51
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Arya G. Models for recovering the energy landscape of conformational transitions from single-molecule pulling experiments. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2015.1123257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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52
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Jadhav VS, Brüggemann D, Wruck F, Hegner M. Single-molecule mechanics of protein-labelled DNA handles. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:138-148. [PMID: 26925362 PMCID: PMC4734302 DOI: 10.3762/bjnano.7.16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 01/18/2016] [Indexed: 05/07/2023]
Abstract
DNA handles are often used as spacers and linkers in single-molecule experiments to isolate and tether RNAs, proteins, enzymes and ribozymes, amongst other biomolecules, between surface-modified beads for nanomechanical investigations. Custom DNA handles with varying lengths and chemical end-modifications are readily and reliably synthesized en masse, enabling force spectroscopic measurements with well-defined and long-lasting mechanical characteristics under physiological conditions over a large range of applied forces. Although these chemically tagged DNA handles are widely used, their further individual modification with protein receptors is less common and would allow for additional flexibility in grabbing biomolecules for mechanical measurements. In-depth information on reliable protocols for the synthesis of these DNA-protein hybrids and on their mechanical characteristics under varying physiological conditions are lacking in literature. Here, optical tweezers are used to investigate different protein-labelled DNA handles in a microfluidic environment under different physiological conditions. Digoxigenin (DIG)-dsDNA-biotin handles of varying sizes (1000, 3034 and 4056 bp) were conjugated with streptavidin or neutravidin proteins. The DIG-modified ends of these hybrids were bound to surface-modified polystyrene (anti-DIG) beads. Using different physiological buffers, optical force measurements showed consistent mechanical characteristics with long dissociation times. These protein-modified DNA hybrids were also interconnected in situ with other tethered biotinylated DNA molecules. Electron-multiplying CCD (EMCCD) imaging control experiments revealed that quantum dot-streptavidin conjugates at the end of DNA handles remain freely accessible. The experiments presented here demonstrate that handles produced with our protein-DNA labelling procedure are excellent candidates for grasping single molecules exposing tags suitable for molecular recognition in time-critical molecular motor studies.
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Affiliation(s)
- Vivek S Jadhav
- CRANN – The Naughton Institute, School of Physics, Trinity College Dublin, Dublin, Ireland
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Dorothea Brüggemann
- CRANN – The Naughton Institute, School of Physics, Trinity College Dublin, Dublin, Ireland
- Institute for Biophysics, University of Bremen, Bremen, Germany
| | - Florian Wruck
- CRANN – The Naughton Institute, School of Physics, Trinity College Dublin, Dublin, Ireland
| | - Martin Hegner
- CRANN – The Naughton Institute, School of Physics, Trinity College Dublin, Dublin, Ireland
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53
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Isabey D, Pelle G, André Dias S, Bottier M, Nguyen NM, Filoche M, Louis B. Multiscale evaluation of cellular adhesion alteration and cytoskeleton remodeling by magnetic bead twisting. Biomech Model Mechanobiol 2015; 15:947-63. [PMID: 26459324 DOI: 10.1007/s10237-015-0734-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/29/2015] [Indexed: 12/19/2022]
Abstract
Cellular adhesion forces depend on local biological conditions meaning that adhesion characterization must be performed while preserving cellular integrity. We presently postulate that magnetic bead twisting provides an appropriate stress, i.e., basically a clamp, for assessment in living cells of both cellular adhesion and mechanical properties of the cytoskeleton. A global dissociation rate obeying a Bell-type model was used to determine the natural dissociation rate ([Formula: see text]) and a reference stress ([Formula: see text]). These adhesion parameters were determined in parallel to the mechanical properties for a variety of biological conditions in which either adhesion or cytoskeleton was selectively weakened or strengthened by changing successively ligand concentration, actin polymerization level (by treating with cytochalasin D), level of exerted stress (by increasing magnetic torque), and cell environment (by using rigid and soft 3D matrices). On the whole, this multiscale evaluation of the cellular and molecular responses to a controlled stress reveals an evolution which is consistent with stochastic multiple bond theories and with literature results obtained with other molecular techniques. Present results confirm the validity of the proposed bead-twisting approach for its capability to probe cellular and molecular responses in a variety of biological conditions.
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Affiliation(s)
- Daniel Isabey
- Inserm, U955, Équipe 13, Biomécanique and Appareil Respiratoire: une approche multi-échelle, UMR S955, CNRS, ERL 7240, Université Paris Est, UPEC, 8, rue du Général Sarrail, 94010, Créteil Cedex, France.
| | - Gabriel Pelle
- Inserm, U955, Équipe 13, Biomécanique and Appareil Respiratoire: une approche multi-échelle, UMR S955, CNRS, ERL 7240, Université Paris Est, UPEC, 8, rue du Général Sarrail, 94010, Créteil Cedex, France.,APHP, Groupe Hospitalier H. Mondor A. Chenevier, Service des Explorations Fonctionnelles, 51, Avenue du Maréchal de Lattre de Tassigny, 94010, Créteil Cedex, France
| | - Sofia André Dias
- Inserm, U955, Équipe 13, Biomécanique and Appareil Respiratoire: une approche multi-échelle, UMR S955, CNRS, ERL 7240, Université Paris Est, UPEC, 8, rue du Général Sarrail, 94010, Créteil Cedex, France
| | - Mathieu Bottier
- Inserm, U955, Équipe 13, Biomécanique and Appareil Respiratoire: une approche multi-échelle, UMR S955, CNRS, ERL 7240, Université Paris Est, UPEC, 8, rue du Général Sarrail, 94010, Créteil Cedex, France
| | - Ngoc-Minh Nguyen
- Inserm, U955, Équipe 13, Biomécanique and Appareil Respiratoire: une approche multi-échelle, UMR S955, CNRS, ERL 7240, Université Paris Est, UPEC, 8, rue du Général Sarrail, 94010, Créteil Cedex, France
| | - Marcel Filoche
- Inserm, U955, Équipe 13, Biomécanique and Appareil Respiratoire: une approche multi-échelle, UMR S955, CNRS, ERL 7240, Université Paris Est, UPEC, 8, rue du Général Sarrail, 94010, Créteil Cedex, France.,Physique de la Matière Condensée, Ecole Polytechnique, CNRS, 91128, Palaiseau, France
| | - Bruno Louis
- Inserm, U955, Équipe 13, Biomécanique and Appareil Respiratoire: une approche multi-échelle, UMR S955, CNRS, ERL 7240, Université Paris Est, UPEC, 8, rue du Général Sarrail, 94010, Créteil Cedex, France
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54
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Avdoshenko SM, Makarov DE. Reaction Coordinates and Pathways of Mechanochemical Transformations. J Phys Chem B 2015; 120:1537-45. [PMID: 26401617 DOI: 10.1021/acs.jpcb.5b07613] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The notions of a reaction path and a reaction coordinate are central to chemistry as they provide low-dimensional descriptions of complex molecular processes. Here we discuss how to define, compute, and use the reaction paths for chemical transformations in molecules that are subjected to mechanical stress and thus driven toward regions of conformational space that are otherwise inaccessible both in computational studies and in reality. We further show that the circuitous nature of mechanochemical pathways often makes their one-dimensional description impossible and describe how multidimensional effects can be detected experimentally.
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Affiliation(s)
- Stanislav M Avdoshenko
- Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Dmitrii E Makarov
- Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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55
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Das P, Reches M. Review insights into the interactions of amino acids and peptides with inorganic materials using single molecule force spectroscopy. Biopolymers 2015; 104:480-94. [DOI: 10.1002/bip.22655] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/18/2015] [Accepted: 03/30/2015] [Indexed: 01/11/2023]
Affiliation(s)
- Priyadip Das
- Institute of Chemistry, The Hebrew University of Jerusalem; 91904 Jerusalem Israel
- The Center for Nanoscience and Nanotechnology; The Hebrew University of Jerusalem; 91904 Jerusalem Israel
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56
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Nguyen TH, Greinacher A, Delcea M. Quantitative description of thermodynamic and kinetic properties of the platelet factor 4/heparin bonds. NANOSCALE 2015; 7:10130-9. [PMID: 25981976 DOI: 10.1039/c5nr02132d] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Heparin is the most important antithrombotic drug in hospitals. It binds to the endogenous tetrameric protein platelet factor 4 (PF4) forming PF4/heparin complexes which may cause a severe immune-mediated adverse drug reaction, so-called heparin-induced thrombocytopenia (HIT). Although new heparin drugs have been synthesized to reduce such a risk, detailed bond dynamics of the PF4/heparin complexes have not been clearly understood. In this study, single molecule force spectroscopy (SMFS) is utilized to characterize the interaction of PF4 with heparins of defined length (5-, 6-, 8-, 12-, and 16-mers). Analysis of the force-distance curves shows that PF4/heparin binding strength rises with increasing heparin length. In addition, two binding pathways in the PF4/short heparins (≤8-mers) and three binding pathways in the PF4/long heparins (≥8-mers) are identified. We provide a model for the PF4/heparin complexes in which short heparins bind to one PF4 tetramer, while long heparins bind to two PF4 tetramers. We propose that the interaction between long heparins and PF4s is not only due to charge differences as generally assumed, but also due to hydrophobic interaction between two PF4s which are brought close to each other by long heparin. This complicated interaction induces PF4/heparin complexes more stable than other ligand-receptor interactions. Our results also reveal that the boundary between antigenic and non-antigenic heparins is between 8- and 12-mers. These observations are particularly important to understand processes in which PF4-heparin interactions are involved and to develop new heparin-derived drugs.
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Affiliation(s)
- Thi-Huong Nguyen
- Nanostructure Group, ZIK HIKE - Center for Innovation Competence, Humoral Immune Reactions in Cardiovascular Diseases, Ernst-Moritz-Arndt-Universität Greifswald, 17489 Greifswald, Germany.
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57
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te Riet J, Reinieren-Beeren I, Figdor CG, Cambi A. AFM force spectroscopy reveals how subtle structural differences affect the interaction strength betweenCandida albicansand DC-SIGN. J Mol Recognit 2015; 28:687-98. [DOI: 10.1002/jmr.2481] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 04/24/2015] [Accepted: 04/27/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Joost te Riet
- Department of Tumor Immunology; Radboud Institute for Molecular Life Sciences, Radboud UMC; P.O. Box 9101 6500HB Nijmegen The Netherlands
| | - Inge Reinieren-Beeren
- Department of Tumor Immunology; Radboud Institute for Molecular Life Sciences, Radboud UMC; P.O. Box 9101 6500HB Nijmegen The Netherlands
| | - Carl G. Figdor
- Department of Tumor Immunology; Radboud Institute for Molecular Life Sciences, Radboud UMC; P.O. Box 9101 6500HB Nijmegen The Netherlands
| | - Alessandra Cambi
- Department of Tumor Immunology; Radboud Institute for Molecular Life Sciences, Radboud UMC; P.O. Box 9101 6500HB Nijmegen The Netherlands
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58
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Cao M, Deng L, Xu H. Study of PNA–DNA hybridization by AFM-based single-molecule force spectroscopy. Colloids Surf A Physicochem Eng Asp 2015. [DOI: 10.1016/j.colsurfa.2015.01.063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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59
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Benichou I, Givli S. Rate dependent response of nanoscale structures having a multiwell energy landscape. PHYSICAL REVIEW LETTERS 2015; 114:095504. [PMID: 25793827 DOI: 10.1103/physrevlett.114.095504] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Indexed: 06/04/2023]
Abstract
A stochastic and rate-dependent response originating from thermal fluctuations over a highly nonconvex energy landscape is a prevailing aspect of the mechanical behavior of nanoscale structures. The overdamped dynamics of a bistable chain subjected to thermal fluctuations is prototypical of such behavior. Based on this approach, we find a new nondimensional quantity, similar in its mathematical structure to Boltzmann's factor, which captures the intricate competition between rate, temperature, and energy barriers underlying the system dynamics. In turn, we obtain simple universal laws for predicting statistical properties of the mechanical response.
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Affiliation(s)
- Itamar Benichou
- Faculty of Mechanical Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Sefi Givli
- Faculty of Mechanical Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
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60
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Tabatabai AP, Kaplan DL, Blair DL. Rheology of reconstituted silk fibroin protein gels: the epitome of extreme mechanics. SOFT MATTER 2015; 11:756-761. [PMID: 25489795 DOI: 10.1039/c4sm02079k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In nature, silk fibroin proteins assemble into hierarchical structures with dramatic mechanical properties. With the hope of creating new classes of on demand silk-based biomaterials, Bombyx mori silk is reconstituted back into stable aqueous solutions that can be reassembled into functionalized materials; one strategy for reassembly is electrogelation. Electrogels (e-gels) are particularly versatile and can be produced using electrolysis with small DC electric fields. We characterize the linear and nonlinear rheological behavior of e-gels to provide fundamental insights into these distinct protein-based materials. We observe that e-gels form robust biopolymer networks that exhibit distinctive strain hardening and are recoverable from strains as large as γ=27, i.e. 2700%. We propose a simple microscopic model that is consistent with local restructuring of single proteins within the e-gel network.
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Affiliation(s)
- A Pasha Tabatabai
- Georgetown University, Department of Physics, The Institute for Soft Matter Synthesis and Metrology, Washington, DC 20057, USA.
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61
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Konda SSM, Avdoshenko SM, Makarov DE. Exploring the topography of the stress-modified energy landscapes of mechanosensitive molecules. J Chem Phys 2014; 140:104114. [PMID: 24628159 DOI: 10.1063/1.4867500] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We propose a method for computing the activation barrier for chemical reactions involving molecules subjected to mechanical stress. The method avoids reactant and transition-state saddle optimizations at every force by, instead, solving the differential equations governing the force dependence of the critical points (i.e., minima and saddles) on the system's potential energy surface (PES). As a result, only zero-force geometry optimization (or, more generally, optimization performed at a single force value) is required by the method. In many cases, minima and transition-state saddles only exist within a range of forces and disappear beyond a certain critical point. Our method identifies such force-induced instabilities as points at which one of the Hessian eigenvalues vanishes. We elucidate the nature of those instabilities as fold and cusp catastrophes, where two or three critical points on the force-modified PES coalesce, and provide a classification of various physically distinct instability scenarios, each illustrated with a concrete chemical example.
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Affiliation(s)
| | - Stanislav M Avdoshenko
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Dmitrii E Makarov
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
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62
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Avdoshenko SM, Konda SSM, Makarov DE. On the calculation of internal forces in mechanically stressed polyatomic molecules. J Chem Phys 2014; 141:134115. [DOI: 10.1063/1.4896944] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Stanislav M. Avdoshenko
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | | | - Dmitrii E. Makarov
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
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63
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Duman M. Probing and mapping the binding sites on streptavidin imprinted polymer surface. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2014; 43:214-20. [PMID: 25175207 DOI: 10.1016/j.msec.2014.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/23/2014] [Accepted: 07/03/2014] [Indexed: 10/25/2022]
Abstract
Molecular imprinting is an effective technique for preparing recognition sites which act as synthetic receptors on polymeric surfaces. Herein, we synthesized MIP surfaces with specific binding sites for streptavidin and characterized them at nanoscale by using two different atomic force microscopy (AFM) techniques. While the single molecule force spectroscopy (SMFS) reveals the unbinding kinetics between streptavidin molecule and binding sites, simultaneous topography and recognition imaging (TREC) was employed, for the first time, to directly map the binding sites on streptavidin imprinted polymers. Streptavidin modified AFM cantilever showed specific unbinding events with an unbinding force around 300 pN and the binding probability was calculated as 35.2% at a given loading rate. In order to prove the specificity of the interaction, free streptavidin molecules were added to AFM liquid cell and the binding probability was significantly decreased to 7.6%. Moreover, the recognition maps show that the smallest recognition site with a diameter of around ~21 nm which corresponds to a single streptavidin molecule binding site. We believe that the potential of combining SMFS and TREC opens new possibilities for the characterization of MIP surfaces with single molecule resolution under physiological conditions.
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Affiliation(s)
- Memed Duman
- Hacettepe University, Institute of Science, Nanotechnology and Nanomedicine Division, Beytepe 06800 Ankara, Turkey.
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64
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Golas EI, Czaplewski C. Rapid communication: Computational simulation and analysis of a candidate for the design of a novel silk-based biopolymer. Biopolymers 2014; 101:915-23. [PMID: 24723330 DOI: 10.1002/bip.22494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/26/2014] [Accepted: 03/20/2014] [Indexed: 11/08/2022]
Abstract
This work theoretically investigates the mechanical properties of a novel silk-derived biopolymer as polymerized in silico from sericin and elastin-like monomers. Molecular Dynamics simulations and Steered Molecular Dynamics were the principal computational methods used, the latter of which applies an external force onto the system and thereby enables an observation of its response to stress. The models explored herein are single-molecule approximations, and primarily serve as tools in a rational design process for the preliminary assessment of properties in a new material candidate.
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Affiliation(s)
- Ewa I Golas
- Department of Chemistry, University of Gdańsk, Ul. Wita Stwosza 63, 80-308, Gdańsk, Poland
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65
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Rakshit S, Sivasankar S. Biomechanics of cell adhesion: how force regulates the lifetime of adhesive bonds at the single molecule level. Phys Chem Chem Phys 2014; 16:2211-23. [PMID: 24419646 DOI: 10.1039/c3cp53963f] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cell adhesion proteins play critical roles in positioning cells during development, segregating cells into distinct tissue compartments and in maintaining tissue integrity. The principle function of these proteins is to bind cells together and resist mechanical force. Adhesive proteins also enable migrating cells to adhere and roll on surfaces even in the presence of shear forces exerted by fluid flow. Recently, several experimental and theoretical studies have provided quantitative insights into the physical mechanisms by which adhesion proteins modulate their unbinding kinetics in response to tensile force. This perspective reviews these biophysical investigations. We focus on single molecule studies of cadherins, selectins, integrins, the von Willebrand factor and FimH adhesion proteins; the effect of mechanical force on the lifetime of these interactions has been extensively characterized. We review both theoretical models and experimental investigations and discuss future directions in this exciting area of research.
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Affiliation(s)
- Sabyasachi Rakshit
- Department of Physics and Astronomy, Iowa State University, Ames, IA 50011, USA.
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66
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Single-molecule force spectroscopy reveals force-enhanced binding of calcium ions by gelsolin. Nat Commun 2014; 5:4623. [PMID: 25100107 PMCID: PMC4143929 DOI: 10.1038/ncomms5623] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 07/08/2014] [Indexed: 01/30/2023] Open
Abstract
Force is increasingly recognized as an important element in controlling biological processes. Forces can deform native protein conformations leading to protein-specific effects. Protein–protein binding affinities may be decreased, or novel protein–protein interaction sites may be revealed, on mechanically stressing one or more components. Here we demonstrate that the calcium-binding affinity of the sixth domain of the actin-binding protein gelsolin (G6) can be enhanced by mechanical force. Our kinetic model suggests that the calcium-binding affinity of G6 increases exponentially with force, up to the point of G6 unfolding. This implies that gelsolin may be activated at lower calcium ion levels when subjected to tensile forces. The demonstration that cation–protein binding affinities can be force-dependent provides a new understanding of the complex behaviour of cation-regulated proteins in stressful cellular environments, such as those found in the cytoskeleton-rich leading edge and at cell adhesions. The application of force can influence biological processes such as ligand and protein–protein binding, with mechanical stress typically hindering such interactions. Here, the authors use atomic force microscopy to show that the binding of calcium to gelsolin can be improved under stress.
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67
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Neundlinger I, Puntheeranurak T, Wildling L, Rankl C, Wang LX, Gruber HJ, Kinne RKH, Hinterdorfer P. Forces and dynamics of glucose and inhibitor binding to sodium glucose co-transporter SGLT1 studied by single molecule force spectroscopy. J Biol Chem 2014; 289:21673-83. [PMID: 24962566 DOI: 10.1074/jbc.m113.529875] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Single molecule force spectroscopy was employed to investigate the dynamics of the sodium glucose co-transporter (SGLT1) upon substrate and inhibitor binding on the single molecule level. CHO cells stably expressing rbSGLT1 were probed by using atomic force microscopy tips carrying either thioglucose, 2'-aminoethyl β-d-glucopyranoside, or aminophlorizin. Poly(ethylene glycol) (PEG) chains of different length and varying end groups were used as tether. Experiments were performed at 10, 25 and 37 °C to address different conformational states of SGLT1. Unbinding forces between ligands and SGLT1 were recorded at different loading rates by changing the retraction velocity, yielding binding probability, width of energy barrier of the binding pocket, and the kinetic off rate constant of the binding reaction. With increasing temperature, width of energy barrier and average life time increased for the interaction of SGLT1 with thioglucose (coupled via acrylamide to a long PEG) but decreased for aminophlorizin binding. The former indicates that in the membrane-bound SGLT1 the pathway to sugar translocation involves several steps with different temperature sensitivity. The latter suggests that also the aglucon binding sites for transport inhibitors have specific, temperature-sensitive conformations.
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Affiliation(s)
- Isabel Neundlinger
- From the Institute for Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Theeraporn Puntheeranurak
- From the Institute for Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria, Department of Biology, Faculty of Science, Mahidol University and Nanotec-MU Center of Excellence on Intelligent Materials and Systems, 272 Rama VI, Ratchathewi, Bangkok 10400, Thailand
| | - Linda Wildling
- From the Institute for Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria
| | | | - Lai-Xi Wang
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, and
| | - Hermann J Gruber
- From the Institute for Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Rolf K H Kinne
- Max Planck Institute of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
| | - Peter Hinterdorfer
- From the Institute for Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria,
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68
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Li Y, Qin M, Li Y, Cao Y, Wang W. Single molecule evidence for the adaptive binding of DOPA to different wet surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:4358-4366. [PMID: 24716607 DOI: 10.1021/la501189n] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
3,4-Dihydroxyphenylalanine (DOPA) is the noncanonical amino acid widely found in mussel holdfast proteins, which is proposed to be responsible for their strong wet adhesion. This feature has also inspired the successful development of a range of DOPA-containing synthetic polymers for wet adhesions and surface coating. Despite the increasing applications of DOPA in material science, the underlying mechanism of DOPA-wet surface interactions remains unclear. In this work, we studied DOPA-surface interactions one bond at a time using atomic force microscope (AFM) based single molecule force spectroscopy. With our recently developed "multiple fishhook" protocol, we were able to perform high-throughput quantification of the binding strength of DOPA to various types of surfaces for the first time. We found that the dissociation forces between DOPA and nine different types of organic and inorganic surfaces are all in the range of 60-90 pN at a pulling speed of 1000 nm s(-1), suggesting the strong and versatile binding capability of DOPA to different types of surfaces. Moreover, by constructing the free energy landscape for the rupture events, we revealed several distinct binding modes between DOPA and different surfaces, which are directly related to the chemistry nature of the surfaces. These results explain the molecular origin of the versatile binding ability of DOPA. Moreover, we could quantitatively predict the relationship between DOPA contents and the binding strength based on the measured rupture kinetics. These serve as the bases for the quantitative prediction of the relationship between DOPA contents and adhesion strength to different wet surfaces, which is important for the design of novel DOPA based materials.
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Affiliation(s)
- Yiran Li
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University , 22 Hankou Road, Nanjing, Jiangsu, China 210093
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69
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Lamprecht C, Plochberger B, Ruprecht V, Wieser S, Rankl C, Heister E, Unterauer B, Brameshuber M, Danzberger J, Lukanov P, Flahaut E, Schütz G, Hinterdorfer P, Ebner A. A single-molecule approach to explore binding, uptake and transport of cancer cell targeting nanotubes. NANOTECHNOLOGY 2014; 25:125704. [PMID: 24577143 DOI: 10.1088/0957-4484/25/12/125704] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In the past decade carbon nanotubes (CNTs) have been widely studied as a potential drug-delivery system, especially with functionality for cellular targeting. Yet, little is known about the actual process of docking to cell receptors and transport dynamics after internalization. Here we performed single-particle studies of folic acid (FA) mediated CNT binding to human carcinoma cells and their transport inside the cytosol. In particular, we employed molecular recognition force spectroscopy, an atomic force microscopy based method, to visualize and quantify docking of FA functionalized CNTs to FA binding receptors in terms of binding probability and binding force. We then traced individual fluorescently labeled, FA functionalized CNTs after specific uptake, and created a dynamic 'roadmap' that clearly showed trajectories of directed diffusion and areas of nanotube confinement in the cytosol. Our results demonstrate the potential of a single-molecule approach for investigation of drug-delivery vehicles and their targeting capacity.
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Affiliation(s)
- C Lamprecht
- Institute of Biophysics, Johannes Kepler University, A-4020 Linz, Austria. Institute of Materials Science, Christian-Albrechts-University of Kiel, D-24114 Kiel, Germany
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70
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Braunger JA, Brückner BR, Nehls S, Pietuch A, Gerke V, Mey I, Janshoff A, Steinem C. Phosphatidylinositol 4,5-bisphosphate alters the number of attachment sites between ezrin and actin filaments: a colloidal probe study. J Biol Chem 2014; 289:9833-43. [PMID: 24500715 DOI: 10.1074/jbc.m113.530659] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Direct linkage between the plasma membrane and the actin cytoskeleton is controlled by the protein ezrin, a member of the ezrin-radixin-moesin protein family. To function as a membrane-cytoskeleton linker, ezrin needs to be activated in a process that involves binding of ezrin to phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphorylation of a conserved threonine residue. Here, we used colloidal probe microscopy to quantitatively analyze the interaction between ezrin and F-actin as a function of these activating factors. We show that the measured individual unbinding forces between ezrin and F-actin are independent of the activating parameters, in the range of approximately 50 piconewtons. However, the cumulative adhesion energy greatly increases in the presence of PIP2 demonstrating that a larger number of bonds between ezrin and F-actin has formed. In contrast, the phosphorylation state, represented by phosphor-mimetic mutants of ezrin, only plays a minor role in the activation process. These results are in line with in vivo experiments demonstrating that an increase in PIP2 concentration recruits more ezrin to the apical plasma membrane of polarized cells and significantly increases the membrane tension serving as a measure of the adhesion sites between the plasma membrane and the F-actin network.
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Affiliation(s)
- Julia A Braunger
- From the Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
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71
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Karsai Á, Kellermayer MSZ, Harris SP. Cross-species mechanical fingerprinting of cardiac myosin binding protein-C. Biophys J 2014; 104:2465-75. [PMID: 23746519 DOI: 10.1016/j.bpj.2013.04.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/19/2013] [Accepted: 04/08/2013] [Indexed: 01/22/2023] Open
Abstract
Cardiac myosin binding protein-C (cMyBP-C) is a member of the immunoglobulin (Ig) superfamily of proteins and consists of 8 Ig- and 3 fibronectin III (FNIII)-like domains along with a unique regulatory sequence referred to as the MyBP-C motif or M-domain. We previously used atomic force microscopy to investigate the mechanical properties of murine cMyBP-C expressed using a baculovirus/insect cell expression system. Here, we investigate whether the mechanical properties of cMyBP-C are conserved across species by using atomic force microscopy to manipulate recombinant human cMyBP-C and native cMyBP-C purified from bovine heart. Force versus extension data obtained in velocity-clamp experiments showed that the mechanical response of the human recombinant protein was remarkably similar to that of the bovine native cMyBP-C. Ig/Fn-like domain unfolding events occurred in a hierarchical fashion across a threefold range of forces starting at relatively low forces of ~50 pN and ending with the unfolding of the highest stability domains at ~180 pN. Force-extension traces were also frequently marked by the appearance of anomalous force drops suggestive of additional mechanical complexity such as structural coupling among domains. Both recombinant and native cMyBP-C exhibited a prominent segment ~100 nm-long that could be stretched by forces <50 pN before the unfolding of Ig- and FN-like domains. Combined with our previous observations of mouse cMyBP-C, these results establish that although the response of cMyBP-C to mechanical load displays a complex pattern, it is highly conserved across species.
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Affiliation(s)
- Árpád Karsai
- University of California - Davis, Davis, CA, USA
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72
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Mártonfalvi Z, Bianco P, Linari M, Caremani M, Nagy A, Lombardi V, Kellermayer M. Low-force transitions in single titin molecules reflect a memory of contractile history. J Cell Sci 2013; 127:858-70. [PMID: 24357719 DOI: 10.1242/jcs.138461] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Titin is a giant elastomeric muscle protein that has been suggested to function as a sensor of sarcomeric stress and strain, but the mechanisms by which it does so are unresolved. To gain insight into its mechanosensory function we manipulated single titin molecules with high-resolution optical tweezers. Discrete, step-wise transitions, with rates faster than canonical Ig domain unfolding occurred during stretch at forces as low as 5 pN. Multiple mechanisms and molecular regions (PEVK, proximal tandem-Ig, N2A) are likely to be involved. The pattern of transitions is sensitive to the history of contractile events. Monte-Carlo simulations of our experimental results predicted that structural transitions begin before the complete extension of the PEVK domain. High-resolution atomic force microscopy (AFM) supported this prediction. Addition of glutamate-rich PEVK domain fragments competitively inhibited the viscoelastic response in both single titin molecules and muscle fibers, indicating that PEVK domain interactions contribute significantly to sarcomere mechanics. Thus, under non-equilibrium conditions across the physiological force range, titin extends by a complex pattern of history-dependent discrete conformational transitions, which, by dynamically exposing ligand-binding sites, could set the stage for the biochemical sensing of the mechanical status of the sarcomere.
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Affiliation(s)
- Zsolt Mártonfalvi
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, Budapest, H1094 Hungary
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73
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Abstract
Playing a dominant role in many biochemical processes are the dynamic properties of molecular linkages; examples include cell adhesion, enzyme-catalyzed reactions, and molecular recognition by antibodies. Dynamic force spectroscopy, namely separating molecular bonds under external force ramps has rapidly become a powerful tool to study the rugged energy landscape of noncovalent ligand-receptor bonds. The picture shows a surface and tip-bound pair being pulled apart and the derived potential energy diagram.
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Affiliation(s)
- A Janshoff
- Institut für Physikalische Chemie, Johannes-Gutenberg Universität, 55128 Mainz, Germany.
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74
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Otten M, Wolf P, Gaub HE. Protein-DNA force assay in a microfluidic format. LAB ON A CHIP 2013; 13:4198-4204. [PMID: 23986395 DOI: 10.1039/c3lc50830g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The detailed study of protein-DNA interactions is a core effort to elucidate physiological processes, including gene regulation, DNA repair and the immune response. The molecular force assay (MFA) is an established method to study DNA-binding proteins. In particular, high-affinity binder dissociation is made possible by the application of force. Microfluidic lab-on-a-chip approaches have proven helpful for parallelization, small sample volumes, reproducibility, and low cost. We report the successful combination of these two principles, forming a microfluidic molecular force assay and representing a novel use for the established MITOMI chip design. We present, characterize, validate and apply this integrated method. An alternative confocal fluorescence microscopy readout and analysis method is introduced and validated. In a multiplexing application, EcoRI binding is detected and characterized. This method paves the way for quantitative on-chip force measurements. It is suited for integration with DNA micro-spotting and in vitro expression of transcription factors to form a high-throughput chip for detailed DNA-protein interaction studies.
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Affiliation(s)
- Marcus Otten
- Lehrstuhl für Angewandte Physik and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Amalienstrasse 54, 80799 Munich, Germany
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75
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Chung JW, Shin D, Kwak JM, Seog J. Direct force measurement of single DNA-peptide interactions using atomic force microscopy. J Mol Recognit 2013; 26:268-75. [PMID: 23595808 DOI: 10.1002/jmr.2269] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/24/2013] [Accepted: 02/01/2013] [Indexed: 11/10/2022]
Abstract
The selective interactions between DNA and miniature (39 residues) engineered peptide were directly measured at the single-molecule level by using atomic force microscopy. This peptide (p007) contains an α-helical recognition site similar to leucine zipper GCN4 and specifically recognizes the ATGAC sequence in the DNA with nanomolar affinity. The average rupture force was 42.1 pN, which is similar to the unbinding forces of the digoxigenin-antidigoxigenin complex, one of the strongest interactions in biological systems. The single linear fit of the rupture forces versus the logarithm of pulling rates showed a single energy barrier with a transition state located at 0.74 nm from the bound state. The smaller koff compared with that of other similar systems was presumably due to the increased stability of the helical structure by putative folding residues in p007. This strong sequence-specific DNA-peptide interaction has a potential to be utilized to prepare well-defined mechanically stable DNA-protein hybrid nanostructures.
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Affiliation(s)
- Ji W Chung
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
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76
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Roca-Cusachs P, Sunyer R, Trepat X. Mechanical guidance of cell migration: lessons from chemotaxis. Curr Opin Cell Biol 2013; 25:543-9. [DOI: 10.1016/j.ceb.2013.04.010] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 04/26/2013] [Indexed: 01/04/2023]
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77
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De Tommasi D, Millardi N, Puglisi G, Saccomandi G. An energetic model for macromolecules unfolding in stretching experiments. J R Soc Interface 2013; 10:20130651. [PMID: 24047874 DOI: 10.1098/rsif.2013.0651] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We propose a simple approach, based on the minimization of the total (entropic plus unfolding) energy of a two-state system, to describe the unfolding of multi-domain macromolecules (proteins, silks, polysaccharides, nanopolymers). The model is fully analytical and enlightens the role of the different energetic components regulating the unfolding evolution. As an explicit example, we compare the analytical results with a titin atomic force microscopy stretch-induced unfolding experiment showing the ability of the model to quantitatively reproduce the experimental behaviour. In the thermodynamic limit, the sawtooth force-elongation unfolding curve degenerates to a constant force unfolding plateau.
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Affiliation(s)
- D De Tommasi
- Dipartimento di Scienze dell' Ingegneria Civile e Architettura, Politecnico di Bari, Bari, Italy
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78
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Stangner T, Singer D, Wagner C, Gutsche C, Ueberschär O, Hoffmann R, Kremer F. FACS-sorted particles reduce the data variance in optical tweezers-assisted dynamic force spectroscopy measurements. Phys Biol 2013; 10:046004. [PMID: 23788010 DOI: 10.1088/1478-3975/10/4/046004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
By combining optical tweezers-assisted dynamic force spectroscopy experiments with fluorescence activated cell sorting (FACS), we demonstrate a new approach to reducing the data variance in measuring receptor-ligand interactions on a single molecule level by ensuring similar coating densities. Therefore, the carboxyfluorescein-labelled monophosphorylated peptide tau226-240[pThr231] is anchored on melamine resin beads and these beads are sorted by FACS to achieve a homogeneous surface coverage. To quantify the impact of the fluorescence dye on the bond parameters between the phosphorylated peptide and the corresponding phosphorylation specific anti-human tau monoclonal antibody HPT-104, we perform dynamic force spectroscopy and compare the results to data using unsorted beads covered with the non-fluorescence peptide analogue. Finally, we demonstrate that the data variance of the relative binding frequency is significantly decreased by a factor of 3.4 using pre-sorted colloids with a homogeneous ligand coating compared to using unsorted colloids.
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Affiliation(s)
- T Stangner
- Department of Experimental Physics I, Leipzig University, Linnéstraße 5, D-04103 Leipzig, Germany.
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79
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Olah MJ, Stefanovic D. Superdiffusive transport by multivalent molecular walkers moving under load. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:062713. [PMID: 23848721 DOI: 10.1103/physreve.87.062713] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 04/10/2013] [Indexed: 06/02/2023]
Abstract
We introduce a model for translational molecular motors to demonstrate that a multivalent catalytic walker with flexible, uncoordinated legs can transform the free energy of surface-bound substrate sites into mechanical work and undergo biased, superdiffusive motion, even in opposition to an external load force. The walker in the model lacks any inherent orientation of body or track, and its legs have no chemomechanical coupling other than the passive constraint imposed by their connection to a common body. Yet, under appropriate kinetic conditions, the walker's motion is biased in the direction of unvisited sites, which allows the walker to move nearly ballistically away from the origin as long as a local supply of unmodified substrate sites is available. The multivalent random walker model is mathematically formulated as a continuous-time Markov process and is studied numerically. We use Monte Carlo simulations to generate ensemble estimates of the mean squared displacement and mean work done for this nonergodic system. Our results show that a residence time bias between visited and unvisited sites leads to superdiffusive motion over significant times and distances. This mechanism can be used to adapt any enzyme-substrate system with appropriate kinetics for use as a functional chemical implementation of a molecular motor, without the need for structural anisotropy or conformationally mediated chemomechanical coordination.
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Affiliation(s)
- Mark J Olah
- Department of Computer Science, University of New Mexico, MSC01 1130, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, USA.
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80
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Peleg O, Savin T, Kolmakov GV, Salib IG, Balazs AC, Kröger M, Vogel V. Fibers with integrated mechanochemical switches: minimalistic design principles derived from fibronectin. Biophys J 2013. [PMID: 23199919 DOI: 10.1016/j.bpj.2012.09.028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Inspired by molecular mechanisms that cells exploit to sense mechanical forces and convert them into biochemical signals, chemists dream of designing mechanochemical switches integrated into materials. Using the adhesion protein fibronectin, whose multiple repeats essentially display distinct molecular recognition motifs, we derived a computational model to explain how minimalistic designs of repeats translate into the mechanical characteristics of their fibrillar assemblies. The hierarchy of repeat-unfolding within fibrils is controlled not only by their relative mechanical stabilities, as found for single molecules, but also by the strength of cryptic interactions between adjacent molecules that become activated by stretching. The force-induced exposure of cryptic sites furthermore regulates the nonlinearity of stress-strain curves, the strain at which such fibers break, and the refolding kinetics and fraction of misfolded repeats. Gaining such computational insights at the mesoscale is important because translating protein-based concepts into novel polymer designs has proven difficult.
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Affiliation(s)
- Orit Peleg
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
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81
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Groote R, Jakobs RTM, Sijbesma RP. Mechanocatalysis: forcing latent catalysts into action. Polym Chem 2013. [DOI: 10.1039/c3py00071k] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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82
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Galectin 3–β-galactobiose interactions. Carbohydr Polym 2013; 92:529-33. [DOI: 10.1016/j.carbpol.2012.08.104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 08/23/2012] [Accepted: 08/26/2012] [Indexed: 11/22/2022]
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83
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84
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Halperin A, Kröger M. Thermoresponsive cell culture substrates based on PNIPAM brushes functionalized with adhesion peptides: theoretical considerations of mechanism and design. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:16623-16637. [PMID: 23121235 DOI: 10.1021/la303443t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Thermoresponsive tissue culture substrates based on PNIPAM brushes are used to harvest confluent cell sheets for tissue engineering. The prospect of clinical use imposes the utilization of culture medium free of bovine serum, thus suggesting conjugation with adhesion peptides containing the RGD minimal recognition sequence. The optimum position of the RGD along the chain should ensure both cell adhesion at 37 °C and cell detachment at T(L) below the lower critical solution temperature of PNIPAM. Design guidelines are formulated from considerations of brush confinement by the cells: (i) Cell adhesion at 37 °C is controlled by the RGDs accessible without brush compression. (ii) Cell detachment at T(L) is driven by a disjoining force due to confinement of the swollen brush by cells retaining integrin-RGD bonds formed at 37 °C. These suggest placing the RGDs at the grafting surface or its vicinity. Randomly placed RGDs do not enable efficient detachment because a large fraction of the integrin-RGD bonds are not sufficiently tensioned at T(L), in line with experimental observations (Ebara, M.; Yamato, M.; Aoyagi, T.; Kikuchi, A.; Sakai, K.; Okano, T. Immobilization of celladhesive peptides to temperature-responsive surfaces facilitates both serum-free cell adhesion and noninvasive cell harvest. Tissue Eng. 2004, 10, 1125-1135). The theory framework enables analysis of culture media based on polymer brushes conjugated with adhesion peptides in general.
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Affiliation(s)
- Avraham Halperin
- University of Grenoble 1/CNRS, LIPhy UMR 5588, BP 87, 38041 Grenoble, France.
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85
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Chen B, Kemkemer R, Deibler M, Spatz J, Gao H. Cyclic stretch induces cell reorientation on substrates by destabilizing catch bonds in focal adhesions. PLoS One 2012; 7:e48346. [PMID: 23152769 PMCID: PMC3495948 DOI: 10.1371/journal.pone.0048346] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 09/24/2012] [Indexed: 01/13/2023] Open
Abstract
A minimal model of cellular mechanosensing system that consists of a single stress fiber adhering on a substrate via two focal adhesions made of catch bonds is adopted to investigate the phenomena of cell reorientation on substrates induced by an applied uniaxial cyclic stretch. The model indicates that the catch bonds in the focal adhesions experience a periodically oscillating internal force with amplitude and frequency controlled by two intrinsic clocks of the stress fiber, one associated with localized activation and the other with homogeneous activation of sarcomere units along the stress fiber. It is shown that this oscillating force due to cyclic stretch tends to destabilize focal adhesions by reducing the lifetime of catch bonds. The resulting slide or relocation of focal adhesions then causes the associated stress fiber to shorten and rotate to configurations nearly perpendicular to the stretching direction. These predicted behaviors from our model are consistent with a wide range of experimental observations.
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Affiliation(s)
- Bin Chen
- Department of Engineering Mechanics, Zhejiang University, Hangzhou, People's Republic of China
- Engineering Mechanics, Institute of High Performance Computing, A*STAR, Singapore, Singapore
| | - Ralf Kemkemer
- Max-Planck-Institute for Intelligent Systems, Department of New Materials and Biosystems, Stuttgart, Germany
| | - Martin Deibler
- Max-Planck-Institute for Intelligent Systems, Department of New Materials and Biosystems, Stuttgart, Germany
- Department of Biophysical Chemistry, University of Heidelberg, Heidelberg, Germany
| | - Joachim Spatz
- Max-Planck-Institute for Intelligent Systems, Department of New Materials and Biosystems, Stuttgart, Germany
- Department of Biophysical Chemistry, University of Heidelberg, Heidelberg, Germany
| | - Huajian Gao
- School of Engineering, Brown University, Providence, Rhode Island, United States of America
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86
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Severin PMD, Gaub HE. DNA-protein binding force chip. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:3269-3273. [PMID: 22887737 DOI: 10.1002/smll.201201088] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Indexed: 06/01/2023]
Affiliation(s)
- Philip M D Severin
- Lehrstuhl für Angewandte Physik and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Amalienstrasse 54, 80799 Munich, Germany
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87
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Valbuena A, Vera AM, Oroz J, Menéndez M, Carrión-Vázquez M. Mechanical properties of β-catenin revealed by single-molecule experiments. Biophys J 2012; 103:1744-52. [PMID: 23083718 DOI: 10.1016/j.bpj.2012.07.051] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 06/20/2012] [Accepted: 07/17/2012] [Indexed: 11/19/2022] Open
Abstract
β-catenin is a central component of the adaptor complex that links cadherins to the actin cytoskeleton in adherens junctions and thus, it is a good candidate to sense and transmit mechanical forces to trigger specific changes inside the cell. To fully understand its molecular physiology, we must first investigate its mechanical role in mechanotransduction within the cadherin system. We have studied the mechanical response of β-catenin to stretching using single-molecule force spectroscopy and molecular dynamics. Unlike most proteins analyzed to date, which have a fixed mechanical unfolding pathway, the β-catenin armadillo repeat region (ARM) displays low mechanostability and multiple alternative unfolding pathways that seem to be modulated by its unstructured termini. These results are supported by steered molecular dynamics simulations, which also predict its mechanical stabilization and unfolding pathway restrictions when the contiguous α-helix of the C-terminal unstructured region is included. Furthermore, simulations of the ARM/E-cadherin cytosolic tail complex emulating the most probable stress geometry occurring in vivo show a mechanical stabilization of the interaction whose magnitude correlates with the length of the stretch of the cadherin cytosolic tail that is in contact with the ARM region.
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Affiliation(s)
- Alejandro Valbuena
- Instituto Cajal/CSIC, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED) and IMDEA Nanociencia, Madrid, Spain
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88
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Lv C, Tan C, Qin M, Zou D, Cao Y, Wang W. Low folding cooperativity of HP35 revealed by single-molecule force spectroscopy and molecular dynamics simulation. Biophys J 2012; 102:1944-51. [PMID: 22768951 DOI: 10.1016/j.bpj.2012.03.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 03/08/2012] [Accepted: 03/14/2012] [Indexed: 10/28/2022] Open
Abstract
Some small proteins, such as HP35, fold at submicrosecond timescale with low folding cooperativity. Although these proteins have been extensively investigated, still relatively little is known about their folding mechanism. Here, using single-molecule force spectroscopy and steered molecule dynamics simulation, we study the unfolding of HP35 under external force. Our results show that HP35 unfolds at extremely low forces without a well-defined unfolding transition state. Subsequently, we probe the structure of unfolded HP35 using the persistence length obtained in the force spectroscopy. We found that the persistence length of unfolded HP35 is around 0.72 nm, >40% longer than typical unstructured proteins, suggesting that there are a significant amount of residual secondary structures in the unfolded HP35. Molecular dynamics simulation further confirmed this finding and revealed that many native contacts are preserved in HP35, even its two ends have been extended up to 8 nm. Our results therefore suggest that retaining a significant amount of secondary structures in the unfolded state of HP35 may be an efficient way to reduce the entropic cost for the formation of tertiary structure and increase the folding speed, although the folding cooperativity is compromised. Moreover, we anticipate that the methods we used in this work can be extended to the study of other proteins with complex folding behaviors and even intrinsically disordered ones.
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Affiliation(s)
- Chunmei Lv
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing, People's Republic of China
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89
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Direct observation of proteolytic cleavage at the S2 site upon forced unfolding of the Notch negative regulatory region. Proc Natl Acad Sci U S A 2012; 109:E2757-65. [PMID: 23011796 DOI: 10.1073/pnas.1205788109] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The conserved Notch signaling pathway plays crucial roles in developing and self-renewing tissues. Notch is activated upon ligand-induced conformation change of the Notch negative regulatory region (NRR) unmasking a key proteolytic site (S2) and facilitating downstream events. Thus far, the molecular mechanism of this signal activation is not defined. However, strong indirect evidence favors a model whereby transendocytosis of the Notch extracellular domain, in tight association with ligand into the ligand-bearing cell, exerts a force on the NRR to drive the required structure change. Here, we demonstrate that force applied to the human Notch2 NRR can indeed expose the S2 site and, crucially, allow cleavage by the metalloprotease TACE (TNF-alpha-converting enzyme). Molecular insight into this process is achieved using atomic force microscopy and molecular dynamics simulations on the human Notch2 NRR. The data show near-sequential unfolding of its constituent LNR (Lin12-Notch repeat) and HD (heterodimerization) domains, at forces similar to those observed for other protein domains with a load-bearing role. Exposure of the S2 site is the first force "barrier" on the unfolding pathway, occurring prior to unfolding of any domain, and achieved via removal of the LNRAB linker region from the HD domain. Metal ions increase the resistance of the Notch2 NRR to forced unfolding, their removal clearly facilitating unfolding at lower forces. The results provide direct demonstration of force-mediated exposure and cleavage of the Notch S2 site and thus firmly establish the feasibility of a mechanotransduction mechanism for ligand-induced Notch activation.
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90
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Torun H, Finkler O, Degertekin FL. Atomic force microscope based biomolecular force-clamp measurements using a micromachined electrostatic actuator. Ultramicroscopy 2012; 122:26-31. [PMID: 22960003 DOI: 10.1016/j.ultramic.2012.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 05/18/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
Abstract
The authors describe a method for biomolecular force clamp measurements using atomic force microscope (AFM) cantilevers and micromachined membrane-based electrostatic actuators. The actuators comprise of Parylene membranes with embedded side actuation electrodes and are fabricated on a silicon substrate. The devices have a displacement range of 1.8 μm with 200 V actuation voltage, and displacement uncertainty is 0.8 nm, including the noise and drift. The settling time, limited by the particular amplifier is 5 ms, with an inherent range down to 20 μs. A force clamp measurement setup using these actuators in a feedback loop has been used to measure bond life-times between human IgG and anti-human IgG molecules to demonstrate the feasibility of this method for biological experiments. The experimental findings are compared with a molecular pulling experiment and the results are found to be in good agreement.
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Affiliation(s)
- Hamdi Torun
- Department of Electrical and Electronics Engineering, Bogazici University, Bebek, TR-34342 Istanbul, Turkey.
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91
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Kusumi A, Fujiwara TK, Chadda R, Xie M, Tsunoyama TA, Kalay Z, Kasai RS, Suzuki KGN. Dynamic organizing principles of the plasma membrane that regulate signal transduction: commemorating the fortieth anniversary of Singer and Nicolson's fluid-mosaic model. Annu Rev Cell Dev Biol 2012; 28:215-50. [PMID: 22905956 DOI: 10.1146/annurev-cellbio-100809-151736] [Citation(s) in RCA: 284] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The recent rapid accumulation of knowledge on the dynamics and structure of the plasma membrane has prompted major modifications of the textbook fluid-mosaic model. However, because the new data have been obtained in a variety of research contexts using various biological paradigms, the impact of the critical conceptual modifications on biomedical research and development has been limited. In this review, we try to synthesize our current biological, chemical, and physical knowledge about the plasma membrane to provide new fundamental organizing principles of this structure that underlie every molecular mechanism that realizes its functions. Special attention is paid to signal transduction function and the dynamic aspect of the organizing principles. We propose that the cooperative action of the hierarchical three-tiered mesoscale (2-300 nm) domains--actin-membrane-skeleton induced compartments (40-300 nm), raft domains (2-20 nm), and dynamic protein complex domains (3-10 nm)--is critical for membrane function and distinguishes the plasma membrane from a classical Singer-Nicolson-type model.
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Affiliation(s)
- Akihiro Kusumi
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8507, Japan.
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92
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Roca-Cusachs P, Iskratsch T, Sheetz MP. Finding the weakest link: exploring integrin-mediated mechanical molecular pathways. J Cell Sci 2012; 125:3025-38. [PMID: 22797926 DOI: 10.1242/jcs.095794] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
From the extracellular matrix to the cytoskeleton, a network of molecular links connects cells to their environment. Molecules in this network transmit and detect mechanical forces, which subsequently determine cell behavior and fate. Here, we reconstruct the mechanical pathway followed by these forces. From matrix proteins to actin through integrins and adaptor proteins, we review how forces affect the lifetime of bonds and stretch or alter the conformation of proteins, and how these mechanical changes are converted into biochemical signals in mechanotransduction events. We evaluate which of the proteins in the network can participate in mechanotransduction and which are simply responsible for transmitting forces in a dynamic network. Besides their individual properties, we also analyze how the mechanical responses of a protein are determined by their serial connections from the matrix to actin, their parallel connections in integrin clusters and by the rate at which force is applied to them. All these define mechanical molecular pathways in cells, which are emerging as key regulators of cell function alongside better studied biochemical pathways.
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Affiliation(s)
- Pere Roca-Cusachs
- University of Barcelona and Institute for Bioengineering of Catalonia, Barcelona, Spain.
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93
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Han X, Qin M, Pan H, Cao Y, Wang W. A versatile "multiple fishhooks" approach for the study of ligand-receptor interactions using single-molecule atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:10020-10025. [PMID: 22690829 DOI: 10.1021/la301903z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Despite the powerfulness of atomic force microscopy (AFM)-based single-molecule force spectroscopy in the study of ligand-receptor interactions, complicated cantilever functionalization and data interpretation have often been a great hurdle for its widespread application. Here, we present a much simplified experimental scheme by using a "multiple fishhooks" approach. In this strategy, multiple ligands are labeled on a single polymer chain, which forms complexes with receptors anchored on the substrate surface. Therefore, multiple single-bond rupture events can be captured in the same force-extension curves, similar to the widely used polyprotein approach. This method also allows nonsingle-molecule events and nonspecific interactions between cantilever and surface to be readily excluded from real data pool and greatly increases the quality and quantity of single-molecule data. The biggest advantage of our approach over the previously reported one is the choice of a naturally occurring polysaccharide, hyaluronan, the conformation of which in solution can be fine-tuned by pH, as the polymer backbone of the "multiple fishhooks" handle. Furthermore, our approach greatly simplifies the chemical synthesis of the polymer handle, allowing bioactive molecules to be easily one-step labeled on the handles in aqueous solution. We validate this strategy using the widely studied streptavidin-biotin system, and our single-molecule AFM results are in good agreement with previously reported ones. We anticipate that this novel strategy can be used as a versatile tool to study other complex and challenging ligand-receptor interactions.
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Affiliation(s)
- Xiaotian Han
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, Jiangsu, People's Republic of China
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94
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Anti-Arrhenius cleavage of covalent bonds in bottlebrush macromolecules on substrate. Proc Natl Acad Sci U S A 2012; 109:9276-80. [PMID: 22645366 DOI: 10.1073/pnas.1118517109] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Spontaneous degradation of bottlebrush macromolecules on aqueous substrates was monitored by atomic force microscopy. Scission of C ─ C covalent bonds in the brush backbone occurred due to steric repulsion between the adsorbed side chains, which generated bond tension on the order of several nano-Newtons. Unlike conventional chemical reactions, the rate of bond scission was shown to decrease with temperature. This apparent anti-Arrhenius behavior was caused by a decrease in the surface energy of the underlying substrate upon heating, which results in a corresponding decrease of bond tension in the adsorbed macromolecules. Even though the tension dropped minimally from 2.16 to 1.89 nN, this was sufficient to overpower the increase in the thermal energy (k(B)T) in the Arrhenius equation. The rate constant of the bond-scission reaction was measured as a function of temperature and surface energy. Fitting the experimental data by a perturbed Morse potential V = V(0)(1 - e(-βx))(2) - fx, we determined the depth and width of the potential to be V(0) = 141 ± 19 kJ/mol and β(-1) = 0.18 ± 0.03 Å, respectively. Whereas the V(0) value is in reasonable agreement with the activation energy E(a) = 80-220 kJ/mol of mechanical and thermal degradation of organic polymers, it is significantly lower than the dissociation energy of a C ─ C bond D(e) = 350 kJ/mol. Moreover, the force constant K(x) = 2β(2)V(0) = 1.45 ± 0.36 kN/m of a strained bottlebrush along its backbone is markedly larger than the force constant of a C ─ C bond K(l) = 0.44 kN/m, which is attributed to additional stiffness due to deformation of the side chains.
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95
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Exploring the Energy Profile of Human IgG/Rat Anti-human IgG Interactions by Dynamic Force Spectroscopy. Protein J 2012; 31:425-31. [DOI: 10.1007/s10930-012-9419-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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96
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Song B, Schönherr H. Atomic Force Microscopy Measurements of Supramolecular Interactions. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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97
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Oroz J, Hervás R, Carrión-Vázquez M. Unequivocal single-molecule force spectroscopy of proteins by AFM using pFS vectors. Biophys J 2012; 102:682-90. [PMID: 22325292 DOI: 10.1016/j.bpj.2011.12.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 11/28/2011] [Accepted: 12/12/2011] [Indexed: 11/28/2022] Open
Abstract
Nanomechanical analysis of proteins by single-molecule force spectroscopy based on atomic force microscopy is increasingly being used to investigate the inner workings of mechanical proteins and substrate proteins of unfoldase machines as well as to gain new insight into the process of protein folding. However, such studies are hindered by a number of technical problems, including the noise of the proximal region, ambiguous single-molecule identification, as well as difficulties in protein expression/folding and full-length purification. To overcome these major drawbacks in protein nanomechanics, we designed a family of cloning/expression vectors, termed pFS (plasmid for force spectroscopy), that essentially has an unstructured region to surmount the noisy proximal region, a homomeric polyprotein marker, a carrier to mechanically protect the protein of interest (only the pFS-2 version) that also acts as a reporter, and two purification tags. pFS-2 enables the unambiguous analysis of proteins with low mechanical stability or/and complex force spectra, such as the increasingly abundant class of intrinsically disordered proteins, which are hard to characterize by traditional bulk techniques and have important biological and clinical implications. The advantages, applications, and potential of this ready-to-go system are illustrated through the analysis of representative proteins.
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Affiliation(s)
- Javier Oroz
- Instituto Cajal/CSIC, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, IMDEA Nanociencia, Madrid, Spain
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98
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Stahl SW, Puchner EM, Alexandrovich A, Gautel M, Gaub HE. A conditional gating mechanism assures the integrity of the molecular force-sensor titin kinase. Biophys J 2012; 101:1978-86. [PMID: 22004752 DOI: 10.1016/j.bpj.2011.09.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 08/11/2011] [Accepted: 09/06/2011] [Indexed: 12/16/2022] Open
Abstract
As more and more recent investigations point out, force plays an important role in cellular regulation mechanisms. Biological responses to mechanical stress are often based on force-induced conformational changes of single molecules. The force sensor, titin kinase, is involved in a signaling complex that regulates protein turnover and transcriptional adaptation in striated muscle. The structural architecture of such a force sensor determines its response to force and must assure both activity and mechanical integrity, which are prerequisites for its function. Here, we use single-molecule force-clamp spectroscopy to show that titin kinase is organized in such a way that the regulatory domains have to unfold before secondary structure elements that determine the overall fold and catalytic function. The stepwise unfolding over many barriers with a topologically determined sequence assures that the protein can react to force by conformational changes while maintaining its structural integrity.
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Affiliation(s)
- Stefan W Stahl
- Center for NanoScience, Ludwig-Maximilians-University Munich, Munich, Germany
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99
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Kusumi A, Fujiwara TK, Morone N, Yoshida KJ, Chadda R, Xie M, Kasai RS, Suzuki KGN. Membrane mechanisms for signal transduction: the coupling of the meso-scale raft domains to membrane-skeleton-induced compartments and dynamic protein complexes. Semin Cell Dev Biol 2012; 23:126-44. [PMID: 22309841 DOI: 10.1016/j.semcdb.2012.01.018] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 01/24/2012] [Indexed: 01/09/2023]
Abstract
Virtually all biological membranes on earth share the basic structure of a two-dimensional liquid. Such universality and peculiarity are comparable to those of the double helical structure of DNA, strongly suggesting the possibility that the fundamental mechanisms for the various functions of the plasma membrane could essentially be understood by a set of simple organizing principles, developed during the course of evolution. As an initial effort toward the development of such understanding, in this review, we present the concept of the cooperative action of the hierarchical three-tiered meso-scale (2-300 nm) domains in the plasma membrane: (1) actin membrane-skeleton-induced compartments (40-300 nm), (2) raft domains (2-20 nm), and (3) dynamic protein complex domains (3-10nm). Special attention is paid to the concept of meso-scale domains, where both thermal fluctuations and weak cooperativity play critical roles, and the coupling of the raft domains to the membrane-skeleton-induced compartments as well as dynamic protein complexes. The three-tiered meso-domain architecture of the plasma membrane provides an excellent perspective for understanding the membrane mechanisms of signal transduction.
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Affiliation(s)
- Akihiro Kusumi
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8507, Japan.
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100
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Taninaka A, Hirano Y, Takeuchi O, Shigekawa H. Force measurement enabling precise analysis by dynamic force spectroscopy. Int J Mol Sci 2011; 13:453-65. [PMID: 22312263 PMCID: PMC3269697 DOI: 10.3390/ijms13010453] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 12/20/2011] [Indexed: 01/12/2023] Open
Abstract
Dynamic force spectroscopy (DFS) makes it possible to investigate specific interactions between two molecules such as ligand-receptor pairs at the single-molecule level. In the DFS method based on the Bell-Evans model, the unbinding force applied to a molecular bond is increased at a constant rate, and the force required to rupture the molecular bond is measured. By analyzing the relationship between the modal rupture force and the logarithm of the loading rate, microscopic potential barrier landscapes and the lifetimes of bonds can be obtained. However, the results obtained, for example, in the case of streptavidin/biotin complexes, have differed among previous studies and some results have been inconsistent with theoretical predictions. In this study, using an atomic force microscopy technique that enables the precise analysis of molecular interactions on the basis of DFS, we investigated the effect of the sampling rate on DFS analysis. The shape of rupture force histograms, for example, was significantly deformed at a sampling rate of 1 kHz in comparison with that of histograms obtained at 100 kHz, indicating the fundamental importance of ensuring suitable experimental conditions for further advances in the DFS method.
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Affiliation(s)
- Atsushi Taninaka
- Institute of Applied Physics, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8573, Japan; E-Mails: (A.T.); (Y.H.); (O.T.)
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