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Mukadum F, Ccoa WJP, Hocky GM. Molecular simulation approaches to probing the effects of mechanical forces in the actin cytoskeleton. Cytoskeleton (Hoboken) 2024:10.1002/cm.21837. [PMID: 38334204 PMCID: PMC11310368 DOI: 10.1002/cm.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024]
Abstract
In this article we give our perspective on the successes and promise of various molecular and coarse-grained simulation approaches to probing the effect of mechanical forces in the actin cytoskeleton.
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Affiliation(s)
- Fatemah Mukadum
- Department of Chemistry, New York University, New York, NY 10003, USA
| | | | - Glen M. Hocky
- Department of Chemistry, New York University, New York, NY 10003, USA
- Simons Center for Computational Physical Chemistry, New York, NY 10003, USA
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2
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Göz M, Steinecker SM, Pohl GM, Walhorn V, Milting H, Anselmetti D. Cardiac desmosomal adhesion relies on ideal-, slip- and catch bonds. Sci Rep 2024; 14:2555. [PMID: 38297017 PMCID: PMC10830561 DOI: 10.1038/s41598-024-52725-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
The cardiac muscle consists of individual cardiomyocytes that are mechanically linked by desmosomes. Desmosomal adhesion is mediated by densely packed and organized cadherins which, in presence of Ca2+, stretch out their extracellular domains (EC) and dimerize with opposing binding partners by exchanging an N-terminal tryptophan. The strand-swap binding motif of cardiac cadherins like desmocollin 2 (Dsc2) (and desmoglein2 alike) is highly specific but of low affinity with average bond lifetimes in the range of approximately 0.3 s. Notably, despite this comparatively weak interaction, desmosomes mediate a stable, tensile-resistant bond. In addition, force mediated dissociation of strand-swap dimers exhibit a reduced bond lifetime as external forces increase (slip bond). Using atomic force microscopy based single molecule force spectroscopy (AFM-SMFS), we demonstrate that Dsc2 has two further binding modes that, in addition to strand-swap dimers, most likely play a significant role in the integrity of the cardiac muscle. At short interaction times, the Dsc2 monomers associate only loosely, as can be seen from short-lived force-independent bonds. These ideal bonds are a precursor state and probably stabilize the formation of the self-inhibiting strand-swap dimer. The addition of tryptophan in the measurement buffer acts as a competitive inhibitor, preventing the N-terminal strand exchange. Here, Dsc2 dimerizes as X-dimer which clearly shows a tri-phasic slip-catch-slip type of dissociation. Within the force-mediated transition (catch) regime, Dsc2 dimers switch between a rather brittle low force and a strengthened high force adhesion state. As a result, we can assume that desmosomal adhesion is mediated not only by strand-swap dimers (slip) but also by their precursor states (ideal bond) and force-activated X-dimers (catch bond).
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Affiliation(s)
- Manuel Göz
- Department of Physics, Experimental Biophysics and Applied Nanoscience, Bielefeld University, Universitätstraße 25, 33615, Bielefeld, Germany
| | - Sylvia M Steinecker
- Department of Physics, Experimental Biophysics and Applied Nanoscience, Bielefeld University, Universitätstraße 25, 33615, Bielefeld, Germany
| | - Greta M Pohl
- Erich & Hanna Klessmann Institute for Cardiovascular Research and Development, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstraße 11, Bad Oeynhausen, Germany
| | - Volker Walhorn
- Department of Physics, Experimental Biophysics and Applied Nanoscience, Bielefeld University, Universitätstraße 25, 33615, Bielefeld, Germany.
| | - Hendrik Milting
- Erich & Hanna Klessmann Institute for Cardiovascular Research and Development, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstraße 11, Bad Oeynhausen, Germany
| | - Dario Anselmetti
- Department of Physics, Experimental Biophysics and Applied Nanoscience, Bielefeld University, Universitätstraße 25, 33615, Bielefeld, Germany
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3
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Ayres CM, Corcelli SA, Baker BM. The Energetic Landscape of Catch Bonds in TCR Interfaces. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:325-332. [PMID: 37459192 PMCID: PMC10361606 DOI: 10.4049/jimmunol.2300121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/14/2023] [Indexed: 07/20/2023]
Abstract
Recognition of peptide/MHC complexes by αβ TCRs has traditionally been viewed through the lens of conventional receptor-ligand theory. Recent work, however, has shown that TCR recognition and T cell signaling can be profoundly influenced and tuned by mechanical forces. One outcome of applied force is the catch bond, where TCR dissociation rates decrease (half-lives increase) when limited force is applied. Although catch bond behavior is believed to be widespread in biology, its counterintuitive nature coupled with the difficulties of describing mechanisms at the structural level have resulted in considerable mystique. In this review, we demonstrate that viewing catch bonds through the lens of energy landscapes, barriers, and the ensuing reaction rates can help demystify catch bonding and provide a foundation on which atomic-level TCR catch bond mechanisms can be built.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
- The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN
| | - Steve A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
- The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN
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4
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Goreke U, Iram S, Singh G, Domínguez-Medina S, Man Y, Bode A, An R, Little JA, Wirth CL, Hinczewski M, Gurkan UA. Catch bonds in sickle cell disease: Shear-enhanced adhesion of red blood cells to laminin. Biophys J 2023; 122:2564-2576. [PMID: 37177783 PMCID: PMC10323024 DOI: 10.1016/j.bpj.2023.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/14/2023] [Accepted: 05/08/2023] [Indexed: 05/15/2023] Open
Abstract
Could the phenomenon of catch bonding-force-strengthened cellular adhesion-play a role in sickle cell disease, where abnormal red blood cell (RBC) adhesion obstructs blood flow? Here, we investigate the dynamics of sickle RBCs adhering to a surface functionalized with the protein laminin (a component of the extracellular matrix around blood vessels) under physiologically relevant microscale flow. First, using total internal reflectance microscopy we characterize the spatial fluctuations of the RBC membrane above the laminin surface before detachment. The complex dynamics we observe suggest the possibility of catch bonding, where the mean detachment time of the cell from the surface initially increases to a maximum and then decreases as a function of shear force. We next conduct a series of shear-induced detachment experiments on blood samples from 25 sickle cell disease patients, quantifying the number and duration of adhered cells under both sudden force jumps and linear force ramps. The experiments reveal that a subset of patients does indeed exhibit catch bonding. By fitting the data to a theoretical model of the bond dynamics, we can extract the mean bond lifetime versus force for each patient. The results show a striking heterogeneity among patients, both in terms of the qualitative behavior (whether or not there is catch bonding) and in the magnitudes of the lifetimes. Patients with large bond lifetimes at physiological forces are more likely to have certain adverse clinical features, like a diagnosis of pulmonary arterial hypertension and intracardiac shunts. By introducing an in vitro platform for fully characterizing RBC-laminin adhesion dynamics, our approach could contribute to the development of patient-specific antiadhesive therapies for sickle cell disease. The experimental setup is also easily generalizable to studying adhesion dynamics in other cell types, for example, leukocytes or cancer cells, and can incorporate disease-relevant environmental conditions like oxygen deprivation.
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Affiliation(s)
- Utku Goreke
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Shamreen Iram
- Department of Physics, Case Western Reserve University, Cleveland, Ohio
| | - Gundeep Singh
- Department of Physics, Case Western Reserve University, Cleveland, Ohio
| | - Sergio Domínguez-Medina
- Department of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Yuncheng Man
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Allison Bode
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Ran An
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Jane A Little
- Division of Hematology and Blood Research Center, Department of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Christopher L Wirth
- Department of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Michael Hinczewski
- Department of Physics, Case Western Reserve University, Cleveland, Ohio.
| | - Umut A Gurkan
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, Ohio; Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio.
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5
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Malektaj H, Drozdov AD, deClaville Christiansen J. Swelling of Homogeneous Alginate Gels with Multi-Stimuli Sensitivity. Int J Mol Sci 2023; 24:ijms24065064. [PMID: 36982139 PMCID: PMC10049665 DOI: 10.3390/ijms24065064] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
A new two-step method is suggested for the preparation of homogeneous alginate gels. In the first step, alginate chains are weakly bonded by Ca2+ ions in an aqueous solution with a low pH. In the next step, the gel is immersed into a strong solution of CaCl2 to finalize the cross-linking process. Homogeneous alginate gels preserve their integrity in aqueous solutions with a pH ranging from 2 to 7 and ionic strength in the interval from 0 to 0.2 M, at temperatures ranging from room temperature up to 50 °C, and can be used in biomedical applications. The immersion of these gels into aqueous solutions with low pH induces the partial breakage of ionic bonds between chains (treated as gel degradation). This degradation affects the equilibrium and transient swelling of homogeneous alginate gels and makes them sensitive to the history of loading and environmental conditions (pH, ionic strength and temperature of aqueous solutions). As sensitivity to the environmental stimuli is a characteristic feature of polymer networks connected by catch bonds, homogeneous alginate gels may serve as a simple model, mimicking the behavior of more sophisticated structures in living matter.
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6
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Wang A, Dunn AR, Weis WI. Mechanism of the cadherin-catenin F-actin catch bond interaction. eLife 2022; 11:80130. [PMID: 35913118 PMCID: PMC9402232 DOI: 10.7554/elife.80130] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Mechanotransduction at cell-cell adhesions is crucial for the structural integrity, organization, and morphogenesis of epithelia. At cell-cell junctions, ternary E-cadherin/β-catenin/αE-catenin complexes sense and transmit mechanical load by binding to F-actin. The interaction with F-actin, described as a two-state catch bond, is weak in solution but is strengthened by applied force due to force-dependent transitions between weak and strong actin-binding states. Here, we provide direct evidence from optical trapping experiments that the catch bond property principally resides in the αE-catenin actin-binding domain (ABD). Consistent with our previously proposed model, deletion of the first helix of the five-helix ABD bundle enables stable interactions with F-actin under minimal load that are well-described by a single-state slip bond, even when αE-catenin is complexed with β-catenin and E-cadherin. Our data argue for a conserved catch bond mechanism for adhesion proteins with structurally similar ABDs. We also demonstrate that a stably bound ABD strengthens load-dependent binding interactions between a neighboring complex and F-actin, but the presence of the other αE-catenin domains weakens this effect. These results provide mechanistic insight to the cooperative binding of the cadherin-catenin complex to F-actin, which regulate dynamic cytoskeletal linkages in epithelial tissues.
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Affiliation(s)
- Amy Wang
- Department of Chemical Engineering, Stanford University, Stanford, United States
| | - Alexander R Dunn
- Department of Chemical Engineering, Stanford University, Stanford, United States
| | - William I Weis
- Department of Chemical Engineering, Stanford University, Stanford, United States
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7
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Stewart V, Ronald PC. Sulfotyrosine residues: interaction specificity determinants for extracellular protein-protein interactions. J Biol Chem 2022; 298:102232. [PMID: 35798140 PMCID: PMC9372746 DOI: 10.1016/j.jbc.2022.102232] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022] Open
Abstract
Tyrosine sulfation, a post-translational modification, can determine and often enhance protein–protein interaction specificity. Sulfotyrosyl residues (sTyrs) are formed by the enzyme tyrosyl-protein sulfotransferase during protein maturation in the Golgi apparatus and most often occur singly or as a cluster within a six-residue span. With both negative charge and aromatic character, sTyr facilitates numerous atomic contacts as visualized in binding interface structural models, thus there is no discernible binding site consensus. Found exclusively in secreted proteins, in this review, we discuss the four broad sequence contexts in which sTyr has been observed: first, a solitary sTyr has been shown to be critical for diverse high-affinity interactions, such as between peptide hormones and their receptors, in both plants and animals. Second, sTyr clusters within structurally flexible anionic segments are essential for a variety of cellular processes, including coreceptor binding to the HIV-1 envelope spike protein during virus entry, chemokine interactions with receptors, and leukocyte rolling cell adhesion. Third, a subcategory of sTyr clusters is found in conserved acidic sequences termed hirudin-like motifs that enable proteins to interact with thrombin; consequently, many proven and potential therapeutic proteins derived from blood-consuming invertebrates depend on sTyrs for their activity. Finally, several proteins that interact with collagen or similar proteins contain one or more sTyrs within an acidic residue array. Refined methods to direct sTyr incorporation in peptides synthesized both in vitro and in vivo, together with continued advances in mass spectrometry and affinity detection, promise to accelerate discoveries of sTyr occurrence and function.
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Affiliation(s)
- Valley Stewart
- Department of Microbiology & Molecular Genetics, University of California, Davis, USA.
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, USA; Genome Center, University of California, Davis, USA.
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8
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Peña Ccoa WJ, Hocky GM. Assessing models of force-dependent unbinding rates via infrequent metadynamics. J Chem Phys 2022; 156:125102. [PMID: 35364872 PMCID: PMC8957391 DOI: 10.1063/5.0081078] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Protein–ligand interactions are crucial for a wide range of physiological processes. Many cellular functions result in these non-covalent “bonds” being mechanically strained, and this can be integral to proper cellular function. Broadly, two classes of force dependence have been observed—slip bonds, where the unbinding rate increases, and catch bonds, where the unbinding rate decreases. Despite much theoretical work, we cannot predict for which protein–ligand pairs, pulling coordinates, and forces a particular rate dependence will appear. Here, we assess the ability of MD simulations combined with enhanced sampling techniques to probe the force dependence of unbinding rates. We show that the infrequent metadynamics technique correctly produces both catch and slip bonding kinetics for model potentials. We then apply it to the well-studied case of a buckyball in a hydrophobic cavity, which appears to exhibit an ideal slip bond. Finally, we compute the force-dependent unbinding rate of biotin–streptavidin. Here, the complex nature of the unbinding process causes the infrequent metadynamics method to begin to break down due to the presence of unbinding intermediates, despite the use of a previously optimized sampling coordinate. Allowing for this limitation, a combination of kinetic and free energy computations predicts an overall slip bond for larger forces consistent with prior experimental results although there are substantial deviations at small forces that require further investigation. This work demonstrates the promise of predicting force-dependent unbinding rates using enhanced sampling MD techniques while also revealing the methodological barriers that must be overcome to tackle more complex targets in the future.
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Affiliation(s)
| | - Glen M. Hocky
- Department of Chemistry, New York University, New York, New York 10003, USA
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9
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Perez-Carrasco R, Franco-Oñate MJ, Walter JC, Dorignac J, Geniet F, Palmeri J, Parmeggiani A, Walliser NO, Nord AL. Relaxation time asymmetry in stator dynamics of the bacterial flagellar motor. SCIENCE ADVANCES 2022; 8:eabl8112. [PMID: 35319986 PMCID: PMC8942351 DOI: 10.1126/sciadv.abl8112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The bacterial flagellar motor is the membrane-embedded rotary motor, which turns the flagellum that provides thrust to many bacteria. This large multimeric complex, composed of a few dozen constituent proteins, is a hallmark of dynamic subunit exchange. The stator units are inner-membrane ion channels that dynamically bind to the peptidoglycan at the rotor periphery and apply torque. Their dynamic exchange is a function of the viscous load on the flagellum, allowing the bacterium to adapt to its local environment, although the molecular mechanisms of mechanosensitivity remain unknown. Here, by actively perturbing the steady-state stator stoichiometry of individual motors, we reveal a stoichiometry-dependent asymmetry in stator remodeling kinetics. We interrogate the potential effect of next-neighbor interactions and local stator unit depletion and find that neither can explain the observed asymmetry. We then simulate and fit two mechanistically diverse models that recapitulate the asymmetry, finding assembly dynamics to be particularly well described by a two-state catch-bond mechanism.
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Affiliation(s)
| | | | - Jean-Charles Walter
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Jérôme Dorignac
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Fred Geniet
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - John Palmeri
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Andrea Parmeggiani
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Nils-Ole Walliser
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Ashley L Nord
- Centre de Biologie Structurale, Univ. Montpellier, CNRS, INSERM, Montpellier, France
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10
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Bongrand P. Is There a Need for a More Precise Description of Biomolecule Interactions to Understand Cell Function? Curr Issues Mol Biol 2022; 44:505-525. [PMID: 35723321 PMCID: PMC8929073 DOI: 10.3390/cimb44020035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/15/2022] [Accepted: 01/17/2022] [Indexed: 11/16/2022] Open
Abstract
An important goal of biological research is to explain and hopefully predict cell behavior from the molecular properties of cellular components. Accordingly, much work was done to build extensive “omic” datasets and develop theoretical methods, including computer simulation and network analysis to process as quantitatively as possible the parameters contained in these resources. Furthermore, substantial effort was made to standardize data presentation and make experimental results accessible to data scientists. However, the power and complexity of current experimental and theoretical tools make it more and more difficult to assess the capacity of gathered parameters to support optimal progress in our understanding of cell function. The purpose of this review is to focus on biomolecule interactions, the interactome, as a specific and important example, and examine the limitations of the explanatory and predictive power of parameters that are considered as suitable descriptors of molecular interactions. Recent experimental studies on important cell functions, such as adhesion and processing of environmental cues for decision-making, support the suggestion that it should be rewarding to complement standard binding properties such as affinity and kinetic constants, or even force dependence, with less frequently used parameters such as conformational flexibility or size of binding molecules.
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Affiliation(s)
- Pierre Bongrand
- Lab Adhesion and Inflammation (LAI), Inserm UMR 1067, Cnrs UMR 7333, Aix-Marseille Université UM 61, Marseille 13009, France
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11
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O’Neill RT, Boulatov R. The Contributions of Model Studies for Fundamental Understanding of Polymer Mechanochemistry. Synlett 2021. [DOI: 10.1055/a-1710-5656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
AbstractThe exciting field of polymer mechanochemistry has made great empirical progress in discovering reactions in which a stretching force accelerates scission of strained bonds using single molecule force spectroscopy and ultrasonication experiments. Understanding why these reactions happen, i.e., the fundamental physical processes that govern coupling of macroscopic motion to chemical reactions, as well as discovering other patterns of mechanochemical reactivity require complementary techniques, which permit a much more detailed characterization of reaction mechanisms and the distribution of force in reacting molecules than are achievable in SMFS or ultrasonication. A molecular force probe allows the specific pattern of molecular strain that is responsible for localized reactions in stretched polymers to be reproduced accurately in non-polymeric substrates using molecular design rather than atomistically intractable collective motions of millions of atoms comprising macroscopic motion. In this review, we highlight the necessary features of a useful molecular force probe and describe their realization in stiff stilbene macrocycles. We describe how studying these macrocycles using classical tools of physical organic chemistry has allowed detailed characterizations of mechanochemical reactivity, explain some of the most unexpected insights enabled by these probes, and speculate how they may guide the next stage of mechanochemistry.
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Affiliation(s)
| | - Roman Boulatov
- Department of Chemistry, University of Liverpool
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University
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12
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Activated nanoscale actin-binding domain motion in the catenin-cadherin complex revealed by neutron spin echo spectroscopy. Proc Natl Acad Sci U S A 2021; 118:2025012118. [PMID: 33753508 DOI: 10.1073/pnas.2025012118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As the core component of the adherens junction in cell-cell adhesion, the cadherin-catenin complex transduces mechanical tension between neighboring cells. Structural studies have shown that the cadherin-catenin complex exists as an ensemble of flexible conformations, with the actin-binding domain (ABD) of α-catenin adopting a variety of configurations. Here, we have determined the nanoscale protein domain dynamics of the cadherin-catenin complex using neutron spin echo spectroscopy (NSE), selective deuteration, and theoretical physics analyses. NSE reveals that, in the cadherin-catenin complex, the motion of the entire ABD becomes activated on nanosecond to submicrosecond timescales. By contrast, in the α-catenin homodimer, only the smaller disordered C-terminal tail of ABD is moving. Molecular dynamics (MD) simulations also show increased mobility of ABD in the cadherin-catenin complex, compared to the α-catenin homodimer. Biased MD simulations further reveal that the applied external forces promote the transition of ABD in the cadherin-catenin complex from an ensemble of diverse conformational states to specific states that resemble the actin-bound structure. The activated motion and an ensemble of flexible configurations of the mechanosensory ABD suggest the formation of an entropic trap in the cadherin-catenin complex, serving as negative allosteric regulation that impedes the complex from binding to actin under zero force. Mechanical tension facilitates the reduction in dynamics and narrows the conformational ensemble of ABD to specific configurations that are well suited to bind F-actin. Our results provide a protein dynamics and entropic explanation for the observed force-sensitive binding behavior of a mechanosensitive protein complex.
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13
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Zhuravlev PI, Hinczewski M, Thirumalai D. Low Force Unfolding of a Single-Domain Protein by Parallel Pathways. J Phys Chem B 2021; 125:1799-1805. [DOI: 10.1021/acs.jpcb.0c11308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Pavel I. Zhuravlev
- Biophysics Program, Institute for Physical Science and Technology, Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Michael Hinczewski
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - D. Thirumalai
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
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14
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O’Neill RT, Boulatov R. The many flavours of mechanochemistry and its plausible conceptual underpinnings. Nat Rev Chem 2021; 5:148-167. [PMID: 37117533 DOI: 10.1038/s41570-020-00249-y] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2020] [Indexed: 12/12/2022]
Abstract
Mechanochemistry describes diverse phenomena in which mechanical load affects chemical reactivity. The fuzziness of this definition means that it includes processes as seemingly disparate as motor protein function, organic synthesis in a ball mill, reactions at a propagating crack, chemical actuation, and polymer fragmentation in fast solvent flows and in mastication. In chemistry, the rate of a reaction in a flask does not depend on how fast the flask moves in space. In mechanochemistry, the rate at which a material is deformed affects which and how many bonds break. In other words, in some manifestations of mechanochemistry, macroscopic motion powers otherwise endergonic reactions. In others, spontaneous chemical reactions drive mechanical motion. Neither requires thermal or electrostatic gradients. Distinct manifestations of mechanochemistry are conventionally treated as being conceptually independent, which slows the field in its transformation from being a collection of observations to a rigorous discipline. In this Review, we highlight observations suggesting that the unifying feature of mechanochemical phenomena may be the coupling between inertial motion at the microscale to macroscale and changes in chemical bonding enabled by transient build-up and relaxation of strains, from macroscopic to molecular. This dynamic coupling across multiple length scales and timescales also greatly complicates the conceptual understanding of mechanochemistry.
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15
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Dansuk KC, Keten S. Self-strengthening biphasic nanoparticle assemblies with intrinsic catch bonds. Nat Commun 2021; 12:85. [PMID: 33397979 PMCID: PMC7782701 DOI: 10.1038/s41467-020-20344-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 11/23/2020] [Indexed: 01/06/2023] Open
Abstract
Protein-ligand complexes with catch bonds exhibit prolonged lifetimes when subject to tensile force, which is a desirable yet elusive attribute for man-made nanoparticle interfaces and assemblies. Most designs proposed so far rely on macromolecular linkers with complicated folds rather than particles exhibiting simple dynamic shapes. Here, we establish a scissor-type X-shaped particle design for achieving intrinsic catch bonding ability with tunable force-enhanced lifetimes under thermal excitations. Molecular dynamics simulations are carried out to illustrate equilibrium self-assembly and force-enhanced bond lifetime of dimers and fibers facilitated by secondary interactions that form under tensile force. The non-monotonic force dependence of the fiber breaking kinetics is well-estimated by an analytical model. Our design concepts for shape-changing particles illuminates a path towards novel nanoparticle or colloidal assemblies that have the passive ability to tune the strength of their interfaces with applied force, setting the stage for self-assembling materials with novel mechanical functions and rheological properties.
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Affiliation(s)
- Kerim C Dansuk
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA.
- Department of Civil & Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA.
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16
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Force-clamp spectroscopy identifies a catch bond mechanism in a Gram-positive pathogen. Nat Commun 2020; 11:5431. [PMID: 33110079 PMCID: PMC7591895 DOI: 10.1038/s41467-020-19216-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/01/2020] [Indexed: 01/17/2023] Open
Abstract
Physical forces have profound effects on cellular behavior, physiology, and disease. Perhaps the most intruiguing and fascinating example is the formation of catch-bonds that strengthen cellular adhesion under shear stresses. Today mannose-binding by the Escherichia coli FimH adhesin remains one of the rare microbial catch-bond thoroughly characterized at the molecular level. Here we provide a quantitative demonstration of a catch-bond in living Gram-positive pathogens using force-clamp spectroscopy. We show that the dock, lock, and latch interaction between staphylococcal surface protein SpsD and fibrinogen is strong, and exhibits an unusual catch-slip transition. The bond lifetime first grows with force, but ultimately decreases to behave as a slip bond beyond a critical force (~1 nN) that is orders of magnitude higher than for previously investigated complexes. This catch-bond, never reported for a staphylococcal adhesin, provides the pathogen with a mechanism to tightly control its adhesive function during colonization and infection.
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17
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Wang X, Bie L, Fei J, Gao J. Insights into the Loop at the E-Selectin Binding Site: From Open to Close Conformation. J Chem Inf Model 2020; 60:5153-5161. [DOI: 10.1021/acs.jcim.0c00939] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Xiaocong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Lihua Bie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Junwen Fei
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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Liu Z, Liu H, Vera AM, Bernardi RC, Tinnefeld P, Nash MA. High force catch bond mechanism of bacterial adhesion in the human gut. Nat Commun 2020; 11:4321. [PMID: 32859904 PMCID: PMC7456326 DOI: 10.1038/s41467-020-18063-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/04/2020] [Indexed: 12/28/2022] Open
Abstract
Bacterial colonization of the human intestine requires firm adhesion of bacteria to insoluble substrates under hydrodynamic flow. Here we report the molecular mechanism behind an ultrastable protein complex responsible for resisting shear forces and adhering bacteria to cellulose fibers in the human gut. Using single-molecule force spectroscopy (SMFS), single-molecule FRET (smFRET), and molecular dynamics (MD) simulations, we resolve two binding modes and three unbinding reaction pathways of a mechanically ultrastable R. champanellensis (Rc) Dockerin:Cohesin (Doc:Coh) complex. The complex assembles in two discrete binding modes with significantly different mechanical properties, with one breaking at ~500 pN and the other at ~200 pN at loading rates from 1-100 nN s-1. A neighboring X-module domain allosterically regulates the binding interaction and inhibits one of the low-force pathways at high loading rates, giving rise to a catch bonding mechanism that manifests under force ramp protocols. Multi-state Monte Carlo simulations show strong agreement with experimental results, validating the proposed kinetic scheme. These results explain mechanistically how gut microbes regulate cell adhesion strength at high shear stress through intricate molecular mechanisms including dual-binding modes, mechanical allostery and catch bonds.
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Affiliation(s)
- Zhaowei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Haipei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Andrés M Vera
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Rafael C Bernardi
- NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA
- Department of Physics, Auburn University, 36849, Auburn, AL, USA
| | - Philip Tinnefeld
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
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Chowdhury D, Ghanti D. Soft mechano-chemistry of molecular hubs in mitotic spindle: biomechanics and mechanical proofreading at microtubule ends. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:284001. [PMID: 32133984 DOI: 10.1088/1361-648x/ab7cc5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A microtubule (MT) is a long stiff tube-shaped filament formed by a hierarchical organization of a large number of tubulin protein molecules. These filaments constitute a major structural component of the scaffold of a multi-component macromolecular machine called mitotic spindle. The plus ends of the MTs are tethered to some specific binding partners by molecular tethers while those of some others are crosslinked by crosslinking molecules. Because of the non-covalent binding involved in the tethering and crosslinking, the attachments formed are intrinsically 'soft'. These attachments are transient because these can get ruptured spontaneously by thermal fluctuations. By implementing in silico the standard protocols of in vitro molecular force spectroscopy, we compute the lifetimes of simple theoretical models of these attachments. The mean lifetime is essentially a mean first-passage time. The stability of cross-linked antiparallel MTs is shown to decrease monotonically with increasing tension, a characteristic of all 'slip-bonds'. This is in sharp contrast to the nonmonotonic variation of the mean lifetime with tension, a mechanical fingerprint of 'catch-bonds', displayed by the MTs tethered to two distinct binding partners. We mention plausible functional implications of these observations in the context of mechanical proofreading.
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Abstract
Integrins, and integrin-mediated adhesions, have long been recognized to provide the main molecular link attaching cells to the extracellular matrix (ECM) and to serve as bidirectional hubs transmitting signals between cells and their environment. Recent evidence has shown that their combined biochemical and mechanical properties also allow integrins to sense, respond to and interact with ECM of differing properties with exquisite specificity. Here, we review this work first by providing an overview of how integrin function is regulated from both a biochemical and a mechanical perspective, affecting integrin cell-surface availability, binding properties, activation or clustering. Then, we address how this biomechanical regulation allows integrins to respond to different ECM physicochemical properties and signals, such as rigidity, composition and spatial distribution. Finally, we discuss the importance of this sensing for major cell functions by taking cell migration and cancer as examples.
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21
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Lim YB, Thingna J, Kong F, Dao M, Cao J, Lim CT. Temperature-Induced Catch-Slip to Slip Bond Transit in Plasmodium falciparum-Infected Erythrocytes. Biophys J 2019; 118:105-116. [PMID: 31813540 DOI: 10.1016/j.bpj.2019.11.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/26/2019] [Accepted: 11/12/2019] [Indexed: 11/28/2022] Open
Abstract
Plasmodium falciparum malaria-infected red blood cells (IRBCs), or erythrocytes, avoid splenic clearance by adhering to host endothelium. Upregulation of endothelial receptors intercellular adhesion molecule-1 (ICAM-1) and cluster of differentiation 36 (CD36) are associated with severe disease pathology. Most in vitro studies of IRBCs interacting with these molecules were conducted at room temperature. However, as IRBCs are exposed to temperature variations between 37°C (body temperature) and 41°C (febrile temperature) in the host, it is important to understand IRBC-receptor interactions at these physiologically relevant temperatures. Here, we probe IRBC interactions against ICAM-1 and CD36 at 37 and 41°C. Single bond force-clamp spectroscopy is used to determine the bond dissociation rates and hence, unravel the nature of the IRBC-receptor interaction. The association rates are also extracted from a multiple bond flow assay using a cellular stochastic model. Surprisingly, IRBC-ICAM-1 bond transits from a catch-slip bond at 37°C toward a slip bond at 41°C. Moreover, binding affinities of both IRBC-ICAM-1 and IRBC-CD36 decrease as the temperature rises from 37 to 41°C. This study highlights the significance of examining receptor-ligand interactions at physiologically relevant temperatures and reveals biophysical insight into the temperature dependence of P. falciparum malaria cytoadherent bonds.
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Affiliation(s)
- Ying Bena Lim
- Department of Biomedical Engineering, National University of Singapore, Singapore; Singapore-Massachusetts Institute of Technology Alliance for Research and Technology Centre, Infectious Diseases IRG, Singapore
| | - Juzar Thingna
- Singapore-Massachusetts Institute of Technology Alliance for Research and Technology Centre, Infectious Diseases IRG, Singapore; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts; Center for Theoretical Physics of Complex Systems, Institute for Basic Science, Daejeon, Republic of Korea
| | - Fang Kong
- Singapore-Massachusetts Institute of Technology Alliance for Research and Technology Centre, Infectious Diseases IRG, Singapore; School of Biological Science, Nanyang Technological University, Singapore
| | - Ming Dao
- Singapore-Massachusetts Institute of Technology Alliance for Research and Technology Centre, Infectious Diseases IRG, Singapore; School of Biological Science, Nanyang Technological University, Singapore; Department of Material Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jianshu Cao
- Singapore-Massachusetts Institute of Technology Alliance for Research and Technology Centre, Infectious Diseases IRG, Singapore; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
| | - Chwee Teck Lim
- Department of Biomedical Engineering, National University of Singapore, Singapore; Singapore-Massachusetts Institute of Technology Alliance for Research and Technology Centre, Infectious Diseases IRG, Singapore; Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore.
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Guo SK, Shi XX, Wang PY, Xie P. Force dependence of unbinding rate of kinesin motor during its processive movement on microtubule. Biophys Chem 2019; 253:106216. [PMID: 31288174 DOI: 10.1016/j.bpc.2019.106216] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/26/2019] [Accepted: 06/30/2019] [Indexed: 12/15/2022]
Abstract
Kinesin is a biological molecular motor that can move continuously on microtubule until it unbinds. Here, we studied computationally the force dependence of the unbinding rate of the motor. Our results showed that while the unbinding rate under the forward load has the expected characteristic of "slip bond", with the unbinding rate increasing monotonically with the increase of the forward load, the unbinding rate under the backward load shows counterintuitive characteristic of "slip-catch-slip bond": as the backward load increases, the unbinding rate increases exponentially firstly, then drops rapidly and then increases again. Our calculated data are in agreement with the available single-molecule data from different research groups. The mechanism of the slip-catch-slip bond was revealed.
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Affiliation(s)
- Si-Kao Guo
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Science, Beijing 100190, China; School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Xuan Shi
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Science, Beijing 100190, China; School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng-Ye Wang
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Science, Beijing 100190, China; School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Xie
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Science, Beijing 100190, China; School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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23
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Mulla Y, MacKintosh FC, Koenderink GH. Origin of Slow Stress Relaxation in the Cytoskeleton. PHYSICAL REVIEW LETTERS 2019; 122:218102. [PMID: 31283330 DOI: 10.1103/physrevlett.122.218102] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 04/26/2019] [Indexed: 06/09/2023]
Abstract
Dynamically cross-linked semiflexible biopolymers such as the actin cytoskeleton govern the mechanical behavior of living cells. Semiflexible biopolymers nonlinearly stiffen in response to mechanical loads, whereas the cross-linker dynamics allow for stress relaxation over time. Here we show, through rheology and theoretical modeling, that the combined nonlinearity in time and stress leads to an unexpectedly slow stress relaxation, similar to the dynamics of disordered systems close to the glass transition. Our work suggests that transient cross-linking combined with internal stress can explain prior reports of soft glassy rheology of cells, in which the shear modulus increases weakly with frequency.
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Affiliation(s)
- Yuval Mulla
- Living Matter Department, AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - F C MacKintosh
- Departments of Chemical & Biomolecular Engineering, Chemistry, and Physics & Astronomy, Rice University, Houston, Texas 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA
- Department of Physics and Astronomy, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Gijsje H Koenderink
- Living Matter Department, AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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24
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Toan NM, Thirumalai D. Forced-rupture of cell-adhesion complexes reveals abrupt switch between two brittle states. J Chem Phys 2018; 148:123332. [PMID: 29604893 DOI: 10.1063/1.5011056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cell adhesion complexes (CACs), which are activated by ligand binding, play key roles in many cellular functions ranging from cell cycle regulation to mediation of cell extracellular matrix adhesion. Inspired by single molecule pulling experiments using atomic force spectroscopy on leukocyte function-associated antigen-1 (LFA-1), expressed in T-cells, bound to intercellular adhesion molecules (ICAM), we performed constant loading rate (rf) and constant force (F) simulations using the self-organized polymer model to describe the mechanism of ligand rupture from CACs. The simulations reproduce the major experimental finding on the kinetics of the rupture process, namely, the dependence of the most probable rupture forces (f*s) on ln rf (rf is the loading rate) exhibits two distinct linear regimes. The first, at low rf, has a shallow slope, whereas the slope at high rf is much larger, especially for a LFA-1/ICAM-1 complex with the transition between the two occurring over a narrow rf range. Locations of the two transition states (TSs) extracted from the simulations show an abrupt change from a high value at low rf or constant force, F, to a low value at high rf or F. This unusual behavior in which the CACs switch from one brittle (TS position is a constant over a range of forces) state to another brittle state is not found in forced-rupture in other protein complexes. We explain this novel behavior by constructing the free energy profiles, F(Λ)s, as a function of a collective reaction coordinate (Λ), involving many key charged residues and a critical metal ion (Mg2+). The TS positions in F(Λ), which quantitatively agree with the parameters extracted using the Bell-Evans model, change abruptly at a critical force, demonstrating that it, rather than the molecular extension, is a good reaction coordinate. Our combined analyses using simulations performed in both the pulling modes (constant rf and F) reveal a new mechanism for the two loading regimes observed in the rupture kinetics in CACs.
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Affiliation(s)
- Ngo Minh Toan
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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25
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Exploring the Sulfatase 1 Catch Bond Free Energy Landscape using Jarzynski's Equality. Sci Rep 2018; 8:16849. [PMID: 30442949 PMCID: PMC6237999 DOI: 10.1038/s41598-018-35120-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/25/2018] [Indexed: 01/29/2023] Open
Abstract
In non-covalent biological adhesion, molecular bonds commonly exhibit a monotonously decreasing life time when subjected to tensile forces (slip bonds). In contrast, catch bonds behave counter intuitively, as they show an increased life time within a certain force interval. To date only a hand full of catch bond displaying systems have been identified. In order to unveil their nature, a number of structural and phenomenological models have been introduced. Regardless of the individual causes for catch bond behavior, it appears evident that the free energy landscapes of these interactions bear more than one binding state. Here, we investigated the catch bond interaction between the hydrophilic domain of the human cell surface sulfatase 1 (Sulf1HD) and its physiological substrate heparan sulfate (HS) by atomic force microscopy based single molecule force spectroscopy (AFM-SMFS). Using Jarzynski’s equality, we estimated the associated Gibbs free energy and provide a comprehensive thermodynamic and kinetic characterization of Sulf1HD/HS interaction. Interestingly, the binding potential landscape exhibits two distinct potential wells which confirms the recently suggested two state binding. Even though structural data of Sulf1HD is lacking, our results allow to draft a detailed picture of the directed and processive desulfation of HS.
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26
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Special issue: Biomolecular forces. J Struct Biol 2018; 197:1-2. [PMID: 28061956 DOI: 10.1016/j.jsb.2016.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Adhikari S, Moran J, Weddle C, Hinczewski M. Unraveling the mechanism of the cadherin-catenin-actin catch bond. PLoS Comput Biol 2018; 14:e1006399. [PMID: 30118477 PMCID: PMC6114904 DOI: 10.1371/journal.pcbi.1006399] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/29/2018] [Accepted: 07/24/2018] [Indexed: 11/19/2022] Open
Abstract
The adherens junctions between epithelial cells involve a protein complex formed by E-cadherin, β-catenin, α-catenin and F-actin. The stability of this complex was a puzzle for many years, since in vitro studies could reconstitute various stable subsets of the individual proteins, but never the entirety. The missing ingredient turned out to be mechanical tension: a recent experiment that applied physiological forces to the complex with an optical tweezer dramatically increased its lifetime, a phenomenon known as catch bonding. However, in the absence of a crystal structure for the full complex, the microscopic details of the catch bond mechanism remain mysterious. Building on structural clues that point to α-catenin as the force transducer, we present a quantitative theoretical model for how the catch bond arises, fully accounting for the experimental lifetime distributions. The underlying hypothesis is that force induces a rotational transition between two conformations of α-catenin, overcoming a significant energy barrier due to a network of salt bridges. This transition allosterically regulates the energies at the interface between α-catenin and F-actin. The model allows us to predict these energetic changes, as well as highlighting the importance of the salt bridge rotational barrier. By stabilizing one of the α-catenin states, this barrier could play a role in how the complex responds to additional in vivo binding partners like vinculin. Since significant conformational energy barriers are a common feature of other adhesion systems that exhibit catch bonds, our model can be adapted into a general theoretical framework for integrating structure and function in a variety of force-regulated protein complexes.
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Affiliation(s)
- Shishir Adhikari
- Department of Physics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Jacob Moran
- Department of Physics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Christopher Weddle
- Department of Physics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Michael Hinczewski
- Department of Physics, Case Western Reserve University, Cleveland, Ohio, United States of America
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Ghanti D, Patra S, Chowdhury D. Molecular force spectroscopy of kinetochore-microtubule attachment in silico: Mechanical signatures of an unusual catch bond and collective effects. Phys Rev E 2018; 97:052414. [PMID: 29906871 DOI: 10.1103/physreve.97.052414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Indexed: 06/08/2023]
Abstract
Measurement of the lifetime of attachments formed by a single microtubule (MT) with a single kinetochore (kt) in vitro under force-clamp conditions had earlier revealed a catch-bond-like behavior. In the past, the physical origin of this apparently counterintuitive phenomenon was traced to the nature of the force dependence of the (de)polymerization kinetics of the MTs. Here, first the same model MT-kt attachment is subjected to external tension that increases linearly with time until rupture occurs. In our force-ramp experiments in silico, the model displays the well known "mechanical signatures" of a catch bond probed by molecular force spectroscopy. Exploiting this evidence, we have further strengthened the analogy between MT-kt attachments and common ligand-receptor bonds in spite of the crucial differences in their underlying physical mechanisms. We then extend the formalism to model the stochastic kinetics of an attachment formed by a bundle of multiple parallel microtubules with a single kt considering the effect of rebinding under force-clamp and force-ramp conditions. From numerical studies of the model we predict the trends of variation of the mean lifetime and mean rupture force with the increasing number of MTs in the bundle. Both the mean lifetime and the mean rupture force display nontrivial nonlinear dependence on the maximum number of MTs that can attach simultaneously to the same kt.
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Affiliation(s)
- Dipanwita Ghanti
- Department of Physics, Indian Institute of Technology Kanpur, 208016, India
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Akbulatov S, Tian Y, Huang Z, Kucharski TJ, Yang QZ, Boulatov R. Experimentally realized mechanochemistry distinct from force-accelerated scission of loaded bonds. Science 2018; 357:299-303. [PMID: 28729509 DOI: 10.1126/science.aan1026] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 06/20/2017] [Indexed: 12/11/2022]
Abstract
Stretching polymer chains accelerates dissociation of a variety of internal covalent bonds, to an extent that correlates well with the force experienced by the scissile bond. Recent theory has also predicted scenarios in which applied force accelerates dissociation of unloaded bonds and kinetically strengthens strained bonds. We report here unambiguous experimental validation of this hypothesis: Detailed kinetic measurements demonstrate that stretching phosphotriesters accelerates dissociation of the unloaded phosphorus-oxygen bond orthogonal to the pulling axis, whereas stretching organosiloxanes inhibits dissociation of the aligned loaded silicon-oxygen bonds. Qualitatively, the outcome is determined by phosphoester elongation and siloxane contraction along the pulling axis in the respective rate-determining transition states. Quantitatively, the results agree with a simple mechanochemical kinetics model.
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Affiliation(s)
- Sergey Akbulatov
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK
| | - Yancong Tian
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK
| | - Zhen Huang
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | | | - Qing-Zheng Yang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Roman Boulatov
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK.
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Abstract
The bacterial flagellar motor (BFM) is the rotary motor powering swimming of many motile bacteria. Many of the components of this molecular machine are dynamic, a property which allows the cell to optimize its behavior in accordance with the surrounding environment. A prime example is the stator unit, a membrane-bound ion channel that is responsible for applying torque to the rotor. The stator units are mechanosensitive, with the number of engaged units dependent on the viscous load on the motor. We measure the kinetics of the stators as a function of the viscous load and find that the mechanosensitivity of the BFM is governed by a catch bond: a counterintuitive type of bond that becomes stronger under force. The bacterial flagellar motor (BFM) is the rotary motor that rotates each bacterial flagellum, powering the swimming and swarming of many motile bacteria. The torque is provided by stator units, ion motive force-powered ion channels known to assemble and disassemble dynamically in the BFM. This turnover is mechanosensitive, with the number of engaged units dependent on the viscous load experienced by the motor through the flagellum. However, the molecular mechanism driving BFM mechanosensitivity is unknown. Here, we directly measure the kinetics of arrival and departure of the stator units in individual motors via analysis of high-resolution recordings of motor speed, while dynamically varying the load on the motor via external magnetic torque. The kinetic rates obtained, robust with respect to the details of the applied adsorption model, indicate that the lifetime of an assembled stator unit increases when a higher force is applied to its anchoring point in the cell wall. This provides strong evidence that a catch bond (a bond strengthened instead of weakened by force) drives mechanosensitivity of the flagellar motor complex. These results add the BFM to a short, but growing, list of systems demonstrating catch bonds, suggesting that this “molecular strategy” is a widespread mechanism to sense and respond to mechanical stress. We propose that force-enhanced stator adhesion allows the cell to adapt to a heterogeneous environmental viscosity and may ultimately play a role in surface-sensing during swarming and biofilm formation.
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31
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Zhang T, Mbanga BL, Yashin VV, Balazs AC. Tailoring the mechanical properties of nanoparticle networks that encompass biomimetic catch bonds. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/polb.24542] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Tao Zhang
- Department of Chemical EngineeringUniversity of PittsburghPittsburgh Pennsylvania 15261
| | - Badel L. Mbanga
- Department of Chemical EngineeringUniversity of PittsburghPittsburgh Pennsylvania 15261
| | - Victor V. Yashin
- Department of Chemical EngineeringUniversity of PittsburghPittsburgh Pennsylvania 15261
| | - Anna C. Balazs
- Department of Chemical EngineeringUniversity of PittsburghPittsburgh Pennsylvania 15261
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32
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Alvarado J, Sheinman M, Sharma A, MacKintosh FC, Koenderink GH. Force percolation of contractile active gels. SOFT MATTER 2017; 13:5624-5644. [PMID: 28812094 DOI: 10.1039/c7sm00834a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Living systems provide a paradigmatic example of active soft matter. Cells and tissues comprise viscoelastic materials that exert forces and can actively change shape. This strikingly autonomous behavior is powered by the cytoskeleton, an active gel of semiflexible filaments, crosslinks, and molecular motors inside cells. Although individual motors are only a few nm in size and exert minute forces of a few pN, cells spatially integrate the activity of an ensemble of motors to produce larger contractile forces (∼nN and greater) on cellular, tissue, and organismal length scales. Here we review experimental and theoretical studies on contractile active gels composed of actin filaments and myosin motors. Unlike other active soft matter systems, which tend to form ordered patterns, actin-myosin systems exhibit a generic tendency to contract. Experimental studies of reconstituted actin-myosin model systems have long suggested that a mechanical interplay between motor activity and the network's connectivity governs this contractile behavior. Recent theoretical models indicate that this interplay can be understood in terms of percolation models, extended to include effects of motor activity on the network connectivity. Based on concepts from percolation theory, we propose a state diagram that unites a large body of experimental observations. This framework provides valuable insights into the mechanisms that drive cellular shape changes and also provides design principles for synthetic active materials.
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Affiliation(s)
- José Alvarado
- Systems Biophysics Department, AMOLF, 1098 XG Amsterdam, The Netherlands.
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Abstract
The adhesion of malaria infected red blood cells (iRBCs) to host endothelial receptors in the microvasculature, or cytoadhesion, is associated with severe disease pathology such as multiple organ failure and cerebral malaria. Malaria iRBCs have been shown to bind to several receptors, of which intercellular adhesion molecule 1 (ICAM-1) upregulation in brain microvasculature is the only one correlated to cerebral malaria. We utilize a biophysical approach to study the interactions between iRBCs and ICAM-1. At the single molecule level, force spectroscopy experiments reveal that ICAM-1 forms catch bond interactions with Plasmodium falciparum parasite iRBCs. Flow experiments are subsequently conducted to understand multiple bond behavior. Using a robust model that smoothly transitions between our single and multiple bond results, we conclusively demonstrate that the catch bond behavior persists even under flow conditions. The parameters extracted from these experimental results revealed that the rate of association of iRBC-ICAM-1 bonds are ten times lower than iRBC-CD36 (cluster of differentiation 36), a receptor that shows no upregulation in the brains of cerebral malaria patients. Yet, the dissociation rates are nearly the same for both iRBC-receptor interactions. Thus, our results suggest that ICAM-1 may not be the sole mediator responsible for cytoadhesion in the brain.
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Helms G, Dasanna AK, Schwarz US, Lanzer M. Modeling cytoadhesion of Plasmodium falciparum-infected erythrocytes and leukocytes-common principles and distinctive features. FEBS Lett 2016; 590:1955-71. [PMID: 26992823 PMCID: PMC5071704 DOI: 10.1002/1873-3468.12142] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/01/2016] [Accepted: 02/07/2016] [Indexed: 12/25/2022]
Abstract
Cytoadhesion of Plasmodium falciparum‐infected erythrocytes to the microvascular endothelial lining shares striking similarities to cytoadhesion of leukocytes. In both cases, adhesins are presented in structures that raise them above the cell surface. Another similarity is the enhancement of adhesion under physical force (catch bonding). Here, we review recent advances in our understanding of the molecular and biophysical mechanisms underlying cytoadherence in both cellular systems. We describe how imaging, flow chamber experiments, single‐molecule measurements, and computational modeling have been used to decipher the relevant processes. We conclude that although the parasite seems to induce processes that resemble the cytoadherence of leukocytes, the mechanics of erythrocytes is such that the resulting behavior in shear flow is fundamentally different.
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Affiliation(s)
- Gesa Helms
- Department of Infectious Diseases, Heidelberg University, Germany
| | - Anil Kumar Dasanna
- BioQuant, Heidelberg, Germany.,Institute for Theoretical Physics, Heidelberg University, Germany
| | - Ulrich S Schwarz
- BioQuant, Heidelberg, Germany.,Institute for Theoretical Physics, Heidelberg University, Germany
| | - Michael Lanzer
- Department of Infectious Diseases, Heidelberg University, Germany
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