1
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Wang Y, Ye J, Liu X, Zhang Z, Shang F, Qi X, Zhang Y, Du J, Sun H, Xu J, Chen H, Yu M, Le S. Mechanically weak and highly dynamic state of mechanosensitive titin Ig domains induced by proline isomerization. Nat Commun 2025; 16:2771. [PMID: 40113761 PMCID: PMC11926396 DOI: 10.1038/s41467-025-57989-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Accepted: 03/07/2025] [Indexed: 03/22/2025] Open
Abstract
Titin, essential for mechano-homeostasis in cardiac and skeletal sarcomere, contains numerous mechanosensitive immunoglobulin-like (Ig) domains in its I-band region. However, how proline isomerization and cysteine-mediated disulfide bond collectively regulate Ig domain dynamics within the physiological force range remains unclear. Here, we use single-molecule force spectroscopy to quantify the proximal Ig1 domain, revealing that proline isomerization leads to two native states-trans and cis states-with distinct mechanical and thermal stabilities. The trans-Ig1 unfolds at forces of ~ 5 pN, which is over 50 pN lower than that of cis-Ig1, and unfolds 1000 times faster under physiological forces. Furthermore, such proline induced dual-state is likely shared feature across majority of I-band Ig domains. Additionally, reduced cis- and trans-Ig1 exhibit catch-slip bond unfolding, while oxidized forms display slip-catch-slip unfolding. This study offers insight into effective modulation of proline isomerization and disulfide bond in regulating mechanosensitive proteins within the physiological force range.
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Affiliation(s)
- Yukai Wang
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, China
- Department of Biochemistry and Division of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiaqing Ye
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Xian Liu
- Department of Biochemistry and Division of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhuwei Zhang
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Fei Shang
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, China
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xingyu Qi
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Yuhang Zhang
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Jingyi Du
- Department of Biochemistry and Division of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Sun
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, China
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Jiashu Xu
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Hu Chen
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, China.
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China.
| | - Miao Yu
- Department of Biochemistry and Division of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Shimin Le
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, China.
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2
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Pancrazi F, De Bei O, Lavecchia di Tocco F, Marchetti M, Campanini B, Cannistraro S, Bettati S, Bizzarri AR. Proline isomerization modulates the bacterial IsdB/hemoglobin interaction: an atomic force spectroscopy study. DISCOVER NANO 2025; 20:20. [PMID: 39918647 PMCID: PMC11805746 DOI: 10.1186/s11671-025-04182-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Accepted: 01/06/2025] [Indexed: 02/11/2025]
Abstract
Iron surface determinant B (IsdB), a Staphylococcus aureus (SA) surface protein involved in both heme iron acquisition from host hemoglobin (Hb) and bacterial adhesion, is a proven virulence factor that can be targeted for the design of antibacterial molecules or vaccines. Recent single-molecule experiments on IsdB interaction with cell adhesion factors revealed an increase of the complex lifetime upon applying a stronger force (catch bond); this was suggested to favor host invasion under shear stress. An increased bond strength under mechanical stress was also detected by Atomic Force Spectroscopy (AFS) for the interaction between IsdB and Hb. Structural information on the underlying molecular mechanisms at the basis of this behaviour in IsdB-based complexes is missing. Here, we show that the single point mutation of Pro173 in the IsdB domain responsible for Hb binding, which weakens the IsdB:Hb interaction without hampering heme extraction, totally abolishes the previously observed behavior. Remarkably, Pro173 does not directly interact with Hb, but undergoes cis-trans isomerization upon IsdB:Hb complex formation, coupled to folding-upon binding of the corresponding protein loop. Our results suggest that these events might represent the molecular basis for the stress-dependence of bond strength observed for wild type IsdB, shedding light on the mechanisms that govern the capability of SA to infect host cells.
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Affiliation(s)
- Francesca Pancrazi
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Largo dell'Università, 01100, Viterbo, Italy
| | - Omar De Bei
- Department of Medicine and Surgery, University of Parma, Via Volturno 39, 43125, Parma, Italy
| | | | - Marialaura Marchetti
- Department of Medicine and Surgery, University of Parma, Via Volturno 39, 43125, Parma, Italy
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - Salvatore Cannistraro
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Largo dell'Università, 01100, Viterbo, Italy
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, Via Volturno 39, 43125, Parma, Italy.
- Institute of Biophysics, National Research Council, via G. Moruzzi, 56124, Pisa, Italy.
| | - Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Largo dell'Università, 01100, Viterbo, Italy.
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3
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Gala M, Paul ED, Čekan P, Žoldák G. Prediction of the Stability of Protein Substructures Using AI/ML Techniques. Methods Mol Biol 2025; 2870:153-182. [PMID: 39543035 DOI: 10.1007/978-1-0716-4213-9_9] [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: 11/17/2024]
Abstract
This chapter explores the innovative application of machine learning techniques to understand and predict the stability of protein substructures. Accurately identifying stable substructures within proteins necessitates incorporating the local context, crucial for elucidating the roles of supersecondary structures. This approach emphasizes the importance of contextual information in understanding the stability and functionality of protein regions, thereby providing a more comprehensive view of protein mechanics and interactions. The chapter focuses on our findings regarding the DnaK Hsp70 chaperone protein, utilizing it as a case study. This research highlights how context-dependent physico-chemical features derived from protein sequences can accurately classify residues into stable and unstable substructures by leveraging logistic regression, random forest, and support vector machine methods. The findings represent a pivotal step towards the rational design of proteins with tailored properties, offering new insights into protein engineering and the fundamental principles underpinning protein supersecondary structures.
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Affiliation(s)
- Michal Gala
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Evan David Paul
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Pavol Čekan
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Gabriel Žoldák
- Faculty of Science, P.J. Šafárik University in Košice, Košice, Slovakia.
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4
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Dawes BA, Kamenetska M. Autoregressive HMM resolves biomolecular transitions from passive optical tweezer force measurements. Biophys J 2024:S0006-3495(24)04057-8. [PMID: 39616441 DOI: 10.1016/j.bpj.2024.11.3320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 11/13/2024] [Accepted: 11/26/2024] [Indexed: 12/13/2024] Open
Abstract
Optical tweezer (OT) single-molecule force spectroscopy is a powerful method to map out the energy landscape of biological complexes and has found increasing applications in academic and pharmaceutical research. The dominant method to extract molecular conformation transitions from the thermal diffusion-broadened trajectories of the microscopic OT probes attached to the single molecule of interest is through hidden Markov models (HMMs). In standard applications, the HMMs assume a white noise spectrum of the probes superimposed onto the molecular signal. Here, we demonstrate, through theoretical derivation, computer modeling and experimental measurements that this standard white noise HMM (wnHMM) misses key features of real OT data. The deviation is most pronounced at higher frequencies because the white noise model does not account for the overdamped nature of particle diffusion in an OT harmonic potential in aqueous environments. To address this, we derive how to incorporate autoregression between consecutive data points into a HMM, and demonstrate through modeling and experiment that such an autoregressive HMM (arHMM) captures real OT data behavior across all frequency ranges. Through analysis of real OT data we recorded on a single DNA hairpin undergoing folding and unfolding transitions, we show that the wnHMM extracts lifetimes that are at least a factor of 2 faster and less consistent than the arHMM results, which match expectations and prior measurements. Overall, our work suggests that arHMM should be the default model choice for analysis OT single-molecule transitions and that its use will improve the fidelity and accuracy of single-molecule force spectroscopy measurements.
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Affiliation(s)
- Brian A Dawes
- Department of Physics, Boston University, Boston, Massachusetts
| | - Maria Kamenetska
- Department of Physics, Boston University, Boston, Massachusetts; Department of Chemistry, Boston University, Boston, Massachusetts; Division of Materials Science and Engineering, Boston University, Boston, Massachusetts.
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5
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Grande V, Schuld J, van der Ven PFM, Gruss OJ, Fürst DO. Filamin-A-interacting protein 1 (FILIP1) is a dual compartment protein linking myofibrils and microtubules during myogenic differentiation and upon mechanical stress. Cell Tissue Res 2023:10.1007/s00441-023-03776-4. [PMID: 37178194 DOI: 10.1007/s00441-023-03776-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023]
Abstract
Variations in the gene encoding filamin-A-interacting protein 1 (FILIP1) were identified to be associated with a combination of neurological and muscular symptoms. While FILIP1 was shown to regulate motility of brain ventricular zone cells, a process important for corticogenesis, the function of the protein in muscle cells has been less well characterized. The expression of FILIP1 in regenerating muscle fibres predicted a role in early muscle differentiation. Here we analysed expression and localization of FILIP1 and its binding partners filamin-C (FLNc) and microtubule plus-end-binding protein EB3 in differentiating cultured myotubes and adult skeletal muscle. Prior to the development of cross-striated myofibrils, FILIP1 is associated with microtubules and colocalizes with EB3. During further myofibril maturation its localization changes, and FILIP1 localizes to myofibrillar Z-discs together with the actin-binding protein FLNc. Forced contractions of myotubes by electrical pulse stimulation (EPS) induce focal disruptions in myofibrils and translocation of both proteins from Z-discs to these lesions, suggesting a role in induction and/or repair of these structures. The immediate proximity of tyrosylated, dynamic microtubules and EB3 to lesions implies that also these play a role in these processes. This implication is supported by the fact that in nocodazole-treated myotubes that lack functional microtubules, the number of lesions induced by EPS is significantly reduced. In summary, we here show that FILIP1 is a cytolinker protein that is associated with both microtubules and actin filaments, and might play a role in the assembly of myofibrils and their stabilization upon mechanical stress to protect them from damage.
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Affiliation(s)
- Valentina Grande
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121, Bonn, Germany
| | - Julia Schuld
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121, Bonn, Germany
| | - Peter F M van der Ven
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121, Bonn, Germany
| | - Oliver J Gruss
- Institute of Genetics, University of Bonn, Karlrobert-Kreiten-Str. 13, 53115, Bonn, Germany
| | - Dieter O Fürst
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121, Bonn, Germany.
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6
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Tapia-Rojo R, Mora M, Board S, Walker J, Boujemaa-Paterski R, Medalia O, Garcia-Manyes S. Enhanced statistical sampling reveals microscopic complexity in the talin mechanosensor folding energy landscape. NATURE PHYSICS 2023; 19:52-60. [PMID: 36660164 PMCID: PMC7614079 DOI: 10.1038/s41567-022-01808-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Statistical mechanics can describe the major conformational ensembles determining the equilibrium free-energy landscape of a folding protein. The challenge is to capture the full repertoire of low-occurrence conformations separated by high kinetic barriers that define complex landscapes. Computationally, enhanced sampling methods accelerate the exploration of molecular rare events. However, accessing the entire protein's conformational space in equilibrium experiments requires technological developments to enable extended observation times. We developed single-molecule magnetic tweezers to capture over a million individual transitions as a single talin protein unfolds and refolds under force in equilibrium. When observed at classically-probed timescales, talin folds in an apparently uncomplicated two-state manner. As the sampling time extends from minutes to days, the underlying energy landscape exhibits gradually larger signatures of complexity, involving a finite number of well-defined rare conformations. A fluctuation analysis allows us to propose plausible structures of each low-probability conformational state. The physiological relevance of each distinct conformation can be connected to the binding of the cytoskeletal protein vinculin, suggesting an extra layer of complexity in talin-mediated mechanotransduction. More generally, our experiments directly test the fundamental notion that equilibrium dynamics depend on the observation timescale.
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Affiliation(s)
- Rafael Tapia-Rojo
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, 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, Strand, WC2R 2LS London, United Kingdom
- Corresponding authors: , ,
| | - Marc Mora
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, 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, Strand, WC2R 2LS London, United Kingdom
- Corresponding authors: , ,
| | - Stephanie Board
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, 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, Strand, WC2R 2LS London, United Kingdom
| | - Jane Walker
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, 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, Strand, WC2R 2LS London, United Kingdom
| | - Rajaa Boujemaa-Paterski
- Department of Biochemistry, Zurich University, Winterhurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, Zurich University, Winterhurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Sergi Garcia-Manyes
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, 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, Strand, WC2R 2LS London, United Kingdom
- Corresponding authors: , ,
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7
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Beedle AEM, Garcia-Manyes S. The role of single protein elasticity in mechanobiology. NATURE REVIEWS. MATERIALS 2023; 8:10-24. [PMID: 37469679 PMCID: PMC7614781 DOI: 10.1038/s41578-022-00488-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/07/2022] [Indexed: 07/21/2023]
Abstract
In addition to biochemical signals and genetic considerations, mechanical forces are rapidly emerging as a master regulator of human physiology. Yet the molecular mechanisms that regulate force-induced functionalities across a wide range of scales, encompassing the cell, tissue or organ levels, are comparatively not so well understood. With the advent, development and refining of single molecule nanomechanical techniques, enabling to exquisitely probe the conformational dynamics of individual proteins under the effect of a calibrated force, we have begun to acquire a comprehensive knowledge on the rich plethora of physicochemical principles that regulate the elasticity of single proteins. Here we review the major advances underpinning our current understanding of how the elasticity of single proteins regulates mechanosensing and mechanotransduction. We discuss the present limitations and future challenges of such a prolific and burgeoning field.
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Affiliation(s)
- Amy EM Beedle
- 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, Strand, WC2R 2LS London, United Kingdom
- Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), 08028 Barcelona, Spain
| | - Sergi Garcia-Manyes
- 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, Strand, WC2R 2LS London, United Kingdom
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, London, UK
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8
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Niu L, Cheng B, Huang G, Nan K, Han S, Ren H, Liu N, Li Y, Genin GM, Xu F. A positive mechanobiological feedback loop controls bistable switching of cardiac fibroblast phenotype. Cell Discov 2022; 8:84. [PMID: 36068215 PMCID: PMC9448780 DOI: 10.1038/s41421-022-00427-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/28/2022] [Indexed: 12/15/2022] Open
Abstract
Cardiac fibrosis is associated with activation of cardiac fibroblasts (CFs), a pathological, phenotypic transition that is widely believed to be irreversible in the late stages of disease development. Sensing of a stiffened mechanical environment through regulation of integrin-based adhesion plaques and activation of the Piezo1 mechanosensitive ion channel is known to factor into this transition. Here, using integrated in vitro and in silico models, we discovered a mutually reinforcing, mechanical positive feedback loop between integrin β1 and Piezo1 activation that forms a bistable switch. The bistable switch is initiated by perturbations in matrix elastic modulus that amplify to trigger downstream signaling involving Ca2+ and YAP that, recursively, leads fibroblasts to further stiffen their environment. By simultaneously interfering with the newly identified mechanical positive feedback loop and modulating matrix elastic modulus, we reversed markers of phenotypical transition of CF, suggesting new therapeutic targets for fibrotic disease.
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Affiliation(s)
- Lele Niu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Bo Cheng
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Guoyou Huang
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei, China
| | - Kai Nan
- Department of Orthopedics Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shuang Han
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Honghui Hospital, Xi'an, Shaanxi, China
| | - Hui Ren
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Na Liu
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yan Li
- Department of Cardiology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Guy M Genin
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Department of Mechanical Engineering & Materials Science, Washington University in St. Louis, St. Louis, MO, USA.,NSF Science and Technology Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China. .,Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, China.
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9
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Tych K, Rief M. Using Single-Molecule Optical Tweezers to Study the Conformational Cycle of the Hsp90 Molecular Chaperone. Methods Mol Biol 2022; 2478:401-425. [PMID: 36063329 DOI: 10.1007/978-1-0716-2229-2_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The heat shock protein 90 (Hsp90) family of chaperones are well-known, highly important components of the cellular systems which regulate protein homeostasis. Essential in eukaryotes, Hsp90s is also found in prokaryotes, including archaea. Hsp90 is a dimeric protein, with each monomer consisting of three separate structural domains, and undergoes large conformational changes as part of its functional cycle. This cycle is driven by interactions with nucleotides, cochaperone proteins, client proteins and allosteric effects enacted by these and by posttranslational modifications. All of these influence the rate and degree of the opening and closing of the dimer as well as the relative domain orientations and its overall rigidity. Optical tweezers, which can access many of these functionally important conformational changes, therefore provide a unique tool for the study of this large and complex molecular chaperone. Here, we provide protocols for the design and implementation of different Hsp90 constructs and optical tweezers experiments for addressing the many open questions about the function of this important molecular chaperone.
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Affiliation(s)
- Katarzyna Tych
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands.
| | - Matthias Rief
- Department of Physics, Technical University of Munich, Garching-bei-München, Germany.
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10
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Alcantara J, Stix R, Huang K, Connor A, East R, Jaramillo-Martinez V, Stollar EJ, Ball KA. An Unbound Proline-Rich Signaling Peptide Frequently Samples Cis Conformations in Gaussian Accelerated Molecular Dynamics Simulations. Front Mol Biosci 2021; 8:734169. [PMID: 34869581 PMCID: PMC8634643 DOI: 10.3389/fmolb.2021.734169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
Disordered proline-rich motifs are common across the proteomes of many species and are often involved in protein-protein interactions. Proline is a unique amino acid due to the covalent bond between the backbone nitrogen and the proline side chain. The resulting five-membered ring allows proline to sample the cis state about its peptide bond, which other residues cannot do as readily. Because proline-rich disordered sequences exist as ensembles that likely include structures with the proline peptide bond in cis, a robust methodology to accurately account for these conformations in the overall ensemble is crucial. Observing the cis conformations of proline in a disordered sequence is challenging both experimentally and computationally. Nitrogen-hydrogen NMR spectroscopy cannot directly observe proline residues, which lack an amide bond, and computational methods struggle to overcome the large kinetic barrier between the cis and trans states, since isomerization usually occurs on the order of seconds. In the current work, Gaussian accelerated molecular dynamics was used to overcome this free energy barrier and simulate proline isomerization in a tetrapeptide (KPTP) and in the 12-residue proline-rich SH3 binding peptide, ArkA. We found that Gaussian accelerated molecular dynamics, when combined with a lowered peptide bond dihedral angle potential energy barrier (15 kcal/mol), allowed sufficient sampling of the proline cis and trans states on a microsecond timescale. All ArkA prolines spend a significant fraction of time in cis, leading to a more compact ensemble with less polyproline II helix structure than an ArkA ensemble with all peptide bonds in trans. The ensemble containing cis prolines also matches more closely to in vitro circular dichroism data than the all-trans ensemble. The ability of the ArkA prolines to isomerize likely affects the peptide's ability to bind its partner SH3 domain, and should be studied further. This is the first molecular dynamics simulation study of proline isomerization in a biologically relevant proline-rich sequence that we know of, and a similar protocol could be applied to study multi-proline isomerization in other proline-containing proteins to improve conformational diversity and agreement with in vitro data.
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Affiliation(s)
- Juan Alcantara
- Department of Chemistry, Skidmore College, Saratoga Springs, NY, United States
| | - Robyn Stix
- Department of Chemistry, Skidmore College, Saratoga Springs, NY, United States
| | - Katherine Huang
- Department of Chemistry, Skidmore College, Saratoga Springs, NY, United States
| | - Acadia Connor
- Department of Chemistry, Skidmore College, Saratoga Springs, NY, United States
| | - Ray East
- Department of Chemistry, Skidmore College, Saratoga Springs, NY, United States
| | - Valeria Jaramillo-Martinez
- Department of Neuroscience and Pharmacology, Texas Teach University Health Science Center, Lubbock, TX, United States
| | - Elliott J Stollar
- School of Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - K Aurelia Ball
- Department of Chemistry, Skidmore College, Saratoga Springs, NY, United States
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11
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Lövenich L, Dreissen G, Hoffmann C, Konrad J, Springer R, Höhfeld J, Merkel R, Hoffmann B. Strain induced mechanoresponse depends on cell contractility and BAG3-mediated autophagy. Mol Biol Cell 2021; 32:ar9. [PMID: 34379447 PMCID: PMC8684750 DOI: 10.1091/mbc.e21-05-0254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Basically all mammalian tissues are constantly exposed to a variety of environmental mechanical signals. Depending on the signal strength, mechanics intervenes in a multitude of cellular processes and is thus capable to induce simple cellular adaptations but also complex differentiation processes and even apoptosis. The underlying recognition typically depends on mechanosensitive proteins, which most often sense the mechanical signal for the induction of a cellular signaling cascade by changing their protein conformation. However, the fate of mechanosensors after mechanical stress application is still poorly understood and it remains unclear whether protein degradation pathways affect the mechanosensitivity of cells. Here, we show that cyclic stretch induces autophagosome formation in a time-dependent manner. Formation depends on the cochaperone BAG3 and thus likely involves BAG3-mediated chaperone-assisted selective autophagy. Furthermore, we demonstrate that strain-induced cell reorientation is clearly delayed upon inhibition of autophagy, suggesting a bidirectional crosstalk between mechanotransduction and autophagic degradation. The strength of the observed delay depends on stable adhesion structures and stress fiber formation in a RhoA-dependent manner.
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Affiliation(s)
- Lukas Lövenich
- Forschungszentrum Jülich, Institute of Biological Information Processing, IBI-2: Mechanobiology, 52428 Jülich, Germany
| | - Georg Dreissen
- Forschungszentrum Jülich, Institute of Biological Information Processing, IBI-2: Mechanobiology, 52428 Jülich, Germany
| | - Christina Hoffmann
- Forschungszentrum Jülich, Institute of Biological Information Processing, IBI-2: Mechanobiology, 52428 Jülich, Germany
| | - Jens Konrad
- Forschungszentrum Jülich, Institute of Biological Information Processing, IBI-2: Mechanobiology, 52428 Jülich, Germany
| | - Ronald Springer
- Forschungszentrum Jülich, Institute of Biological Information Processing, IBI-2: Mechanobiology, 52428 Jülich, Germany
| | - Jörg Höhfeld
- Institute for Cell Biology, University of Bonn, 53121 Bonn, Germany
| | - Rudolf Merkel
- Forschungszentrum Jülich, Institute of Biological Information Processing, IBI-2: Mechanobiology, 52428 Jülich, Germany
| | - Bernd Hoffmann
- Forschungszentrum Jülich, Institute of Biological Information Processing, IBI-2: Mechanobiology, 52428 Jülich, Germany
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12
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Höhfeld J, Benzing T, Bloch W, Fürst DO, Gehlert S, Hesse M, Hoffmann B, Hoppe T, Huesgen PF, Köhn M, Kolanus W, Merkel R, Niessen CM, Pokrzywa W, Rinschen MM, Wachten D, Warscheid B. Maintaining proteostasis under mechanical stress. EMBO Rep 2021; 22:e52507. [PMID: 34309183 PMCID: PMC8339670 DOI: 10.15252/embr.202152507] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 12/11/2022] Open
Abstract
Cell survival, tissue integrity and organismal health depend on the ability to maintain functional protein networks even under conditions that threaten protein integrity. Protection against such stress conditions involves the adaptation of folding and degradation machineries, which help to preserve the protein network by facilitating the refolding or disposal of damaged proteins. In multicellular organisms, cells are permanently exposed to stress resulting from mechanical forces. Yet, for long time mechanical stress was not recognized as a primary stressor that perturbs protein structure and threatens proteome integrity. The identification and characterization of protein folding and degradation systems, which handle force-unfolded proteins, marks a turning point in this regard. It has become apparent that mechanical stress protection operates during cell differentiation, adhesion and migration and is essential for maintaining tissues such as skeletal muscle, heart and kidney as well as the immune system. Here, we provide an overview of recent advances in our understanding of mechanical stress protection.
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Affiliation(s)
- Jörg Höhfeld
- Institute for Cell BiologyRheinische Friedrich‐Wilhelms University BonnBonnGermany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Wilhelm Bloch
- Institute of Cardiovascular Research and Sports MedicineGerman Sport UniversityCologneGermany
| | - Dieter O Fürst
- Institute for Cell BiologyRheinische Friedrich‐Wilhelms University BonnBonnGermany
| | - Sebastian Gehlert
- Institute of Cardiovascular Research and Sports MedicineGerman Sport UniversityCologneGermany
- Department for the Biosciences of SportsInstitute of Sports ScienceUniversity of HildesheimHildesheimGermany
| | - Michael Hesse
- Institute of Physiology I, Life & Brain CenterMedical FacultyRheinische Friedrich‐Wilhelms UniversityBonnGermany
| | - Bernd Hoffmann
- Institute of Biological Information Processing, IBI‐2: MechanobiologyForschungszentrum JülichJülichGermany
| | - Thorsten Hoppe
- Institute for GeneticsCologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) and CMMCUniversity of CologneCologneGermany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA3Forschungszentrum JülichJülichGermany
- CECADUniversity of CologneCologneGermany
| | - Maja Köhn
- Institute of Biology IIIFaculty of Biology, and Signalling Research Centres BIOSS and CIBSSAlbert‐Ludwigs‐University FreiburgFreiburgGermany
| | - Waldemar Kolanus
- LIMES‐InstituteRheinische Friedrich‐Wilhelms University BonnBonnGermany
| | - Rudolf Merkel
- Institute of Biological Information Processing, IBI‐2: MechanobiologyForschungszentrum JülichJülichGermany
| | - Carien M Niessen
- Department of Dermatology and CECADUniversity of CologneCologneGermany
| | | | - Markus M Rinschen
- Department of Biomedicine and Aarhus Institute of Advanced StudiesAarhus UniversityAarhusDenmark
- Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Dagmar Wachten
- Institute of Innate ImmunityUniversity Hospital BonnBonnGermany
| | - Bettina Warscheid
- Institute of Biology IIFaculty of Biology, and Signalling Research Centres BIOSS and CIBSSAlbert‐Ludwigs‐University FreiburgFreiburgGermany
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13
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Sengupta A, Rognoni LE, Merkel U, Žoldák G, Rief M. SlyD Accelerates trans-to- cis Prolyl Isomerization in a Mechanosignaling Protein under Load. J Phys Chem B 2021; 125:8712-8721. [PMID: 34279937 DOI: 10.1021/acs.jpcb.1c03648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prolyl isomerization is recognized as one of the key regulatory mechanisms, which plays a crucial role in cell signaling, ion channel gating, phage virus infection, and molecular timing. This isomerization is usually slow but often accelerated by an enzyme, called peptidyl-prolyl isomerase (PPIase). In the current project, we investigate using single-molecule force spectroscopy (SMFS) the impact of a bacterial PPIase, SlyD, on the cis-trans isomerization of the proline 2225 (P2225) in an isolated 20th domain of a cytoskeletal mechanosensing protein filamin-A (FlnA20). To explore the FlnA20-PPIase interaction, we have used multiple SMFS modes, like constant velocity, constant distance, and jumping trap experiments. In our previous study, we reported the unique nature of the P2225, which is conserved in all naturally occurring filamins and can slowly (minutes) interconvert between cis-trans isomers, in absence of any PPIase. Our current results show a staggering 25-fold acceleration of the trans-to-cis isomerization rate in the presence of saturating SlyD concentration (7.25 μM) compared to the unenzymatic condition. A SlyD concentration-dependent depletion of the trans isomeric lifetime was also observed. Additionally, we observed that SlyD stabilizes the cis-isomer in the native state of FlnA20 by ∼2 kBT. This is the first single-molecule observation of the cis-trans isomerization catalysis by a PPIase in a mechanosensing protein.
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Affiliation(s)
- Abhigyan Sengupta
- Technische Universität München, Physik Department, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 8, D-85748 Garching, Germany
| | - Lorenz E Rognoni
- Technische Universität München, Physik Department, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 8, D-85748 Garching, Germany
| | - Ulrich Merkel
- Technische Universität München, Physik Department, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 8, D-85748 Garching, Germany
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Trieda SNP 1, 040 11Košice, Slovakia
| | - Matthias Rief
- Technische Universität München, Physik Department, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 8, D-85748 Garching, Germany
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14
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Maschio MC, Fregoni J, Molteni C, Corni S. Proline isomerization effects in the amyloidogenic protein β2-microglobulin. Phys Chem Chem Phys 2021; 23:356-367. [DOI: 10.1039/d0cp04780e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The protein β2-microglobulin can aggregate in insoluble amyloid fibrils. By relying on extensive sampling simulations, we study the Pro32 isomerization as a possible triggering factor leading to structural modifications in β2-m.
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Affiliation(s)
| | - Jacopo Fregoni
- CNR-Nano S3
- Modena
- Italy
- Department of Chemical Sciences
- University of Padova
| | - Carla Molteni
- Department of Physics
- King's College London
- Strand
- London WC2R 2LS
- UK
| | - Stefano Corni
- CNR-Nano S3
- Modena
- Italy
- Department of Chemical Sciences
- University of Padova
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15
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Mehlich A, Fang J, Pelz B, Li H, Stigler J. Slow Transition Path Times Reveal a Complex Folding Barrier in a Designed Protein. Front Chem 2020; 8:587824. [PMID: 33365300 PMCID: PMC7750197 DOI: 10.3389/fchem.2020.587824] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/26/2020] [Indexed: 11/30/2022] Open
Abstract
De-novo designed proteins have received wide interest as potential platforms for nano-engineering and biomedicine. While much work is being done in the design of thermodynamically stable proteins, the folding process of artificially designed proteins is not well-studied. Here we used single-molecule force spectroscopy by optical tweezers to study the folding of ROSS, a de-novo designed 2x2 Rossmann fold. We measured a barrier crossing time in the millisecond range, much slower than what has been reported for other systems. While long transition times can be explained by barrier roughness or slow diffusion, we show that isotropic roughness cannot explain the measured transition path time distribution. Instead, this study shows that the slow barrier crossing of ROSS is caused by the population of three short-lived high-energy intermediates. In addition, we identify incomplete and off-pathway folding events with different barrier crossing dynamics. Our results hint at the presence of a complex transition barrier that may be a common feature of many artificially designed proteins.
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Affiliation(s)
- Alexander Mehlich
- Physics Department E22, Technische Universität München, Garching, Germany
| | - Jie Fang
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Benjamin Pelz
- Physics Department E22, Technische Universität München, Garching, Germany
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Johannes Stigler
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
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16
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Buwa N, Mazumdar D, Balasubramanian N. Caveolin1 Tyrosine-14 Phosphorylation: Role in Cellular Responsiveness to Mechanical Cues. J Membr Biol 2020; 253:509-534. [PMID: 33089394 DOI: 10.1007/s00232-020-00143-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/05/2020] [Indexed: 02/07/2023]
Abstract
The plasma membrane is a dynamic lipid bilayer that engages with the extracellular microenvironment and intracellular cytoskeleton. Caveolae are distinct plasma membrane invaginations lined by integral membrane proteins Caveolin1, 2, and 3. Caveolae formation and stability is further supported by additional proteins including Cavin1, EHD2, Pacsin2 and ROR1. The lipid composition of caveolar membranes, rich in cholesterol and phosphatidylserine, actively contributes to caveolae formation and function. Post-translational modifications of Cav1, including its phosphorylation of the tyrosine-14 residue (pY14Cav1) are vital to its function in and out of caveolae. Cells that experience significant mechanical stress are seen to have abundant caveolae. They play a vital role in regulating cellular signaling and endocytosis, which could further affect the abundance and distribution of caveolae at the PM, contributing to sensing and/or buffering mechanical stress. Changes in membrane tension in cells responding to multiple mechanical stimuli affects the organization and function of caveolae. These mechanical cues regulate pY14Cav1 levels and function in caveolae and focal adhesions. This review, along with looking at the mechanosensitive nature of caveolae, focuses on the role of pY14Cav1 in regulating cellular mechanotransduction.
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Affiliation(s)
- Natasha Buwa
- Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Debasmita Mazumdar
- Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Nagaraj Balasubramanian
- Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.
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17
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Deletion of a Peptidylprolyl Isomerase Gene Results in the Inability of Caldicellulosiruptor bescii To Grow on Crystalline Cellulose without Affecting Protein Glycosylation or Growth on Soluble Substrates. Appl Environ Microbiol 2020; 86:AEM.00909-20. [PMID: 32769195 DOI: 10.1128/aem.00909-20] [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: 04/16/2020] [Accepted: 07/30/2020] [Indexed: 11/20/2022] Open
Abstract
Caldicellulosiruptor bescii secretes a large number of complementary multifunctional enzymes with unique activities for biomass deconstruction. The most abundant enzymes in the C. bescii secretome are found in a unique gene cluster containing a glycosyl transferase (GT39) and a putative peptidyl prolyl cis-trans isomerase. Deletion of the glycosyl transferase in this cluster resulted in loss of detectable protein glycosylation in C. bescii, and its activity has been shown to be responsible for the glycosylation of the proline-threonine rich linkers found in many of the multifunctional cellulases. The presence of a putative peptidyl prolyl cis-trans isomerase within this gene cluster suggested that it might also play a role in cellulase modification. Here, we identify this gene as a putative prsA prolyl cis-trans isomerase. Deletion of prsA2 leads to the inability of C. bescii to grow on insoluble substrates such as Avicel, the model cellulose substrate, while exhibiting no differences in phenotype with the wild-type strain on soluble substrates. Finally, we provide evidence that the prsA2 gene is likely needed to increase solubility of multifunctional cellulases and that this unique gene cluster was likely acquired by members of the Caldicellulosiruptor genus with a group of genes to optimize the production and activity of multifunctional cellulases.IMPORTANCE Caldicellulosiruptor has the ability to digest complex plant biomass without pretreatment and have been engineered to convert biomass, a sustainable, carbon neutral substrate, to fuels. Their strategy for deconstructing plant cell walls relies on an interesting class of cellulases consisting of multiple catalytic modules connected by linker regions and carbohydrate binding modules. The best studied of these enzymes, CelA, has a unique deconstruction mechanism. CelA is located in a cluster of genes that likely allows for optimal expression, secretion, and activity. One of the genes in this cluster is a putative isomerase that modifies the CelA protein. In higher eukaryotes, these isomerases are essential for the proper folding of glycoproteins in the endoplasmic reticulum, but little is known about the role of isomerization in cellulase activity. We show that the stability and activity of CelA is dependent on the activity of this isomerase.
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18
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Schuld J, Orfanos Z, Chevessier F, Eggers B, Heil L, Uszkoreit J, Unger A, Kirfel G, van der Ven PFM, Marcus K, Linke WA, Clemen CS, Schröder R, Fürst DO. Homozygous expression of the myofibrillar myopathy-associated p.W2710X filamin C variant reveals major pathomechanisms of sarcomeric lesion formation. Acta Neuropathol Commun 2020; 8:154. [PMID: 32887649 PMCID: PMC7650280 DOI: 10.1186/s40478-020-01001-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/22/2020] [Indexed: 01/06/2023] Open
Abstract
Filamin C (FLNc) is mainly expressed in striated muscle cells where it localizes to Z-discs, myotendinous junctions and intercalated discs. Recent studies have revealed numerous mutations in the FLNC gene causing familial and sporadic myopathies and cardiomyopathies with marked clinical variability. The most frequent myopathic mutation, p.W2710X, which is associated with myofibrillar myopathy, deletes the carboxy-terminal 16 amino acids from FLNc and abolishes the dimerization property of Ig-like domain 24. We previously characterized "knock-in" mice heterozygous for this mutation (p.W2711X), and have now investigated homozygous mice using protein and mRNA expression analyses, mass spectrometry, and extensive immunolocalization and ultrastructural studies. Although the latter mice display a relatively mild myopathy under normal conditions, our analyses identified major mechanisms causing the pathophysiology of this disease: in comparison to wildtype animals (i) the expression level of FLNc protein is drastically reduced; (ii) mutant FLNc is relocalized from Z-discs to particularly mechanically strained parts of muscle cells, i.e. myotendinous junctions and myofibrillar lesions; (iii) the number of lesions is greatly increased and these lesions lack Bcl2-associated athanogene 3 (BAG3) protein; (iv) the expression of heat shock protein beta-7 (HSPB7) is almost completely abolished. These findings indicate grave disturbances of BAG3-dependent and -independent autophagy pathways that are required for efficient lesion repair. In addition, our studies reveal general mechanisms of lesion formation and demonstrate that defective FLNc dimerization via its carboxy-terminal domain does not disturb assembly and basic function of myofibrils. An alternative, more amino-terminally located dimerization site might compensate for that loss. Since filamins function as stress sensors, our data further substantiate that FLNc is important for mechanosensing in the context of Z-disc stabilization and maintenance.
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19
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Iqbal NS, Jascur TA, Harrison SM, Edwards AB, Smith LT, Choi ES, Arevalo MK, Chen C, Zhang S, Kern AJ, Scheuerle AE, Sanchez EJ, Xing C, Baker LA. Prune belly syndrome in surviving males can be caused by Hemizygous missense mutations in the X-linked Filamin A gene. BMC MEDICAL GENETICS 2020; 21:38. [PMID: 32085749 PMCID: PMC7035669 DOI: 10.1186/s12881-020-0973-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 02/12/2020] [Indexed: 12/12/2022]
Abstract
Background Prune belly syndrome (PBS) is a rare, multi-system congenital myopathy primarily affecting males that is poorly described genetically. Phenotypically, its morbidity spans from mild to lethal, however, all isolated PBS cases manifest three cardinal pathological features: 1) wrinkled flaccid ventral abdominal wall with skeletal muscle deficiency, 2) urinary tract dilation with poorly contractile smooth muscle, and 3) intra-abdominal undescended testes. Despite evidence for a genetic basis, previously reported PBS autosomal candidate genes only account for one consanguineous family and single cases. Methods We performed whole exome sequencing (WES) of two maternal adult half-brothers with syndromic PBS (PBS + Otopalatodigital spectrum disorder [OPDSD]) and two unrelated sporadic individuals with isolated PBS and further functionally validated the identified mutations. Results We identified three unreported hemizygous missense point mutations in the X-chromosome gene Filamin A (FLNA) (c.4952 C > T (p.A1448V), c.6727C > T (p.C2160R), c.5966 G > A (p.G2236E)) in two related cases and two unrelated sporadic individuals. Two of the three PBS mutations map to the highly regulatory, stretch-sensing Ig19–21 region of FLNA and enhance binding to intracellular tails of the transmembrane receptor β-integrin 1 (ITGβ1). Conclusions FLNA is a regulatory actin-crosslinking protein that functions in smooth muscle cells as a mechanosensing molecular scaffold, transmitting force signals from the actin-myosin motor units and cytoskeleton via binding partners to the extracellular matrix. This is the first evidence for an X-linked cause of PBS in multiple unrelated individuals and expands the phenotypic spectrum associated with FLNA in males surviving even into adulthood.
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Affiliation(s)
- Nida S Iqbal
- Department of Urology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA.
| | - Thomas A Jascur
- Department of Urology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA
| | - Steven M Harrison
- Department of Urology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Angelena B Edwards
- Department of Urology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA
| | - Luke T Smith
- Department of Urology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA
| | - Erin S Choi
- Department of Urology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA
| | - Michelle K Arevalo
- Department of Urology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA
| | - Catherine Chen
- Department of Urology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA
| | - Shaohua Zhang
- Department of Urology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA
| | - Adam J Kern
- Department of Urology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA
| | - Angela E Scheuerle
- Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA.,McDermott Center for Human Growth and Development, Department of Bioinformatics, Department of Clinical Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA
| | - Emma J Sanchez
- Department of Urology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA.,Children's Health Dallas, 2350 N. Stemmons Freeway, Suite F4300, Dallas, TX, 75207, USA
| | - Chao Xing
- McDermott Center for Human Growth and Development, Department of Bioinformatics, Department of Clinical Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA
| | - Linda A Baker
- Department of Urology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA. .,Children's Health Dallas, 2350 N. Stemmons Freeway, Suite F4300, Dallas, TX, 75207, USA.
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20
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Zhu C, Chen Y, Ju LA. Dynamic bonds and their roles in mechanosensing. Curr Opin Chem Biol 2019; 53:88-97. [PMID: 31563813 PMCID: PMC6926149 DOI: 10.1016/j.cbpa.2019.08.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 07/14/2019] [Accepted: 08/22/2019] [Indexed: 12/25/2022]
Abstract
Mechanical forces are ubiquitous in a cell's internal structure and external environment. Mechanosensing is the process that the cell employs to sense its mechanical environment. In receptor-mediated mechanosensing, cell surface receptors interact with immobilized ligands to provide a specific way to receive extracellular force signals to targeted force-transmitting, force-transducing and force-supporting structures inside the cell. Conversely, forces generated endogenously by the cell can be transmitted via cytoplasmic protein-protein interactions and regulate cell surface receptor activities in an 'inside-out' manner. Dynamic force spectroscopy analyzes these interactions on and inside cells to reveal various dynamic bonds. What is more, by integrating analysis of molecular interactions with that of cell signaling events involved in force-sensing and force-responding processes, one can investigate how dynamic bonds regulate the reception, transmission and transduction of mechanical signals.
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Affiliation(s)
- Cheng Zhu
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Yunfeng Chen
- Department of Molecular Medicine, MERU-Roon Research Center on Vascular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lining Arnold Ju
- School of Biomedical Engineering, The University of Sydney, Camperdown, NSW 2006, Australia; Charles Perkins Centre, The University of Sydney, Camperdown, NSW 2006, Australia; Heart Research Institute, The University of Sydney, Camperdown, NSW 2006, Australia
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21
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Blanco PM, Madurga S, Mas F, Garcés JL. Effect of Charge Regulation and Conformational Equilibria in the Stretching Properties of Weak Polyelectrolytes. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b01160] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Pablo M. Blanco
- Physical Chemistry Unit, Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB) of Barcelona University (UB), Barcelona 08028, Catalonia, Spain
| | - Sergio Madurga
- Physical Chemistry Unit, Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB) of Barcelona University (UB), Barcelona 08028, Catalonia, Spain
| | - Francesc Mas
- Physical Chemistry Unit, Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB) of Barcelona University (UB), Barcelona 08028, Catalonia, Spain
| | - Josep L. Garcés
- Chemistry Department, Technical School of Agricultural Engineering & AGROTECNIO of Lleida University (UdL), Lleida 25198, Catalonia, Spain
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Peptidyl prolyl cis/ trans isomerase activity on the cell surface correlates with extracellular matrix development. Commun Biol 2019; 2:58. [PMID: 30775459 PMCID: PMC6370856 DOI: 10.1038/s42003-019-0315-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/08/2019] [Indexed: 11/25/2022] Open
Abstract
Interactions with the extracellular matrix (ECM) dictate cell fates. However, the complexity of dense ECM network and cell-surface molecules prevent the study of their dynamic interaction at the molecular level on living cells. Here, we focus on peptidyl prolyl cis/trans isomerases (PPIases) to dissect prolyl isomerization from other dynamic events. We reveal the contribution of PPIase on the mechanical properties of various ECM materials and on the dynamic cell–ECM interaction. To avoid complications associated with the existing spectroscopy-based methods such as light scattering, an assay was developed for detecting PPIase activity on living cell surface. This assay allows us to correlate PPIase activity with ECM development, and with the physiological and pathological states of the cells, including the functional properties of cancer cells and immune effector cells. Weilin Lin et al. report a new assay for measuring the activity of peptidyl prolyl cis/trans isomerase (PPIase) at the cell surface using ultra performance liquid chromatography. They find that PPIase activity correlates with development and functional properties of the extracellular matrix in primary healthy and leukemic cells.
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Kanoldt V, Fischer L, Grashoff C. Unforgettable force – crosstalk and memory of mechanosensitive structures. Biol Chem 2018; 400:687-698. [DOI: 10.1515/hsz-2018-0328] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/11/2018] [Indexed: 12/11/2022]
Abstract
Abstract
The ability of cells to sense and respond to mechanical stimuli is crucial for many developmental and homeostatic processes, while mechanical dysfunction of cells has been associated with numerous pathologies including muscular dystrophies, cardiovascular defects and epithelial disorders. Yet, how cells detect and process mechanical information is still largely unclear. In this review, we outline major mechanisms underlying cellular mechanotransduction and we summarize the current understanding of how cells integrate information from distinct mechanosensitive structures to mediate complex mechanoresponses. We also discuss the concept of mechanical memory and describe how cells store information on previous mechanical events for different periods of time.
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Affiliation(s)
- Verena Kanoldt
- Group of Molecular Mechanotransduction , Max Planck Institute of Biochemistry , 82152 Martinsried , Germany
| | - Lisa Fischer
- Group of Molecular Mechanotransduction , Max Planck Institute of Biochemistry , 82152 Martinsried , Germany
| | - Carsten Grashoff
- Group of Molecular Mechanotransduction , Max Planck Institute of Biochemistry , 82152 Martinsried , Germany
- Department of Quantitative Cell Biology , Institute of Molecular Cell Biology, University of Münster , 48149 Münster , Germany
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24
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Tych KM, Jahn M, Gegenfurtner F, Hechtl VK, Buchner J, Hugel T, Rief M. Nucleotide-Dependent Dimer Association and Dissociation of the Chaperone Hsp90. J Phys Chem B 2018; 122:11373-11380. [PMID: 30179494 DOI: 10.1021/acs.jpcb.8b07301] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hsp90 is an essential molecular chaperone, which has to be in a dimeric form for its correct function. While the affinity of the dimer has previously been measured, little is known about how it associates and dissociates and the factors that influence this. We perform an in-depth single molecule characterization of the C-terminal association and dissociation of Hsp90. We find more than one dissociation rate, indicating that the dimer has a stable and an unstable state. Furthermore, we find that the stability of the C-terminal association is dependent on the presence of ATP, despite the C-terminal dimerization interface being distal to the catalytic site.
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Affiliation(s)
| | | | | | | | | | - Thorsten Hugel
- Institute of Physical Chemistry , University of Freiburg , Freiburg , Baden-Württemberg 79104 , Germany
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25
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Zosel F, Mercadante D, Nettels D, Schuler B. A proline switch explains kinetic heterogeneity in a coupled folding and binding reaction. Nat Commun 2018; 9:3332. [PMID: 30127362 PMCID: PMC6102232 DOI: 10.1038/s41467-018-05725-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/19/2018] [Indexed: 11/22/2022] Open
Abstract
The interactions of intrinsically disordered proteins (IDPs) with their molecular targets are essential for the regulation of many cellular processes. IDPs can perform their functions while disordered, and they may fold to structured conformations on binding. Here we show that the cis/trans isomerization of peptidyl−prolyl bonds can have a pronounced effect on the interactions of IDPs. By single-molecule spectroscopy, we identify a conserved proline residue in NCBD (the nuclear-coactivator binding domain of CBP) whose cis/trans isomerization in the unbound state modulates the association and dissociation rates with its binding partner, ACTR. As a result, NCBD switches on a time scale of tens of seconds between two populations that differ in their affinities to ACTR by about an order of magnitude. Molecular dynamics simulations indicate as a cause reduced packing of the complex for the cis isomer. Peptidyl-prolyl cis/trans isomerization may be an important previously unidentified mechanism for regulating IDP interactions. How intrinsically disordered proteins (IDPs) undergo a coupled folding and binding reaction with their molecular targets remains to be understood. Here authors use single-molecule FRET to assess the contribution of cis/trans isomerization of peptidyl-prolyl bonds in regulating IDP interactions.
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Affiliation(s)
- Franziska Zosel
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Måløv, Denmark
| | - Davide Mercadante
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. .,Department of Physics, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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26
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Zhao J, Zhang B, Zhu J, Nussinov R, Ma B. Structure and energetic basis of overrepresented λ light chain in systemic light chain amyloidosis patients. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2294-2303. [PMID: 29241665 PMCID: PMC5927852 DOI: 10.1016/j.bbadis.2017.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/29/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022]
Abstract
Amyloid formation and deposition of immunoglobulin light-chain proteins in systemic amyloidosis (AL) cause major organ failures. While the κ light-chain is dominant (λ/κ=1:2) in healthy individuals, λ is highly overrepresented (λ/κ=3:1) in AL patients. The structural basis of the amyloid formation and the sequence preference are unknown. We examined the correlation between sequence and structural stability of dimeric variable domains of immunoglobulin light chains using molecular dynamics simulations of 24 representative dimer interfaces, followed by energy evaluation of conformational ensembles for 20 AL patients' light chain sequences. We identified a stable interface with displaced N-terminal residues, provides the structural basis for AL protein fibrils formation. Proline isomerization may cause the N-terminus to adopt amyloid-prone conformations. We found that λ light-chains prefer misfolded dimer conformation, while κ chain structures are stabilized by a natively folded dimer. Our study may facilitate structure-based small molecule and antibody design to inhibit AL. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.
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Affiliation(s)
- Jun Zhao
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Baohong Zhang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jianwei Zhu
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Jecho Laboratories, Inc., 7320A Executive Way, Frederick, MD 21704, USA
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA; Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA.
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27
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Parobek A, Black JW, Kamenetska M, Ganim Z. Force-detected nanoscale absorption spectroscopy in water at room temperature using an optical trap. J Chem Phys 2018; 148:144201. [PMID: 29655351 DOI: 10.1063/1.5017853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Measuring absorption spectra of single molecules presents a fundamental challenge for standard transmission-based instruments because of the inherently low signal relative to the large background of the excitation source. Here we demonstrate a new approach for performing absorption spectroscopy in solution using a force measurement to read out optical excitation at the nanoscale. The photoinduced force between model chromophores and an optically trapped gold nanoshell has been measured in water at room temperature. This photoinduced force is characterized as a function of wavelength to yield the force spectrum, which is shown to be correlated to the absorption spectrum for four model systems. The instrument constructed for these measurements combines an optical tweezer with frequency domain absorption spectroscopy over the 400-800 nm range. These measurements provide proof-of-principle experiments for force-detected nanoscale spectroscopies that operate under ambient chemical conditions.
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Affiliation(s)
- Alexander Parobek
- Department of Chemistry, Yale University, 350 Edwards St., New Haven, Connecticut 06520, USA
| | - Jacob W Black
- Department of Chemistry, Yale University, 350 Edwards St., New Haven, Connecticut 06520, USA
| | - Maria Kamenetska
- Department of Chemistry, Yale University, 350 Edwards St., New Haven, Connecticut 06520, USA
| | - Ziad Ganim
- Department of Chemistry, Yale University, 350 Edwards St., New Haven, Connecticut 06520, USA
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28
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Black JW, Kamenetska M, Ganim Z. An Optical Tweezers Platform for Single Molecule Force Spectroscopy in Organic Solvents. NANO LETTERS 2017; 17:6598-6605. [PMID: 28972764 DOI: 10.1021/acs.nanolett.7b02413] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Observation at the single molecule level has been a revolutionary tool for molecular biophysics and materials science, but single molecule studies of solution-phase chemistry are less widespread. In this work we develop an experimental platform for solution-phase single molecule force spectroscopy in organic solvents. This optical-tweezer-based platform was designed for broad chemical applicability and utilizes optically trapped core-shell microspheres, synthetic polymer tethers, and click chemistry linkages formed in situ. We have observed stable optical trapping of the core-shell microspheres in ten different solvents, and single molecule link formation in four different solvents. These experiments demonstrate how to use optical tweezers for single molecule force application in the study of solution-phase chemistry.
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Affiliation(s)
- Jacob W Black
- Department of Chemistry, Yale University , 350 Edwards St., New Haven, Connecticut 06520, United States
| | - Maria Kamenetska
- Department of Chemistry, Yale University , 350 Edwards St., New Haven, Connecticut 06520, United States
| | - Ziad Ganim
- Department of Chemistry, Yale University , 350 Edwards St., New Haven, Connecticut 06520, United States
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29
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30
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Mechanically switching single-molecule fluorescence of GFP by unfolding and refolding. Proc Natl Acad Sci U S A 2017; 114:11052-11056. [PMID: 29073015 DOI: 10.1073/pnas.1704937114] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Green fluorescent protein (GFP) variants are widely used as genetically encoded fluorescent fusion tags, and there is an increasing interest in engineering their structure to develop in vivo optical sensors, such as for optogenetics and force transduction. Ensemble experiments have shown that the fluorescence of GFP is quenched upon denaturation. Here we study the dependence of fluorescence on protein structure by driving single molecules of GFP into different conformational states with optical tweezers and simultaneously probing the chromophore with fluorescence. Our results show that fluorescence is lost during the earliest events in unfolding, 3.5 ms before secondary structure is disrupted. No fluorescence is observed from the unfolding intermediates or the ensemble of compact and extended states populated during refolding. We further demonstrate that GFP can be mechanically switched between emissive and dark states. These data definitively establish that complete structural integrity is necessary to observe single-molecule fluorescence of GFP.
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31
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Abstract
Chemical reactions can be accelerated by various means, including applied mechanical forces. If the direction of the force does not project well onto the desired reaction coordinate, then only poor acceleration is achieved. Recent developments in single polymer mechanics illustrate how to overcome this limitation, in a simple cis-trans isomerization reaction. Generalizing the approach, synthetic chemistry can be used to attach tethers to different parts of reacting molecular fragments to direct the force usefully. This Perspective explores the prospects for using applied mechanical forces to create exciting new chemistries. For example, it is possible to imagine making polymers that sense mechanical forces within hard-to-reach places, like biological cells, or using mechanical forces to make nanoscale electrical devices using conjugated polymers.
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Affiliation(s)
- Hongbin Li
- Department of Chemistry, University of British Columbia , Vancouver, BC V6T 1Z1, Canada
| | - Gilbert C Walker
- Department of Chemistry, University of Toronto , Toronto, ON M5S 3H6, Canada
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32
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Hwang W, Lee IB, Hong SC, Hyeon C. Decoding Single Molecule Time Traces with Dynamic Disorder. PLoS Comput Biol 2016; 12:e1005286. [PMID: 28027304 PMCID: PMC5226833 DOI: 10.1371/journal.pcbi.1005286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 01/11/2017] [Accepted: 12/07/2016] [Indexed: 12/11/2022] Open
Abstract
Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted dynamic disorder in certain classes of biomolecules, whose dynamic pattern of conformational transitions is affected by slower transition dynamics of internal state hidden in a low dimensional projection. A systematic means to analyze such data is, however, currently not well developed. Here we report a new algorithm—Variational Bayes-double chain Markov model (VB-DCMM)—to analyze single molecule time trajectories that display dynamic disorder. The proposed analysis employing VB-DCMM allows us to detect the presence of dynamic disorder, if any, in each trajectory, identify the number of internal states, and estimate transition rates between the internal states as well as the rates of conformational transition within each internal state. Applying VB-DCMM algorithm to single molecule FRET data of H-DNA in 100 mM-Na+ solution, followed by data clustering, we show that at least 6 kinetic paths linking 4 distinct internal states are required to correctly interpret the duplex-triplex transitions of H-DNA. We have developed a new algorithm to better decode single molecule data with dynamic disorder. Our new algorithm, which represents a substantial improvement over other methodologies, can detect the presence of dynamic disorder in each trajectory and quantify the kinetic characteristics of underlying energy landscape. As a model system, we applied our algorithm to the single molecule FRET time traces of H-DNA. While duplex-triplex transitions of H-DNA are conventionally interpreted in terms of two-state kinetics, slowly varying dynamic patterns corresponding to hidden internal states can also be identified from the individual time traces. Our algorithm reveals that at least 4 distinct internal states are required to correctly interpret the data.
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Affiliation(s)
- Wonseok Hwang
- Korea Institute for Advanced Study, Seoul, Republic of Korea
| | - Il-Buem Lee
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Seok-Cheol Hong
- Korea Institute for Advanced Study, Seoul, Republic of Korea
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul, Republic of Korea
- * E-mail:
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33
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Mukhortava A, Schlierf M. Efficient Formation of Site-Specific Protein–DNA Hybrids Using Copper-Free Click Chemistry. Bioconjug Chem 2016; 27:1559-63. [DOI: 10.1021/acs.bioconjchem.6b00120] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ann Mukhortava
- B CUBE − Center for
Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße
18, 01307 Dresden, Germany
| | - Michael Schlierf
- B CUBE − Center for
Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße
18, 01307 Dresden, Germany
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34
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Radiom M, Kong P, Maroni P, Schäfer M, Kilbinger AFM, Borkovec M. Mechanically induced cis-to-trans isomerization of carbon–carbon double bonds using atomic force microscopy. Phys Chem Chem Phys 2016; 18:31202-31210. [DOI: 10.1039/c6cp05696b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Single molecule force spectroscopy can be used to induce cis-to-trans isomerization in carbon–carbon double bonds.
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Affiliation(s)
- Milad Radiom
- Department of Inorganic and Analytical Chemistry
- University of Geneva
- Geneva
- Switzerland
| | - Phally Kong
- Department of Chemistry
- University of Fribourg
- Fribourg
- Switzerland
| | - Plinio Maroni
- Department of Inorganic and Analytical Chemistry
- University of Geneva
- Geneva
- Switzerland
| | - Mark Schäfer
- Department of Chemistry
- University of Fribourg
- Fribourg
- Switzerland
| | | | - Michal Borkovec
- Department of Inorganic and Analytical Chemistry
- University of Geneva
- Geneva
- Switzerland
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35
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Zhao Y, Shapiro SS, Eto M. F-actin clustering and cell dysmotility induced by the pathological W148R missense mutation of filamin B at the actin-binding domain. Am J Physiol Cell Physiol 2015; 310:C89-98. [PMID: 26491051 DOI: 10.1152/ajpcell.00274.2015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/19/2015] [Indexed: 11/22/2022]
Abstract
Filamin B (FLNB) is a dimeric actin-binding protein that orchestrates the reorganization of the actin cytoskeleton. Congenital mutations of FLNB at the actin-binding domain (ABD) are known to cause abnormalities of skeletal development, such as atelosteogenesis types I and III and Larsen's syndrome, although the underlying mechanisms are poorly understood. Here, using fluorescence microscopy, we characterized the reorganization of the actin cytoskeleton in cells expressing each of six pathological FLNB mutants that have been linked to skeletal abnormalities. The subfractionation assay showed a greater accumulation of the FLNB ABD mutants W148R and E227K than the wild-type protein to the cytoskeleton. Ectopic expression of FLNB-W148R and, to a lesser extent, FLNB-E227K induced prominent F-actin accumulations and the consequent rearrangement of focal adhesions, myosin II, and septin filaments and results in a delayed directional migration of the cells. The W148R protein-induced cytoskeletal rearrangement was partially attenuated by the inhibition of myosin II, p21-activated protein kinase, or Rho-associated protein kinase. The expression of a single-head ABD fragment with the mutations partially mimicked the rearrangement induced by the dimer. The F-actin clustering through the interaction with the mutant FLNB ABD may limit the cytoskeletal reorganization, preventing normal skeletal development.
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Affiliation(s)
- Yongtong Zhao
- Department of Molecular Physiology and Biophysics, Sidney Kimmel Medical College at Thomas Jefferson University, and Sidney Kimmel Cancer Center, Philadelphia, Pennsylvania
| | - Sandor S Shapiro
- Department of Molecular Physiology and Biophysics, Sidney Kimmel Medical College at Thomas Jefferson University, and Sidney Kimmel Cancer Center, Philadelphia, Pennsylvania
| | - Masumi Eto
- Department of Molecular Physiology and Biophysics, Sidney Kimmel Medical College at Thomas Jefferson University, and Sidney Kimmel Cancer Center, Philadelphia, Pennsylvania
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36
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Abstract
Mechanical stimuli are known to be potent regulators of the form and function of cells and organisms. Although biological regulation has classically been understood in terms of principles from solution biochemistry, advancements in many fields have led to the development of a suite of techniques that are able to reveal the interplay between mechanical loading and changes in the biochemical properties of proteins in systems ranging from single molecules to living organisms. Here, we review these techniques and highlight the emergence of a new molecular-scale understanding of the mechanisms mediating the detection and response of cells to mechanical stimuli, a process termed mechanotransduction. Specifically, we focus on the role of subcellular adhesion structures in sensing the stiffness of the surrounding environment because this process is pertinent to applications in tissue engineering as well the onset of several mechanosensitive disease states, including cancer.
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Affiliation(s)
- Andrew S LaCroix
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708;
| | - Katheryn E Rothenberg
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708;
| | - Brenton D Hoffman
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708;
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37
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Mak M, Kim T, Zaman MH, Kamm RD. Multiscale mechanobiology: computational models for integrating molecules to multicellular systems. Integr Biol (Camb) 2015; 7:1093-108. [PMID: 26019013 DOI: 10.1039/c5ib00043b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mechanical signals exist throughout the biological landscape. Across all scales, these signals, in the form of force, stiffness, and deformations, are generated and processed, resulting in an active mechanobiological circuit that controls many fundamental aspects of life, from protein unfolding and cytoskeletal remodeling to collective cell motions. The multiple scales and complex feedback involved present a challenge for fully understanding the nature of this circuit, particularly in development and disease in which it has been implicated. Computational models that accurately predict and are based on experimental data enable a means to integrate basic principles and explore fine details of mechanosensing and mechanotransduction in and across all levels of biological systems. Here we review recent advances in these models along with supporting and emerging experimental findings.
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Affiliation(s)
- Michael Mak
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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38
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Chen Y, Radford SE, Brockwell DJ. Force-induced remodelling of proteins and their complexes. Curr Opin Struct Biol 2015; 30:89-99. [PMID: 25710390 PMCID: PMC4499843 DOI: 10.1016/j.sbi.2015.02.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/29/2015] [Accepted: 02/02/2015] [Indexed: 11/23/2022]
Abstract
Force can drive conformational changes in proteins, as well as modulate their stability and the affinity of their complexes, allowing a mechanical input to be converted into a biochemical output. These properties have been utilised by nature and force is now recognised to be widely used at the cellular level. The effects of force on the biophysical properties of biological systems can be large and varied. As these effects are only apparent in the presence of force, studies on the same proteins using traditional ensemble biophysical methods can yield apparently conflicting results. Where appropriate, therefore, force measurements should be integrated with other experimental approaches to understand the physiological context of the system under study.
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Affiliation(s)
- Yun Chen
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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39
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Schmidpeter PAM, Schmid FX. Prolyl isomerization and its catalysis in protein folding and protein function. J Mol Biol 2015; 427:1609-31. [PMID: 25676311 DOI: 10.1016/j.jmb.2015.01.023] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/30/2015] [Indexed: 12/20/2022]
Abstract
Prolyl isomerizations are intrinsically slow processes. They determine the rates of many protein folding reactions and control regulatory events in folded proteins. Prolyl isomerases are able to catalyze these isomerizations, and thus, they have the potential to assist protein folding and to modulate protein function. Here, we provide examples for how prolyl isomerizations limit protein folding and are accelerated by prolyl isomerases and how native-state prolyl isomerizations regulate protein functions. The roles of prolines in protein folding and protein function are closely interrelated because both of them depend on the coupling between cis/trans isomerization and conformational changes that can involve extended regions of a protein.
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Affiliation(s)
- Philipp A M Schmidpeter
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Franz X Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biologie, Universität Bayreuth, 95440 Bayreuth, Germany.
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40
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Tych KM, Hughes ML, Bourke J, Taniguchi Y, Kawakami M, Brockwell DJ, Dougan L. Optimizing the calculation of energy landscape parameters from single-molecule protein unfolding experiments. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:012710. [PMID: 25679645 DOI: 10.1103/physreve.91.012710] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Indexed: 06/04/2023]
Abstract
Single-molecule force spectroscopy using an atomic force microscope (AFM) can be used to measure the average unfolding force of proteins in a constant velocity experiment. In combination with Monte Carlo simulations and through the application of the Zhurkov-Bell model, information about the parameters describing the underlying unfolding energy landscape of the protein can be obtained. Using this approach, we have completed protein unfolding experiments on the polyprotein (I27)(5) over a range of pulling velocities. In agreement with previous work, we find that the observed number of protein unfolding events observed in each approach-retract cycle varies between one and five, due to the nature of the interactions between the polyprotein, the AFM tip, and the substrate, and there is an unequal unfolding probability distribution. We have developed a Monte Carlo simulation that incorporates the impact of this unequal unfolding probability distribution on the median unfolding force and the calculation of the protein unfolding energy landscape parameters. These results show that while there is a significant, unequal unfolding probability distribution, the unfolding energy landscape parameters obtained from use of the Zhurkov-Bell model are not greatly affected. This result is important because it demonstrates that the minimum acceptance criteria typically used in force extension experiments are justified and do not skew the calculation of the unfolding energy landscape parameters. We further validate this approach by determining the error in the energy landscape parameters for two extreme cases, and we provide suggestions for methods that can be employed to increase the level of accuracy in single-molecule experiments using polyproteins.
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Affiliation(s)
- Katarzyna M Tych
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Megan L Hughes
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - James Bourke
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yukinori Taniguchi
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Masaru Kawakami
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lorna Dougan
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
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41
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DeMali KA, Sun X, Bui GA. Force transmission at cell-cell and cell-matrix adhesions. Biochemistry 2014; 53:7706-17. [PMID: 25474123 DOI: 10.1021/bi501181p] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
All cells are subjected to mechanical forces throughout their lifetimes. These forces are sensed by cell surface adhesion receptors and trigger robust actin cytoskeletal rearrangements and growth of the associated adhesion complex to counter the applied force. In this review, we discuss how integrins and cadherins sense force and transmit these forces into the cell interior. We focus on the complement of proteins each adhesion complex recruits to bear the force and the signal transduction pathways activated to allow the cell to tune its contractility. A discussion of the similarities, differences, and crosstalk between cadherin- and integrin-mediated force transmission is also presented.
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Affiliation(s)
- Kris A DeMali
- Department of Biochemistry and Interdisciplinary Program in Molecular and Cellular Biology, Roy J. and Lucille A. Carver College of Medicine , Iowa City, Iowa 52242, United States
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