1
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Carlucci LA, Johnson KC, Thomas WE. FimH-mannose noncovalent bonds survive minutes to hours under force. Biophys J 2024:S0006-3495(24)00440-5. [PMID: 38961621 DOI: 10.1016/j.bpj.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/10/2024] [Accepted: 07/01/2024] [Indexed: 07/05/2024] Open
Abstract
The adhesin FimH is expressed by commensal Escherichia coli and is implicated in urinary tract infections, where it mediates adhesion to mannosylated glycoproteins on urinary and intestinal epithelial cells in the presence of a high-shear fluid environment. The FimH-mannose bond exhibits catch behavior in which bond lifetime increases with force, because tensile force induces a transition in FimH from a compact native to an elongated activated conformation with a higher affinity to mannose. However, the lifetime of the activated state of FimH has not been measured under force. Here we apply multiplexed magnetic tweezers to apply a preload force to activate FimH bonds with yeast mannan, then we measure the lifetime of these activated bonds under a wide range of forces above and below the preload force. A higher fraction of FimH-mannan bonds were activated above than below a critical preload force, confirming the FimH catch bond behavior. Once activated, FimH detached from mannose with multi-state kinetics, suggesting the existence of two bound states with a 20-fold difference in dissociation rates. The average lifetime of activated FimH-mannose bonds was 1000 to 10,000 s at forces of 30-70 pN. Structural explanations of the two bound states and the high force resistance provide insights into structural mechanisms for long-lived, force-resistant biomolecular interactions.
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Affiliation(s)
- Laura A Carlucci
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Keith C Johnson
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Wendy E Thomas
- Department of Bioengineering, University of Washington, Seattle, Washington.
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2
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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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3
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Tapia-Rojo R, Mora M, Garcia-Manyes S. Single-molecule magnetic tweezers to probe the equilibrium dynamics of individual proteins at physiologically relevant forces and timescales. Nat Protoc 2024; 19:1779-1806. [PMID: 38467905 PMCID: PMC7616092 DOI: 10.1038/s41596-024-00965-5] [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: 04/26/2023] [Accepted: 12/18/2023] [Indexed: 03/13/2024]
Abstract
The reversible unfolding and refolding of proteins is a regulatory mechanism of tissue elasticity and signalling used by cells to sense and adapt to extracellular and intracellular mechanical forces. However, most of these proteins exhibit low mechanical stability, posing technical challenges to the characterization of their conformational dynamics under force. Here, we detail step-by-step instructions for conducting single-protein nanomechanical experiments using ultra-stable magnetic tweezers, which enable the measurement of the equilibrium conformational dynamics of single proteins under physiologically relevant low forces applied over biologically relevant timescales. We report the basic principles determining the functioning of the magnetic tweezer instrument, review the protein design strategy and the fluid chamber preparation and detail the procedure to acquire and analyze the unfolding and refolding trajectories of individual proteins under force. This technique adds to the toolbox of single-molecule nanomechanical techniques and will be of particular interest to those interested in proteins involved in mechanosensing and mechanotransduction. The procedure takes 4 d to complete, plus an additional 6 d for protein cloning and production, requiring basic expertise in molecular biology, surface chemistry and data analysis.
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Affiliation(s)
- Rafael Tapia-Rojo
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK.
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King's College London, London, UK.
| | - Marc Mora
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK.
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King's College London, London, UK.
| | - Sergi Garcia-Manyes
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK.
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King's College London, London, UK.
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4
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Panagaki F, Tapia-Rojo R, Zhu T, Milmoe N, Paracuellos P, Board S, Mora M, Walker J, Rostkova E, Stannard A, Infante E, Garcia-Manyes S. Structural anisotropy results in mechano-directional transport of proteins across nuclear pores. NATURE PHYSICS 2024; 20:1180-1193. [PMID: 39036650 PMCID: PMC11254768 DOI: 10.1038/s41567-024-02438-8] [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: 02/08/2023] [Accepted: 02/08/2024] [Indexed: 07/23/2024]
Abstract
The nuclear pore complex regulates nucleocytoplasmic transport by means of a tightly synchronized suite of biochemical reactions. The physicochemical properties of the translocating cargos are emerging as master regulators of their shuttling dynamics. As well as being affected by molecular weight and surface-exposed amino acids, the kinetics of the nuclear translocation of protein cargos also depend on their nanomechanical properties, yet the mechanisms underpinning the mechanoselectivity of the nuclear pore complex are unclear. Here we show that proteins with locally soft regions in the vicinity of the nuclear-localization sequence exhibit higher nuclear-import rates, and that such mechanoselectivity is specifically impaired upon knocking down nucleoporin 153, a key protein in the nuclear pore complex. This allows us to design a short, easy-to-express and chemically inert unstructured peptide tag that accelerates the nuclear-import rate of stiff protein cargos. We also show that U2OS osteosarcoma cells expressing the peptide-tagged myocardin-related transcription factor import this mechanosensitive protein to the nucleus at higher rates and display faster motility. Locally unstructured regions lower the free-energy barrier of protein translocation and might offer a control mechanism for nuclear mechanotransduction.
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Affiliation(s)
- Fani Panagaki
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Rafael Tapia-Rojo
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Tong Zhu
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Natalie Milmoe
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Patricia Paracuellos
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Stephanie Board
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Marc Mora
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Jane Walker
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Elena Rostkova
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Andrew Stannard
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Elvira Infante
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Sergi Garcia-Manyes
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
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5
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Mora M, Tapia-Rojo R, Garcia-Manyes S. Unfolding and Refolding Proteins Using Single-Molecule AFM. Methods Mol Biol 2024; 2694:339-354. [PMID: 37824012 DOI: 10.1007/978-1-0716-3377-9_16] [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] [Indexed: 10/13/2023]
Abstract
Single-molecule atomic force microscopy (AFM) allows capturing the conformational dynamics of an individual molecule under force. In this chapter, we describe a protocol for conducting a protein nanomechanical experiment using AFM, covering both the force-extension and force-clamp modes. Combined, these experiments provide an integrated vista of the molecular mechanisms-and their associated kinetics-underpinning the mechanical unfolding and refolding of individual proteins when exposed to mechanical load.
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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, London, UK
| | - Rafael Tapia-Rojo
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King's College London, London, UK
| | - Sergi Garcia-Manyes
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King's College London, London, UK.
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6
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Lei H, Ma Q, Wang Z, Zhang D, Huang X, Qin M, Ma H, Wang W, Cao Y. Ester Bond: Chemically Labile Yet Mechanically Stable. ACS NANO 2023; 17:16870-16878. [PMID: 37646337 DOI: 10.1021/acsnano.3c03807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Due to the dynamic nature of ester linkages, ester-bond-containing materials are well known for their outstanding degradability and stimuli responsiveness. However, whether ester hydrolysis is affected by mechanical forces remains unclear. Here, we develop a single-molecule assay to quantitatively study the force-dependent ester hydrolysis using an engineered circular permutant protein with a caged ester bond as a model. Our single-molecule force spectroscopy results show that the ester hydrolysis rate is surprisingly insensitive to forces, with a ∼7 s-1 dissociation rate that remains almost unchanged in the force range of 80 to 200 pN. Quantum calculations reveal that the ester hydrolysis involves an intermediate state formed by either H3O+- or OH--bonded tetrahedral intermediates. The measured ester-hydrolysis kinetics at the single-molecule level may primarily correspond to the rupture of these intermediate states. However, the rate-limiting step appears to be the formation of the tetrahedral intermediates, which cannot be quantitatively characterized in our experiments. Nonetheless, based on the quantum calculations, this step is also insensitive to applied forces. Altogether, our study suggests that the ester bond is chemically labile yet mechanically stable, serving as the basis for the design of responsive materials using ester bonds as mechanically inert units.
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Affiliation(s)
- Hai Lei
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- School of Physics, Zhejiang University, Hangzhou 310027, China
- Institute for Advanced Study in Physics, Zhejiang University, Hangzhou 310027, China
| | - Quan Ma
- Zhejiang Laboratory, Hangzhou, Zhejiang 311121, China
| | - Zhangxia Wang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Di Zhang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Xiaoyu Huang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Meng Qin
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Haibo Ma
- Qingdao Institute for Theoretical and Computational Sciences, Qingdao Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
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7
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Interdomain Linker Effect on the Mechanical Stability of Ig Domains in Titin. Int J Mol Sci 2022; 23:ijms23179836. [PMID: 36077234 PMCID: PMC9456048 DOI: 10.3390/ijms23179836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
Titin is the largest protein in humans, composed of more than one hundred immunoglobulin (Ig) domains, and plays a critical role in muscle’s passive elasticity. Thus, the molecular design of this giant polyprotein is responsible for its mechanical function. Interestingly, most of these Ig domains are connected directly with very few interdomain residues/linker, which suggests such a design is necessary for its mechanical stability. To understand this design, we chose six representative Ig domains in titin and added nine glycine residues (9G) as an artificial interdomain linker between these Ig domains. We measured their mechanical stabilities using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) and compared them to the natural sequence. The AFM results showed that the linker affected the mechanical stability of Ig domains. The linker mostly reduces its mechanical stability to a moderate extent, but the opposite situation can happen. Thus, this effect is very complex and may depend on each particular domain’s property.
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8
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Chetrit E, Sharma S, Maayan U, Pelah MG, Klausner Z, Popa I, Berkovich R. Nonexponential kinetics in captured in sequential unfolding of polyproteins over a range of loads. Curr Res Struct Biol 2022; 4:106-117. [PMID: 35540955 PMCID: PMC9079174 DOI: 10.1016/j.crstbi.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 11/08/2022] Open
Abstract
While performing under mechanical loads in vivo, polyproteins are vitally involved in cellular mechanisms such as regulation of tissue elasticity and mechano-transduction by unfolding their comprising domains and extending them. It is widely thought that the process of sequential unfolding of polyproteins follows an exponential kinetics as the individual unfolding events exhibit identical and identically distributed (iid) Poisson behavior. However, it was shown that under high loads, the sequential unfolding kinetics displays nonexponential kinetics that alludes to aging by a subdiffusion process. Statistical order analysis of this kinetics indicated that the individual unfolding events are not iid, and cannot be defined as a Poisson (memoryless) process. Based on numerical simulations it was argued that this behavior becomes less pronounced with lowering the load, therefore it is to be expected that polyproteins unfolding under lower forces will follow a Poisson behavior. This expectation serves as the motivation of the current study, in which we investigate the effect of force lowering on the unfolding kinetics of Poly-L8 under varying loads, specifically high (150, 100 pN) and moderate-low (45, 30, 20 pN) forces. We found that a hierarchy among the unfolding events still exists even under low loads, again resulting in nonexponential behavior. We observe that analyzing the dwell-time distributions with stretched-exponentials and power laws give rise to different phenomenological trends. Using statistical order analysis, we demonstrated that even under the lowest load, the sequential unfolding cannot be considered as iid, in accord with the power law distribution. Additional free energy analysis revealed the contribution of the unfolded segments elasticity that scales with the force on the overall one-dimensional contour of the energy landscape, but more importantly, it discloses the hierarchy within the activation barriers during sequential unfolding that account for the observed nonexponentiality. Poly-L8 unfolding shows nonexponential kinetics at forces ranging from 150 to 20 pN. Different phenomenological trends are observed for the dwell-time distributions. The unfolding events were shown to be dependent and not identically distributed. Free energy analysis reveals elastic impact and hierarchy in the unfolding barriers.
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9
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Schönfelder J, Alonso-Caballero A, Perez-Jimenez R. Mechanochemical Evolution of Disulfide Bonds in Proteins. Methods Mol Biol 2022; 2376:283-300. [PMID: 34845615 DOI: 10.1007/978-1-0716-1716-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Disulfide bonds play a pivotal role in the mechanical stability of proteins. Numerous proteins that are known to be exposed to mechanical forces in vivo contain disulfide bonds. The presence of cryptic disulfide bonds in a protein structure may be related to its resistance to an applied mechanical force. Disulfide bonds in proteins tend to be highly conserved but their evolution might be directly related to the evolution of the protein mechanical stability. Hence, tracking the evolution of disulfide bonds in a protein can help to derive crucial stability/function correlations in proteins that are exposed to mechanical forces. Phylogenic analysis and ancestral sequence reconstruction (ASR) allow tracking the evolution of proteins from the past ancestors to our modern days and also establish correlations between proteins from different species. In addition, ASR can be combined with single-molecule force spectroscopy (smFS) to investigate the mechanical properties of proteins including the occurrence and function of disulfide bonds. Here we present a detailed protocol to study the mechanochemical evolution of proteins using a fragment of the giant muscle protein titin as example. The protocol can be easily adapted to AFS studies of any resurrected mechanical force bearing protein of interest.
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Affiliation(s)
- Jörg Schönfelder
- CIC nanoGUNE, San Sebastián, Spain
- IMDEA Nanosciences, Madrid, Spain
| | | | - Raul Perez-Jimenez
- CIC nanoGUNE, San Sebastián, Spain.
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
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10
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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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11
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Suay-Corredera C, Pricolo MR, Velázquez-Carreras D, Pathak D, Nandwani N, Pimenta-Lopes C, Sánchez-Ortiz D, Urrutia-Irazabal I, Vilches S, Dominguez F, Frisso G, Monserrat L, García-Pavía P, de Sancho D, Spudich JA, Ruppel KM, Herrero-Galán E, Alegre-Cebollada J. Nanomechanical Phenotypes in Cardiac Myosin-Binding Protein C Mutants That Cause Hypertrophic Cardiomyopathy. ACS NANO 2021; 15:10203-10216. [PMID: 34060810 PMCID: PMC8514129 DOI: 10.1021/acsnano.1c02242] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Hypertrophic cardiomyopathy (HCM) is a disease of the myocardium caused by mutations in sarcomeric proteins with mechanical roles, such as the molecular motor myosin. Around half of the HCM-causing genetic variants target contraction modulator cardiac myosin-binding protein C (cMyBP-C), although the underlying pathogenic mechanisms remain unclear since many of these mutations cause no alterations in protein structure and stability. As an alternative pathomechanism, here we have examined whether pathogenic mutations perturb the nanomechanics of cMyBP-C, which would compromise its modulatory mechanical tethers across sliding actomyosin filaments. Using single-molecule atomic force spectroscopy, we have quantified mechanical folding and unfolding transitions in cMyBP-C domains targeted by HCM mutations that do not induce RNA splicing alterations or protein thermodynamic destabilization. Our results show that domains containing mutation R495W are mechanically weaker than wild-type at forces below 40 pN and that R502Q mutant domains fold faster than wild-type. None of these alterations are found in control, nonpathogenic variants, suggesting that nanomechanical phenotypes induced by pathogenic cMyBP-C mutations contribute to HCM development. We propose that mutation-induced nanomechanical alterations may be common in mechanical proteins involved in human pathologies.
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Affiliation(s)
| | - Maria Rosaria Pricolo
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029, Madrid, Spain
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, 80131, Naples, Italy
| | | | - Divya Pathak
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Neha Nandwani
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, United States
| | | | - David Sánchez-Ortiz
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029, Madrid, Spain
| | | | - Silvia Vilches
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro, 28222, Madrid, Spain
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART, http://guardheart.ern-net.eu/), 28222, Madrid, Spain
| | - Fernando Dominguez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029, Madrid, Spain
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro, 28222, Madrid, Spain
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART, http://guardheart.ern-net.eu/), 28222, Madrid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029, Madrid, Spain
| | - Giulia Frisso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, 80131, Naples, Italy
- CEINGE Biotecnologie Avanzate, scarl, 80145, Naples, Italy
| | | | - Pablo García-Pavía
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro, 28222, Madrid, Spain
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART, http://guardheart.ern-net.eu/), 28222, Madrid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029, Madrid, Spain
- Universidad Francisco de Vitoria (UFV), 28223, Pozuelo de Alarcón, Madrid, Spain
| | - David de Sancho
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, 20018, Donostia-San Sebastián, Spain
- Donostia International Physics Center (DIPC), 20018, Donostia-San Sebastián, Spain
| | - James A Spudich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Kathleen M Ruppel
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Elías Herrero-Galán
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029, Madrid, Spain
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12
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Müller DJ, Dumitru AC, Lo Giudice C, Gaub HE, Hinterdorfer P, Hummer G, De Yoreo JJ, Dufrêne YF, Alsteens D. Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems. Chem Rev 2020; 121:11701-11725. [PMID: 33166471 DOI: 10.1021/acs.chemrev.0c00617] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During the last three decades, a series of key technological improvements turned atomic force microscopy (AFM) into a nanoscopic laboratory to directly observe and chemically characterize molecular and cell biological systems under physiological conditions. Here, we review key technological improvements that have established AFM as an analytical tool to observe and quantify native biological systems from the micro- to the nanoscale. Native biological systems include living tissues, cells, and cellular components such as single or complexed proteins, nucleic acids, lipids, or sugars. We showcase the procedures to customize nanoscopic chemical laboratories by functionalizing AFM tips and outline the advantages and limitations in applying different AFM modes to chemically image, sense, and manipulate biosystems at (sub)nanometer spatial and millisecond temporal resolution. We further discuss theoretical approaches to extract the kinetic and thermodynamic parameters of specific biomolecular interactions detected by AFM for single bonds and extend the discussion to multiple bonds. Finally, we highlight the potential of combining AFM with optical microscopy and spectroscopy to address the full complexity of biological systems and to tackle fundamental challenges in life sciences.
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Affiliation(s)
- Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 28, 4056 Basel, Switzerland
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Cristina Lo Giudice
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Hermann E Gaub
- Applied Physics, Ludwig-Maximilians-Universität Munich, Amalienstrasse 54, 80799 München, Germany
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics and Department of Physics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.,Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
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13
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Loescher CM, Breitkreuz M, Li Y, Nickel A, Unger A, Dietl A, Schmidt A, Mohamed BA, Kötter S, Schmitt JP, Krüger M, Krüger M, Toischer K, Maack C, Leichert LI, Hamdani N, Linke WA. Regulation of titin-based cardiac stiffness by unfolded domain oxidation (UnDOx). Proc Natl Acad Sci U S A 2020; 117:24545-24556. [PMID: 32929035 PMCID: PMC7533878 DOI: 10.1073/pnas.2004900117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The relationship between oxidative stress and cardiac stiffness is thought to involve modifications to the giant muscle protein titin, which in turn can determine the progression of heart disease. In vitro studies have shown that S-glutathionylation and disulfide bonding of titin fragments could alter the elastic properties of titin; however, whether and where titin becomes oxidized in vivo is less certain. Here we demonstrate, using multiple models of oxidative stress in conjunction with mechanical loading, that immunoglobulin domains preferentially from the distal titin spring region become oxidized in vivo through the mechanism of unfolded domain oxidation (UnDOx). Via oxidation type-specific modification of titin, UnDOx modulates human cardiomyocyte passive force bidirectionally. UnDOx also enhances titin phosphorylation and, importantly, promotes nonconstitutive folding and aggregation of unfolded domains. We propose a mechanism whereby UnDOx enables the controlled homotypic interactions within the distal titin spring to stabilize this segment and regulate myocardial passive stiffness.
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Affiliation(s)
| | - Martin Breitkreuz
- Institute of Physiology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Yong Li
- Institute of Physiology II, University of Munster, 48149 Munster, Germany
| | - Alexander Nickel
- Comprehensive Heart Failure Center Wuerzburg, University Clinic Wuerzburg, 97078 Wuerzburg, Germany
| | - Andreas Unger
- Institute of Physiology II, University of Munster, 48149 Munster, Germany
| | - Alexander Dietl
- Department of Internal Medicine II, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Andreas Schmidt
- Institute for Genetics, University of Cologne, 50931 Cologne, Germany
| | - Belal A Mohamed
- Department of Cardiology and Pneumology, University Medicine Goettingen, 37075 Goettingen, Germany
| | - Sebastian Kötter
- Department of Cardiovascular Physiology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Joachim P Schmitt
- Department of Pharmacology and Clinical Pharmacology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Marcus Krüger
- Institute for Genetics, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine and Excellence Cluster "Cellular Stress Responses in Aging-Associated Diseases" (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Martina Krüger
- Department of Cardiovascular Physiology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Karl Toischer
- Department of Cardiology and Pneumology, University Medicine Goettingen, 37075 Goettingen, Germany
| | - Christoph Maack
- Comprehensive Heart Failure Center Wuerzburg, University Clinic Wuerzburg, 97078 Wuerzburg, Germany
| | - Lars I Leichert
- Institute for Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Nazha Hamdani
- Institute of Physiology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Wolfgang A Linke
- Institute of Physiology II, University of Munster, 48149 Munster, Germany;
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14
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An C, Hu W, Gao J, Ju BF, Obeidy P, Zhao YC, Tu X, Fang W, Ju LA, Chen W. Ultra-stable Biomembrane Force Probe for Accurately Determining Slow Dissociation Kinetics of PD-1 Blockade Antibodies on Single Living Cells. NANO LETTERS 2020; 20:5133-5140. [PMID: 32530632 DOI: 10.1021/acs.nanolett.0c01360] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Immune checkpoint blockade with monoclonal antibodies (mAbs) that target programmed cell death protein-1 (PD-1) has remarkably revolutionized cancer therapy. Their binding kinetics measured by surface plasmon resonance does not always correlate well with their immunotherapeutic efficacies, mainly due to the lack of two-dimensional cell plasma membrane and the capability of force sensing and manipulation. In this regard, based on a more suitable and ultra-sensitive biomechanical nanotool, biomembrane force probe (BFP), we developed a Double-edge Smart Feedback control system as an ultra-stable platform to characterize ultra-long bond lifetimes of receptor-ligand binding on living cells. We further benchmarked the dissociation kinetics for three clinically approved PD-1 blockade mAbs (Nivolumab, Pembrolizumab, and Camrelizumab), intriguingly correlating well with the objective response rates in the hepatocellular carcinoma second-line treatment. This ultra-stable BFP potentially provides a compelling kinetic platform to direct the screening, optimization, and clinical selection of therapeutic antibodies in the future.
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Affiliation(s)
- Chenyi An
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Fluid Power and Mechatronic Systems, Key Laboratory for Biomedical Engineering of Ministry of Education, and School of Mechanical Engineering, Zhejiang University, Hangzhou, China, 310058
| | - Wei Hu
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Fluid Power and Mechatronic Systems, Key Laboratory for Biomedical Engineering of Ministry of Education, and School of Mechanical Engineering, Zhejiang University, Hangzhou, China, 310058
| | - Jie Gao
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Fluid Power and Mechatronic Systems, Key Laboratory for Biomedical Engineering of Ministry of Education, and School of Mechanical Engineering, Zhejiang University, Hangzhou, China, 310058
| | - Bing-Feng Ju
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Fluid Power and Mechatronic Systems, Key Laboratory for Biomedical Engineering of Ministry of Education, and School of Mechanical Engineering, Zhejiang University, Hangzhou, China, 310058
| | - Peyman Obeidy
- School of Biomedical Engineering, Faculty of Engineering and Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales Australia, 2006
| | - Yunduo Charles Zhao
- School of Biomedical Engineering, Faculty of Engineering and Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales Australia, 2006
| | - Xiaoxuan Tu
- Department of Medical Oncology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310000
| | - Weijia Fang
- Department of Medical Oncology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310000
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310000
| | - Lining Arnold Ju
- School of Biomedical Engineering, Faculty of Engineering and Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales Australia, 2006
- Heart Research Institute, Newtown, New South Wales Australia, 2042
| | - Wei Chen
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Fluid Power and Mechatronic Systems, Key Laboratory for Biomedical Engineering of Ministry of Education, and School of Mechanical Engineering, Zhejiang University, Hangzhou, China, 310058
- State Key Laboratory for Modern Optical Instrumentation and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China, 310058
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15
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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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16
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Rivas-Pardo JA, Li Y, Mártonfalvi Z, Tapia-Rojo R, Unger A, Fernández-Trasancos Á, Herrero-Galán E, Velázquez-Carreras D, Fernández JM, Linke WA, Alegre-Cebollada J. A HaloTag-TEV genetic cassette for mechanical phenotyping of proteins from tissues. Nat Commun 2020; 11:2060. [PMID: 32345978 PMCID: PMC7189229 DOI: 10.1038/s41467-020-15465-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 03/09/2020] [Indexed: 11/09/2022] Open
Abstract
Single-molecule methods using recombinant proteins have generated transformative hypotheses on how mechanical forces are generated and sensed in biological tissues. However, testing these mechanical hypotheses on proteins in their natural environment remains inaccesible to conventional tools. To address this limitation, here we demonstrate a mouse model carrying a HaloTag-TEV insertion in the protein titin, the main determinant of myocyte stiffness. Using our system, we specifically sever titin by digestion with TEV protease, and find that the response of muscle fibers to length changes requires mechanical transduction through titin's intact polypeptide chain. In addition, HaloTag-based covalent tethering enables examination of titin dynamics under force using magnetic tweezers. At pulling forces < 10 pN, titin domains are recruited to the unfolded state, and produce 41.5 zJ mechanical work during refolding. Insertion of the HaloTag-TEV cassette in mechanical proteins opens opportunities to explore the molecular basis of cellular force generation, mechanosensing and mechanotransduction.
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Affiliation(s)
- Jaime Andrés Rivas-Pardo
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
- Center for Genomics and Bioinformatics, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Yong Li
- Institute of Physiology II, University of Muenster, Muenster, Germany
| | - Zsolt Mártonfalvi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Rafael Tapia-Rojo
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Andreas Unger
- Institute of Physiology II, University of Muenster, Muenster, Germany
| | | | | | | | - Julio M Fernández
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Wolfgang A Linke
- Institute of Physiology II, University of Muenster, Muenster, Germany.
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17
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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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18
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Echarri A, Pavón DM, Sánchez S, García-García M, Calvo E, Huerta-López C, Velázquez-Carreras D, Viaris de Lesegno C, Ariotti N, Lázaro-Carrillo A, Strippoli R, De Sancho D, Alegre-Cebollada J, Lamaze C, Parton RG, Del Pozo MA. An Abl-FBP17 mechanosensing system couples local plasma membrane curvature and stress fiber remodeling during mechanoadaptation. Nat Commun 2019; 10:5828. [PMID: 31862885 PMCID: PMC6925243 DOI: 10.1038/s41467-019-13782-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/22/2019] [Indexed: 12/19/2022] Open
Abstract
Cells remodel their structure in response to mechanical strain. However, how mechanical forces are translated into biochemical signals that coordinate the structural changes observed at the plasma membrane (PM) and the underlying cytoskeleton during mechanoadaptation is unclear. Here, we show that PM mechanoadaptation is controlled by a tension-sensing pathway composed of c-Abl tyrosine kinase and membrane curvature regulator FBP17. FBP17 is recruited to caveolae to induce the formation of caveolar rosettes. FBP17 deficient cells have reduced rosette density, lack PM tension buffering capacity under osmotic shock, and cannot adapt to mechanical strain. Mechanistically, tension is transduced to the FBP17 F-BAR domain by direct phosphorylation mediated by c-Abl, a mechanosensitive molecule. This modification inhibits FBP17 membrane bending activity and releases FBP17-controlled inhibition of mDia1-dependent stress fibers, favoring membrane adaptation to increased tension. This mechanoprotective mechanism adapts the cell to changes in mechanical tension by coupling PM and actin cytoskeleton remodeling. Mechanical forces are sensed by cells and can alter plasma membrane properties, but biochemical changes underlying this are not clear. Here the authors show tension is sensed by c-Abl and FBP17, which couples changes in mechanical tension to remodelling of the plasma membrane and actin cytoskeleton.
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Affiliation(s)
- Asier Echarri
- Mechanoadaptation and Caveolae Biology Laboratory, Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029, Madrid, Spain.
| | - Dácil M Pavón
- Mechanoadaptation and Caveolae Biology Laboratory, Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Sara Sánchez
- Mechanoadaptation and Caveolae Biology Laboratory, Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - María García-García
- Mechanoadaptation and Caveolae Biology Laboratory, Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Enrique Calvo
- Proteomics Unit, Vascular Pathophysiology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Carla Huerta-López
- Molecular Mechanics of the Cardiovascular System Laboratory, Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Diana Velázquez-Carreras
- Molecular Mechanics of the Cardiovascular System Laboratory, Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Christine Viaris de Lesegno
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie - Centre de Recherche, PSL Research University, CNRS UMR3666, INSERM U1143, 75248, Paris, France
| | - Nicholas Ariotti
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ana Lázaro-Carrillo
- Mechanoadaptation and Caveolae Biology Laboratory, Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029, Madrid, Spain.,Departamento de Biología, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | | | - David De Sancho
- Departamento de Ciencia y Tecnología de Polímeros, Euskal Herriko Unibertsitatea, 20018, Donostia-San Sebastián, Spain.,Donostia International Physics Center, Manuel Lardizabal Ibilbidea, 4, 20018, Donostia-San Sebastián, Spain
| | - Jorge Alegre-Cebollada
- Molecular Mechanics of the Cardiovascular System Laboratory, Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Christophe Lamaze
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie - Centre de Recherche, PSL Research University, CNRS UMR3666, INSERM U1143, 75248, Paris, France
| | - Robert G Parton
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,The Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Miguel A Del Pozo
- Mechanoadaptation and Caveolae Biology Laboratory, Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029, Madrid, Spain.
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19
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Feng L, Torun H. Miniaturized magnetic bead-actuators for force-clamp spectroscopy-based single-molecule measurements. Ultramicroscopy 2019; 209:112888. [PMID: 31734437 DOI: 10.1016/j.ultramic.2019.112888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 10/27/2019] [Accepted: 11/09/2019] [Indexed: 10/25/2022]
Abstract
Force-clamp spectroscopy can mimic the physiological conditions for the proteins under investigation. In addition, it is a direct way of observing the relationship between bond lifetime and molecular forces. However, traditional force-clamp methods rely on active feedback controllers that can introduce artefacts. In this work, we introduce a new method to enable force-clamp spectroscopy without a need for an active feedback. The method is based on miniaturized magnetic beads offering improved stability. As a case study, we performed force-clamp experiments using biotin-streptavidin molecule pairs with and without active feedback. Our results demonstrate the feasibility of force-clamp experiments without feedback and illustrate the advantages of our method.
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Affiliation(s)
- L Feng
- Faculty of Engineering and Environment, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom
| | - H Torun
- Faculty of Engineering and Environment, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom.
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20
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Infante E, Stannard A, Board SJ, Rico-Lastres P, Panagaki F, Beedle AE, Rajan VS, Rostkova E, Lezamiz A, Wang YJ, Breen SG, Shanahan C, Roca-Cusachs P, Garcia-Manyes S. The mechanical stability of proteins regulates their translocation rate into the cell nucleus. NATURE PHYSICS 2019; 15:973-981. [PMID: 37484710 PMCID: PMC7614795 DOI: 10.1038/s41567-019-0551-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 05/10/2019] [Indexed: 07/25/2023]
Abstract
The translocation of mechanosensitive transcription factors (TFs) across the nuclear envelope is a crucial step in cellular mechanotransduction. Yet the molecular mechanisms by which external mechanical cues control the nuclear shuttling dynamics of TFs through the nuclear pore complex (NPC) to activate gene expression are poorly understood. Here, we show that the nuclear import rate of myocardin-related transcription factor A (MRTFA) - a protein that regulates cytoskeletal dynamics via the activation of the TF serum response factor (SRF) - inversely correlates with the protein's nanomechanical stability and does not relate to its thermodynamic stability. Tagging MRTFA with mechanically resistant proteins results in the downregulation of SRF-mediated myosin light-chain 9 (MYL9) gene expression and subsequent slowing down of cell migration. We conclude that the mechanical unfolding of proteins regulates their nuclear translocation rate through the NPC, and highlight the role of the NPC as a selective mechanosensor able to discriminate forces as low as ~10 pN. The modulation of the mechanical stability of TFs may represent a new strategy for the control of gene expression.
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Affiliation(s)
- Elvira Infante
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Andrew Stannard
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Stephanie J. Board
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Palma Rico-Lastres
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Fani Panagaki
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Amy E.M. Beedle
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Vinoth Sundar Rajan
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Elena Rostkova
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Ainhoa Lezamiz
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Yong Jian Wang
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Samuel Gulaidi Breen
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Catherine Shanahan
- Cardiovascular Division, James Black Centre, King’s College London, London SE5 9NU, UK Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and
| | - Pere Roca-Cusachs
- Technology (BIST) and University of Barcelona, 08028 Barcelona, Spain
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
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21
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Multiplexed protein force spectroscopy reveals equilibrium protein folding dynamics and the low-force response of von Willebrand factor. Proc Natl Acad Sci U S A 2019; 116:18798-18807. [PMID: 31462494 PMCID: PMC6754583 DOI: 10.1073/pnas.1901794116] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-molecule force spectroscopy has provided unprecedented insights into protein folding, force regulation, and function. So far, the field has relied primarily on atomic force microscope and optical tweezers assays that, while powerful, are limited in force resolution, throughput, and require feedback for constant force measurements. Here, we present a modular approach based on magnetic tweezers (MT) for highly multiplexed protein force spectroscopy. Our approach uses elastin-like polypeptide linkers for the specific attachment of proteins, requiring only short peptide tags on the protein of interest. The assay extends protein force spectroscopy into the low force (<1 pN) regime and enables parallel and ultra-stable measurements at constant forces. We present unfolding and refolding data for the small, single-domain protein ddFLN4, commonly used as a molecular fingerprint in force spectroscopy, and for the large, multidomain dimeric protein von Willebrand factor (VWF) that is critically involved in primary hemostasis. For both proteins, our measurements reveal exponential force dependencies of unfolding and refolding rates. We directly resolve the stabilization of the VWF A2 domain by Ca2+ and discover transitions in the VWF C domain stem at low forces that likely constitute the first steps of VWF's mechano-activation. Probing the force-dependent lifetime of biotin-streptavidin bonds, we find that monovalent streptavidin constructs with specific attachment geometry are significantly more force stable than commercial, multivalent streptavidin. We expect our modular approach to enable multiplexed force-spectroscopy measurements for a wide range of proteins, in particular in the physiologically relevant low-force regime.
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22
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Eckels EC, Tapia-Rojo R, Rivas-Pardo JA, Fernández JM. The Work of Titin Protein Folding as a Major Driver in Muscle Contraction. Annu Rev Physiol 2019; 80:327-351. [PMID: 29433413 DOI: 10.1146/annurev-physiol-021317-121254] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Single-molecule atomic force microscopy and magnetic tweezers experiments have demonstrated that titin immunoglobulin (Ig) domains are capable of folding against a pulling force, generating mechanical work that exceeds that produced by a myosin motor. We hypothesize that upon muscle activation, formation of actomyosin cross bridges reduces the force on titin, causing entropic recoil of the titin polymer and triggering the folding of the titin Ig domains. In the physiological force range of 4-15 pN under which titin operates in muscle, the folding contraction of a single Ig domain can generate 200% of the work of entropic recoil and occurs at forces that exceed the maximum stalling force of single myosin motors. Thus, titin operates like a mechanical battery, storing elastic energy efficiently by unfolding Ig domains and delivering the charge back by folding when the motors are activated during a contraction. We advance the hypothesis that titin folding and myosin activation act as inextricable partners during muscle contraction.
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Affiliation(s)
- Edward C Eckels
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; , .,Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Medical Center, New York, NY 10032, USA
| | - Rafael Tapia-Rojo
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; ,
| | | | - Julio M Fernández
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; ,
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23
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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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24
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The extracellular matrix-myosin pathway in mechanotransduction: from molecule to tissue. Emerg Top Life Sci 2018; 2:727-737. [PMID: 33530663 PMCID: PMC7289002 DOI: 10.1042/etls20180043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 12/23/2022]
Abstract
Mechanotransduction via the extracellular matrix (ECM)–myosin pathway is involved in determining cell morphology during development and in coupling external transient mechanical stimuli to the reorganization of the cytoskeleton. Here, we present a review on the molecular mechanisms involved in this pathway and how they influence cellular development and organization. We investigate key proteins involved in the ECM–myosin pathway and discuss how specific binding events and conformational changes under force are related to mechanical signaling. We connect these molecular mechanisms with observed morphological changes at the cellular and organism level. Finally, we propose a model encompassing the biomechanical signals along the ECM–myosin pathway and how it could be involved in cell adhesion, cell migration, and tissue architecture.
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25
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The power of the force: mechano-physiology of the giant titin. Emerg Top Life Sci 2018; 2:681-686. [PMID: 33530662 DOI: 10.1042/etls20180046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 01/18/2023]
Abstract
Titin - the largest protein in the human body - spans half of the muscle sarcomere from the Z-disk to the M-band through a single polypeptide chain. More than 30 000 amino acid residues coded from a single gene (TTN, in humans Q8WZ42) form a long filamentous protein organized in individual globular domains concatenated in tandem. Owing to its location and close interaction with the other muscle filaments, titin is considered the third filament of muscle, after the thick-myosin and the thin-actin filaments.
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26
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Herrero-Galán E, Martínez-Martín I, Alegre-Cebollada J. Redox regulation of protein nanomechanics in health and disease: Lessons from titin. Redox Biol 2018; 21:101074. [PMID: 30584979 PMCID: PMC6305763 DOI: 10.1016/j.redox.2018.101074] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/22/2018] [Accepted: 12/07/2018] [Indexed: 01/11/2023] Open
Abstract
The nanomechanics of sarcomeric proteins is a key contributor to the mechanical output of muscle. Among them, titin emerges as a main target for the regulation of the stiffness of striated muscle. In the last years, single-molecule experiments by Atomic Force Microscopy (AFM) have demonstrated that redox posttranslational modifications are strong modulators of the mechanical function of titin. Here, we provide an overview of the recent development of the redox mechanobiology of titin, and suggest avenues of research to better understand how the stiffness of molecules, cells and tissues are modulated by redox signaling in health and disease.
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28
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Uhlig MR, Amo CA, Garcia R. Dynamics of breaking intermolecular bonds in high-speed force spectroscopy. NANOSCALE 2018; 10:17112-17116. [PMID: 30182101 DOI: 10.1039/c8nr05715j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Atomic force microscope based single-molecule force spectroscopy provides a description of a variety of intermolecular interactions such as those occurring between receptor molecules and their ligands. Advances in force spectroscopy have enabled performing measurements at high-speeds and sub-microsecond resolutions. We report experiments performed on a biotin-avidin system that reveal that the measured force decreases with the loading rate at high rates. This result is at odds with the established Bell-Evans theory that predicts a monotonic increase of the rupture force with the loading rate. We demonstrate that inertial and hydrodynamic forces generated during the breaking of the bond dominate the measured force at high loading rates. We develop a correction factor to incorporate those effects into the Bell-Evans theory. The correction is necessary to obtain accurate values of the intermolecular forces at high speeds.
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Affiliation(s)
- Manuel R Uhlig
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid, CSIC, Sor Juana Inés de la Cruz, 28049 Madrid, Spain.
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29
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Khoury LR, Nowitzke J, Dahal N, Shmilovich K, Eis A, Popa I. Force-Clamp Rheometry for Characterizing Protein-based Hydrogels. J Vis Exp 2018. [PMID: 30199039 DOI: 10.3791/58280] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Here, we describe a force-clamp rheometry method to characterize the biomechanical properties of protein-based hydrogels. This method uses an analog proportional-integral-derivative (PID) system to apply controlled-force protocols on cylindrical protein-based hydrogel samples, which are tethered between a linear voice-coil motor and a force transducer. During operation, the PID system adjusts the extension of the hydrogel sample to follow a predefined force protocol by minimizing the difference between the measured and set-point forces. This unique approach to protein-based hydrogels enables the tethering of extremely low-volume hydrogel samples (< 5 µL) with different protein concentrations. Under force-ramp protocols, where the applied stress increases and decreases linearly with time, the system enables the study of the elasticity and hysteresis behaviors associated with the (un)folding of proteins and the measurement of standard elastic and viscoelastic parameters. Under constant-force, where the force pulse has a step-like shape, the elastic response, due to the change in force, is decoupled from the viscoelastic response, which comes from protein domain unfolding and refolding. Due to its low-volume sample and versatility in applying various mechanical perturbations, force-clamp rheometry is optimized to investigate the mechanical response of proteins under force using a bulk approach.
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Affiliation(s)
- Luai R Khoury
- Department of Physics, University of Wisconsin-Milwaukee
| | - Joel Nowitzke
- Department of Physics, University of Wisconsin-Milwaukee
| | - Narayan Dahal
- Department of Physics, University of Wisconsin-Milwaukee
| | | | - Annie Eis
- Department of Physics, University of Wisconsin-Milwaukee
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee;
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30
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Beedle AEM, Mora M, Davis CT, Snijders AP, Stirnemann G, Garcia-Manyes S. Forcing the reversibility of a mechanochemical reaction. Nat Commun 2018; 9:3155. [PMID: 30089863 PMCID: PMC6082871 DOI: 10.1038/s41467-018-05115-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/13/2018] [Indexed: 11/09/2022] Open
Abstract
Mechanical force modifies the free-energy surface of chemical reactions, often enabling thermodynamically unfavoured reaction pathways. Most of our molecular understanding of force-induced reactivity is restricted to the irreversible homolytic scission of covalent bonds and ring-opening in polymer mechanophores. Whether mechanical force can by-pass thermodynamically locked reactivity in heterolytic bimolecular reactions and how this impacts the reaction reversibility remains poorly understood. Using single-molecule force-clamp spectroscopy, here we show that mechanical force promotes the thermodynamically disfavored SN2 cleavage of an individual protein disulfide bond by poor nucleophilic organic thiols. Upon force removal, the transition from the resulting high-energy unstable mixed disulfide product back to the initial, low-energy disulfide bond reactant becomes suddenly spontaneous, rendering the reaction fully reversible. By rationally varying the nucleophilicity of a series of small thiols, we demonstrate how force-regulated chemical kinetics can be finely coupled with thermodynamics to predict and modulate the reversibility of bimolecular mechanochemical reactions.
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Affiliation(s)
- Amy E M Beedle
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London, WC2R 2LS, UK
| | - Marc Mora
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London, WC2R 2LS, UK
| | - Colin T Davis
- The Francis Crick Institute, Protein analysis and Proteomics Science Technology Platform, 1 Midland Road, London, NW1 1AT, UK
| | - Ambrosius P Snijders
- The Francis Crick Institute, Protein analysis and Proteomics Science Technology Platform, 1 Midland Road, London, NW1 1AT, UK
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Univ. Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London, WC2R 2LS, UK.
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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31
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Haining AWM, Rahikainen R, Cortes E, Lachowski D, Rice A, von Essen M, Hytönen VP, del Río Hernández A. Mechanotransduction in talin through the interaction of the R8 domain with DLC1. PLoS Biol 2018; 16:e2005599. [PMID: 30028837 PMCID: PMC6054372 DOI: 10.1371/journal.pbio.2005599] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 06/19/2018] [Indexed: 11/19/2022] Open
Abstract
The mechanical unfolding of proteins is a cellular mechanism for force transduction with potentially broad implications in cell fate. Despite this, the mechanism by which protein unfolding elicits differential downstream signalling pathways remains poorly understood. Here, we used protein engineering, atomic force microscopy, and biophysical tools to delineate how protein unfolding controls cell mechanics. Deleted in liver cancer 1 (DLC1) is a negative regulator of Ras homolog family member A (RhoA) and cell contractility that regulates cell behaviour when localised to focal adhesions bound to folded talin. Using a talin mutant resistant to force-induced unfolding of R8 domain, we show that talin unfolding determines DLC1 downstream signalling and, consequently, cell mechanics. We propose that this new mechanism of mechanotransduction may have implications for a wide variety of associated cellular processes.
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Affiliation(s)
- Alexander William M. Haining
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Rolle Rahikainen
- Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Finland and Fimlab Laboratories, Tampere, Finland
| | - Ernesto Cortes
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Dariusz Lachowski
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Alistair Rice
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Magdalena von Essen
- Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Finland and Fimlab Laboratories, Tampere, Finland
| | - Vesa P. Hytönen
- Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Finland and Fimlab Laboratories, Tampere, Finland
| | - Armando del Río Hernández
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, United Kingdom
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32
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Johnson KC, Thomas WE. How Do We Know when Single-Molecule Force Spectroscopy Really Tests Single Bonds? Biophys J 2018; 114:2032-2039. [PMID: 29742396 PMCID: PMC5961468 DOI: 10.1016/j.bpj.2018.04.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 03/16/2018] [Accepted: 04/02/2018] [Indexed: 01/04/2023] Open
Abstract
Single-molecule force spectroscopy makes it possible to measure the mechanical strength of single noncovalent receptor-ligand-type bonds. A major challenge in this technique is to ensure that measurements reflect bonds between single biomolecules because the molecules cannot be directly observed. This perspective evaluates different methodologies for identifying and reducing the contribution of multiple molecule interactions to single-molecule measurements to help the reader design experiments or assess publications in the single-molecule force spectroscopy field. We apply our analysis to the large body of literature that purports to measure the strength of single bonds between biotin and streptavidin as a demonstration that measurements are only reproducible when the most reliable methods for ensuring single molecules are used.
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Affiliation(s)
- Keith C Johnson
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Wendy E Thomas
- Department of Bioengineering, University of Washington, Seattle, Washington.
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33
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Mykuliak VV, Haining AWM, von Essen M, del Río Hernández A, Hytönen VP. Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin. PLoS Comput Biol 2018; 14:e1006126. [PMID: 29698481 PMCID: PMC5940241 DOI: 10.1371/journal.pcbi.1006126] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/08/2018] [Accepted: 04/06/2018] [Indexed: 11/18/2022] Open
Abstract
Mechanical stability is a key feature in the regulation of structural scaffolding proteins and their functions. Despite the abundance of α-helical structures among the human proteome and their undisputed importance in health and disease, the fundamental principles of their behavior under mechanical load are poorly understood. Talin and α-catenin are two key molecules in focal adhesions and adherens junctions, respectively. In this study, we used a combination of atomistic steered molecular dynamics (SMD) simulations, polyprotein engineering, and single-molecule atomic force microscopy (smAFM) to investigate unfolding of these proteins. SMD simulations revealed that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. While the 5-helix bundles were found to be mechanically stable, a second stable conformation corresponding to the 3-helix state was revealed. Mechanically weaker 4-helix bundles easily unfolded into a stable 3-helix conformation. The results of smAFM experiments were in agreement with the findings of the computational simulations. The disulfide clamp mutants, designed to protect the stable state, support the 3-helix intermediate model in both experimental and computational setups. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered. Better understanding of the mechanical unfolding mechanism of α-helix proteins is a key step towards comprehensive models describing the mechanoregulation of proteins.
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Affiliation(s)
- Vasyl V. Mykuliak
- Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Finland and Fimlab Laboratories, Tampere, Finland
| | - Alexander William M. Haining
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Magdaléna von Essen
- Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Finland and Fimlab Laboratories, Tampere, Finland
| | - Armando del Río Hernández
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, United Kingdom
- * E-mail: (AdRH); (VPH)
| | - Vesa P. Hytönen
- Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Finland and Fimlab Laboratories, Tampere, Finland
- * E-mail: (AdRH); (VPH)
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34
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Efremova MV, Veselov MM, Barulin AV, Gribanovsky SL, Le-Deygen IM, Uporov IV, Kudryashova EV, Sokolsky-Papkov M, Majouga AG, Golovin YI, Kabanov AV, Klyachko NL. In Situ Observation of Chymotrypsin Catalytic Activity Change Actuated by Nonheating Low-Frequency Magnetic Field. ACS NANO 2018; 12:3190-3199. [PMID: 29570975 DOI: 10.1021/acsnano.7b06439] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Magnetomechanical modulation of biochemical processes is a promising instrument for bioengineering and nanomedicine. This work demonstrates two approaches to control activity of an enzyme, α-chymotrypsin immobilized on the surface of gold-coated magnetite magnetic nanoparticles (GM-MNPs) using a nonheating low-frequency magnetic field (LF MF). The measurement of the enzyme reaction rate was carried out in situ during exposure to the magnetic field. The first approach involves α-chymotrypsin-GM-MNPs conjugates, in which the enzyme undergoes mechanical deformations with the reorientation of the MNPs under LF MF (16-410 Hz frequency, 88 mT flux density). Such mechanical deformations result in conformational changes in α-chymotrypsin structure, as confirmed by infrared spectroscopy and molecular modeling, and lead to a 63% decrease of enzyme initial activity. The second approach involves an α-chymotrypsin-GM-MNPs/trypsin inhibitor-GM-MNPs complex, in which the activity of the enzyme is partially inhibited. In this case the reorientation of MNPs in the field leads to disruption of the enzyme-inhibitor complex and an almost 2-fold increase of enzyme activity. The results further demonstrate the utility of magnetomechanical actuation at the nanoscale for the remote modulation of biochemical reactions.
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Affiliation(s)
- Maria V Efremova
- Laboratory for Chemical Design of Bionanomaterials, Chemistry Department , M.V. Lomonosov Moscow State University , Moscow 119991 , Russian Federation
- National University of Science and Technology MISIS , Moscow 119049 , Russian Federation
| | - Maxim M Veselov
- Laboratory for Chemical Design of Bionanomaterials, Chemistry Department , M.V. Lomonosov Moscow State University , Moscow 119991 , Russian Federation
| | - Alexander V Barulin
- Laboratory for Chemical Design of Bionanomaterials, Chemistry Department , M.V. Lomonosov Moscow State University , Moscow 119991 , Russian Federation
| | | | - Irina M Le-Deygen
- Laboratory for Chemical Design of Bionanomaterials, Chemistry Department , M.V. Lomonosov Moscow State University , Moscow 119991 , Russian Federation
| | - Igor V Uporov
- Laboratory for Chemical Design of Bionanomaterials, Chemistry Department , M.V. Lomonosov Moscow State University , Moscow 119991 , Russian Federation
| | - Elena V Kudryashova
- Laboratory for Chemical Design of Bionanomaterials, Chemistry Department , M.V. Lomonosov Moscow State University , Moscow 119991 , Russian Federation
| | - Marina Sokolsky-Papkov
- Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Alexander G Majouga
- Laboratory for Chemical Design of Bionanomaterials, Chemistry Department , M.V. Lomonosov Moscow State University , Moscow 119991 , Russian Federation
- National University of Science and Technology MISIS , Moscow 119049 , Russian Federation
- D. Mendeleev University of Chemical Technology of Russia , Moscow 125047 , Russian Federation
| | - Yuri I Golovin
- Laboratory for Chemical Design of Bionanomaterials, Chemistry Department , M.V. Lomonosov Moscow State University , Moscow 119991 , Russian Federation
- G.R. Derzhavin Tambov State University , Tambov 392036 , Russian Federation
| | - Alexander V Kabanov
- Laboratory for Chemical Design of Bionanomaterials, Chemistry Department , M.V. Lomonosov Moscow State University , Moscow 119991 , Russian Federation
- Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Natalia L Klyachko
- Laboratory for Chemical Design of Bionanomaterials, Chemistry Department , M.V. Lomonosov Moscow State University , Moscow 119991 , Russian Federation
- National University of Science and Technology MISIS , Moscow 119049 , Russian Federation
- Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
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35
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Zhao D, Liu S, Gao Y. Single-molecule manipulation and detection. Acta Biochim Biophys Sin (Shanghai) 2018; 50:231-237. [PMID: 29377975 DOI: 10.1093/abbs/gmx146] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/23/2017] [Indexed: 11/13/2022] Open
Abstract
Compared to conventional ensemble methods, studying macromolecules at single-molecule level can reveal extraordinary clear and even surprising views for a biological reaction. In the past 20 years, single-molecule techniques have been undergoing a very rapid development, and these cutting edge technologies have revolutionized the biological research by facilitating single-molecule manipulation and detection. Here we give a brief review about these advanced techniques, including optical tweezers, magnetic tweezers, atomic force microscopy (AFM), hydrodynamic flow-stretching assay, and single-molecule fluorescence resonance energy transfer (smFRET). We are trying to describe their basic principles and provide a few examples of applications for each technique. This review aims to give a rather introductory survey of single-molecule techniques for audiences with biological or biophysical background.
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Affiliation(s)
- Deyu Zhao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Siyun Liu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Ying Gao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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36
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Perales-Calvo J, Giganti D, Stirnemann G, Garcia-Manyes S. The force-dependent mechanism of DnaK-mediated mechanical folding. SCIENCE ADVANCES 2018; 4:eaaq0243. [PMID: 29487911 PMCID: PMC5817926 DOI: 10.1126/sciadv.aaq0243] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/09/2018] [Indexed: 05/27/2023]
Abstract
It is well established that chaperones modulate the protein folding free-energy landscape. However, the molecular determinants underlying chaperone-mediated mechanical folding remain largely elusive, primarily because the force-extended unfolded conformation fundamentally differs from that characterized in biochemistry experiments. We use single-molecule force-clamp spectroscopy, combined with molecular dynamics simulations, to study the effect that the Hsp70 system has on the mechanical folding of three mechanically stiff model proteins. Our results demonstrate that, when working independently, DnaJ (Hsp40) and DnaK (Hsp70) work as holdases, blocking refolding by binding to distinct substrate conformations. Whereas DnaK binds to molten globule-like forms, DnaJ recognizes a cryptic sequence in the extended state in an unanticipated force-dependent manner. By contrast, the synergetic coupling of the Hsp70 system exhibits a marked foldase behavior. Our results offer unprecedented molecular and kinetic insights into the mechanisms by which mechanical force finely regulates chaperone binding, directly affecting protein elasticity.
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Affiliation(s)
- Judit Perales-Calvo
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King’s College London, WC2R 2LS London, UK
| | - David Giganti
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King’s College London, WC2R 2LS London, UK
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Univ. Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King’s College London, WC2R 2LS London, UK
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37
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Khoury LR, Nowitzke J, Shmilovich K, Popa I. Study of Biomechanical Properties of Protein-Based Hydrogels Using Force-Clamp Rheometry. Macromolecules 2018. [DOI: 10.1021/acs.macromol.7b02160] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Luai R. Khoury
- Department of Physics, University of Wisconsin—Milwaukee, 3135 North Maryland Ave., Milwaukee, Wisconsin 53211, United States
| | - Joel Nowitzke
- Department of Physics, University of Wisconsin—Milwaukee, 3135 North Maryland Ave., Milwaukee, Wisconsin 53211, United States
| | - Kirill Shmilovich
- Department of Physics, University of Wisconsin—Milwaukee, 3135 North Maryland Ave., Milwaukee, Wisconsin 53211, United States
| | - Ionel Popa
- Department of Physics, University of Wisconsin—Milwaukee, 3135 North Maryland Ave., Milwaukee, Wisconsin 53211, United States
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38
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Disulfide isomerization reactions in titin immunoglobulin domains enable a mode of protein elasticity. Nat Commun 2018; 9:185. [PMID: 29330363 PMCID: PMC5766482 DOI: 10.1038/s41467-017-02528-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 12/04/2017] [Indexed: 12/31/2022] Open
Abstract
The response of titin to mechanical forces is a major determinant of the function of the heart. When placed under a pulling force, the unstructured regions of titin uncoil while its immunoglobulin (Ig) domains unfold and extend. Using single-molecule atomic force microscopy, we show that disulfide isomerization reactions within Ig domains enable a third mechanism of titin elasticity. Oxidation of Ig domains leads to non-canonical disulfide bonds that stiffen titin while enabling force-triggered isomerization reactions to more extended states of the domains. Using sequence and structural analyses, we show that 21% of titin’s I-band Ig domains contain a conserved cysteine triad that can engage in disulfide isomerization reactions. We propose that imbalance of the redox status of myocytes can have immediate consequences for the mechanical properties of the sarcomere via alterations of the oxidation state of titin domains. Titin regulates myocyte stiffness through uncoiling and unfolding but these two processes cannot fully explain its elasticity. Here, the authors use atomic force microscopy to study the properties of titin disulfide bonds, showing that disulfide isomerization represents a third mode of titin elasticity.
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39
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Elosegui-Artola A, Andreu I, Beedle AE, Lezamiz A, Uroz M, Kosmalska AJ, Oria R, Kechagia JZ, Rico-Lastres P, Le Roux AL, Shanahan CM, Trepat X, Navajas D, Garcia-Manyes S, Roca-Cusachs P. Force Triggers YAP Nuclear Entry by Regulating Transport across Nuclear Pores. Cell 2017; 171:1397-1410.e14. [DOI: 10.1016/j.cell.2017.10.008] [Citation(s) in RCA: 519] [Impact Index Per Article: 74.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/14/2017] [Accepted: 10/04/2017] [Indexed: 12/28/2022]
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40
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Zhao X, Zeng X, Lu C, Yan J. Studying the mechanical responses of proteins using magnetic tweezers. NANOTECHNOLOGY 2017; 28:414002. [PMID: 28766506 DOI: 10.1088/1361-6528/aa837e] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The mechanical stability of proteins has been extensively studied using AFM as a single-molecule force spectroscopy method. While this has led to many important results, these studies have been mainly limited to fast unfolding at a high-force regime due to the rapid mechanical drift in most AFM stretching experiments. Therefore, there is a gap between the knowledge obtained at a high-force regime and the mechanical properties of proteins at a lower force regime which is often more physiologically relevant. Recent studies have demonstrated that this gap can be addressed by stretching single protein molecules using magnetic tweezers, due to the excellent mechanical stability this technology offers. Here we review magnetic tweezers technology and its current application in studies of the force-dependent stability and interactions of proteins.
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Affiliation(s)
- Xiaodan Zhao
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore
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41
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Valle-Orero J, Tapia-Rojo R, Eckels EC, Rivas-Pardo JA, Popa I, Fernández JM. Proteins Breaking Bad: A Free Energy Perspective. J Phys Chem Lett 2017; 8:3642-3647. [PMID: 28723106 PMCID: PMC5957541 DOI: 10.1021/acs.jpclett.7b01509] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Protein aging may manifest as a mechanical disease that compromises tissue elasticity. As proved recently, while proteins respond to changes in force with an instantaneous elastic recoil followed by a folding contraction, aged proteins break bad, becoming unstructured polymers. Here, we explain this phenomenon in the context of a free energy model, predicting the changes in the folding landscape of proteins upon oxidative aging. Our findings validate that protein folding under force is constituted by two separable components, polymer properties and hydrophobic collapse, and demonstrate that the latter becomes irreversibly blocked by oxidative damage. We run Brownian dynamics simulations on the landscape of protein L octamer, reproducing all experimental observables, for a naive and damaged polyprotein. This work provides a unique tool to understand the evolving free energy landscape of elastic proteins upon physiological changes, opening new perspectives to predict age-related diseases in tissues.
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42
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Beedle AEM, Mora M, Lynham S, Stirnemann G, Garcia-Manyes S. Tailoring protein nanomechanics with chemical reactivity. Nat Commun 2017; 8:15658. [PMID: 28585528 PMCID: PMC5467162 DOI: 10.1038/ncomms15658] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 04/13/2017] [Indexed: 12/22/2022] Open
Abstract
The nanomechanical properties of elastomeric proteins determine the elasticity of a variety of tissues. A widespread natural tactic to regulate protein extensibility lies in the presence of covalent disulfide bonds, which significantly enhance protein stiffness. The prevalent in vivo strategy to form disulfide bonds requires the presence of dedicated enzymes. Here we propose an alternative chemical route to promote non-enzymatic oxidative protein folding via disulfide isomerization based on naturally occurring small molecules. Using single-molecule force-clamp spectroscopy, supported by DFT calculations and mass spectrometry measurements, we demonstrate that subtle changes in the chemical structure of a transient mixed-disulfide intermediate adduct between a protein cysteine and an attacking low molecular-weight thiol have a dramatic effect on the protein's mechanical stability. This approach provides a general tool to rationalize the dynamics of S-thiolation and its role in modulating protein nanomechanics, offering molecular insights on how chemical reactivity regulates protein elasticity. Post-translational modifications modulate nanomechanics of proteins. Here the authors use single-molecule force-clamp spectroscopy supported by density functional theory calculations to show how reactive low-weight molecular thiol compounds directly affect mechanical protein folding.
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Affiliation(s)
- Amy E M Beedle
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, WC2R 2LS London, UK
| | - Marc Mora
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, WC2R 2LS London, UK
| | - Steven Lynham
- Centre of Excellence for Mass Spectrometry, King's College London, SE5 8AF London, UK
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Univ. Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, WC2R 2LS London, UK
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43
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Relat-Goberna J, Beedle AEM, Garcia-Manyes S. The Nanomechanics of Lipid Multibilayer Stacks Exhibits Complex Dynamics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1700147. [PMID: 28503797 DOI: 10.1002/smll.201700147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/17/2017] [Indexed: 06/07/2023]
Abstract
The nanomechanics of lipid membranes regulates a large number of cellular functions. However, the molecular mechanisms underlying the plastic rupture of individual bilayers remain elusive. This study uses force clamp spectroscopy to capture the force-dependent dynamics of membrane failure on a model diphytanoylphosphatidylcholine multilayer stack, which is devoid of surface effects. The obtained kinetic measurements demonstrate that the rupture of an individual lipid bilayer, occurring in the bilayer parallel plane, is a stochastic process that follows a log-normal distribution, compatible with a pore formation mechanism. Furthermore, the vertical individual force-clamp trajectories, occurring in the bilayer orthogonal bilayer plane, reveal that rupturing process occurs through distinct intermediate mechanical transition states that can be ascribed to the fine chemical composition of the hydrated phospholipid moiety. Altogether, these results provide a first description of unanticipated complexity in the energy landscape governing the mechanically induced bilayer rupture process.
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Affiliation(s)
- Josep Relat-Goberna
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, Strand, London, WC2R 2LS, UK
| | - Amy E M Beedle
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, Strand, London, WC2R 2LS, UK
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, Strand, London, WC2R 2LS, UK
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44
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Abstract
Advancements in single-molecule force spectroscopy techniques such as atomic force microscopy and magnetic tweezers allow investigation of how domain folding under force can play a physiological role. Combining these techniques with protein engineering and HaloTag covalent attachment, we investigate similarities and differences between four model proteins: I10 and I91-two immunoglobulin-like domains from the muscle protein titin, and two α + β fold proteins-ubiquitin and protein L. These proteins show a different mechanical response and have unique extensions under force. Remarkably, when normalized to their contour length, the size of the unfolding and refolding steps as a function of force reduces to a single master curve. This curve can be described using standard models of polymer elasticity, explaining the entropic nature of the measured steps. We further validate our measurements with a simple energy landscape model, which combines protein folding with polymer physics and accounts for the complex nature of tandem domains under force. This model can become a useful tool to help in deciphering the complexity of multidomain proteins operating under force.
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Affiliation(s)
- Jessica Valle-Orero
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
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45
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Echelman DJ, Lee AQ, Fernández JM. Mechanical forces regulate the reactivity of a thioester bond in a bacterial adhesin. J Biol Chem 2017; 292:8988-8997. [PMID: 28348083 DOI: 10.1074/jbc.m117.777466] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/17/2017] [Indexed: 11/06/2022] Open
Abstract
Bacteria must withstand large mechanical shear forces when adhering to and colonizing hosts. Recent structural studies on a class of Gram-positive bacterial adhesins have revealed an intramolecular Cys-Gln thioester bond that can react with surface-associated ligands to covalently anchor to host surfaces. Two other examples of such internal thioester bonds occur in certain anti-proteases and in the immune complement system, both of which react with the ligand only after the thioester bond is exposed by a proteolytic cleavage. We hypothesized that mechanical forces in bacterial adhesion could regulate thioester reactivity to ligand analogously to such proteolytic gating. Studying the pilus tip adhesin Spy0125 of Streptococcus pyogenes, we developed a single molecule assay to unambiguously resolve the state of the thioester bond. We found that when Spy0125 was in a folded state, its thioester bond could be cleaved with the small-molecule nucleophiles methylamine and histamine, but when Spy0125 was mechanically unfolded and subjected to forces of 50-350 piconewtons, thioester cleavage was no longer observed. For folded Spy0125 without mechanical force exposure, thioester cleavage was in equilibrium with spontaneous thioester reformation, which occurred with a half-life of several minutes. Functionally, this equilibrium reactivity allows thioester-containing adhesins to sample potential substrates without irreversible cleavage and inactivation. We propose that such reversible thioester reactivity would circumvent potential soluble inhibitors, such as histamine released at sites of inflammation, and allow the bacterial adhesin to selectively associate with surface-bound ligands.
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Affiliation(s)
- Daniel J Echelman
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Alex Q Lee
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Julio M Fernández
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
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46
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Maki K, Nakao N, Adachi T. Nano-mechanical characterization of tension-sensitive helix bundles in talin rod. Biochem Biophys Res Commun 2017; 484:372-377. [PMID: 28131835 DOI: 10.1016/j.bbrc.2017.01.127] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 01/23/2017] [Indexed: 01/11/2023]
Abstract
Tension-induced exposure of a cryptic signaling binding site is one of the most fundamental mechanisms in molecular mechanotransduction. Helix bundles in rod domains of talin, a tension-sensing protein at focal adhesions, unfurl under tension to expose cryptic vinculin binding sites. Although the difference in their mechanical stabilities would determine which helix bundle is tension-sensitive, their respective mechanical behaviors under tension have not been characterized. In this study, we evaluated the mechanical behaviors of residues 486-654 and 754-889 of talin, which form helix bundles with low and high tension-sensitivity, by employing AFM nano-tensile testing. As a result, residues 754-889 exhibited lower unfolding energy for complete unfolding than residues 486-654. In addition, we found that residues 754-889 transition into intermediate conformations under lower tension than residues 486-654. Furthermore, residues 754-889 showed shorter persistence length in the intermediate conformation than residues 486-654, suggesting that residues 754-889 under tension exhibit separated α-helices, while residues 486-654 assume a compact conformation with inter-helix interactions. Therefore, we suggest that residues 754-889 of talin work as a tension-sensitive domain to recruit vinculin at the early stage of focal adhesion development, while residues 486-654 contribute to rather robust tension-sensitivity by recruiting vinculin under high tension.
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Affiliation(s)
- Koichiro Maki
- Laboratory of Biomechanics, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo, Kyoto 606-8507, Japan; Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Yoshida Honmachi, Sakyo, Kyoto 606-8501, Japan
| | - Nobuhiko Nakao
- Laboratory of Biomechanics, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo, Kyoto 606-8507, Japan; Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Yoshida Honmachi, Sakyo, Kyoto 606-8501, Japan
| | - Taiji Adachi
- Laboratory of Biomechanics, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo, Kyoto 606-8507, Japan; Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Yoshida Honmachi, Sakyo, Kyoto 606-8501, Japan.
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47
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Huang W, Zhu Z, Wen J, Wang X, Qin M, Cao Y, Ma H, Wang W. Single Molecule Study of Force-Induced Rotation of Carbon-Carbon Double Bonds in Polymers. ACS NANO 2017; 11:194-203. [PMID: 28114764 DOI: 10.1021/acsnano.6b07119] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Carbon-carbon double bonds (C═C) are ubiquitous in natural and synthetic polymers. In bulk studies, due to limited ways to control applied force, they are thought to be mechanically inert and not to contribute to the extensibility of polymers. Here, we report a single molecule force spectroscopy study on a polymer containing C═C bonds using atomic force microscope. Surprisingly, we found that it is possible to directly observe the cis-to-trans isomerization of C═C bonds at the time scale of ∼1 ms at room temperature by applying a tensile force ∼1.7 nN. The reaction proceeds through a diradical intermediate state, as confirmed by both a free radical quenching experiment and quantum chemical modeling. The force-free activation length to convert the cis C═C bonds to the transition state is ∼0.5 Å, indicating that the reaction rate is accelerated by ∼109 times at the transition force. On the basis of the density functional theory optimized structure, we propose that because the pulling direction is not parallel to C═C double bonds in the polymer, stretching the polymer not only provides tension to lower the transition barrier but also provides torsion to facilitate the rotation of cis C═C bonds. This explains the apparently low transition force for such thermally "forbidden" reactions and offers an additional explanation of the "lever-arm effect" of polymer backbones on the activation force for many mechanophores. This work demonstrates the importance of precisely controlling the force direction at the nanoscale to the force-activated reactions and may have many implications on the design of stress-responsive materials.
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Affiliation(s)
- Wenmao Huang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University , Nanjing 210093, P.R. China
| | - Zhenshu Zhu
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University , Nanjing 210093, P.R. China
- Department of Pharmaceutical Analysis, Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University , Nanjing 210009, P.R. China
| | - Jing Wen
- Key Laboratory of Mesoscopic Chemistry of MOE, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, P. R. China
| | - Xin Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University , Nanjing 210093, P.R. China
| | - Meng Qin
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University , Nanjing 210093, P.R. China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University , Nanjing 210093, P.R. China
| | - Haibo Ma
- Key Laboratory of Mesoscopic Chemistry of MOE, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, P. R. China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University , Nanjing 210093, P.R. China
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48
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Kim Y, Kim W, Park JW. Principles and Applications of Force Spectroscopy Using Atomic Force Microscopy. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.11022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Youngkyu Kim
- Department of Chemistry; Pohang University of Science and Technology; Pohang 37673 Korea
| | - Woong Kim
- Department of Chemistry; Pohang University of Science and Technology; Pohang 37673 Korea
| | - Joon Won Park
- Department of Chemistry; Pohang University of Science and Technology; Pohang 37673 Korea
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49
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Sevim S, Ozer S, Feng L, Wurzel J, Fakhraee A, Shamsudhin N, Jang B, Alcantara C, Ergeneman O, Pellicer E, Sort J, Lühmann T, Pané S, Nelson BJ, Torun H. Dually actuated atomic force microscope with miniaturized magnetic bead-actuators for single-molecule force measurements. NANOSCALE HORIZONS 2016; 1:488-495. [PMID: 32260713 DOI: 10.1039/c6nh00134c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We report a novel atomic force microscopy (AFM) technique with dual actuation capabilities using both piezo and magnetic bead actuation for advanced single-molecule force spectroscopy experiments. The experiments are performed by manipulating magnetic microbeads using an electromagnet against a stationary cantilever. Magnetic actuation has been demonstrated before to actuate cantilevers, but here we keep the cantilever stationary and accomplish actuation via free-manipulated microstructures. The developed method benefits from significant reduction of drift, since the experiments are performed without a substrate contact and the measured force is inherently differential. In addition, shrinking the size of the actuator can minimize hydrodynamic forces affecting the cantilever. The new method reported herein allows for the application of constant force to perform force-clamp experiments without any active feedback, profiled for a deeper understanding of biomolecular interactions.
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Affiliation(s)
- Semih Sevim
- Department of Electrical and Electronics Engineering, Bogazici University, Bebek, 34342 Istanbul, Turkey.
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50
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Manibog K, Yen CF, Sivasankar S. Measuring Force-Induced Dissociation Kinetics of Protein Complexes Using Single-Molecule Atomic Force Microscopy. Methods Enzymol 2016; 582:297-320. [PMID: 28062039 DOI: 10.1016/bs.mie.2016.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Proteins respond to mechanical force by undergoing conformational changes and altering the kinetics of their interactions. However, the biophysical relationship between mechanical force and the lifetime of protein complexes is not completely understood. In this chapter, we provide a step-by-step tutorial on characterizing the force-dependent regulation of protein interactions using in vitro and in vivo single-molecule force clamp measurements with an atomic force microscope (AFM). While we focus on the force-induced dissociation of E-cadherins, a critical cell-cell adhesion protein, the approaches described here can be readily adapted to study other protein complexes. We begin this chapter by providing a brief overview of theoretical models that describe force-dependent kinetics of biomolecular interactions. Next, we present step-by-step methods for measuring the response of single receptor-ligand bonds to tensile force in vitro. Finally, we describe methods for quantifying the mechanical response of single protein complexes on the surface of living cells. We describe general protocols for conducting such measurements, including sample preparation, AFM force clamp measurements, and data analysis. We also highlight critical limitations in current technologies and discuss solutions to these challenges.
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Affiliation(s)
- K Manibog
- Iowa State University, Ames, IA, United States; Ames Laboratory, U.S. Department of Energy, Ames, IA, United States
| | - C F Yen
- Iowa State University, Ames, IA, United States; Ames Laboratory, U.S. Department of Energy, Ames, IA, United States
| | - S Sivasankar
- Iowa State University, Ames, IA, United States; Ames Laboratory, U.S. Department of Energy, Ames, IA, United States.
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