physical; creation of a hydrated polymer brush to inhibit surface interactions, (ii) chemical; absence of molecular recognition clues needed for engulfment and (iii) mechanical; strength that maintains the camouflage layer during surface stretching.
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Affiliation(s)
- Daniel T. Peters
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | | | - Azzeldin Madkour
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Helen Waller
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Brendan Kenny
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Raul Perez-Jimenez
- CIC nanoGUNE BRTA, San Sebastian, Spain
- Ikerbasque Foundation for Science, Bilbao, Spain
| | - Jeremy H. Lakey
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail:
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15
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Nagy K, Dukic B, Hodula O, Ábrahám Á, Csákvári E, Dér L, Wetherington MT, Noorlag J, Keymer JE, Galajda P. Emergence of Resistant Escherichia coli Mutants in Microfluidic On-Chip Antibiotic Gradients. Front Microbiol 2022; 13:820738. [PMID: 35391738 PMCID: PMC8981919 DOI: 10.3389/fmicb.2022.820738] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Spatiotemporal structures and heterogeneities are common in natural habitats, yet their role in the evolution of antibiotic resistance is still to be uncovered. We applied a microfluidic gradient generator device to study the emergence of resistant bacteria in spatial ciprofloxacin gradients. We observed biofilm formation in regions with sub-inhibitory concentrations of antibiotics, which quickly expanded into the high antibiotic regions. In the absence of an explicit structure of the habitat, this multicellular formation led to a spatial structure of the population with local competition and limited migration. Therefore, such structures can function as amplifiers of selection and aid the spread of beneficial mutations. We found that the physical environment itself induces stress-related mutations that later prove beneficial when cells are exposed to antibiotics. This shift in function suggests that exaptation occurs in such experimental scenarios. The above two processes pave the way for the subsequent emergence of highly resistant specific mutations.
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Affiliation(s)
- Krisztina Nagy
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- *Correspondence: Krisztina Nagy,
| | - Barbara Dukic
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Orsolya Hodula
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Ágnes Ábrahám
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | - Eszter Csákvári
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - László Dér
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | | | - Janneke Noorlag
- Department of Natural Sciences and Technology, University of Aysén, Coyhaique, Chile
| | - Juan E. Keymer
- Department of Natural Sciences and Technology, University of Aysén, Coyhaique, Chile
| | - Péter Galajda
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Péter Galajda,
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16
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Shapiro DM, Mandava G, Yalcin SE, Arranz-Gibert P, Dahl PJ, Shipps C, Gu Y, Srikanth V, Salazar-Morales AI, O'Brien JP, Vanderschuren K, Vu D, Batista VS, Malvankar NS, Isaacs FJ. Protein nanowires with tunable functionality and programmable self-assembly using sequence-controlled synthesis. Nat Commun 2022; 13:829. [PMID: 35149672 PMCID: PMC8837800 DOI: 10.1038/s41467-022-28206-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/13/2022] [Indexed: 12/17/2022] Open
Abstract
Advances in synthetic biology permit the genetic encoding of synthetic chemistries at monomeric precision, enabling the synthesis of programmable proteins with tunable properties. Bacterial pili serve as an attractive biomaterial for the development of engineered protein materials due to their ability to self-assemble into mechanically robust filaments. However, most biomaterials lack electronic functionality and atomic structures of putative conductive proteins are not known. Here, we engineer high electronic conductivity in pili produced by a genomically-recoded E. coli strain. Incorporation of tryptophan into pili increased conductivity of individual filaments >80-fold. Computationally-guided ordering of the pili into nanostructures increased conductivity 5-fold compared to unordered pili networks. Site-specific conjugation of pili with gold nanoparticles, facilitated by incorporating the nonstandard amino acid propargyloxy-phenylalanine, increased filament conductivity ~170-fold. This work demonstrates the sequence-defined production of highly-conductive protein nanowires and hybrid organic-inorganic biomaterials with genetically-programmable electronic functionalities not accessible in nature or through chemical-based synthesis. Bacterial hairs called pili become highly-conductive electric wires upon addition of both natural and synthetic amino acids conjugated with gold nanoparticles. Here the authors use computationally-guided ordering further increasing their conductivity, thus yielding genetically-programmable materials.
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Affiliation(s)
- Daniel Mark Shapiro
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, 06520, USA.,Systems Biology Institute, Yale University, West Haven, CT, 06516, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA
| | - Gunasheil Mandava
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA
| | - Sibel Ebru Yalcin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA
| | - Pol Arranz-Gibert
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, 06520, USA.,Systems Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Peter J Dahl
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA
| | - Catharine Shipps
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA
| | - Yangqi Gu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA
| | - Vishok Srikanth
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA
| | - Aldo I Salazar-Morales
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA
| | - J Patrick O'Brien
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA
| | - Koen Vanderschuren
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, 06520, USA.,Systems Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Dennis Vu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Nikhil S Malvankar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA. .,Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA.
| | - Farren J Isaacs
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, 06520, USA. .,Systems Biology Institute, Yale University, West Haven, CT, 06516, USA. .,Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA.
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17
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Stirnemann G. Recent Advances and Emerging Challenges in the Molecular Modeling of Mechanobiological Processes. J Phys Chem B 2022; 126:1365-1374. [PMID: 35143190 DOI: 10.1021/acs.jpcb.1c10715] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many biological processes result from the effect of mechanical forces on macromolecular structures and on their interactions. In particular, the cell shape, motion, and differentiation directly depend on mechanical stimuli from the extracellular matrix or from neighboring cells. The development of experimental techniques that can measure and characterize the tiny forces acting at the cellular scale and down to the single-molecule, biomolecular level has enabled access to unprecedented details about the involved mechanisms. However, because the experimental observables often do not provide a direct atomistic picture of the corresponding phenomena, particle-based simulations performed at various scales are instrumental in complementing these experiments and in providing a molecular interpretation. Here, we will review the recent key achievements in the field, and we will highlight and discuss the many technical challenges these simulations are facing, as well as suggest future directions for improvement.
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Affiliation(s)
- Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France
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18
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Furniss RCD, Kaderabkova N, Barker D, Bernal P, Maslova E, Antwi AA, McNeil HE, Pugh HL, Dortet L, Blair JM, Larrouy-Maumus GJ, McCarthy RR, Gonzalez D, Mavridou DA. Breaking antimicrobial resistance by disrupting extracytoplasmic protein folding. eLife 2022; 11:57974. [PMID: 35025730 PMCID: PMC8863373 DOI: 10.7554/elife.57974] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 01/11/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance in Gram-negative bacteria is one of the greatest threats to global health. New antibacterial strategies are urgently needed, and the development of antibiotic adjuvants that either neutralize resistance proteins or compromise the integrity of the cell envelope is of ever-growing interest. Most available adjuvants are only effective against specific resistance proteins. Here, we demonstrate that disruption of cell envelope protein homeostasis simultaneously compromises several classes of resistance determinants. In particular, we find that impairing DsbA-mediated disulfide bond formation incapacitates diverse β-lactamases and destabilizes mobile colistin resistance enzymes. Furthermore, we show that chemical inhibition of DsbA sensitizes multidrug-resistant clinical isolates to existing antibiotics and that the absence of DsbA, in combination with antibiotic treatment, substantially increases the survival of Galleria mellonella larvae infected with multidrug-resistant Pseudomonas aeruginosa. This work lays the foundation for the development of novel antibiotic adjuvants that function as broad-acting resistance breakers. Antibiotics, like penicillin, are the foundation of modern medicine, but bacteria are evolving to resist their effects. Some of the most harmful pathogens belong to a group called the 'Gram-negative bacteria', which have an outer layer – called the cell envelope – that acts as a drug barrier. This envelope contains antibiotic resistance proteins that can deactivate or repel antibiotics or even pump them out of the cell once they get in. One way to tackle antibiotic resistance could be to stop these proteins from working. Proteins are long chains of building blocks called amino acids that fold into specific shapes. In order for a protein to perform its role correctly, it must fold in the right way. In bacteria, a protein called DsbA helps other proteins fold correctly by holding them in place and inserting links called disulfide bonds. It was unclear whether DsbA plays a role in the folding of antibiotic resistance proteins, but if it did, it might open up new ways to treat antibiotic resistant infections. To find out more, Furniss, Kaderabkova et al. collected the genes that code for several antibiotic resistance proteins and put them into Escherichia coli bacteria, which made the bacteria resistant to antibiotics. Furniss, Kaderabkova et al. then stopped the modified E. coli from making DsbA, which led to the antibiotic resistance proteins becoming unstable and breaking down because they could not fold correctly. Further experiments showed that blocking DsbA with a chemical inhibitor in other pathogenic species of Gram-negative bacteria made these bacteria more sensitive to antibiotics that they would normally resist. To demonstrate that using this approach could work to stop infections by these bacteria, Furniss, Kaderabkova et al. used Gram-negative bacteria that produced antibiotic resistance proteins but could not make DsbA to infect insect larvae. The larvae were then treated with antibiotics, which increased their survival rate, indicating that blocking DsbA may be a good approach to tackling antibiotic resistant bacteria. According to the World Health Organization, developing new treatments against Gram-negative bacteria is of critical importance, but the discovery of new drugs has ground to a halt. One way around this is to develop ways to make existing drugs work better. Making drugs that block DsbA could offer a way to treat resistant infections using existing antibiotics in the future.
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Affiliation(s)
| | - Nikol Kaderabkova
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
| | - Declan Barker
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Patricia Bernal
- Department of Microbiology, Universidad de Sevilla, Seville, Spain
| | - Evgenia Maslova
- Department of Life Sciences, Brunel University London, London, United Kingdom
| | - Amanda Aa Antwi
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Helen E McNeil
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Hannah L Pugh
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Laurent Dortet
- Department of Bacteriology-Hygiene, Paris-Sud University, Paris, France
| | - Jessica Ma Blair
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | | | - Ronan R McCarthy
- Department of Life Sciences, Brunel University London, London, United Kingdom
| | - Diego Gonzalez
- Department of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - Despoina Ai Mavridou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
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19
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Nie J, Tian F, Zheng B, Wang Z, Zheng P. Exploration of Metal-Ligand Coordination Bonds in Proteins by Single-molecule Force Spectroscopy. CHEM LETT 2021. [DOI: 10.1246/cl.210307] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Ziyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
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20
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Eckels EC, Chaudhuri D, Chakraborty S, Echelman DJ, Haldar S. DsbA is a redox-switchable mechanical chaperone. Chem Sci 2021; 12:11109-11120. [PMID: 34522308 PMCID: PMC8386657 DOI: 10.1039/d1sc03048e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 07/17/2021] [Indexed: 12/18/2022] Open
Abstract
DsbA is a ubiquitous bacterial oxidoreductase that associates with substrates during and after translocation, yet its involvement in protein folding and translocation remains an open question. Here we demonstrate a redox-controlled chaperone activity of DsbA, on both cysteine-containing and cysteine-free substrates, using magnetic tweezers-based single molecule force spectroscopy that enables independent measurements of oxidoreductase activity and chaperone behavior. Interestingly we found that this chaperone activity is tuned by the oxidation state of DsbA; oxidized DsbA is a strong promoter of folding, but the effect is weakened by the reduction of the catalytic CXXC motif. We further localize the chaperone binding site of DsbA using a seven-residue peptide which effectively blocks the chaperone activity. We found that the DsbA assisted folding of proteins in the periplasm generates enough mechanical work to decrease the ATP consumption needed for periplasmic translocation by up to 33%.
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Affiliation(s)
- Edward C Eckels
- Department of Biological Sciences, Columbia University New York NY 10027 USA
- Department of Internal Medicine, Columbia University Medical Center New York NY 10032 USA
| | - Deep Chaudhuri
- Department of Biological Sciences, Ashoka University Sonepat Haryana 131029 India
| | - Soham Chakraborty
- Department of Biological Sciences, Ashoka University Sonepat Haryana 131029 India
| | - Daniel J Echelman
- Department of Biological Sciences, Columbia University New York NY 10027 USA
| | - Shubhasis Haldar
- Department of Biological Sciences, Ashoka University Sonepat Haryana 131029 India
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21
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Alegre-Cebollada J. Protein nanomechanics in biological context. Biophys Rev 2021; 13:435-454. [PMID: 34466164 PMCID: PMC8355295 DOI: 10.1007/s12551-021-00822-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/05/2021] [Indexed: 12/20/2022] Open
Abstract
How proteins respond to pulling forces, or protein nanomechanics, is a key contributor to the form and function of biological systems. Indeed, the conventional view that proteins are able to diffuse in solution does not apply to the many polypeptides that are anchored to rigid supramolecular structures. These tethered proteins typically have important mechanical roles that enable cells to generate, sense, and transduce mechanical forces. To fully comprehend the interplay between mechanical forces and biology, we must understand how protein nanomechanics emerge in living matter. This endeavor is definitely challenging and only recently has it started to appear tractable. Here, I introduce the main in vitro single-molecule biophysics methods that have been instrumental to investigate protein nanomechanics over the last 2 decades. Then, I present the contemporary view on how mechanical force shapes the free energy of tethered proteins, as well as the effect of biological factors such as post-translational modifications and mutations. To illustrate the contribution of protein nanomechanics to biological function, I review current knowledge on the mechanobiology of selected muscle and cell adhesion proteins including titin, talin, and bacterial pilins. Finally, I discuss emerging methods to modulate protein nanomechanics in living matter, for instance by inducing specific mechanical loss-of-function (mLOF). By interrogating biological systems in a causative manner, these new tools can contribute to further place protein nanomechanics in a biological context.
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22
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Baker JL, Dahlberg T, Bullitt E, Andersson M. Impact of an alpha helix and a cysteine-cysteine disulfide bond on the resistance of bacterial adhesion pili to stress. Proc Natl Acad Sci U S A 2021; 118:e2023595118. [PMID: 34011607 PMCID: PMC8166124 DOI: 10.1073/pnas.2023595118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Escherichia coli express adhesion pili that mediate attachment to host cell surfaces and are exposed to body fluids in the urinary and gastrointestinal tracts. Pilin subunits are organized into helical polymers, with a tip adhesin for specific host binding. Pili can elastically unwind when exposed to fluid flow forces, reducing the adhesin load, thereby facilitating sustained attachment. Here we investigate biophysical and structural differences of pili commonly expressed on bacteria that inhabit the urinary and intestinal tracts. Optical tweezers measurements reveal that class 1a pili of uropathogenic E. coli (UPEC), as well as class 1b of enterotoxigenic E. coli (ETEC), undergo an additional conformational change beyond pilus unwinding, providing significantly more elasticity to their structure than ETEC class 5 pili. Examining structural and steered molecular dynamics simulation data, we find that this difference in class 1 pili subunit behavior originates from an α-helical motif that can unfold when exposed to force. A disulfide bond cross-linking β-strands in class 1 pili stabilizes subunits, allowing them to tolerate higher forces than class 5 pili that lack this covalent bond. We suggest that these extra contributions to pilus resiliency are relevant for the UPEC niche, since resident bacteria are exposed to stronger, more transient drag forces compared to those experienced by ETEC bacteria in the mucosa of the intestinal tract. Interestingly, class 1b ETEC pili include the same structural features seen in UPEC pili, while requiring lower unwinding forces that are more similar to those of class 5 ETEC pili.
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Affiliation(s)
- Joseph L Baker
- Department of Chemistry, The College of New Jersey, Ewing, NJ 08628;
| | | | - Esther Bullitt
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA 02118
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23
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Applications of atomic force microscopy in modern biology. Emerg Top Life Sci 2021; 5:103-111. [PMID: 33600596 DOI: 10.1042/etls20200255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/25/2020] [Accepted: 01/22/2021] [Indexed: 01/20/2023]
Abstract
Single-molecule force spectroscopy (SMFS) is an emerging tool to investigate mechanical properties of biomolecules and their responses to mechanical forces, and one of the most-used techniques for mechanical manipulation is the atomic force microscope (AFM). AFM was invented as an imaging tool which can be used to image biomolecules in sub-molecular resolution in physiological conditions. It can also be used as a molecular force probe for applying mechanical forces on biomolecules. In this brief review, we will provide exciting examples from recent literature which show how the advances in AFM have enabled us to gain deep insights into mechanical properties and mechanobiology of biomolecules. AFM has been applied to study mechanical properties of cells, tissues, microorganisms, viruses as well as biological macromolecules such as proteins. It has found applications in biomedical fields like cancer biology, where it has been used both in the diagnostic phases as well as drug discovery. AFM has been able to answer questions pertaining to mechanosensing by neurons, and mechanical changes in viruses during infection by the viral particles as well as the fundamental processes such as cell division. Fundamental questions related to protein folding have also been answered by SMFS like determination of energy landscape properties of variety of proteins and their correlation with their biological functions. A multipronged approach is needed to diversify the research, as a combination with optical spectroscopy and computer-based steered molecular dynamic simulations along with SMFS can help us gain further insights into the field of biophysics and modern biology.
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24
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Beaussart A, Feuillie C, El-Kirat-Chatel S. The microbial adhesive arsenal deciphered by atomic force microscopy. NANOSCALE 2020; 12:23885-23896. [PMID: 33289756 DOI: 10.1039/d0nr07492f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Microbes employ a variety of strategies to adhere to abiotic and biotic surfaces, as well as host cells. In addition to their surface physicochemical properties (e.g. charge, hydrophobic balance), microbes produce appendages (e.g. pili, fimbriae, flagella) and express adhesion proteins embedded in the cell wall or cell membrane, with adhesive domains targeting specific ligands or chemical properties. Atomic force microscopy (AFM) is perfectly suited to deciphering the adhesive properties of microbial cells. Notably, AFM imaging has revealed the cell wall topographical organization of live cells at unprecedented resolution, and AFM has a dual capability to probe adhesion at the single-cell and single-molecule levels. AFM is thus a powerful tool for unravelling the molecular mechanisms of microbial adhesion at scales ranging from individual molecular interactions to the behaviours of entire cells. In this review, we cover some of the major breakthroughs facilitated by AFM in deciphering the microbial adhesive arsenal, including the exciting development of anti-adhesive strategies.
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25
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Song G, Ding X, Liu H, Yuan G, Tian F, Shi S, Yang Y, Li G, Zheng P. Single-Molecule Force Spectroscopy Reveals that the Fe-N Bond Enables Multiple Rupture Pathways of the 2Fe2S Cluster in a MitoNEET Monomer. Anal Chem 2020; 92:14783-14789. [PMID: 33048522 DOI: 10.1021/acs.analchem.0c03536] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The mitochondrial outer membrane protein, mitoNEET (mNT), is an iron-sulfur protein containing an Fe2S2(His)1(Cys)3 cluster with a unique single Fe-N bond. Previous studies have shown that this Fe(III)-N(His) bond is essential for metal cluster transfer and protein function. To further understand the effect of this unique Fe-N bond on the metal cluster and protein, we used atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to investigate the mechanical unfolding mechanism of an mNT monomer, focusing on the rupture pathway and kinetic stability of the cluster. We found that the Fe-N bond was the weakest point of the cluster, the rupture of which occurred first, and could be independent of the cluster break. Moreover, this Fe-N bond enabled a dynamic and labile iron-sulfur cluster, as multiple unfolding pathways of mNT with a unique Fe2S2(Cys)3 intermediate were observed accordingly.
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Affiliation(s)
- Guobin Song
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Xuan Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Huaxing Liu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Guodong Yuan
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Yang Yang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Guoqiang Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
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26
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He LH, Wang H, Liu Y, Kang M, Li T, Li CC, Tong AP, Zhu YB, Song YJ, Savarino SJ, Prouty MG, Xia D, Bao R. Chaperone-tip adhesin complex is vital for synergistic activation of CFA/I fimbriae biogenesis. PLoS Pathog 2020; 16:e1008848. [PMID: 33007034 PMCID: PMC7531860 DOI: 10.1371/journal.ppat.1008848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 07/30/2020] [Indexed: 02/05/2023] Open
Abstract
Colonization factor CFA/I defines the major adhesive fimbriae of enterotoxigenic Escherichia coli and mediates bacterial attachment to host intestinal epithelial cells. The CFA/I fimbria consists of a tip-localized minor adhesive subunit, CfaE, and thousands of copies of the major subunit CfaB polymerized into an ordered helical rod. Biosynthesis of CFA/I fimbriae requires the assistance of the periplasmic chaperone CfaA and outer membrane usher CfaC. Although the CfaE subunit is proposed to initiate the assembly of CFA/I fimbriae, how it performs this function remains elusive. Here, we report the establishment of an in vitro assay for CFA/I fimbria assembly and show that stabilized CfaA-CfaB and CfaA-CfaE binary complexes together with CfaC are sufficient to drive fimbria formation. The presence of both CfaA-CfaE and CfaC accelerates fimbria formation, while the absence of either component leads to linearized CfaB polymers in vitro. We further report the crystal structure of the stabilized CfaA-CfaE complex, revealing features unique for biogenesis of Class 5 fimbriae.
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Affiliation(s)
- Li-hui He
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Wang
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
- Enteric Diseases Department, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Yang Liu
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
- Enteric Diseases Department, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Mei Kang
- Department of Laboratory medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Chang-cheng Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ai-ping Tong
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yi-bo Zhu
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ying-jie Song
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Stephen J. Savarino
- Enteric Diseases Department, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, United States of America
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Michael G. Prouty
- Enteric Diseases Department, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Rui Bao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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27
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Zyla D, Echeverria B, Glockshuber R. Donor strand sequence, rather than donor strand orientation, determines the stability and non-equilibrium folding of the type 1 pilus subunit FimA. J Biol Chem 2020; 295:12437-12448. [PMID: 32651228 DOI: 10.1074/jbc.ra120.014324] [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: 05/11/2020] [Revised: 07/07/2020] [Indexed: 11/06/2022] Open
Abstract
FimA is the main structural subunit of adhesive type 1 pili from uropathogenic Escherichia coli strains. Up to 3000 copies of FimA assemble to the helical pilus rod through a mechanism termed donor strand complementation, in which the incomplete immunoglobulin-like fold of each FimA subunit is complemented by the N-terminal extension (Nte) of the next subunit. The Nte of FimA, which exhibits a pseudo-palindromic sequence, is inserted in an antiparallel orientation relative to the last β-strand of the preceding subunit in the pilus. The resulting subunit-subunit interactions are extraordinarily stable against dissociation and unfolding. Alternatively, FimA can fold to a self-complemented monomer with anti-apoptotic activity, in which the Nte inserts intramolecularly into the FimA core in the opposite, parallel orientation. The FimA monomers, however, show dramatically lower thermodynamic stability compared with FimA subunits in the assembled pilus. Using self-complemented FimA variants with reversed, pseudo-palindromic extensions, we demonstrate that the high stability of FimA polymers is primarily caused by the specific interactions between the side chains of the Nte residues and the FimA core and not by the antiparallel orientation of the donor strand alone. In addition, we demonstrate that nonequilibrium two-state folding, a hallmark of FimA with the Nte inserted in the pilus rod-like, antiparallel orientation, only depends on the identity of the inserted Nte side chains and not on Nte orientation.
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Affiliation(s)
- Dawid Zyla
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Blanca Echeverria
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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28
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Sharma S, Subramani S, Popa I. Does protein unfolding play a functional role in vivo? FEBS J 2020; 288:1742-1758. [PMID: 32761965 DOI: 10.1111/febs.15508] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022]
Abstract
Unfolding and refolding of multidomain proteins under force have yet to be recognized as a major mechanism of function for proteins in vivo. In this review, we discuss the inherent properties of multidomain proteins under a force vector from a structural and functional perspective. We then characterize three main systems where multidomain proteins could play major roles through mechanical unfolding: muscular contraction, cellular mechanotransduction, and bacterial adhesion. We analyze how key multidomain proteins for each system can produce a gain-of-function from the perspective of a fine-tuned quantized response, a molecular battery, delivery of mechanical work through refolding, elasticity tuning, protection and exposure of cryptic sites, and binding-induced mechanical changes. Understanding how mechanical unfolding and refolding affect function will have important implications in designing mechano-active drugs against conditions such as muscular dystrophy, cancer, or novel antibiotics.
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Affiliation(s)
- Sabita Sharma
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Smrithika Subramani
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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29
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El-Kirat-Chatel S, Beaussart A, Mathelié-Guinlet M, Dufrêne YF. The importance of force in microbial cell adhesion. Curr Opin Colloid Interface Sci 2020. [DOI: 10.1016/j.cocis.2019.12.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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30
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Yang B, Liu Z, Liu H, Nash MA. Next Generation Methods for Single-Molecule Force Spectroscopy on Polyproteins and Receptor-Ligand Complexes. Front Mol Biosci 2020; 7:85. [PMID: 32509800 PMCID: PMC7248566 DOI: 10.3389/fmolb.2020.00085] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/16/2020] [Indexed: 12/31/2022] Open
Abstract
Single-molecule force spectroscopy with the atomic force microscope provides molecular level insights into protein function, allowing researchers to reconstruct energy landscapes and understand functional mechanisms in biology. With steadily advancing methods, this technique has greatly accelerated our understanding of force transduction, mechanical deformation, and mechanostability within single- and multi-domain polyproteins, and receptor-ligand complexes. In this focused review, we summarize the state of the art in terms of methodology and highlight recent methodological improvements for AFM-SMFS experiments, including developments in surface chemistry, considerations for protein engineering, as well as theory and algorithms for data analysis. We hope that by condensing and disseminating these methods, they can assist the community in improving data yield, reliability, and throughput and thereby enhance the information that researchers can extract from such experiments. These leading edge methods for AFM-SMFS will serve as a groundwork for researchers cognizant of its current limitations who seek to improve the technique in the future for in-depth studies of molecular biomechanics.
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Affiliation(s)
- Byeongseon Yang
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Zhaowei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Haipei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michael A. Nash
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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31
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Corsetti F, Alonso-Caballero A, Poly S, Perez-Jimenez R, Artacho E. Entropic bonding of the type 1 pilus from experiment and simulation. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200183. [PMID: 32431906 PMCID: PMC7211842 DOI: 10.1098/rsos.200183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/19/2020] [Indexed: 06/11/2023]
Abstract
The type 1 pilus is a bacterial filament consisting of a long coiled proteic chain of subunits joined together by non-covalent bonding between complementing β -strands. Its strength and structural stability are critical for its anchoring function in uropathogenic Escherichia coli bacteria. The pulling and unravelling of the FimG subunit of the pilus was recently studied by atomic force microscopy experiments and steered molecular dynamics simulations (Alonso-Caballero et al. 2018 Nat. Commun. 9, 2758. (doi:10.1038/s41467-018-05107-6)). In this work, we perform a quantitative comparison between experiment and simulation, showing a good agreement in the underlying work values for the unfolding. The simulation results are then used to estimate the free energy difference for the detachment of FimG from the complementing strand of the neighbouring subunit in the chain, FimF. Finally, we show that the large free energy difference for the unravelling and detachment of the subunits which leads to the high stability of the chain is entirely entropic in nature.
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Affiliation(s)
- Fabiano Corsetti
- Department of Materials, Imperial College London, London SW7 2AZ, UK
- Department of Physics, Imperial College London, London SW7 2AZ, UK
- The Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, UK
- CIC nanoGUNE, 20018 Donostia-San Sebastián, Spain
| | - Alvaro Alonso-Caballero
- CIC nanoGUNE, 20018 Donostia-San Sebastián, Spain
- Department of Biological Sciences, Columbia University, NY 10027, USA
| | - Simon Poly
- CIC nanoGUNE, 20018 Donostia-San Sebastián, Spain
- Chimie et Biologie des Membranes et des Nanoobjets CBMN, Université de Bordeaux, 33600 Pessac, France
| | - Raul Perez-Jimenez
- CIC nanoGUNE, 20018 Donostia-San Sebastián, Spain
- Basque Foundation for Science Ikerbasque, 48011 Bilbao, Spain
| | - Emilio Artacho
- CIC nanoGUNE, 20018 Donostia-San Sebastián, Spain
- Basque Foundation for Science Ikerbasque, 48011 Bilbao, Spain
- Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
- Donostia International Physics Center DIPC, 20018 Donostia-San Sebastián, Spain
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32
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Dahal N, Nowitzke J, Eis A, Popa I. Binding-Induced Stabilization Measured on the Same Molecular Protein Substrate Using Single-Molecule Magnetic Tweezers and Heterocovalent Attachments. J Phys Chem B 2020; 124:3283-3290. [DOI: 10.1021/acs.jpcb.0c00167] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Narayan Dahal
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Joel Nowitzke
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Annie Eis
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
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33
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Extreme mechanical stability in protein complexes. Curr Opin Struct Biol 2020; 60:124-130. [DOI: 10.1016/j.sbi.2019.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/14/2019] [Accepted: 11/27/2019] [Indexed: 12/21/2022]
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34
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Viela F, Mathelié-Guinlet M, Viljoen A, Dufrêne YF. What makes bacterial pathogens so sticky? Mol Microbiol 2020; 113:683-690. [PMID: 31916325 DOI: 10.1111/mmi.14448] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/06/2020] [Indexed: 01/06/2023]
Abstract
Pathogenic bacteria use a variety of cell surface adhesins to promote binding to host tissues and protein-coated biomaterials, as well as cell-cell aggregation. These cellular interactions represent the first essential step that leads to host colonization and infection. Atomic force microscopy (AFM) has greatly contributed to increase our understanding of the specific interactions at play during microbial adhesion, down to the single-molecule level. A key asset of AFM is that adhesive interactions are studied under mechanical force, which is highly relevant as surface-attached pathogens are often exposed to physical stresses in the human body. These studies have identified sophisticated binding mechanisms in adhesins, which represent promising new targets for antiadhesion therapy.
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Affiliation(s)
- Felipe Viela
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Marion Mathelié-Guinlet
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Albertus Viljoen
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium.,Walloon Excellence in Life sciences and Biotechnology (WELBIO), Wavre, Belgium
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35
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Bernardi RC, Durner E, Schoeler C, Malinowska KH, Carvalho BG, Bayer EA, Luthey-Schulten Z, Gaub HE, Nash MA. Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy. J Am Chem Soc 2019; 141:14752-14763. [PMID: 31464132 PMCID: PMC6939381 DOI: 10.1021/jacs.9b06776] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Can molecular dynamics
simulations predict the mechanical behavior of protein complexes?
Can simulations decipher the role of protein domains of unknown function
in large macromolecular complexes? Here, we employ a wide-sampling
computational approach to demonstrate that molecular dynamics simulations,
when carefully performed and combined with single-molecule atomic
force spectroscopy experiments, can predict and explain the behavior
of highly mechanostable protein complexes. As a test case, we studied
a previously unreported homologue from Ruminococcus flavefaciens called X-module-Dockerin (XDoc) bound to its partner Cohesin (Coh).
By performing dozens of short simulation replicas near the rupture
event, and analyzing dynamic network fluctuations, we were able to
generate large simulation statistics and directly compare them with
experiments to uncover the mechanisms involved in mechanical stabilization.
Our single-molecule force spectroscopy experiments show that the XDoc-Coh
homologue complex withstands forces up to 1 nN at loading rates of
105 pN/s. Our simulation results reveal that this remarkable
mechanical stability is achieved by a protein architecture that directs
molecular deformation along paths that run perpendicular to the pulling
axis. The X-module was found to play a crucial role in shielding the
adjacent protein complex from mechanical rupture. These mechanisms
of protein mechanical stabilization have potential applications in
biotechnology for the development of systems exhibiting shear enhanced
adhesion or tunable mechanics.
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Affiliation(s)
- Rafael C Bernardi
- Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Ellis Durner
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , 80799 Munich , Germany
| | - Constantin Schoeler
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , 80799 Munich , Germany
| | - Klara H Malinowska
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , 80799 Munich , Germany
| | - Bruna G Carvalho
- School of Chemical Engineering , University of Campinas , 13083-852 Campinas , Brazil
| | - Edward A Bayer
- Department of Biomolecular Sciences , Weizmann Institute of Science , 76100 Rehovot , Israel
| | - Zaida Luthey-Schulten
- Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , 80799 Munich , Germany
| | - Michael A Nash
- Department of Chemistry , University of Basel , 4058 Basel , Switzerland.,Department of Biosystems Science and Engineering , ETH Zurich , 4058 Basel , Switzerland
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36
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Liu H, Schittny V, Nash MA. Removal of a Conserved Disulfide Bond Does Not Compromise Mechanical Stability of a VHH Antibody Complex. NANO LETTERS 2019; 19:5524-5529. [PMID: 31257893 PMCID: PMC6975629 DOI: 10.1021/acs.nanolett.9b02062] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/28/2019] [Indexed: 05/28/2023]
Abstract
Single-domain VHH antibodies are promising reagents for medical therapy. A conserved disulfide bond within the VHH framework region is known to be critical for thermal stability, however, no prior studies have investigated its influence on the stability of VHH antibody-antigen complexes under mechanical load. Here, we used single-molecule force spectroscopy to test the influence of a VHH domain's conserved disulfide bond on the mechanical strength of the interaction with its antigen mCherry. We found that although removal of the disulfide bond through cysteine-to-alanine mutagenesis significantly lowered VHH domain denaturation temperature, it had no significant impact on the mechanical strength of the VHH:mCherry interaction with complex rupture occurring at ∼60 pN at 103-104 pN/sec regardless of disulfide bond state. These results demonstrate that mechanostable binding interactions can be built on molecular scaffolds that may be thermodynamically compromised at equilibrium.
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Affiliation(s)
- Haipei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Valentin Schittny
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Michael A. Nash
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
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37
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Abstract
The chaperone-usher (CU) pathway is a conserved secretion system dedicated to the assembly of a superfamily of virulence-associated surface structures by a wide range of Gram-negative bacteria. Pilus biogenesis by the CU pathway requires two specialized assembly components: a dedicated periplasmic chaperone and an integral outer membrane assembly and secretion platform termed the usher. The CU pathway assembles a variety of surface fibers, ranging from thin, flexible filaments to rigid, rod-like organelles. Pili typically act as adhesins and function as virulence factors that mediate contact with host cells and colonization of host tissues. Pilus-mediated adhesion is critical for early stages of infection, allowing bacteria to establish a foothold within the host. Pili are also involved in modulation of host cell signaling pathways, bacterial invasion into host cells, and biofilm formation. Pili are critical for initiating and sustaining infection and thus represent attractive targets for the development of antivirulence therapeutics. Such therapeutics offer a promising alternative to broad-spectrum antibiotics and provide a means to combat antibiotic resistance and treat infection while preserving the beneficial microbiota. A number of strategies have been taken to develop antipilus therapeutics, including vaccines against pilus proteins, competitive inhibitors of pilus-mediated adhesion, and small molecules that disrupt pilus biogenesis. Here we provide an overview of the function and assembly of CU pili and describe current efforts aimed at interfering with these critical virulence structures.
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Deng Y, Wu T, Wang M, Shi S, Yuan G, Li X, Chong H, Wu B, Zheng P. Enzymatic biosynthesis and immobilization of polyprotein verified at the single-molecule level. Nat Commun 2019; 10:2775. [PMID: 31235796 PMCID: PMC6591319 DOI: 10.1038/s41467-019-10696-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/23/2019] [Indexed: 11/09/2022] Open
Abstract
The recent development of chemical and bio-conjugation techniques allows for the engineering of various protein polymers. However, most of the polymerization process is difficult to control. To meet this challenge, we develop an enzymatic procedure to build polyprotein using the combination of a strict protein ligase OaAEP1 (Oldenlandia affinis asparaginyl endopeptidases 1) and a protease TEV (tobacco etch virus). We firstly demonstrate the use of OaAEP1-alone to build a sequence-uncontrolled ubiquitin polyprotein and covalently immobilize the coupled protein on the surface. Then, we construct a poly-metalloprotein, rubredoxin, from the purified monomer. Lastly, we show the feasibility of synthesizing protein polymers with rationally-controlled sequences by the synergy of the ligase and protease, which are verified by protein unfolding using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS). Thus, this study provides a strategy for polyprotein engineering and immobilization.
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Affiliation(s)
- Yibing Deng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Tao Wu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Mengdi Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Guodong Yuan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Xi Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Hanchung Chong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China.
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Hospenthal MK, Waksman G. The Remarkable Biomechanical Properties of the Type 1 Chaperone-Usher Pilus: A Structural and Molecular Perspective. Microbiol Spectr 2019; 7. [PMID: 30681068 DOI: 10.1128/microbiolspec.psib-0010-2018] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Indexed: 01/02/2023] Open
Abstract
Chaperone-usher (CU) pili are long, supramolecular protein fibers tethered to the surface of numerous bacterial pathogens. These virulence factors function primarily in bacterial adhesion to host tissues, but they also mediate biofilm formation. Type 1 and P pili of uropathogenic Escherichia coli (UPEC) are the two best-studied CU pilus examples, and here we primarily focus on the former. UPEC can be transmitted to the urinary tract by fecal shedding. It can then ascend up the urinary tract and cause disease by invading and colonizing host tissues of the bladder, causing cystitis, and the kidneys, causing pyelonephritis. FimH is the subunit displayed at the tip of type 1 pili and mediates adhesion to mannosylated host cells via a unique catch-bond mechanism. In response to shear forces caused by urine flow, FimH can transition from a low-affinity to high-affinity binding mode. This clever allosteric mechanism allows UPEC cells to remain tightly attached during periods of urine flow, while loosening their grip to allow dissemination through the urinary tract during urine stasis. Moreover, the bulk of a CU pilus is made up of the rod, which can reversibly uncoil in response to urine flow to evenly spread the tensile forces over the entire pilus length. We here explore the novel structural and mechanistic findings relating to the type 1 pilus FimH catch-bond and rod uncoiling and explain how they function together to enable successful attachment, spread, and persistence in the hostile urinary tract.
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Affiliation(s)
- Manuela K Hospenthal
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London WC1E 7HX, United Kingdom
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London WC1E 7HX, United Kingdom
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40
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Mechanobiology: protein refolding under force. Emerg Top Life Sci 2018; 2:687-699. [PMID: 33530665 DOI: 10.1042/etls20180044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/19/2018] [Accepted: 09/19/2018] [Indexed: 02/03/2023]
Abstract
The application of direct force to a protein enables to probe wide regions of its energy surface through conformational transitions as unfolding, extending, recoiling, collapsing, and refolding. While unfolding under force typically displayed a two-state behavior, refolding under force, from highly extended unfolded states, displayed a more complex behavior. The first recording of protein refolding at a force quench step displayed an initial rapid elastic recoil, followed by a plateau phase at some extension, concluding with a collapse to a final state, at which refolding occurred. These findings stirred a lively discussion, which led to further experimental and theoretical investigation of this behavior. It was demonstrated that the polymeric chain of the unfolded protein is required to fully collapse to a globular conformation for the maturation of native structure. This behavior was modeled using one-dimensional free energy landscape over the end-to-end length reaction coordinate, the collective measured variable. However, at low forces, conformational space is not well captured by such models, and using two-dimensional energy surfaces provides further insight into the dynamics of this process. This work reviews the main concepts of protein refolding under constant force, which is essential for understanding how mechanotransducing proteins operate in vivo.
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