1
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Galmozzi CV, Tippmann F, Wruck F, Auburger JJ, Kats I, Guennigmann M, Till K, O Brien EP, Tans SJ, Kramer G, Bukau B. Proteome-wide determinants of co-translational chaperone binding in bacteria. Nat Commun 2025; 16:4361. [PMID: 40348781 PMCID: PMC12065913 DOI: 10.1038/s41467-025-59067-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Accepted: 04/10/2025] [Indexed: 05/14/2025] Open
Abstract
Chaperones are essential to the co-translational folding of most proteins. However, the principles of co-translational chaperone interaction throughout the proteome are poorly understood, as current methods are restricted to few substrates and cannot capture nascent protein folding or chaperone binding sites, precluding a comprehensive understanding of productive and erroneous protein biosynthesis. Here, by integrating genome-wide selective ribosome profiling, single-molecule tools, and computational predictions using AlphaFold we show that the binding of the main E. coli chaperones involved in co-translational folding, Trigger Factor (TF) and DnaK correlates with "unsatisfied residues" exposed on nascent partial folds - residues that have begun to form tertiary structure but cannot yet form all native contacts due to ongoing translation. This general principle allows us to predict their co-translational binding across the proteome based on sequence only, which we verify experimentally. The results show that TF and DnaK stably bind partially folded rather than unfolded conformers. They also indicate a synergistic action of TF guiding intra-domain folding and DnaK preventing premature inter-domain contacts, and reveal robustness in the larger chaperone network (TF, DnaK, GroEL). Given the complexity of translation, folding, and chaperone functions, our predictions based on general chaperone binding rules indicate an unexpected underlying simplicity.
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Affiliation(s)
- Carla Verónica Galmozzi
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Frank Tippmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Josef Johannes Auburger
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ilia Kats
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manuel Guennigmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Edward P O Brien
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, PA, USA
| | - Sander J Tans
- AMOLF, Amsterdam, The Netherlands.
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands.
| | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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2
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Silbermann L, Fottner M, van der Meulen R, Migdad N, Lang K, Tych K. One-pot dual protein labeling for simultaneous mechanical and fluorescent readouts in optical tweezers. Protein Sci 2025; 34:e70098. [PMID: 40099877 PMCID: PMC11915586 DOI: 10.1002/pro.70098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 02/14/2025] [Accepted: 02/28/2025] [Indexed: 03/20/2025]
Abstract
Optical tweezers are widely used in the study of biological macromolecules but are limited by their one-directional probing capability, potentially missing critical conformational changes. Combining fluorescence microscopy with optical tweezers, employing Förster resonance energy transfer (FRET) pairs, addresses this issue. When integrating fluorescence microscopy with optical tweezers, orthogonal protein conjugation methods are needed to enable simultaneous, site-specific attachment of fluorophores and DNA handles, commonly used to apply force to molecules of interest. In this study, we utilized commercially available reagents for dual site-specific labeling of the homodimeric heat shock protein 90 (Hsp90) using thiol-maleimide and inverse electron demand Diels-Alder cycloaddition (IEDDAC) bioorthogonal reactions. In a one-pot approach, Hsp90 modified with a cysteine mutation and the non-canonical amino acid cyclopropene-L-lysine (CpK) was labeled with the FRET pair maleimide-Atto 550 and maleimide-Atto 647N, alongside single-stranded methyltetrazine-modified DNA oligonucleotide. Optical tweezers experiments with this labeled Hsp90 construct revealed structural transitions consistent with previous studies, validating the approach. Fluorescence measurements confirmed the proximity of FRET pairs in the N-terminally closed state of Hsp90 in this experimental setup. This integrative method provides a powerful tool for probing complex protein conformational dynamics beyond the limitations of traditional optical tweezers.
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Affiliation(s)
- Laura‐Marie Silbermann
- Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenthe Netherlands
| | - Maximilian Fottner
- Laboratory for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences (D‐CHAB)ETH ZurichZurichSwitzerland
| | - Ronald van der Meulen
- Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenthe Netherlands
| | - Nora Migdad
- Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenthe Netherlands
| | - Kathrin Lang
- Laboratory for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences (D‐CHAB)ETH ZurichZurichSwitzerland
| | - Katarzyna Tych
- Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenthe Netherlands
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3
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Vorobevskaia E, Loot C, Mazel D, Schlierf M. The recombination efficiency of the bacterial integron depends on the mechanical stability of the synaptic complex. SCIENCE ADVANCES 2024; 10:eadp8756. [PMID: 39671485 PMCID: PMC11641012 DOI: 10.1126/sciadv.adp8756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 11/05/2024] [Indexed: 12/15/2024]
Abstract
Multiple antibiotic resistances are a major global health threat. The predominant tool for adaptation in Gram-negative bacteria is the integron. Under stress, it rearranges gene cassettes to offer an escape using the tyrosine recombinase IntI, recognizing folded DNA hairpins, the attC sites. Four recombinases and two attC sites form the synaptic complex. Yet, for unclear reasons, the recombination efficiency varies greatly. Here, we established an optical tweezers force spectroscopy assay to probe the synaptic complex stability and revealed, for seven combinations of attC sites, significant variability in the mechanical stability. We found a strong correlation between mechanical stability and recombination efficiency of attC sites in vivo, indicating a regulatory mechanism from the DNA structure to the macromolecular complex stability. Taking into account known forces during DNA metabolism, we propose that the variation of the integron in vivo recombination efficiency is mediated by the synaptic complex stability. We anticipate that further recombination processes are also affected by their corresponding mechanical stability.
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Affiliation(s)
| | - Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, F-75015 Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, F-75015 Paris, France
| | - Michael Schlierf
- B CUBE, TU Dresden, Tatzberg 41, 01307 Dresden, Germany
- Physics of Life, DFG Cluster of Excellence, TU Dresden, 01062 Dresden, Germany
- Faculty of Physics, TU Dresden, 01062 Dresden, Germany
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4
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Avellaneda MJ, Koers EJ, Sunderlikova V, Tans SJ. Protein Tethering for Single-Molecule Force Spectroscopy. Methods Mol Biol 2024; 2694:57-67. [PMID: 37823999 DOI: 10.1007/978-1-0716-3377-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Molecular manipulation by optical tweezers is a central technique to study the folded states of individual proteins and how they depend on interactions with molecules including DNA, ligands, and other proteins. One of the key challenges of this approach is to stably attach DNA handles in an efficient manner. Here, we provide detailed descriptions of a universal approach to covalently link long DNA tethers of up to 5000 base pairs to proteins with or without native cysteines.
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5
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Scalvini B, Heling LWHJ, Sheikhhassani V, Sunderlikova V, Tans SJ, Mashaghi A. Cytosolic Interactome Protects Against Protein Unfolding in a Single Molecule Experiment. Adv Biol (Weinh) 2023; 7:e2300105. [PMID: 37409427 DOI: 10.1002/adbi.202300105] [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: 03/08/2023] [Revised: 06/13/2023] [Indexed: 07/07/2023]
Abstract
Single molecule techniques are particularly well suited for investigating the processes of protein folding and chaperone assistance. However, current assays provide only a limited perspective on the various ways in which the cellular environment can influence the folding pathway of a protein. In this study, a single molecule mechanical interrogation assay is developed and used to monitor protein unfolding and refolding within a cytosolic solution. This allows to test the cumulative topological effect of the cytoplasmic interactome on the folding process. The results reveal a stabilization against forced unfolding for partial folds, which are attributed to the protective effect of the cytoplasmic environment against unfolding and aggregation. This research opens the possibility of conducting single molecule molecular folding experiments in quasi-biological environments.
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Affiliation(s)
- Barbara Scalvini
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
- Centre for Interdisciplinary Genome Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
| | - Laurens W H J Heling
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
- Centre for Interdisciplinary Genome Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
| | - Vahid Sheikhhassani
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
- Centre for Interdisciplinary Genome Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
| | | | - Sander J Tans
- AMOLF, Science Park 104, Amsterdam, 1098 XG, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629HZ, The Netherlands
| | - Alireza Mashaghi
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
- Centre for Interdisciplinary Genome Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
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6
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Choudhary D, Mediani L, Avellaneda MJ, Bjarnason S, Alberti S, Boczek EE, Heidarsson PO, Mossa A, Carra S, Tans SJ, Cecconi C. Human Small Heat Shock Protein B8 Inhibits Protein Aggregation without Affecting the Native Folding Process. J Am Chem Soc 2023. [PMID: 37411010 PMCID: PMC10360156 DOI: 10.1021/jacs.3c02022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Small Heat Shock Proteins (sHSPs) are key components of our Protein Quality Control system and are thought to act as reservoirs that neutralize irreversible protein aggregation. Yet, sHSPs can also act as sequestrases, promoting protein sequestration into aggregates, thus challenging our understanding of their exact mechanisms of action. Here, we employ optical tweezers to explore the mechanisms of action of the human small heat shock protein HSPB8 and its pathogenic mutant K141E, which is associated with neuromuscular disease. Through single-molecule manipulation experiments, we studied how HSPB8 and its K141E mutant affect the refolding and aggregation processes of the maltose binding protein. Our data show that HSPB8 selectively suppresses protein aggregation without affecting the native folding process. This anti-aggregation mechanism is distinct from previous models that rely on the stabilization of unfolded polypeptide chains or partially folded structures, as has been reported for other chaperones. Rather, it appears that HSPB8 selectively recognizes and binds to aggregated species formed at the early stages of aggregation, preventing them from growing into larger aggregated structures. Consistently, the K141E mutation specifically targets the affinity for aggregated structures without impacting native folding, and hence impairs its anti-aggregation activity.
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Affiliation(s)
- Dhawal Choudhary
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Laura Mediani
- Department of Biomedical, Metabolic and Neural Sciences, and Centre for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
| | - Mario J Avellaneda
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Sveinn Bjarnason
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102 Reykjavík, Iceland
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, D-01307 Dresden, Germany
| | - Edgar E Boczek
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, D-01307 Dresden, Germany
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102 Reykjavík, Iceland
| | - Alessandro Mossa
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy
- INFN Firenze, Via Sansone 1, 50019 Sesto Fiorentino, Italy
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, and Centre for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
| | - Sander J Tans
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Ciro Cecconi
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy
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7
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Haghizadeh A, Iftikhar M, Dandpat SS, Simpson T. Looking at Biomolecular Interactions through the Lens of Correlated Fluorescence Microscopy and Optical Tweezers. Int J Mol Sci 2023; 24:2668. [PMID: 36768987 PMCID: PMC9916863 DOI: 10.3390/ijms24032668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
Understanding complex biological events at the molecular level paves the path to determine mechanistic processes across the timescale necessary for breakthrough discoveries. While various conventional biophysical methods provide some information for understanding biological systems, they often lack a complete picture of the molecular-level details of such dynamic processes. Studies at the single-molecule level have emerged to provide crucial missing links to understanding complex and dynamic pathways in biological systems, which are often superseded by bulk biophysical and biochemical studies. Latest developments in techniques combining single-molecule manipulation tools such as optical tweezers and visualization tools such as fluorescence or label-free microscopy have enabled the investigation of complex and dynamic biomolecular interactions at the single-molecule level. In this review, we present recent advances using correlated single-molecule manipulation and visualization-based approaches to obtain a more advanced understanding of the pathways for fundamental biological processes, and how this combination technique is facilitating research in the dynamic single-molecule (DSM), cell biology, and nanomaterials fields.
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8
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Geiger F, Wendlandt T, Berking T, Spatz JP, Wege C. Convenient site-selective protein coupling from bacterial raw lysates to coenzyme A-modified tobacco mosaic virus (TMV) by Bacillus subtilis Sfp phosphopantetheinyl transferase. Virology 2023; 578:61-70. [PMID: 36473278 DOI: 10.1016/j.virol.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
A facile enzyme-mediated strategy enables site-specific covalent one-step coupling of genetically tagged luciferase molecules to coenzyme A-modified tobacco mosaic virus (TMV-CoA) both in solution and on solid supports. Bacillus subtilis surfactin phosphopantetheinyl transferase Sfp produced in E. coli mediated the conjugation of firefly luciferase N-terminally extended by eleven amino acids forming a 'ybbR tag' as Sfp-selective substrate, which even worked in bacterial raw lysates. The enzymes displayed on the protein coat of the TMV nanocarriers exhibited high activity. As TMV has proven a beneficial high surface-area adapter template stabilizing enzymes in different biosensing layouts in recent years, the use of TMV-CoA for fishing ybbR-tagged proteins from complex mixtures might become an advantageous concept for the versatile equipment of miniaturized devices with biologically active proteins. It comes along with new opportunities for immobilizing multiple functionalities on TMV adapter coatings, as desired, e.g., in handheld systems for point-of-care detection.
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Affiliation(s)
- Fania Geiger
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Jahnstraße 29, 69120, Heidelberg, Germany; Heidelberg University, Institute for Molecular Systems Engineering and Advanced Materials (IMSEAM), Im Neuenheimer Feld 225, 69120, Heidelberg, Germany
| | - Tim Wendlandt
- University of Stuttgart, Institute of Biomaterials and Biomolecular Systems, Research Unit Molecular and Synthetic Plant Virology, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Tim Berking
- University of Stuttgart, Institute of Organic Chemistry, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Joachim P Spatz
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Jahnstraße 29, 69120, Heidelberg, Germany; Heidelberg University, Institute for Molecular Systems Engineering and Advanced Materials (IMSEAM), Im Neuenheimer Feld 225, 69120, Heidelberg, Germany; Max Planck School Matter to Life, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Christina Wege
- University of Stuttgart, Institute of Biomaterials and Biomolecular Systems, Research Unit Molecular and Synthetic Plant Virology, Pfaffenwaldring 57, 70569, Stuttgart, Germany.
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9
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Mulla Y, Avellaneda MJ, Roland A, Baldauf L, Jung W, Kim T, Tans SJ, Koenderink GH. Weak catch bonds make strong networks. NATURE MATERIALS 2022; 21:1019-1023. [PMID: 36008604 PMCID: PMC7613626 DOI: 10.1038/s41563-022-01288-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 05/11/2022] [Indexed: 05/12/2023]
Abstract
Molecular catch bonds are ubiquitous in biology and essential for processes like leucocyte extravasion1 and cellular mechanosensing2. Unlike normal (slip) bonds, catch bonds strengthen under tension. The current paradigm is that this feature provides 'strength on demand3', thus enabling cells to increase rigidity under stress1,4-6. However, catch bonds are often weaker than slip bonds because they have cryptic binding sites that are usually buried7,8. Here we show that catch bonds render reconstituted cytoskeletal actin networks stronger than slip bonds, even though the individual bonds are weaker. Simulations show that slip bonds remain trapped in stress-free areas, whereas weak binding allows catch bonds to mitigate crack initiation by moving to high-tension areas. This 'dissociation on demand' explains how cells combine mechanical strength with the adaptability required for shape change, and is relevant to diseases where catch bonding is compromised7,9, including focal segmental glomerulosclerosis10 caused by the α-actinin-4 mutant studied here. We surmise that catch bonds are the key to create life-like materials.
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Affiliation(s)
- Yuval Mulla
- Living Matter Department, AMOLF, Amsterdam, The Netherlands
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - Mario J Avellaneda
- Living Matter Department, AMOLF, Amsterdam, The Netherlands
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Antoine Roland
- Living Matter Department, AMOLF, Amsterdam, The Netherlands
| | - Lucia Baldauf
- Living Matter Department, AMOLF, Amsterdam, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
| | - Wonyeong Jung
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Taeyoon Kim
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | - Sander J Tans
- Living Matter Department, AMOLF, Amsterdam, The Netherlands.
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands.
| | - Gijsje H Koenderink
- Living Matter Department, AMOLF, Amsterdam, The Netherlands.
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands.
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10
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Determination of protein-protein interactions at the single-molecule level using optical tweezers. Q Rev Biophys 2022; 55:e8. [PMID: 35946323 DOI: 10.1017/s0033583522000075] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Biomolecular interactions are at the base of all physical processes within living organisms; the study of these interactions has led to the development of a plethora of different methods. Among these, single-molecule (in singulo) experiments have become relevant in recent years because these studies can give insight into mechanisms and interactions that are hidden for ensemble-based (in multiplo) methods. The focus of this review is on optical tweezer (OT) experiments, which can be used to apply and measure mechanical forces in molecular systems. OTs are based on optical trapping, where a laser is used to exert a force on a dielectric bead; and optically trap the bead at a controllable position in all three dimensions. Different experimental approaches have been developed to study protein–protein interactions using OTs, such as: (1) refolding and unfolding in trans interaction where one protein is tethered between the beads and the other protein is in the solution; (2) constant force in cis interaction where each protein is bound to a bead, and the tension is suddenly increased. The interaction may break after some time, giving information about the lifetime of the binding at that tension. And (3) force ramp in cis interaction where each protein is attached to a bead and a ramp force is applied until the interaction breaks. With these experiments, parameters such as kinetic constants (koff, kon), affinity values (KD), energy to the transition state ΔG≠, distance to the transition state Δx≠ can be obtained. These parameters characterize the energy landscape of the interaction. Some parameters such as distance to the transition state can only be obtained from force spectroscopy experiments such as those described here.
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11
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Naqvi MM, Avellaneda MJ, Roth A, Koers EJ, Roland A, Sunderlikova V, Kramer G, Rye HS, Tans SJ. Protein chain collapse modulation and folding stimulation by GroEL-ES. SCIENCE ADVANCES 2022; 8:eabl6293. [PMID: 35245117 PMCID: PMC8896798 DOI: 10.1126/sciadv.abl6293] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
The collapse of polypeptides is thought important to protein folding, aggregation, intrinsic disorder, and phase separation. However, whether polypeptide collapse is modulated in cells to control protein states is unclear. Here, using integrated protein manipulation and imaging, we show that the chaperonin GroEL-ES can accelerate the folding of proteins by strengthening their collapse. GroEL induces contractile forces in substrate chains, which draws them into the cavity and triggers a general compaction and discrete folding transitions, even for slow-folding proteins. This collapse enhancement is strongest in the nucleotide-bound states of GroEL and is aided by GroES binding to the cavity rim and by the amphiphilic C-terminal tails at the cavity bottom. Collapse modulation is distinct from other proposed GroEL-ES folding acceleration mechanisms, including steric confinement and misfold unfolding. Given the prevalence of collapse throughout the proteome, we conjecture that collapse modulation is more generally relevant within the protein quality control machinery.
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Affiliation(s)
| | | | - Andrew Roth
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA
| | | | | | | | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Hays S. Rye
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA
| | - Sander J. Tans
- AMOLF, Science Park 104, 1098 XG Amsterdam, Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
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12
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Tych K, Rief M. Using Single-Molecule Optical Tweezers to Study the Conformational Cycle of the Hsp90 Molecular Chaperone. Methods Mol Biol 2022; 2478:401-425. [PMID: 36063329 DOI: 10.1007/978-1-0716-2229-2_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The heat shock protein 90 (Hsp90) family of chaperones are well-known, highly important components of the cellular systems which regulate protein homeostasis. Essential in eukaryotes, Hsp90s is also found in prokaryotes, including archaea. Hsp90 is a dimeric protein, with each monomer consisting of three separate structural domains, and undergoes large conformational changes as part of its functional cycle. This cycle is driven by interactions with nucleotides, cochaperone proteins, client proteins and allosteric effects enacted by these and by posttranslational modifications. All of these influence the rate and degree of the opening and closing of the dimer as well as the relative domain orientations and its overall rigidity. Optical tweezers, which can access many of these functionally important conformational changes, therefore provide a unique tool for the study of this large and complex molecular chaperone. Here, we provide protocols for the design and implementation of different Hsp90 constructs and optical tweezers experiments for addressing the many open questions about the function of this important molecular chaperone.
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Affiliation(s)
- Katarzyna Tych
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands.
| | - Matthias Rief
- Department of Physics, Technical University of Munich, Garching-bei-München, Germany.
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13
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Shinde A, Illath K, Gupta P, Shinde P, Lim KT, Nagai M, Santra TS. A Review of Single-Cell Adhesion Force Kinetics and Applications. Cells 2021; 10:577. [PMID: 33808043 PMCID: PMC8000588 DOI: 10.3390/cells10030577] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
Abstract
Cells exert, sense, and respond to the different physical forces through diverse mechanisms and translating them into biochemical signals. The adhesion of cells is crucial in various developmental functions, such as to maintain tissue morphogenesis and homeostasis and activate critical signaling pathways regulating survival, migration, gene expression, and differentiation. More importantly, any mutations of adhesion receptors can lead to developmental disorders and diseases. Thus, it is essential to understand the regulation of cell adhesion during development and its contribution to various conditions with the help of quantitative methods. The techniques involved in offering different functionalities such as surface imaging to detect forces present at the cell-matrix and deliver quantitative parameters will help characterize the changes for various diseases. Here, we have briefly reviewed single-cell mechanical properties for mechanotransduction studies using standard and recently developed techniques. This is used to functionalize from the measurement of cellular deformability to the quantification of the interaction forces generated by a cell and exerted on its surroundings at single-cell with attachment and detachment events. The adhesive force measurement for single-cell microorganisms and single-molecules is emphasized as well. This focused review should be useful in laying out experiments which would bring the method to a broader range of research in the future.
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Affiliation(s)
- Ashwini Shinde
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (A.S.); (K.I.); (P.G.); (P.S.)
| | - Kavitha Illath
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (A.S.); (K.I.); (P.G.); (P.S.)
| | - Pallavi Gupta
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (A.S.); (K.I.); (P.G.); (P.S.)
| | - Pallavi Shinde
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (A.S.); (K.I.); (P.G.); (P.S.)
| | - Ki-Taek Lim
- Department of Biosystems Engineering, Kangwon National University, Chuncheon-Si, Gangwon-Do 24341, Korea;
| | - Moeto Nagai
- Department of Mechanical Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan;
| | - Tuhin Subhra Santra
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (A.S.); (K.I.); (P.G.); (P.S.)
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Lehmann K, Shayegan M, Blab GA, Forde NR. Optical Tweezers Approaches for Probing Multiscale Protein Mechanics and Assembly. Front Mol Biosci 2020; 7:577314. [PMID: 33134316 PMCID: PMC7573139 DOI: 10.3389/fmolb.2020.577314] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023] Open
Abstract
Multi-step assembly of individual protein building blocks is key to the formation of essential higher-order structures inside and outside of cells. Optical tweezers is a technique well suited to investigate the mechanics and dynamics of these structures at a variety of size scales. In this mini-review, we highlight experiments that have used optical tweezers to investigate protein assembly and mechanics, with a focus on the extracellular matrix protein collagen. These examples demonstrate how optical tweezers can be used to study mechanics across length scales, ranging from the single-molecule level to fibrils to protein networks. We discuss challenges in experimental design and interpretation, opportunities for integration with other experimental modalities, and applications of optical tweezers to current questions in protein mechanics and assembly.
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Affiliation(s)
- Kathrin Lehmann
- Department of Physics, Simon Fraser University, Burnaby, BC, Canada.,Soft Condensed Matter and Biophysics, Utrecht University, Utrecht, Netherlands
| | - Marjan Shayegan
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States
| | - Gerhard A Blab
- Soft Condensed Matter and Biophysics, Utrecht University, Utrecht, Netherlands
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, Burnaby, BC, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada.,Centre for Cell Biology, Development and Disease (C2D2), Simon Fraser University, Burnaby, BC, Canada
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