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Sun H, Guo Z, Hong H, Zhang Z, Zhang Y, Wang Y, Le S, Chen H. Free Energy Landscape of Type III Fibronectin Domain with Identified Intermediate State and Hierarchical Symmetry. PHYSICAL REVIEW LETTERS 2023; 131:218402. [PMID: 38072617 DOI: 10.1103/physrevlett.131.218402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 10/23/2023] [Indexed: 12/18/2023]
Abstract
The tenth domain of type III fibronectin (FNIII_{10}) mediates cell adhesion to the extracellular matrix. Despite its structural similarity to immunoglobulin domains, FNIII_{10} exhibits unique unfolding behaviors. We employed magnetic tweezers to investigate the unfolding and folding dynamics of FNIII_{10} under physiological forces (4-50 pN). Our results showed that FNIII_{10} follows a consistent transition pathway with an intermediate state characterized by detached A and G β strands. We determined the folding free energies and all force-dependent transition rates of FNIII_{10} and found that both unfolding rates from the native state to the intermediate state and from the intermediate state to the unfolded state deviate from Bell's model. We constructed a quantitative free energy landscape with well-defined traps and barriers that exhibits a hierarchical symmetrical pattern. Our findings provide a comprehensive understanding of FNIII_{10} conformational dynamics and demonstrate how free energy landscape of multistate biomolecules can be precisely mapped, illuminating the relationship between thermal stability, intermediate states, and folding rates in protein folding.
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Affiliation(s)
- Hao Sun
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Zilong Guo
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Haiyan Hong
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
| | - Zhuwei Zhang
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Yuhang Zhang
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
| | - Yang Wang
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Shimin Le
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
| | - Hu Chen
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
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2
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Chen G, Wang H, Bumba L, Masin J, Sebo P, Li H. The adenylate cyclase toxin RTX domain follows a series templated folding mechanism with implications for toxin activity. J Biol Chem 2023; 299:105150. [PMID: 37567473 PMCID: PMC10511787 DOI: 10.1016/j.jbc.2023.105150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023] Open
Abstract
Folding of the Repeats-in-toxin (RTX) domain of the bacterial adenylate cyclase toxin-hemolysin (CyaA) is critical to its toxin activities and the virulence of the whooping cough agent Bordetella pertussis. The RTX domain (RD) contains five RTX blocks (RTX-i to RTX-v) and their folding is driven by the binding of calcium. However, the detailed molecular mechanism via which the folding signal transmits within the five RTX blocks remains unknown. By combining single molecule optical tweezers, protein engineering, and toxin activity assays, here we demonstrate that the folding of the RD follows a strict hierarchy, with the folding starting from its C-terminal block RTX-v and proceeding towards the N-terminal RTX-i block sequentially. Our results reveal a strict series, templated folding mechanism, where the folding signal is transmitted along the RD in a series fashion from its C terminus continuously to the N terminus. Due to the series nature of this folding signal transmission pathway, the folding of RD can be disrupted at any given RTX block, rendering the RTX blocks located N-terminally to the disruption site and the acylation region of CyaA unfolded and abolishing CyaA's toxin activities. Our results reveal key mechanistic insights into the secretion and folding process of CyaA and may open up new potential avenues towards designing new therapeutics to abolish toxin activity of CyaA and combat B. pertussis.
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Affiliation(s)
- Guojun Chen
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Han Wang
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ladislav Bumba
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Prague, Czech Republic
| | - Jiri Masin
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Prague, Czech Republic
| | - Peter Sebo
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Prague, Czech Republic
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
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3
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Goult BT, von Essen M, Hytönen VP. The mechanical cell - the role of force dependencies in synchronising protein interaction networks. J Cell Sci 2022; 135:283155. [PMID: 36398718 PMCID: PMC9845749 DOI: 10.1242/jcs.259769] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The role of mechanical signals in the proper functioning of organisms is increasingly recognised, and every cell senses physical forces and responds to them. These forces are generated both from outside the cell or via the sophisticated force-generation machinery of the cell, the cytoskeleton. All regions of the cell are connected via mechanical linkages, enabling the whole cell to function as a mechanical system. In this Review, we define some of the key concepts of how this machinery functions, highlighting the critical requirement for mechanosensory proteins, and conceptualise the coupling of mechanical linkages to mechanochemical switches that enables forces to be converted into biological signals. These mechanical couplings provide a mechanism for how mechanical crosstalk might coordinate the entire cell, its neighbours, extending into whole collections of cells, in tissues and in organs, and ultimately in the coordination and operation of entire organisms. Consequently, many diseases manifest through defects in this machinery, which we map onto schematics of the mechanical linkages within a cell. This mapping approach paves the way for the identification of additional linkages between mechanosignalling pathways and so might identify treatments for diseases, where mechanical connections are affected by mutations or where individual force-regulated components are defective.
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Affiliation(s)
- Benjamin T. Goult
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK,Authors for correspondence (; )
| | - Magdaléna von Essen
- Faculty of Medicine and Health Technology, Tampere University, FI-33100 Tampere, Finland
| | - Vesa P. Hytönen
- Faculty of Medicine and Health Technology, Tampere University, FI-33100 Tampere, Finland,Fimlab Laboratories, FI-33520 Tampere, Finland,Authors for correspondence (; )
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4
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Ferenczy GG, Kellermayer M. Contribution of Hydrophobic Interactions to Protein Mechanical Stability. Comput Struct Biotechnol J 2022; 20:1946-1956. [PMID: 35521554 PMCID: PMC9062142 DOI: 10.1016/j.csbj.2022.04.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 04/07/2022] [Accepted: 04/17/2022] [Indexed: 11/26/2022] Open
Abstract
The role of hydrophobic and polar interactions in providing thermodynamic stability to folded proteins has been intensively studied, but the relative contribution of these interactions to the mechanical stability is less explored. We used steered molecular dynamics simulations with constant-velocity pulling to generate force-extension curves of selected protein domains and monitor hydrophobic surface unravelling upon extension. Hydrophobic contribution was found to vary between one fifth and one third of the total force while the rest of the contribution is attributed primarily to hydrogen bonds. Moreover, hydrophobic force peaks were shifted towards larger protein extensions with respect to the force peaks attributed to hydrogen bonds. The higher importance of hydrogen bonds compared to hydrophobic interactions in providing mechanical resistance is in contrast with the relative importance of the hydrophobic interactions in providing thermodynamic stability of proteins. The different contributions of these interactions to the mechanical stability are explained by the steeper free energy dependence of hydrogen bonds compared to hydrophobic interactions on the relative positions of interacting atoms. Comparative analyses for several protein domains revealed that the variation of hydrophobic forces is modest, while the contribution of hydrogen bonds to the force peaks becomes increasingly important for mechanically resistant protein domains.
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Alegre-Cebollada J. Protein nanomechanics in biological context. Biophys Rev 2021; 13:435-454. [PMID: 34466164 PMCID: PMC8355295 DOI: 10.1007/s12551-021-00822-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/05/2021] [Indexed: 12/20/2022] Open
Abstract
How proteins respond to pulling forces, or protein nanomechanics, is a key contributor to the form and function of biological systems. Indeed, the conventional view that proteins are able to diffuse in solution does not apply to the many polypeptides that are anchored to rigid supramolecular structures. These tethered proteins typically have important mechanical roles that enable cells to generate, sense, and transduce mechanical forces. To fully comprehend the interplay between mechanical forces and biology, we must understand how protein nanomechanics emerge in living matter. This endeavor is definitely challenging and only recently has it started to appear tractable. Here, I introduce the main in vitro single-molecule biophysics methods that have been instrumental to investigate protein nanomechanics over the last 2 decades. Then, I present the contemporary view on how mechanical force shapes the free energy of tethered proteins, as well as the effect of biological factors such as post-translational modifications and mutations. To illustrate the contribution of protein nanomechanics to biological function, I review current knowledge on the mechanobiology of selected muscle and cell adhesion proteins including titin, talin, and bacterial pilins. Finally, I discuss emerging methods to modulate protein nanomechanics in living matter, for instance by inducing specific mechanical loss-of-function (mLOF). By interrogating biological systems in a causative manner, these new tools can contribute to further place protein nanomechanics in a biological context.
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Arora N, Hazra JP, Rakshit S. Anisotropy in mechanical unfolding of protein upon partner-assisted pulling and handle-assisted pulling. Commun Biol 2021; 4:925. [PMID: 34326473 PMCID: PMC8322310 DOI: 10.1038/s42003-021-02445-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023] Open
Abstract
Proteins as force-sensors respond to mechanical cues and regulate signaling in physiology. Proteins commonly connect the source and response points of mechanical cues in two conformations, independent proteins in end-to-end geometry and protein complexes in handshake geometry. The force-responsive property of independent proteins in end-to-end geometry is studied extensively using single-molecule force spectroscopy (SMFS). The physiological significance of the complex conformations in force-sensing is often disregarded as mere surge protectors. However, with the potential of force-steering, protein complexes possess a distinct mechano-responsive property over individual force-sensors. To decipher, we choose a force-sensing protein, cadherin-23, from tip-link complex and perform SMFS using end-to-end geometry and handshake complex geometry. We measure higher force-resilience of cadherin-23 with preferential shorter extensions in handshake mode of pulling over the direct mode. The handshake geometry drives the force-response of cadherin-23 through different potential-energy landscapes than direct pulling. Analysis of the dynamic network structure of cadherin-23 under tension indicates narrow force-distributions among residues in cadherin-23 in direct pulling, resulting in low force-dissipation paths and low resilience to force. Overall, the distinct and superior mechanical responses of cadherin-23 in handshake geometry than single protein geometry highlight a probable evolutionary drive of protein-protein complexes as force-conveyors over independent ones.
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Affiliation(s)
- Nisha Arora
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
| | - Jagadish Prasad Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
| | - Sabyasachi Rakshit
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
- Centre for Protein Science Design and Engineering, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
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7
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Probing fibronectin adsorption on chemically defined surfaces by means of single molecule force microscopy. Sci Rep 2020; 10:15662. [PMID: 32973270 PMCID: PMC7518417 DOI: 10.1038/s41598-020-72617-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/02/2020] [Indexed: 12/18/2022] Open
Abstract
Atomic force microscope (AFM) based single molecule force spectroscopy (SMFS) and a quartz crystal microbalance (QCM) were respectively employed to probe interfacial characteristics of fibronectin fragment FNIII8–14 and full-length fibronectin (FN) on CH3–, OH–, COOH–, and NH2-terminated alkane-thiol self-assembled monolayers (SAMs). Force-distance curves acquired between hexahistidine-tagged FNIII8–14 immobilised on trisNTA-Ni2+ functionalized AFM cantilevers and the OH and COOH SAM surfaces were predominantly ‘loop-like’ (76% and 94% respectively), suggesting domain unfolding and preference for ‘end-on’ oriented binding, while those generated with NH2 and CH3 SAMs were largely ‘mixed type’ (81% and 86%, respectively) commensurate with unravelling and desorption, and ‘side-on’ binding. Time-dependent binding of FN to SAM-coated QCM crystals occurred in at least two phases: initial rapid coverage over the first 5 min; and variably diminishing adsorption thereafter (5–70 min). Loading profiles and the final hydrated surface concentrations reached (~ 950, ~ 1200, ~ 1400, ~ 1500 ng cm−2 for CH3, OH, COOH and NH2 SAMs) were consistent with: space-filling ‘side-on’ orientation and unfolding on CH3 SAM; greater numbers of FN molecules arranged ‘end-on’ on OH and especially COOH SAMs; and initial ‘side-on’ contact, followed by either (1) gradual tilting to a space-saving ‘end-on’ configuration, or (2) bi-/multi-layer adsorption on NH2 SAM.
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8
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Yang B, Liu Z, Liu H, Nash MA. Next Generation Methods for Single-Molecule Force Spectroscopy on Polyproteins and Receptor-Ligand Complexes. Front Mol Biosci 2020; 7:85. [PMID: 32509800 PMCID: PMC7248566 DOI: 10.3389/fmolb.2020.00085] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/16/2020] [Indexed: 12/31/2022] Open
Abstract
Single-molecule force spectroscopy with the atomic force microscope provides molecular level insights into protein function, allowing researchers to reconstruct energy landscapes and understand functional mechanisms in biology. With steadily advancing methods, this technique has greatly accelerated our understanding of force transduction, mechanical deformation, and mechanostability within single- and multi-domain polyproteins, and receptor-ligand complexes. In this focused review, we summarize the state of the art in terms of methodology and highlight recent methodological improvements for AFM-SMFS experiments, including developments in surface chemistry, considerations for protein engineering, as well as theory and algorithms for data analysis. We hope that by condensing and disseminating these methods, they can assist the community in improving data yield, reliability, and throughput and thereby enhance the information that researchers can extract from such experiments. These leading edge methods for AFM-SMFS will serve as a groundwork for researchers cognizant of its current limitations who seek to improve the technique in the future for in-depth studies of molecular biomechanics.
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Affiliation(s)
- Byeongseon Yang
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Zhaowei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Haipei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michael A. Nash
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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9
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Nasif AO, Mahfuz MU. Spatial Nanomechanical Communications Based on State Transitions. IEEE Trans Nanobioscience 2020; 19:457-467. [PMID: 32287001 DOI: 10.1109/tnb.2020.2986299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this paper, we present a novel framework of a nanomechanical communication (NMC) system where nanomechanical (NM) systems can communicate using mechanical movements to encode and transfer information between a transmitter (TX) nanomachine and a receiver (RX) nanomachine. First, some unique features of the envisioned NMC system have been presented in contrast to traditional communications systems. It is demonstrated that the encoding of distinct repeatable movements or motions is the key to information transfer in an NMC system. Using a state transition framework, we identify rest states (RSs) and motional degrees of freedom (MDoF) as the two essential concepts that determine the transmission rate of an NMC system in the spatial domain in two different modes, namely, synchronous and asynchronous transmissions. While the synchronous transmission is found to achieve much higher transmission rate compared to the asynchronous transmission in the noise-free case, the asynchronous mode is less restrictive and may have wider applicability. A stochastic model is considered to incorporate the influence of thermal noise in the system. A closed-form expression of the symbol error rate (SER) and its bounds have been derived for a particular symbol of a synchronous sliding motion NMC system with MDoF = 2. Numerical results show a promising SER performance in support of developing an NMC system model for nanoscale communications networks.
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10
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Distinct mechanical properties in homologous spectrin-like repeats of utrophin. Sci Rep 2019; 9:5210. [PMID: 30914715 PMCID: PMC6435810 DOI: 10.1038/s41598-019-41569-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 03/12/2019] [Indexed: 11/09/2022] Open
Abstract
Patients with Duchenne muscular dystrophy (DMD) lack the protein dystrophin, which is a critical molecular component of the dystrophin-glycoprotein complex (DGC). Dystrophin is hypothesized to function as a molecular shock absorber that mechanically stabilizes the sarcolemma of striated muscle through interaction with the cortical actin cytoskeleton via its N-terminal half and with the transmembrane protein β-dystroglycan via its C-terminal region. Utrophin is a fetal homologue of dystrophin that can subserve many dystrophin functions and is therefore under active investigation as a dystrophin replacement therapy for DMD. Here, we report the first mechanical characterization of utrophin using atomic force microscopy (AFM). Our data indicate that the mechanical properties of spectrin-like repeats in utrophin are more in line with the PEVK and Ig-like repeats of titin rather than those reported for repeats in spectrin or dystrophin. Moreover, we measured markedly different unfolding characteristics for spectrin repeats within the N-terminal actin-binding half of utrophin compared to those in the C-terminal dystroglycan-binding half, even though they exhibit identical thermal denaturation profiles. Our results demonstrate dramatic differences in the mechanical properties of structurally homologous utrophin constructs and suggest that utrophin may function as a stiff elastic element in series with titin at the myotendinous junction.
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Nadler H, Shaulov L, Blitsman Y, Mordechai M, Jopp J, Sal-Man N, Berkovich R. Deciphering the Mechanical Properties of Type III Secretion System EspA Protein by Single Molecule Force Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:6261-6270. [PMID: 29726683 DOI: 10.1021/acs.langmuir.8b01198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bacterial pathogens inject virulence factors into host cells during bacterial infections using type III secretion systems. In enteropathogenic Escherichia coli, this system contains an external filament, formed by a self-oligomerizing protein called E. coli secreted protein A (EspA). The EspA filament penetrates the thick viscous mucus layer to facilitate the attachment of the bacteria to the gut-epithelium. To do that, the EspA filament requires noteworthy mechanical endurance considering the mechanical shear stresses found within the intestinal tract. To date, the mechanical properties of the EspA filament and the structural and biophysical knowledge of monomeric EspA are very limited, mostly due to the strong tendency of the protein to self-oligomerize. To overcome this limitation, we employed a single molecule force spectroscopy (SMFS) technique and studied the mechanical properties of EspA. Force extension dynamic of (I91)4-EspA-(I91)4 chimera revealed two structural unfolding events occurring at low forces during EspA unfolding, thus indicating no unique mechanical stability of the monomeric protein. SMFS examination of purified monomeric EspA protein, treated by a gradually refolding protocol, exhibited similar mechanical properties as the EspA protein within the (I91)4-EspA-(I91)4 chimera. Overall, our results suggest that the mechanical integrity of the EspA filament likely originates from the interactions between EspA monomers and not from the strength of an individual monomer.
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Affiliation(s)
- Hila Nadler
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Lihi Shaulov
- Department of Microbiology, Immunology and Genetics , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Yossi Blitsman
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Moran Mordechai
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Jürgen Jopp
- The Ilse Katz Institute for Nanoscale Science and Technology , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Neta Sal-Man
- Department of Microbiology, Immunology and Genetics , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Ronen Berkovich
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
- The Ilse Katz Institute for Nanoscale Science and Technology , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
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13
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Valle‐Orero J, Rivas‐Pardo JA, Tapia‐Rojo R, Popa I, Echelman DJ, Haldar S, Fernández JM. Mechanical Deformation Accelerates Protein Ageing. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703630] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | | | - Rafael Tapia‐Rojo
- Department of Biological Sciences Columbia University New York NY 10027 USA
| | - Ionel Popa
- Department of Biological Sciences Columbia University New York NY 10027 USA
- Current address: Department of Physics University of Wisconsin Milwaukee WI 53211 USA
| | - Daniel J. Echelman
- Department of Biological Sciences Columbia University New York NY 10027 USA
| | - Shubhasis Haldar
- Department of Biological Sciences Columbia University New York NY 10027 USA
| | - Julio M. Fernández
- Department of Biological Sciences Columbia University New York NY 10027 USA
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14
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Valle-Orero J, Tapia-Rojo R, Eckels EC, Rivas-Pardo JA, Popa I, Fernández JM. Proteins Breaking Bad: A Free Energy Perspective. J Phys Chem Lett 2017; 8:3642-3647. [PMID: 28723106 PMCID: PMC5957541 DOI: 10.1021/acs.jpclett.7b01509] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Protein aging may manifest as a mechanical disease that compromises tissue elasticity. As proved recently, while proteins respond to changes in force with an instantaneous elastic recoil followed by a folding contraction, aged proteins break bad, becoming unstructured polymers. Here, we explain this phenomenon in the context of a free energy model, predicting the changes in the folding landscape of proteins upon oxidative aging. Our findings validate that protein folding under force is constituted by two separable components, polymer properties and hydrophobic collapse, and demonstrate that the latter becomes irreversibly blocked by oxidative damage. We run Brownian dynamics simulations on the landscape of protein L octamer, reproducing all experimental observables, for a naive and damaged polyprotein. This work provides a unique tool to understand the evolving free energy landscape of elastic proteins upon physiological changes, opening new perspectives to predict age-related diseases in tissues.
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15
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Cao L, Nicosia J, Larouche J, Zhang Y, Bachman H, Brown AC, Holmgren L, Barker TH. Detection of an Integrin-Binding Mechanoswitch within Fibronectin during Tissue Formation and Fibrosis. ACS NANO 2017; 11:7110-7117. [PMID: 28699736 PMCID: PMC5842356 DOI: 10.1021/acsnano.7b02755] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Fibronectin (Fn) is an extracellular matrix protein that orchestrates complex cell adhesion and signaling through cell surface integrin receptors during tissue development, remodeling, and disease, such as fibrosis. Fn is sensitive to mechanical forces in its tandem type III repeats, resulting in extensive molecular enlongation. As such, it has long been hypothesized that cell- and tissue-derived forces may activate an "integrin switch" within the critical integrin-binding ninth and 10th type III repeats-conferring differential integrin-binding specificity, leading to differential cell responses. Yet, no direct evidence exists to prove the hypothesis nor demonstrate the physiological existence of the switch. We report direct experimental evidence for the Fn integrin switch both in vitro and ex vivo using a scFv engineered to detect the transient, force-induced conformational change, representing an opportunity for detection and targeting of early molecular signatures of cell contractile forces in tissue repair and disease.
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Affiliation(s)
- Lizhi Cao
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - John Nicosia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Jacqueline Larouche
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yuanyuan Zhang
- Department of Oncology and Pathology, Cancer Centrum Karolinska, Karolinska Institutet, SE-17176 Stockholm, Sweden
| | - Haylee Bachman
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ashley C. Brown
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, North Carolina 27695, United States
| | - Lars Holmgren
- Department of Oncology and Pathology, Cancer Centrum Karolinska, Karolinska Institutet, SE-17176 Stockholm, Sweden
| | - Thomas H. Barker
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
- Corresponding Author:
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Baumann F, Bauer MS, Rees M, Alexandrovich A, Gautel M, Pippig DA, Gaub HE. Increasing evidence of mechanical force as a functional regulator in smooth muscle myosin light chain kinase. eLife 2017; 6. [PMID: 28696205 PMCID: PMC5505704 DOI: 10.7554/elife.26473] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/20/2017] [Indexed: 11/18/2022] Open
Abstract
Mechanosensitive proteins are key players in cytoskeletal remodeling, muscle contraction, cell migration and differentiation processes. Smooth muscle myosin light chain kinase (smMLCK) is a member of a diverse group of serine/threonine kinases that feature cytoskeletal association. Its catalytic activity is triggered by a conformational change upon Ca2+/calmodulin (Ca2+/CaM) binding. Due to its significant homology with the force-activated titin kinase, smMLCK is suspected to be also regulatable by mechanical stress. In this study, a CaM-independent activation mechanism for smMLCK by mechanical release of the inhibitory elements is investigated via high throughput AFM single-molecule force spectroscopy. The characteristic pattern of transitions between different smMLCK states and their variations in the presence of different substrates and ligands are presented. Interaction between kinase domain and regulatory light chain (RLC) substrate is identified in the absence of CaM, indicating restored substrate-binding capability due to mechanically induced removal of the auto-inhibitory regulatory region. DOI:http://dx.doi.org/10.7554/eLife.26473.001
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Affiliation(s)
- Fabian Baumann
- Chair for Applied Physics and Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Magnus Sebastian Bauer
- Chair for Applied Physics and Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany.,Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin Rees
- Randall Division of Cell and Molecular Biophysics, King's College London BHF Centre of Research Excellence, London, United Kingdom
| | - Alexander Alexandrovich
- Randall Division of Cell and Molecular Biophysics, King's College London BHF Centre of Research Excellence, London, United Kingdom
| | - Mathias Gautel
- Randall Division of Cell and Molecular Biophysics, King's College London BHF Centre of Research Excellence, London, United Kingdom
| | - Diana Angela Pippig
- Chair for Applied Physics and Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hermann Eduard Gaub
- Chair for Applied Physics and Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
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17
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Durner E, Ott W, Nash MA, Gaub HE. Post-Translational Sortase-Mediated Attachment of High-Strength Force Spectroscopy Handles. ACS OMEGA 2017; 2:3064-3069. [PMID: 30023682 PMCID: PMC6044863 DOI: 10.1021/acsomega.7b00478] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 05/26/2017] [Indexed: 05/27/2023]
Abstract
Single-molecule force spectroscopy greatly benefits from site-specific surface immobilization and specific probing with a functionalized cantilever. Here, we describe a streamlined approach to such experiments by covalently attaching mechanically stable receptors onto proteins of interest (POI) to improve pickup efficiency and specificity. This platform provides improved throughput, allows precise control over the pulling geometry, and allows for multiple constructs to be probed with the same ligand-modified cantilever. We employ two orthogonal enzymatic ligation reactions [sortase and phosphopantetheinyl transferase (Sfp)] to covalently immobilize POI to a pegylated surface and to subsequently ligate the POI to a mechanically stable dockerin domain at the protein's C-terminus for use as a high-strength pulling handle. Our configuration permits expression and folding of the POI to proceed independently from the mechanically stable receptor used for specific probing and requires only two short terminal peptide sequences (i.e., ybbR-tag and sortase C-tag). We applied this system successfully to proteins expressed using in vitro transcription and translation reactions without a protein purification step and to purified proteins expressed in Escherichia coli.
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Affiliation(s)
- Ellis Durner
- Lehrstuhl
für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Wolfgang Ott
- Lehrstuhl
für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Michael A. Nash
- Department
of Chemistry, University of Basel, 4056 Basel, Switzerland
- Department
of Biosystems Science & Engineering, Swiss Federal Institute of Technology (ETH-Zurich), 4058 Basel, Switzerland
| | - Hermann E. Gaub
- Lehrstuhl
für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
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18
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Valle-Orero J, Rivas-Pardo JA, Tapia-Rojo R, Popa I, Echelman DJ, Haldar S, Fernández JM. Mechanical Deformation Accelerates Protein Ageing. Angew Chem Int Ed Engl 2017; 56:9741-9746. [PMID: 28470663 DOI: 10.1002/anie.201703630] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Indexed: 01/15/2023]
Abstract
A hallmark of tissue ageing is the irreversible oxidative modification of its proteins. We show that single proteins, kept unfolded and extended by a mechanical force, undergo accelerated ageing in times scales of minutes to days. A protein forced to be continuously unfolded completely loses its ability to contract by folding, becoming a labile polymer. Ageing rates vary among different proteins, but in all cases they lose their mechanical integrity. Random oxidative modification of cryptic side chains exposed by mechanical unfolding can be slowed by the addition of antioxidants such as ascorbic acid, or accelerated by oxidants. By contrast, proteins kept in the folded state and probed over week-long experiments show greatly reduced rates of ageing. We demonstrate a novel approach whereby protein ageing can be greatly accelerated: the constant unfolding of a protein for hours to days is equivalent to decades of exposure to free radicals under physiological conditions.
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Affiliation(s)
- Jessica Valle-Orero
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | | | - Rafael Tapia-Rojo
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Ionel Popa
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.,Current address: Department of Physics, University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Daniel J Echelman
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Shubhasis Haldar
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Julio M Fernández
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
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19
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Malhotra P, Udgaonkar JB. How cooperative are protein folding and unfolding transitions? Protein Sci 2016; 25:1924-1941. [PMID: 27522064 PMCID: PMC5079258 DOI: 10.1002/pro.3015] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/09/2016] [Accepted: 08/09/2016] [Indexed: 11/12/2022]
Abstract
A thermodynamically and kinetically simple picture of protein folding envisages only two states, native (N) and unfolded (U), separated by a single activation free energy barrier, and interconverting by cooperative two-state transitions. The folding/unfolding transitions of many proteins occur, however, in multiple discrete steps associated with the formation of intermediates, which is indicative of reduced cooperativity. Furthermore, much advancement in experimental and computational approaches has demonstrated entirely non-cooperative (gradual) transitions via a continuum of states and a multitude of small energetic barriers between the N and U states of some proteins. These findings have been instrumental towards providing a structural rationale for cooperative versus noncooperative transitions, based on the coupling between interaction networks in proteins. The cooperativity inherent in a folding/unfolding reaction appears to be context dependent, and can be tuned via experimental conditions which change the stabilities of N and U. The evolution of cooperativity in protein folding transitions is linked closely to the evolution of function as well as the aggregation propensity of the protein. A large activation energy barrier in a fully cooperative transition can provide the kinetic control required to prevent the accumulation of partially unfolded forms, which may promote aggregation. Nevertheless, increasing evidence for barrier-less "downhill" folding, as well as for continuous "uphill" unfolding transitions, indicate that gradual non-cooperative processes may be ubiquitous features on the free energy landscape of protein folding.
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Affiliation(s)
- Pooja Malhotra
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.
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20
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Wołek K, Gómez-Sicilia À, Cieplak M. Determination of contact maps in proteins: A combination of structural and chemical approaches. J Chem Phys 2016; 143:243105. [PMID: 26723590 DOI: 10.1063/1.4929599] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Contact map selection is a crucial step in structure-based molecular dynamics modelling of proteins. The map can be determined in many different ways. We focus on the methods in which residues are represented as clusters of effective spheres. One contact map, denoted as overlap (OV), is based on the overlap of such spheres. Another contact map, named Contacts of Structural Units (CSU), involves the geometry in a different way and, in addition, brings chemical considerations into account. We develop a variant of the CSU approach in which we also incorporate Coulombic effects such as formation of the ionic bridges and destabilization of possible links through repulsion. In this way, the most essential and well defined contacts are identified. The resulting residue-residue contact map, dubbed repulsive CSU (rCSU), is more sound in its physico-chemical justification than CSU. It also provides a clear prescription for validity of an inter-residual contact: the number of attractive atomic contacts should be larger than the number of repulsive ones - a feature that is not present in CSU. However, both of these maps do not correlate well with the experimental data on protein stretching. Thus, we propose to use rCSU together with the OV map. We find that the combined map, denoted as OV+rCSU, performs better than OV. In most situations, OV and OV+rCSU yield comparable folding properties but for some proteins rCSU provides contacts which improve folding in a substantial way. We discuss the likely residue-specificity of the rCSU contacts. Finally, we make comparisons to the recently proposed shadow contact map, which is derived from different principles.
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Affiliation(s)
- Karol Wołek
- Institute of Physics, Polish Academy of Science, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Àngel Gómez-Sicilia
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), Av. Doctor Arce, 37, 28002 Madrid, Spain
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Science, Al. Lotników 32/46, 02-668 Warsaw, Poland
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21
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Curli mediate bacterial adhesion to fibronectin via tensile multiple bonds. Sci Rep 2016; 6:33909. [PMID: 27652888 PMCID: PMC5031991 DOI: 10.1038/srep33909] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/02/2016] [Indexed: 01/25/2023] Open
Abstract
Many enteric bacteria including pathogenic Escherichia coli and Salmonella strains produce curli fibers that bind to host surfaces, leading to bacterial internalization into host cells. By using a nanomechanical force-sensing approach, we obtained real-time information about the distribution of molecular bonds involved in the adhesion of curliated bacteria to fibronectin. We found that curliated E. coli and fibronectin formed dense quantized and multiple specific bonds with high tensile strength, resulting in tight bacterial binding. Nanomechanical recognition measurements revealed that approximately 10 bonds were disrupted either sequentially or simultaneously under force load. Thus the curli formation of bacterial surfaces leads to multi-bond structural components of fibrous nature, which may explain the strong mechanical binding of curliated bacteria to host cells and unveil the functions of these proteins in bacterial internalization and invasion.
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22
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Scholl ZN, Josephs EA, Marszalek PE. Modular, Nondegenerate Polyprotein Scaffolds for Atomic Force Spectroscopy. Biomacromolecules 2016; 17:2502-5. [PMID: 27276010 PMCID: PMC4940236 DOI: 10.1021/acs.biomac.6b00548] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zackary N. Scholl
- Computational Biology and Bioinformatics Program, Edmund
T. Pratt, Jr. School of Engineering, Duke University, Durham, North Carolina, United
States
| | - Eric A. Josephs
- Department of Mechanical Engineering and Materials
Science, Edmund T. Pratt, Jr. School of Engineering, Duke University, Durham, North
Carolina, United States
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials
Science, Edmund T. Pratt, Jr. School of Engineering, Duke University, Durham, North
Carolina, United States
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23
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Hughes ML, Dougan L. The physics of pulling polyproteins: a review of single molecule force spectroscopy using the AFM to study protein unfolding. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2016; 79:076601. [PMID: 27309041 DOI: 10.1088/0034-4885/79/7/076601] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
One of the most exciting developments in the field of biological physics in recent years is the ability to manipulate single molecules and probe their properties and function. Since its emergence over two decades ago, single molecule force spectroscopy has become a powerful tool to explore the response of biological molecules, including proteins, DNA, RNA and their complexes, to the application of an applied force. The force versus extension response of molecules can provide valuable insight into its mechanical stability, as well as details of the underlying energy landscape. In this review we will introduce the technique of single molecule force spectroscopy using the atomic force microscope (AFM), with particular focus on its application to study proteins. We will review the models which have been developed and employed to extract information from single molecule force spectroscopy experiments. Finally, we will end with a discussion of future directions in this field.
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Affiliation(s)
- Megan L Hughes
- School of Physics and Astronomy, University of Leeds, LS2 9JT, UK. Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, UK
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24
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Significance of 1B and 2B domains in modulating elastic properties of lamin A. Sci Rep 2016; 6:27879. [PMID: 27301336 PMCID: PMC4908593 DOI: 10.1038/srep27879] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/23/2016] [Indexed: 12/20/2022] Open
Abstract
Nuclear lamins are type V intermediate filament proteins which form an elastic
meshwork underlying the inner nuclear membrane. Lamins directly contribute to
maintain the nuclear shape and elasticity. More than 400 mutations have been
reported in lamin A that are involved in diseases known as laminopathies. These
mutations are scattered mainly in the lamin rod domain along with some in its
C-terminal domain. The contribution of the rod domain towards the elasticity of
lamin A molecule was hitherto unknown. Here, we have elucidated the significance of
the 1B and 2B domains of the rod in modulating the elastic behavior of lamin A by
single-molecule force spectroscopy. In addition, we have also studied the network
forming capacity of these domains and their corresponding viscoelastic behavior. We
have shown that the 1B domain has the ability to form a lamin-like network and
resists larger deformation. However at the single-molecular level, both the domains
have comparable mechanical properties. The self-assembly of the 1B domain
contributes to the elasticity of the lamin A network.
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25
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Kelly CM, Muzard J, Brooks BR, Lee GU, Buchete NV. Structure and dynamics of the fibronectin-III domains of Aplysia californica cell adhesion molecules. Phys Chem Chem Phys 2016; 17:9634-43. [PMID: 25729787 DOI: 10.1039/c4cp05307a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Due to their homophilic and heterophilic binding properties, cell adhesion molecules (CAMs) such as integrin, cadherin and the immunoglobulin superfamily CAMs are of primary importance in cell-cell and cell-substrate interactions, signalling pathways and other crucial biological processes. We study the molecular structures and conformational dynamics of the two fibronectin type III (Fn-III) extracellular domains of the Aplysia californica CAM (apCAM) protein, by constructing and probing an atomically-detailed structural model based on apCAM's homology with other CAMs. The stability and dynamic properties of the Fn-III domains, individually and in tandem, are probed and analysed using all-atom explicit-solvent molecular dynamics (MD) simulations and normal mode analysis of their corresponding elastic network models. The refined structural model of the Fn-III tandem of apCAM reveals a specific pattern of amino acid interactions that controls the stability of the β-sheet rich structure and could affect apCAM's response to physical or chemical changes of its environment. It also exposes the important role of several specific charged residues in modulating the structural properties of the linker segment connecting the two Fn-III domains, as well as of the inter-domain interface.
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Affiliation(s)
- Catherine M Kelly
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland.
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26
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Beedle AEM, Lezamiz A, Stirnemann G, Garcia-Manyes S. The mechanochemistry of copper reports on the directionality of unfolding in model cupredoxin proteins. Nat Commun 2015; 6:7894. [PMID: 26235284 PMCID: PMC4532836 DOI: 10.1038/ncomms8894] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 06/24/2015] [Indexed: 11/09/2022] Open
Abstract
Understanding the directionality and sequence of protein unfolding is crucial to elucidate the underlying folding free energy landscape. An extra layer of complexity is added in metalloproteins, where a metal cofactor participates in the correct, functional fold of the protein. However, the precise mechanisms by which organometallic interactions are dynamically broken and reformed on (un)folding are largely unknown. Here we use single molecule force spectroscopy AFM combined with protein engineering and MD simulations to study the individual unfolding pathways of the blue-copper proteins azurin and plastocyanin. Using the nanomechanical properties of the native copper centre as a structurally embedded molecular reporter, we demonstrate that both proteins unfold via two independent, competing pathways. Our results provide experimental evidence of a novel kinetic partitioning scenario whereby the protein can stochastically unfold through two distinct main transition states placed at the N and C termini that dictate the direction in which unfolding occurs.
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Affiliation(s)
- Amy E M Beedle
- Department of Physics, King's College London, London WC2R 2LS, UK
| | - Ainhoa Lezamiz
- Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
| | - Guillaume Stirnemann
- CNRS - Institut de Biologie Physico-Chimique - PSL Research University, Laboratoire de Biochimie Théorique, 75005 Paris, France
| | - Sergi Garcia-Manyes
- Department of Physics, King's College London, London WC2R 2LS, UK.,Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
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27
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Otten M, Ott W, Jobst MA, Milles LF, Verdorfer T, Pippig DA, Nash MA, Gaub HE. From genes to protein mechanics on a chip. Nat Methods 2014; 11:1127-1130. [PMID: 25194847 PMCID: PMC4216144 DOI: 10.1038/nmeth.3099] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 07/29/2014] [Indexed: 01/28/2023]
Abstract
Single-molecule force spectroscopy enables mechanical testing of individual proteins, but low experimental throughput limits the ability to screen constructs in parallel. We describe a microfluidic platform for on-chip expression, covalent surface attachment and measurement of single-molecule protein mechanical properties. A dockerin tag on each protein molecule allowed us to perform thousands of pulling cycles using a single cohesin-modified cantilever. The ability to synthesize and mechanically probe protein libraries enables high-throughput mechanical phenotyping.
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Affiliation(s)
- Marcus Otten
- Lehrstuhl für Angewandte Physik, Ludwig-Maximilians-Universität, 80799 Munich, Germany
- Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Wolfgang Ott
- Lehrstuhl für Angewandte Physik, Ludwig-Maximilians-Universität, 80799 Munich, Germany
- Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Markus A Jobst
- Lehrstuhl für Angewandte Physik, Ludwig-Maximilians-Universität, 80799 Munich, Germany
- Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Lukas F Milles
- Lehrstuhl für Angewandte Physik, Ludwig-Maximilians-Universität, 80799 Munich, Germany
- Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Tobias Verdorfer
- Lehrstuhl für Angewandte Physik, Ludwig-Maximilians-Universität, 80799 Munich, Germany
- Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Diana A Pippig
- Lehrstuhl für Angewandte Physik, Ludwig-Maximilians-Universität, 80799 Munich, Germany
- Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, 80799 Munich, Germany
- Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Michael A Nash
- Lehrstuhl für Angewandte Physik, Ludwig-Maximilians-Universität, 80799 Munich, Germany
- Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik, Ludwig-Maximilians-Universität, 80799 Munich, Germany
- Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, 80799 Munich, Germany
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28
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29
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Ramanujam V, Kotamarthi HC, Ainavarapu SRK. Ca2+ binding enhanced mechanical stability of an archaeal crystallin. PLoS One 2014; 9:e94513. [PMID: 24728085 PMCID: PMC3984160 DOI: 10.1371/journal.pone.0094513] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/12/2014] [Indexed: 12/22/2022] Open
Abstract
Structural topology plays an important role in protein mechanical stability. Proteins with β-sandwich topology consisting of Greek key structural motifs, for example, I27 of muscle titin and 10FNIII of fibronectin, are mechanically resistant as shown by single-molecule force spectroscopy (SMFS). In proteins with β-sandwich topology, if the terminal strands are directly connected by backbone H-bonding then this geometry can serve as a “mechanical clamp”. Proteins with this geometry are shown to have very high unfolding forces. Here, we set out to explore the mechanical properties of a protein, M-crystallin, which belongs to β-sandwich topology consisting of Greek key motifs but its overall structure lacks the “mechanical clamp” geometry at the termini. M-crystallin is a Ca2+ binding protein from Methanosarcina acetivorans that is evolutionarily related to the vertebrate eye lens β and γ-crystallins. We constructed an octamer of crystallin, (M-crystallin)8, and using SMFS, we show that M-crystallin unfolds in a two-state manner with an unfolding force ∼90 pN (at a pulling speed of 1000 nm/sec), which is much lower than that of I27. Our study highlights that the β-sandwich topology proteins with a different strand-connectivity than that of I27 and 10FNIII, as well as lacking “mechanical clamp” geometry, can be mechanically resistant. Furthermore, Ca2+ binding not only stabilizes M-crystallin by 11.4 kcal/mol but also increases its unfolding force by ∼35 pN at the same pulling speed. The differences in the mechanical properties of apo and holo M-crystallins are further characterized using pulling speed dependent measurements and they show that Ca2+ binding reduces the unfolding potential width from 0.55 nm to 0.38 nm. These results are explained using a simple two-state unfolding energy landscape.
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Affiliation(s)
- Venkatraman Ramanujam
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Hema Chandra Kotamarthi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
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30
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Glyakina AV, Balabaev NK, Galzitskaya OV. Experimental and theoretical studies of mechanical unfolding of different proteins. BIOCHEMISTRY (MOSCOW) 2014; 78:1216-27. [PMID: 24460936 DOI: 10.1134/s0006297913110023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mechanical properties of proteins are important for a wide range of biological processes including cell adhesion, muscle contraction, and protein translocation across biological membranes. It is necessary to reveal how proteins achieve their required mechanical stability under natural conditions in order to understand the biological processes and also to use the knowledge for constructing new biomaterials for medical and industrial purposes. In this connection, it is important to know how a protein will behave in response to various impacts. Theoretical and experimental works on mechanical unfolding of globular proteins will be considered in detail in this review.
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Affiliation(s)
- A V Glyakina
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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31
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Brucale M, Schuler B, Samorì B. Single-molecule studies of intrinsically disordered proteins. Chem Rev 2014; 114:3281-317. [PMID: 24432838 DOI: 10.1021/cr400297g] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marco Brucale
- Institute for the Study of Nanostructured Materials (ISMN), Italian National Council of Research (CNR) , Area della Ricerca Roma1, Via Salaria km 29.3 00015 Monterotondo (Rome), Italy
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32
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Zheng P, Chou CC, Guo Y, Wang Y, Li H. Single Molecule Force Spectroscopy Reveals the Molecular Mechanical Anisotropy of the FeS4 Metal Center in Rubredoxin. J Am Chem Soc 2013; 135:17783-92. [DOI: 10.1021/ja406695g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Peng Zheng
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
| | - Chih-Chung Chou
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
| | - Ying Guo
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
| | - Yanyan Wang
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin, 30072 P. R. China
| | - Hongbin Li
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin, 30072 P. R. China
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33
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Sevilla CA, Dalecki D, Hocking DC. Regional fibronectin and collagen fibril co-assembly directs cell proliferation and microtissue morphology. PLoS One 2013; 8:e77316. [PMID: 24116223 PMCID: PMC3792918 DOI: 10.1371/journal.pone.0077316] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 09/03/2013] [Indexed: 11/19/2022] Open
Abstract
The extracellular matrix protein, fibronectin stimulates cells to self-assemble into three-dimensional multicellular structures by a mechanism that requires the cell-dependent conversion of soluble fibronectin molecules into insoluble fibrils. Fibronectin also binds to collagen type I and mediates the co-assembly of collagen fibrils into the extracellular matrix. Here, the role of collagen-fibronectin binding in fibronectin-induced cellular self-assembly was investigated using fibronectin-null fibroblasts in an in vitro model of tissue formation. High resolution, two-photon immunofluorescence microscopy was combined with second harmonic generation imaging to examine spatial and temporal relationships among fibronectin and collagen fibrils, actin organization, cell proliferation, and microtissue morphology. Time course studies coupled with simultaneous 4-channel multiphoton imaging identified regional differences in fibronectin fibril conformation, collagen fibril remodeling, actin organization, and cell proliferation during three-dimensional cellular self-assembly. Regional differences in cell proliferation and fibronectin structure were dependent on both soluble fibronectin concentration and fibronectin-collagen interactions. Fibronectin-collagen binding was not necessary for either fibronectin matrix formation or intercellular cohesion. However, inhibiting fibronectin binding to collagen reduced collagen fibril remodeling, decreased fibronectin fibril extension, blocked fibronectin-induced cell proliferation, and altered microtissue morphology. Furthermore, continual fibronectin-collagen binding was necessary to maintain both cell proliferation and microtissue morphology. Collectively, these data suggest that the complex changes in extracellular matrix and cytoskeletal remodeling that mediate tissue assembly are driven, in part, by regional variations in cell-mediated fibronectin-collagen co-assembly.
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Affiliation(s)
- Carlos A. Sevilla
- Department of Biomedical Engineering, University of Rochester, Rochester, New York, United States of America
| | - Diane Dalecki
- Department of Biomedical Engineering, University of Rochester, Rochester, New York, United States of America
| | - Denise C. Hocking
- Department of Biomedical Engineering, University of Rochester, Rochester, New York, United States of America
- Department of Pharmacology and Physiology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
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A transformation for the mechanical fingerprints of complex biomolecular interactions. Proc Natl Acad Sci U S A 2013; 110:16432-7. [PMID: 24062442 DOI: 10.1073/pnas.1309101110] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biological processes are carried out through molecular conformational transitions, ranging from the structural changes within biomolecules to the formation of macromolecular complexes and the associations between the complexes themselves. These transitions cover a vast range of timescales and are governed by a tangled network of molecular interactions. The resulting hierarchy of interactions, in turn, becomes encoded in the experimentally measurable "mechanical fingerprints" of the biomolecules, their force-extension curves. However, how can we decode these fingerprints so that they reveal the kinetic barriers and the associated timescales of a biological process? Here, we show that this can be accomplished with a simple, model-free transformation that is general enough to be applicable to molecular interactions involving an arbitrarily large number of kinetic barriers. Specifically, the transformation converts the mechanical fingerprints of the system directly into a map of force-dependent rate constants. This map reveals the kinetics of the multitude of rate processes in the system beyond what is typically accessible to direct measurements. With the contributions from individual barriers to the interaction network now "untangled", the map is straightforward to analyze in terms of the prominent barriers and timescales. Practical implementation of the transformation is illustrated with simulated biomolecular interactions that comprise different patterns of complexity--from a cascade of activation barriers to competing dissociation pathways.
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Vadillo-Rodríguez V, Bruque JM, Gallardo-Moreno AM, González-Martín ML. Surface-dependent mechanical stability of adsorbed human plasma fibronectin on Ti6Al4V: domain unfolding and stepwise unraveling of single compact molecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:8554-8560. [PMID: 23772866 DOI: 10.1021/la401776e] [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
In this study, the structure and mechanical stability of human plasma fibronectin (HFN), a major protein component of blood plasma, have been evaluated in detail upon adsorption on the nonirradiated and irradiated Ti6Al4V material through the use of atomic force microscopy. The results indicated that the material surface changes occurring after the irradiation process reduce the disulfide bonds that typically preclude the mechanical denaturation of individual HFN domains and interfere significantly with the intraionic interactions stabilizing the compact conformation of the adsorbed HFN molecules. In particular, upon adsorption on this material, the molecules adopt a more flexible conformation and become mechanically more compliant. Unexpected observations also indicated that, regardless the material surface, a single HFN molecule can be pulled into an extended conformation without the unfolding of its domains through a series of three unraveling steps. The forces involved in the unraveling process were found to be generally lower than the forces required to unfold the individual protein domains. This report is the first one to present the force displacement details associated to the straightening of a single compact protein at the molecular level.
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Affiliation(s)
- Virginia Vadillo-Rodríguez
- Department of Applied Physics and Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), University of Extremadura, Avda de Elvas s/n, 06006 Badajoz, Spain.
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36
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Gao X, Qin M, Yin P, Liang J, Wang J, Cao Y, Wang W. Single-molecule experiments reveal the flexibility of a Per-ARNT-Sim domain and the kinetic partitioning in the unfolding pathway under force. Biophys J 2012; 102:2149-57. [PMID: 22824279 DOI: 10.1016/j.bpj.2012.03.042] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 02/21/2012] [Accepted: 03/20/2012] [Indexed: 10/28/2022] Open
Abstract
Per-ARNT-Sim (PAS) domains serve as versatile binding motifs in many signal-transduction proteins and are able to respond to a wide spectrum of chemical or physical signals. Despite their diverse functions, PAS domains share a conserved structure. It has been suggested that the structure of PAS domains is flexible and thus adaptable to many binding partners. However, direct measurement of the flexibility of PAS domains has not yet been provided. Here, we quantitatively measure the mechanical unfolding of a PAS domain, ARNT PAS-B, using single-molecule atomic force microscopy. Our force spectroscopy results indicate that the structure of ARNT PAS-B can be unraveled under mechanical forces as low as ~30 pN due to its broad potential well for the mechanical unfolding transition of ~2 nm. This allows the PAS-B domain to extend by up to 75% of its resting end-to-end distance without unfolding. Moreover, we found that the ARNT PAS-B domain unfolds in two distinct pathways via a kinetic partitioning mechanism. Sixty-seven percent of ARNT PAS-B unfolds through a simple two-state pathway, whereas the other 33% unfolds with a well-defined intermediate state in which the C-terminal β-hairpin is detached. We propose that the structural flexibility and force-induced partial unfolding of PAS-B domains may provide a unique mechanism for them to recruit diverse binding partners and lower the free-energy barrier for the formation of the binding interface.
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Affiliation(s)
- Xiang Gao
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing, People's Republic of China
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37
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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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38
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Molecular origin of the sawtooth behavior and the toughness of nacre. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2012; 32:1542-7. [DOI: 10.1016/j.msec.2012.04.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 03/05/2012] [Accepted: 04/20/2012] [Indexed: 11/21/2022]
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39
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Elter P, Weihe T, Bühler S, Gimsa J, Beck U. Low fibronectin concentration overcompensates for reduced initial fibroblasts adhesion to a nanoscale topography: Single-cell force spectroscopy. Colloids Surf B Biointerfaces 2012; 95:82-9. [DOI: 10.1016/j.colsurfb.2012.02.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Revised: 01/18/2012] [Accepted: 02/14/2012] [Indexed: 11/29/2022]
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40
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Toofanny RD, Daggett V. Understanding protein unfolding from molecular simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1088] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Rudesh D. Toofanny
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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41
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Bradshaw MJ, Smith ML. Contribution of unfolding and intermolecular architecture to fibronectin fiber extensibility. Biophys J 2012; 101:1740-8. [PMID: 21961600 DOI: 10.1016/j.bpj.2011.08.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 08/13/2011] [Accepted: 08/18/2011] [Indexed: 10/17/2022] Open
Abstract
The extracellular matrix contains components with remarkable mechanical properties, including fibronectin (Fn) fibers with extensibilities of >700% strain. We utilized what we consider a novel technique to quantify the extent of molecular unfolding that contributes to Fn fiber extension, and we compared this behavior with stochastic models of Fn fibers with different molecular arrangements. In vitro unfolding as a function of strain was measured by fluorescently labeling cysteines in modules FnIII7 and III15 in artificial Fn fibers. A calibration technique we also consider novel made it possible to demonstrate that 44% of cysteines in these modules were exposed in Fn fibers strained to 421% extension, up from 8% exposure without strain. In silico unfolding was measured by applying a constant strain rate to a fiber represented by a network of wormlike chain springs, each representing an individual Fn molecule. Unfolding rates were calculated with a tension-dependent stochastic model applied to FnIII modules in each molecule. A comparison of these approaches revealed that only a molecular arrangement permitting unequal mechanical loading of Fn molecules recapitulates in vitro unfolding. These data have implications for Fn-dependent mechanotransduction and give insight into how the molecular architecture of natural materials permits such remarkable extensibility.
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Affiliation(s)
- Mark J Bradshaw
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts, USA
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42
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de Graff AMR, Shannon G, Farrell DW, Williams PM, Thorpe MF. Protein unfolding under force: crack propagation in a network. Biophys J 2011; 101:736-44. [PMID: 21806942 DOI: 10.1016/j.bpj.2011.05.072] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 04/24/2011] [Accepted: 05/19/2011] [Indexed: 10/17/2022] Open
Abstract
The mechanical unfolding of a set of 12 proteins with diverse topologies is investigated using an all-atom constraint-based model. Proteins are represented as polypeptides cross-linked by hydrogen bonds, salt bridges, and hydrophobic contacts, each modeled as a harmonic inequality constraint capable of supporting a finite load before breaking. Stereochemically acceptable unfolding pathways are generated by minimally overloading the network in an iterative fashion, analogous to crack propagation in solids. By comparing the pathways to those from molecular dynamics simulations and intermediates identified from experiment, it is demonstrated that the dominant unfolding pathways for 9 of the 12 proteins studied are well described by crack propagation in a network.
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Affiliation(s)
- Adam M R de Graff
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
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43
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Atomic force microscopy studies of the influence of convex and concave nanostructures on the adsorption of fibronectin. Colloids Surf B Biointerfaces 2011; 89:139-46. [PMID: 21978554 DOI: 10.1016/j.colsurfb.2011.09.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 08/30/2011] [Accepted: 09/04/2011] [Indexed: 11/23/2022]
Abstract
Atomic force microscopy (AFM)-based force spectroscopy was used to analyze the adsorption of bovine plasma fibronectin on periodically grooved nanostructures (groove/summit width: 90 nm; depth: 120 nm). We present a simple procedure that allowed us to directly compare the local protein density and conformation for the convex summits, the concave grooves and planar reference regions of the substrate. At a bulk fibronectin concentration of 5 μg/ml, the amount of adsorbed protein per surface area was significantly higher in all regions of the nanostructure than on the planar reference, and fibronectin tended to adsorb preferentially in the concave grooves. The increased surface concentration resulted in an additional stabilization of the molecules by protein-protein interactions and a lower degree of denaturized fibronectin in the nanostructured regions. The stabilization was less pronounced in concave regions, indicating that the increased contact area in the grooves counteracted the stabilization by increased protein-substrate interactions and must be compensated for by additional protein-protein interactions. Less favorable sites were occupied at higher bulk fibronectin concentrations (25 μg/ml, 100 μg/ml), and a high degree of native folded fibronectin was observed in both the nanostructured and planar regions. Our results demonstrate that the amount of adsorbed fibronectin per surface area can be increased if a substrate is provided with a topographic nanostructure. Our results also show that the local conformational state of fibronectin is determined by the locally different interplay of protein-protein and protein-substrate interactions.
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44
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Horejs C, Ristl R, Tscheliessnig R, Sleytr UB, Pum D. Single-molecule force spectroscopy reveals the individual mechanical unfolding pathways of a surface layer protein. J Biol Chem 2011; 286:27416-24. [PMID: 21690085 PMCID: PMC3149335 DOI: 10.1074/jbc.m111.251322] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 06/15/2011] [Indexed: 12/14/2022] Open
Abstract
Surface layers (S-layers) represent an almost universal feature of archaeal cell envelopes and are probably the most abundant bacterial cell proteins. S-layers are monomolecular crystalline structures of single protein or glycoprotein monomers that completely cover the cell surface during all stages of the cell growth cycle, thereby performing their intrinsic function under a constant intra- and intermolecular mechanical stress. In gram-positive bacteria, the individual S-layer proteins are anchored by a specific binding mechanism to polysaccharides (secondary cell wall polymers) that are linked to the underlying peptidoglycan layer. In this work, atomic force microscopy-based single-molecule force spectroscopy and a polyprotein approach are used to study the individual mechanical unfolding pathways of an S-layer protein. We uncover complex unfolding pathways involving the consecutive unfolding of structural intermediates, where a mechanical stability of 87 pN is revealed. Different initial extensibilities allow the hypothesis that S-layer proteins adapt highly stable, mechanically resilient conformations that are not extensible under the presence of a pulling force. Interestingly, a change of the unfolding pathway is observed when individual S-layer proteins interact with secondary cell wall polymers, which is a direct signature of a conformational change induced by the ligand. Moreover, the mechanical stability increases up to 110 pN. This work demonstrates that single-molecule force spectroscopy offers a powerful tool to detect subtle changes in the structure of an individual protein upon binding of a ligand and constitutes the first conformational study of surface layer proteins at the single-molecule level.
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Affiliation(s)
| | - Robin Ristl
- From the Department for Nanobiotechnology and
| | - Rupert Tscheliessnig
- the Austrian Centre of Industrial Biotechnology, c/o Institute for Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | | | - Dietmar Pum
- From the Department for Nanobiotechnology and
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45
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Sarangapani KK, Qian J, Chen W, Zarnitsyna VI, Mehta P, Yago T, McEver RP, Zhu C. Regulation of catch bonds by rate of force application. J Biol Chem 2011; 286:32749-61. [PMID: 21775439 DOI: 10.1074/jbc.m111.240044] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The current paradigm for receptor-ligand dissociation kinetics assumes off-rates as functions of instantaneous force without impact from its prior history. This a priori assumption is the foundation for predicting dissociation from a given initial state using kinetic equations. Here we have invalidated this assumption by demonstrating the impact of force history with single-bond kinetic experiments involving selectins and their ligands that mediate leukocyte tethering and rolling on vascular surfaces during inflammation. Dissociation of bonds between L-selectin and P-selectin glycoprotein ligand-1 (PSGL-1) loaded at a constant ramp rate to a constant hold force behaved as catch-slip bonds at low ramp rates that transformed to slip-only bonds at high ramp rates. Strikingly, bonds between L-selectin and 6-sulfo-sialyl Lewis X were impervious to ramp rate changes. This ligand-specific force history effect resembled the effect of a point mutation at the L-selectin surface (L-selectinA108H) predicted to contact the former but not the latter ligand, suggesting that the high ramp rate induced similar structural changes as the mutation. Although the A108H substitution in L-selectin eliminated the ramp rate responsiveness of its dissociation from PSGL-1, the inverse mutation H108A in P-selectin acquired the ramp rate responsiveness. Our data are well explained by the sliding-rebinding model for catch-slip bonds extended to incorporate the additional force history dependence, with Ala-108 playing a pivotal role in this structural mechanism. These results call for a paradigm shift in modeling the mechanical regulation of receptor-ligand bond dissociation, which includes conformational coupling between binding pocket and remote regions of the interacting molecules.
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Affiliation(s)
- Krishna K Sarangapani
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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46
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Velocity-dependent mechanical unfolding of bacteriorhodopsin is governed by a dynamic interaction network. Biophys J 2011; 100:1109-19. [PMID: 21320457 DOI: 10.1016/j.bpj.2011.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 01/03/2011] [Accepted: 01/05/2011] [Indexed: 12/17/2022] Open
Abstract
Bacteriorhodopsin is a model system for membrane proteins. This seven transmembrane helical protein is embedded within a membrane structure called purple membrane. Its structural stability against mechanical stress was recently investigated by atomic force microscopy experiments, in which single proteins were extracted from the purple membrane. Here, we study this process by all-atom molecular dynamics simulations, in which single bacteriorhodopsin molecules were extracted and unfolded from an atomistic purple membrane model. In our simulations, key features from the experiments like force profiles and location of key residues that resist mechanical unfolding were reproduced. These key residues were seen to be stabilized by a dynamic network of intramolecular interactions. Further, the unfolding pathway was found to be velocity-dependent. Simulations in which the mechanical stress was released during unfolding revealed relaxation motions that allowed characterization of the nonequilibrium processes during fast extraction.
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47
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Graham TGW, Best RB. Force-Induced Change in Protein Unfolding Mechanism: Discrete or Continuous Switch? J Phys Chem B 2011; 115:1546-61. [DOI: 10.1021/jp110738m] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Thomas G. W. Graham
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Robert B. Best
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
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48
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Complex unfolding kinetics of single-domain proteins in the presence of force. Biophys J 2010; 99:1620-7. [PMID: 20816075 PMCID: PMC2931718 DOI: 10.1016/j.bpj.2010.06.039] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 06/11/2010] [Accepted: 06/17/2010] [Indexed: 02/02/2023] Open
Abstract
Single-molecule force spectroscopy is providing unique, and sometimes unexpected, insights into the free-energy landscapes of proteins. Despite the complexity of the free-energy landscapes revealed by mechanical probes, forced unfolding experiments are often analyzed using one-dimensional models that predict a logarithmic dependence of the unfolding force on the pulling velocity. We previously found that the unfolding force of the protein filamin at low pulling speed did not decrease logarithmically with the pulling speed. Here we present results from a large number of unfolding simulations of a coarse-grain model of the protein filamin under a broad range of constant forces. These show that a two-path model is physically plausible and produces a deviation from the behavior predicted by one-dimensional models analogous to that observed experimentally. We also show that the analysis of the distributions of unfolding forces (p[F]) contains crucial and exploitable information, and that a proper description of the unfolding of single-domain proteins needs to account for the intrinsic multidimensionality of the underlying free-energy landscape, especially when the applied perturbation is small.
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49
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Nguyen CM, Levy AJ. The mechanics of atherosclerotic plaque rupture by inclusion/matrix interfacial decohesion. J Biomech 2010; 43:2702-8. [DOI: 10.1016/j.jbiomech.2010.06.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 06/11/2010] [Accepted: 06/12/2010] [Indexed: 10/19/2022]
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50
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Averett LE, Akhremitchev BB, Schoenfisch MH, Gorkun OV. Calcium dependence of fibrin nanomechanics: the γ1 calcium mediates the unfolding of fibrinogen induced by force applied to the "A-a" bond. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:14716-14722. [PMID: 20731339 DOI: 10.1021/la1017664] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The interactions between the constituent monomers of fibrin, the polymerized protein network that provides the structural stability of blood clots, are frequently under stress because of the dynamic nature of blood flow. Herein, the calcium dependence of the structural unfolding linked to the forced dissociation of the "A-a" knob-hole bond between fibrin monomers is reported. The presence of calcium was shown to influence the incidence of the last event in the unfolding pattern characteristic of "A-a" rupture. This effect, attributed to the function of the γ1 calcium-binding site, was found to be reversible and specific. Our results indicate that binding of calcium at the γ1 site has no effect on the strength of the knob-hole bond prior to unfolding of the hole-containing γ module. Rather, calcium bound at the γ1 site makes the structure of the hole more resilient to such forced unfolding, leading to survival of the "A-a" knob-hole bond during larger extensions of the fibrinogen molecule but at the cost of rupture of the bond at lower forces.
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Affiliation(s)
- Laurel E Averett
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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