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Stransky F, Kostrz D, Follenfant M, Pomplun S, Meyners C, Strick T, Hausch F, Gosse C. Use of DNA forceps to measure receptor-ligand dissociation equilibrium constants in a single-molecule competition assay. Methods Enzymol 2024; 694:51-82. [PMID: 38492958 DOI: 10.1016/bs.mie.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
The ability of biophysicists to decipher the behavior of individual biomolecules has steadily improved over the past thirty years. However, it still remains unclear how an ensemble of data acquired at the single-molecule level compares with the data acquired on an ensemble of the same molecules. We here propose an assay to tackle this question in the context of dissociation equilibrium constant measurements. A sensor is built by engrafting a receptor and a ligand onto a flexible dsDNA scaffold and mounting this assembly on magnetic tweezers. This way, looking at the position of the magnetic bead enables one to determine in real-time if the two molecular partners are associated or not. Next, to quantify the affinity of the scrutinized single-receptor for a given competitor, various amounts of the latter molecule are introduced in solution and the equilibrium response of the sensor is monitored throughout the titration protocol. Proofs of concept are established for the binding of three rapamycin analogs to the FKBP12 cis-trans prolyl isomerase. For each of these drugs the mean affinity constant obtained on a ten of individual receptors agrees with the one previously determined in a bulk assay. Furthermore, experimental contingencies are sufficient to explain the dispersion observed over the single-molecule values.
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Affiliation(s)
- François Stransky
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Dorota Kostrz
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Maryne Follenfant
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Sebastian Pomplun
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Christian Meyners
- Department of Chemistry and Biochemistry, Technical University Darmstadt, Darmstadt, Germany
| | - Terence Strick
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Felix Hausch
- Department of Chemistry and Biochemistry, Technical University Darmstadt, Darmstadt, Germany; Centre for Synthetic Biology, Technical University Darmstadt, Darmstadt, Germany
| | - Charlie Gosse
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France.
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2
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Zhou Y, Tang Q, Zhao X, Zeng X, Chong C, Yan J. A novel design for magnetic tweezers with wide-range temperature control. Biophys J 2023; 122:3860-3868. [PMID: 37563833 PMCID: PMC10560670 DOI: 10.1016/j.bpj.2023.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/19/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023] Open
Abstract
Single-molecule manipulation technologies have proven to be powerful tools for studying the molecular mechanisms and physical principles underlying many essential biological processes. However, achieving wide-range temperature control has been challenging due to thermal drift that undermines the stability of the instrument. This limitation has made it difficult to study biomolecules from thermophiles at their physiologically relevant temperatures and has also hindered the convenient measurement of temperature-sensitive biomolecular interactions and the fundamental thermodynamic properties of biomolecules. In this work, we present a novel design of magnetic tweezers that uses a reflective coverslip and dry objective lens to insulate the heat conductance between the sample and the objective lens, enabling stable temperature changes from ambient up to 70°C during experiments without significant thermal drift of the instrument. The performance of the technology is demonstrated through the quantification of the free energy change of a DNA hairpin over a temperature range of 22°C-72°C, from which the entropy and enthalpy changes are determined.
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Affiliation(s)
- Yu Zhou
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Qingnan Tang
- Department of Physics, National University of Singapore, Singapore, Singapore
| | - Xiaodan Zhao
- Department of Physics, National University of Singapore, Singapore, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Xiangjun Zeng
- Department of Physics, National University of Singapore, Singapore, Singapore
| | - Clarence Chong
- Department of Physics, National University of Singapore, Singapore, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore; Department of Physics, National University of Singapore, Singapore, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore; Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou, China.
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3
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Cheung E, Xia Y, Caporini MA, Gilmore JL. Tools shaping drug discovery and development. BIOPHYSICS REVIEWS 2022; 3:031301. [PMID: 38505278 PMCID: PMC10903431 DOI: 10.1063/5.0087583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/21/2022] [Indexed: 03/21/2024]
Abstract
Spectroscopic, scattering, and imaging methods play an important role in advancing the study of pharmaceutical and biopharmaceutical therapies. The tools more familiar to scientists within industry and beyond, such as nuclear magnetic resonance and fluorescence spectroscopy, serve two functions: as simple high-throughput techniques for identification and purity analysis, and as potential tools for measuring dynamics and structures of complex biological systems, from proteins and nucleic acids to membranes and nanoparticle delivery systems. With the expansion of commercial small-angle x-ray scattering instruments into the laboratory setting and the accessibility of industrial researchers to small-angle neutron scattering facilities, scattering methods are now used more frequently in the industrial research setting, and probe-less time-resolved small-angle scattering experiments are now able to be conducted to truly probe the mechanism of reactions and the location of individual components in complex model or biological systems. The availability of atomic force microscopes in the past several decades enables measurements that are, in some ways, complementary to the spectroscopic techniques, and wholly orthogonal in others, such as those related to nanomechanics. As therapies have advanced from small molecules to protein biologics and now messenger RNA vaccines, the depth of biophysical knowledge must continue to serve in drug discovery and development to ensure quality of the drug, and the characterization toolbox must be opened up to adapt traditional spectroscopic methods and adopt new techniques for unraveling the complexities of the new modalities. The overview of the biophysical methods in this review is meant to showcase the uses of multiple techniques for different modalities and present recent applications for tackling particularly challenging situations in drug development that can be solved with the aid of fluorescence spectroscopy, nuclear magnetic resonance spectroscopy, atomic force microscopy, and small-angle scattering.
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Affiliation(s)
- Eugene Cheung
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Yan Xia
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Marc A. Caporini
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Jamie L. Gilmore
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
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4
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Dahal N, Sharma S, Phan B, Eis A, Popa I. Mechanical regulation of talin through binding and history-dependent unfolding. SCIENCE ADVANCES 2022; 8:eabl7719. [PMID: 35857491 DOI: 10.1126/sciadv.abl7719] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Talin is a force-sensing multidomain protein and a major player in cellular mechanotransduction. Here, we use single-molecule magnetic tweezers to investigate the mechanical response of the R8 rod domain of talin. We find that under various force cycles, the R8 domain of talin can display a memory-dependent behavior: At the same low force (<10 pN), the same protein molecule shows vastly different unfolding kinetics. This history-dependent behavior indicates the evolution of a unique force-induced native state. We measure through mechanical unfolding that talin R8 domain binds one of its ligands, DLC1, with much higher affinity than previously reported. This strong interaction can explain the antitumor response of DLC1 by regulating inside-out activation of integrins. Together, our results paint a complex picture for the mechanical unfolding of talin in the physiological range and a new mechanism of function of DLC1 to regulate inside-out activation of integrins.
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Affiliation(s)
- Narayan Dahal
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, WI 53211, USA
| | - Sabita Sharma
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, WI 53211, USA
| | - Binh Phan
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, WI 53211, USA
| | - Annie Eis
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, WI 53211, USA
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, WI 53211, USA
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5
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Yadav J, Kumar Y, Singaraju GS, Patil S. Interaction of chloramphenicol with titin I27 probed using single-molecule force spectroscopy. J Biol Phys 2021; 47:191-204. [PMID: 34075502 DOI: 10.1007/s10867-021-09573-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 05/05/2021] [Indexed: 11/28/2022] Open
Abstract
Titin is a giant elastic protein which is responsible for passive muscle stiffness when muscle sarcomeres are stretched. Chloramphenicol, besides being a broad-spectrum antibiotic, also acts as a muscle relaxant. Therefore, it is important to study the interaction between titin I27 and chloramphenicol. We investigated the interaction of chloramphenicol with octamer of titin I27 using single-molecule force spectroscopy and fluorescence spectroscopy. The fluorescence data indicated that binding of chloramphenicol with I27 results in fluorescence quenching. Furthermore, it is observed that chloramphenicol binds to I27 at a particular concentration ([Formula: see text] 40 μM). Single-molecule force spectroscopy shows that, in the presence of 40 μM chloramphenicol concentration, the I27 monomers become mechanically stable, resulting in an increment of the unfolding force. The stability was further confirmed by chemical denaturation experiments on monomers of I27, which corroborate the evidence for enhanced mechanical stability at 40 μM drug concentration. The free energy of stabilization for I27 (wild type) was found to be 1.95 ± 0.93 kcal/mole and I27 with 40 μM drug was 3.25 ± 0.63 kcal/mole. The results show a direct effect of the broad-spectrum antibiotic chloramphenicol on the passive elasticity of muscle protein titin. The I27 is stabilized both mechanically and chemically by chloramphenicol.
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Affiliation(s)
- Jyoti Yadav
- Indian Institute of Science Education and Research, Pune, India
| | - Yashwant Kumar
- Indian Institute of Science Education and Research, Pune, India
| | | | - Shivprasad Patil
- Indian Institute of Science Education and Research, Pune, India.
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6
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Modulation of a protein-folding landscape revealed by AFM-based force spectroscopy notwithstanding instrumental limitations. Proc Natl Acad Sci U S A 2021; 118:2015728118. [PMID: 33723041 DOI: 10.1073/pnas.2015728118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Single-molecule force spectroscopy is a powerful tool for studying protein folding. Over the last decade, a key question has emerged: how are changes in intrinsic biomolecular dynamics altered by attachment to μm-scale force probes via flexible linkers? Here, we studied the folding/unfolding of α3D using atomic force microscopy (AFM)-based force spectroscopy. α3D offers an unusual opportunity as a prior single-molecule fluorescence resonance energy transfer (smFRET) study showed α3D's configurational diffusion constant within the context of Kramers theory varies with pH. The resulting pH dependence provides a test for AFM-based force spectroscopy's ability to track intrinsic changes in protein folding dynamics. Experimentally, however, α3D is challenging. It unfolds at low force (<15 pN) and exhibits fast-folding kinetics. We therefore used focused ion beam-modified cantilevers that combine exceptional force precision, stability, and temporal resolution to detect state occupancies as brief as 1 ms. Notably, equilibrium and nonequilibrium force spectroscopy data recapitulated the pH dependence measured using smFRET, despite differences in destabilization mechanism. We reconstructed a one-dimensional free-energy landscape from dynamic data via an inverse Weierstrass transform. At both neutral and low pH, the resulting constant-force landscapes showed minimal differences (∼0.2 to 0.5 k B T) in transition state height. These landscapes were essentially equal to the predicted entropic barrier and symmetric. In contrast, force-dependent rates showed that the distance to the unfolding transition state increased as pH decreased and thereby contributed to the accelerated kinetics at low pH. More broadly, this precise characterization of a fast-folding, mechanically labile protein enables future AFM-based studies of subtle transitions in mechanoresponsive proteins.
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7
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Abstract
Multiple gram-negative bacteria encode type III secretion systems (T3SS) that allow them to inject effector proteins directly into host cells to facilitate colonization. To be secreted, effector proteins must be at least partially unfolded to pass through the narrow needle-like channel (diameter <2 nm) of the T3SS. Fusion of effector proteins to tightly packed proteins-such as GFP, ubiquitin, or dihydrofolate reductase (DHFR)-impairs secretion and results in obstruction of the T3SS. Prior observation that unfolding can become rate-limiting for secretion has led to the model that T3SS effector proteins have low thermodynamic stability, facilitating their secretion. Here, we first show that the unfolding free energy ([Formula: see text]) of two Salmonella effector proteins, SptP and SopE2, are 6.9 and 6.0 kcal/mol, respectively, typical for globular proteins and similar to published [Formula: see text] for GFP, ubiquitin, and DHFR. Next, we mechanically unfolded individual SptP and SopE2 molecules by atomic force microscopy (AFM)-based force spectroscopy. SptP and SopE2 unfolded at low force (F unfold ≤ 17 pN at 100 nm/s), making them among the most mechanically labile proteins studied to date by AFM. Moreover, their mechanical compliance is large, as measured by the distance to the transition state (Δx ‡ = 1.6 and 1.5 nm for SptP and SopE2, respectively). In contrast, prior measurements of GFP, ubiquitin, and DHFR show them to be mechanically robust (F unfold > 80 pN) and brittle (Δx ‡ < 0.4 nm). These results suggest that effector protein unfolding by T3SS is a mechanical process and that mechanical lability facilitates efficient effector protein secretion.
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8
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Gupta M, Venkatramani R, Ainavarapu SRK. Role of Ligand Binding Site in Modulating the Mechanical Stability of Proteins with β-Grasp Fold. J Phys Chem B 2021; 125:1009-1019. [PMID: 33492970 DOI: 10.1021/acs.jpcb.0c08085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite many studies on ligand-modulated protein mechanics, a comparative analysis of the role of ligand binding site on any specific protein fold is yet to be made. In this study, we explore the role of ligand binding site on the mechanical properties of β-grasp fold proteins, namely, ubiquitin and small ubiquitin related modifier 1 (SUMO1). The terminal segments directly connected through hydrogen bonds constitute the β-clamp geometry (or mechanical clamp), which confers high mechanical resilience to the β-grasp fold. Here, we study ubiquitin complexed with CUE2-1, a ubiquitin-binding domain (UBD) from yeast endonuclease protein Cue2, using a combination of single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations. Our study reveals that CUE2-1 does not alter the mechanical properties of ubiquitin, despite directly interacting with its β-clamp. To explore the role of ligand binding site, we compare the mechanical properties of the ubiquitin/CUE2-1 complex with that of previously studied SUMO1/S12, another β-grasp protein complex, using SMD simulations. Simulations on the SUMO1/S12 complex corroborate previous experimentally observed enhancement in the mechanical stability of SUMO1, even though S12 binds away from the β-clamp. Differences in ligand binding-induced structural impact at the transition state of the two complexes explain the differences in ligand modulated protein mechanics. Contrary to previous reports, our study demonstrates that direct binding of ligands to the mechanical clamp does not necessarily alter the mechanical stability of β-grasp fold proteins. Rather, binding interactions away from the clamp can reinforce protein stability provided by the β-grasp fold. Our study highlights the importance of binding site and binding modes of ligands in modulating the mechanical stability of β-grasp fold proteins.
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Affiliation(s)
- Mona Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr Homi Bhabha Road, Colaba, Mumbai 400005, India
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9
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Sonar P, Bellucci L, Mossa A, Heidarsson PO, Kragelund BB, Cecconi C. Effects of Ligand Binding on the Energy Landscape of Acyl-CoA-Binding Protein. Biophys J 2020; 119:1821-1832. [PMID: 33080224 PMCID: PMC7677128 DOI: 10.1016/j.bpj.2020.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/14/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Binding of ligands is often crucial for function yet the effects of ligand binding on the mechanical stability and energy landscape of proteins are incompletely understood. Here, we use a combination of single-molecule optical tweezers and MD simulations to investigate the effect of ligand binding on the energy landscape of acyl-coenzyme A (CoA)-binding protein (ACBP). ACBP is a topologically simple and highly conserved four-α-helix bundle protein that acts as an intracellular transporter and buffer for fatty-acyl-CoA and is active in membrane assembly. We have previously described the behavior of ACBP under tension, revealing a highly extended transition state (TS) located almost halfway between the unfolded and native states. Here, we performed force-ramp and force-jump experiments, in combination with advanced statistical analysis, to show that octanoyl-CoA binding increases the activation free energy for the unfolding reaction of ACBP without affecting the position of the transition state along the reaction coordinate. It follows that ligand binding enhances the mechanical resistance and thermodynamic stability of the protein, without changing its mechanical compliance. Steered molecular dynamics simulations allowed us to rationalize the results in terms of key interactions that octanoyl-CoA establishes with the four α-helices of ACBP and showed that the unfolding pathway is marginally affected by the ligand. The results show that ligand-induced mechanical stabilization effects can be complex and may prove useful for the rational design of stabilizing ligands.
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Affiliation(s)
- Punam Sonar
- Physik-Department E22, Technische Universität München, Garching Germany
| | - Luca Bellucci
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, Pisa, Italy
| | - Alessandro Mossa
- INFN Firenze, Sesto Fiorentino, Italy; Istituto Statale di Istruzione Superiore "Leonardo da Vinci", Firenze, Italy.
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
| | - Ciro Cecconi
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Modena, Italy; Center S3, CNR Institute Nanoscience, Modena, Italy.
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10
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Optical imaging of single-protein size, charge, mobility, and binding. Nat Commun 2020; 11:4768. [PMID: 32958747 PMCID: PMC7505846 DOI: 10.1038/s41467-020-18547-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/31/2020] [Indexed: 12/28/2022] Open
Abstract
Detection and identification of proteins are typically achieved by analyzing protein size, charge, mobility and binding to antibodies, which are critical for biomedical research and disease diagnosis and treatment. Despite the importance, measuring these quantities with one technology and at the single-molecule level has not been possible. Here we tether a protein to a surface with a flexible polymer, drive it into oscillation with an electric field, and image the oscillation with a near field optical imaging method, from which we determine the size, charge, and mobility of the protein. We also measure antibody binding and conformation changes in the protein. The work demonstrates a capability for comprehensive protein analysis and precision protein biomarker detection at the single molecule level. Protein identification at the single-molecule level is the ultimate goal for biological research and disease diagnosis. Here, the authors identify the size, charge, mobility, and binding of individual protein molecules by measuring the optical and electrical responses of each protein molecule tethered to a surface.
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11
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Sharma S, Subramani S, Popa I. Does protein unfolding play a functional role in vivo? FEBS J 2020; 288:1742-1758. [PMID: 32761965 DOI: 10.1111/febs.15508] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022]
Abstract
Unfolding and refolding of multidomain proteins under force have yet to be recognized as a major mechanism of function for proteins in vivo. In this review, we discuss the inherent properties of multidomain proteins under a force vector from a structural and functional perspective. We then characterize three main systems where multidomain proteins could play major roles through mechanical unfolding: muscular contraction, cellular mechanotransduction, and bacterial adhesion. We analyze how key multidomain proteins for each system can produce a gain-of-function from the perspective of a fine-tuned quantized response, a molecular battery, delivery of mechanical work through refolding, elasticity tuning, protection and exposure of cryptic sites, and binding-induced mechanical changes. Understanding how mechanical unfolding and refolding affect function will have important implications in designing mechano-active drugs against conditions such as muscular dystrophy, cancer, or novel antibiotics.
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Affiliation(s)
- Sabita Sharma
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Smrithika Subramani
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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12
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Hughes MDG, Cussons S, Mahmoudi N, Brockwell DJ, Dougan L. Single molecule protein stabilisation translates to macromolecular mechanics of a protein network. SOFT MATTER 2020; 16:6389-6399. [PMID: 32578583 DOI: 10.1039/c9sm02484k] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Folded globular proteins are attractive building blocks for biopolymer-based materials, as their mechanically resistant structures carry out diverse biological functionality. While much is now understood about the mechanical response of single folded proteins, a major challenge is to understand and predictably control how single protein mechanics translates to the collective response of a network of connected folded proteins. Here, by utilising the binding of maltose to hydrogels constructed from photo-chemically cross-linked maltose binding protein (MBP), we investigate the effects of protein stabilisation at the molecular level on the macroscopic mechanical and structural properties of a protein-based hydrogel. Rheological measurements show an enhancement in the mechanical strength and energy dissipation of MBP hydrogels in the presence of maltose. Circular dichroism spectroscopy and differential scanning calorimetry measurements show that MBP remains both folded and functional in situ. By coupling these mechanical measurements with mesoscopic structural information obtained by small angle scattering, we propose an occupation model in which higher proportions of stabilised, ligand occupied, protein building blocks translate their increased stability to the macroscopic properties of the hydrogel network. This provides powerful opportunities to exploit environmentally responsive folded protein-based biomaterials for many broad applications.
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Affiliation(s)
- Matt D G Hughes
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds, UK.
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13
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Dahal N, Nowitzke J, Eis A, Popa I. Binding-Induced Stabilization Measured on the Same Molecular Protein Substrate Using Single-Molecule Magnetic Tweezers and Heterocovalent Attachments. J Phys Chem B 2020; 124:3283-3290. [DOI: 10.1021/acs.jpcb.0c00167] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Narayan Dahal
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Joel Nowitzke
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Annie Eis
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
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14
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Mora M, Stannard A, Garcia-Manyes S. The nanomechanics of individual proteins. Chem Soc Rev 2020; 49:6816-6832. [DOI: 10.1039/d0cs00426j] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This tutorial review provides an overview of the single protein force spectroscopy field, including the main techniques and the basic tools for analysing the data obtained from the single molecule experiments.
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Affiliation(s)
- Marc Mora
- Department of Physics and Randall Centre for Cell and Molecular Biophysics
- King's College London
- London
- UK
- The Francis Crick Institute
| | - Andrew Stannard
- Department of Physics and Randall Centre for Cell and Molecular Biophysics
- King's College London
- London
- UK
- The Francis Crick Institute
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Centre for Cell and Molecular Biophysics
- King's College London
- London
- UK
- The Francis Crick Institute
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15
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Xia J, Zuo J, Li H. Single molecule force spectroscopy reveals that the oxidation state of cobalt ions plays an important role in enhancing the mechanical stability of proteins. NANOSCALE 2019; 11:19791-19796. [PMID: 31612899 DOI: 10.1039/c9nr06912g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Engineered bi-histidine (biHis)-based metal chelation is a general and robust method to enhance the mechanical stability of proteins. Here we used single molecule force spectroscopy techniques to investigate the effect of binding of Co2+/Co3+ on the mechanical stability of an engineered biHis mutant of protein GB1, G6-53. We found that the binding of Co2+/Co3+ can lead to an enhancement of the mechanical stability of G6-53, but the degree of enhancement is drastically different. The binding of Co2+ can only lead to marginal enhancement of G6-53's mechanical stability, while Co3+ has a much stronger effect. This large difference is likely due to the large difference in thermodynamic stability and kinetic lability of Co2+ and Co3+ complexes. These results opened up new avenues towards fine tuning the mechanical properties of proteins.
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Affiliation(s)
- Jiahao Xia
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada. and Key Laboratory of Organic Optoelectronic and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing, 10084, P. R. China
| | - Jiacheng Zuo
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
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16
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Abstract
![]()
Life is an emergent property of transient
interactions between
biomolecules and other organic and inorganic molecules that somehow
leads to harmony and order. Measurement and quantitation of these
biological interactions are of value to scientists and are major goals
of biochemistry, as affinities provide insight into biological processes.
In an organism, these interactions occur in the context of forces
and the need for a consideration of binding affinities in the context
of a changing mechanical landscape necessitates a new way to consider
the biochemistry of protein–protein interactions. In the past
few decades, the field of mechanobiology has exploded, as both the
appreciation of, and the technical advances required to facilitate
the study of, how forces impact biological processes have become evident.
The aim of this review is to introduce the concept of force dependence
of biomolecular interactions and the requirement to be able to measure
force-dependent binding constants. The focus of this discussion will
be on the mechanotransduction that occurs at the integrin-mediated
adhesions with the extracellular matrix and the major mechanosensors
talin and vinculin. However, the approaches that the cell uses to
sense and respond to forces can be applied to other systems, and this
therefore provides a general discussion of the force dependence of
biomolecule interactions.
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Affiliation(s)
- Yinan Wang
- Department of Physics , National University of Singapore , 117542 Singapore
| | - Jie Yan
- Department of Physics , National University of Singapore , 117542 Singapore.,Mechanobiology Institute , National University of Singapore , 117411 Singapore
| | - Benjamin T Goult
- School of Biosciences , University of Kent , Canterbury , Kent CT2 7NJ , U.K
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17
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Wang WB, Zhu JZ, Li XY, Li CH, Su JG, Li JY. Enhancement of protein mechanical stability: Correlated deformations are handcuffed by ligand binding. J Chem Phys 2019; 150:155102. [PMID: 31005084 DOI: 10.1063/1.5054932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
As revealed by previous experiments, protein mechanical stability can be effectively regulated by ligand binding with the binding site distant from the force-bearing region. However, the mechanism for such long-range allosteric control of protein mechanics is still largely unknown. In this work, we use protein topology-based elastic network model (ENM) and all-atomic steered molecular dynamics (SMD) simulations to study the impact of ligand binding on protein mechanical stability in two systems, i.e., GB1 and CheY-binding P2-domain of CheA (CBDCheA). Both ENM and SMD results show that the ligand binding has considerable and negligible effects on the mechanical stability of these two proteins, respectively. These results are consistent with the experimental observations. A physical mechanism for the enhancement of protein mechanical stability was then proposed: the correlated deformations of the force-bearing region and the binding site are handcuffed by the binding of ligand. The handcuff effect suppresses the propagation of internal force in the force-bearing region, thus improving the resistance to the loading force. Our study indicates that ENM method can effectively identify the structure motifs allosterically related to the deformation in the force bearing region, as well as the force propagation pathway within the structure of the studied proteins. Hence, it should be helpful to understand the molecular origin of the different mechanical properties in response to ligand binding for GB1 and CBDCheA.
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Affiliation(s)
- Wei Bu Wang
- Key Laboratory for Microstructural Material Physics of Hebei Province, College of Science, Yanshan University, Qinhuangdao 066004, China
| | - Jian Zhuo Zhu
- Key Laboratory for Microstructural Material Physics of Hebei Province, College of Science, Yanshan University, Qinhuangdao 066004, China
| | - Xing Yuan Li
- Key Laboratory for Microstructural Material Physics of Hebei Province, College of Science, Yanshan University, Qinhuangdao 066004, China
| | - Chun Hua Li
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Ji Guo Su
- Key Laboratory for Microstructural Material Physics of Hebei Province, College of Science, Yanshan University, Qinhuangdao 066004, China
| | - Jing Yuan Li
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
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18
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Abstract
The genome-wide occurrence of G-quadruplexes and their demonstrated biological activities call for detailed understanding on the stability and transition kinetics of the structures. Although the core structural element in a G-quadruplex is simple and requires only four tandem repeats of Guanine rich sequences, there is rather rich conformational diversity in this structure. Corresponding to this structural diversity, it displays involved transition kinetics within individual G-quadruplexes and complicated interconversion among different G-quadruplex species. Due to the inherently high signal-to-noise ratio in the measurement, single-molecule tools offer a unique capability to investigate the thermodynamic, kinetic, and mechanical properties of G-quadruplexes with dynamic conformations. In this chapter, we describe different single molecule methods such as atomic-force microscopy (AFM), single-molecule fluorescence resonance energy transfer (smFRET), optical, magnetic, and magneto-optical tweezers to investigate G-quadruplex structures as well as their interactions with small-molecule ligands.
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Affiliation(s)
- Shankar Mandal
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA
| | | | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA.
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19
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Xiao A, Li H. Direct monitoring of equilibrium protein folding–unfolding by atomic force microscopy: pushing the limit. Chem Commun (Camb) 2019; 55:12920-12923. [DOI: 10.1039/c9cc06293a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the direct observation of equilibrium folding–unfolding dynamics of a mechanically labile, three helix bundle protein GA using a commercial atomic force microscope (AFM).
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Affiliation(s)
- Adam Xiao
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
| | - Hongbin Li
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
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20
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Izadi D, Chen Y, Whitmore ML, Slivka JD, Ching K, Lapidus LJ, Comstock MJ. Combined Force Ramp and Equilibrium High-Resolution Investigations Reveal Multipath Heterogeneous Unfolding of Protein G. J Phys Chem B 2018; 122:11155-11165. [DOI: 10.1021/acs.jpcb.8b06199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Dena Izadi
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yujie Chen
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Miles L. Whitmore
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Joseph D. Slivka
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kevin Ching
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Lisa J. Lapidus
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Matthew J. Comstock
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
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21
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Hua B, Wang Y, Park S, Han KY, Singh D, Kim JH, Cheng W, Ha T. The Single-Molecule Centroid Localization Algorithm Improves the Accuracy of Fluorescence Binding Assays. Biochemistry 2018; 57:1572-1576. [PMID: 29457977 PMCID: PMC6149537 DOI: 10.1021/acs.biochem.7b01293] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Here, we demonstrate that the use of the single-molecule centroid localization algorithm can improve the accuracy of fluorescence binding assays. Two major artifacts in this type of assay, i.e., nonspecific binding events and optically overlapping receptors, can be detected and corrected during analysis. The effectiveness of our method was confirmed by measuring two weak biomolecular interactions, the interaction between the B1 domain of streptococcal protein G and immunoglobulin G and the interaction between double-stranded DNA and the Cas9-RNA complex with limited sequence matches. This analysis routine requires little modification to common experimental protocols, making it readily applicable to existing data and future experiments.
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Affiliation(s)
- Boyang Hua
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Yanbo Wang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Seongjin Park
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kyu Young Han
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Digvijay Singh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Jin H. Kim
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wei Cheng
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
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22
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Walder R, Van Patten WJ, Adhikari A, Perkins TT. Going Vertical To Improve the Accuracy of Atomic Force Microscopy Based Single-Molecule Force Spectroscopy. ACS NANO 2018; 12:198-207. [PMID: 29244486 DOI: 10.1021/acsnano.7b05721] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Single-molecule force spectroscopy (SMFS) is a powerful technique to characterize the energy landscape of individual proteins, the mechanical properties of nucleic acids, and the strength of receptor-ligand interactions. Atomic force microscopy (AFM)-based SMFS benefits from ongoing progress in improving the precision and stability of cantilevers and the AFM itself. Underappreciated is that the accuracy of such AFM studies remains hindered by inadvertently stretching molecules at an angle while measuring only the vertical component of the force and extension, degrading both measurements. This inaccuracy is particularly problematic in AFM studies using double-stranded DNA and RNA due to their large persistence length (p ≈ 50 nm), often limiting such studies to other SMFS platforms (e.g., custom-built optical and magnetic tweezers). Here, we developed an automated algorithm that aligns the AFM tip above the DNA's attachment point to a coverslip. Importantly, this algorithm was performed at low force (10-20 pN) and relatively fast (15-25 s), preserving the connection between the tip and the target molecule. Our data revealed large uncorrected lateral offsets for 100 and 650 nm DNA molecules [24 ± 18 nm (mean ± standard deviation) and 180 ± 110 nm, respectively]. Correcting this offset yielded a 3-fold improvement in accuracy and precision when characterizing DNA's overstretching transition. We also demonstrated high throughput by acquiring 88 geometrically corrected force-extension curves of a single individual 100 nm DNA molecule in ∼40 min and versatility by aligning polyprotein- and PEG-based protein-ligand assays. Importantly, our software-based algorithm was implemented on a commercial AFM, so it can be broadly adopted. More generally, this work illustrates how to enhance AFM-based SMFS by developing more sophisticated data-acquisition protocols.
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Affiliation(s)
- Robert Walder
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
| | - William J Van Patten
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
| | - Ayush Adhikari
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado , Boulder, Colorado 80309, United States
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23
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Edwards DT, Faulk JK, LeBlanc MA, Perkins TT. Force Spectroscopy with 9-μs Resolution and Sub-pN Stability by Tailoring AFM Cantilever Geometry. Biophys J 2017; 113:2595-2600. [PMID: 29132641 DOI: 10.1016/j.bpj.2017.10.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 10/11/2017] [Indexed: 01/08/2023] Open
Abstract
Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is a powerful yet accessible means to characterize the unfolding/refolding dynamics of individual molecules and resolve closely spaced, transiently occupied folding intermediates. On a modern commercial AFM, these applications and others are now limited by the mechanical properties of the cantilever. Specifically, AFM-based SMFS data quality is degraded by a commercial cantilever's limited combination of temporal resolution, force precision, and force stability. Recently, we modified commercial cantilevers with a focused ion beam to optimize their properties for SMFS. Here, we extend this capability by modifying a 40 × 18 μm2 cantilever into one terminated with a gold-coated, 4 × 4 μm2 reflective region connected to an uncoated 2-μm-wide central shaft. This "Warhammer" geometry achieved 8.5-μs resolution coupled with improved force precision and sub-pN stability over 100 s when measured on a commercial AFM. We highlighted this cantilever's biological utility by first resolving a calmodulin unfolding intermediate previously undetected by AFM and then measuring the stabilization of calmodulin by myosin light chain kinase at dramatically higher unfolding velocities than in previous AFM studies. More generally, enhancing data quality via an improved combination of time resolution, force precision, and force stability will broadly benefit biological applications of AFM.
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Affiliation(s)
- Devin T Edwards
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado
| | - Jaevyn K Faulk
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado
| | - Marc-André LeBlanc
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado; Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado.
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24
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Camunas-Soler J, Alemany A, Ritort F. Experimental measurement of binding energy, selectivity, and allostery using fluctuation theorems. Science 2017; 355:412-415. [PMID: 28126820 DOI: 10.1126/science.aah4077] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/16/2016] [Indexed: 12/13/2022]
Abstract
Thermodynamic bulk measurements of binding reactions rely on the validity of the law of mass action and the assumption of a dilute solution. Yet, important biological systems such as allosteric ligand-receptor binding, macromolecular crowding, or misfolded molecules may not follow these assumptions and may require a particular reaction model. Here we introduce a fluctuation theorem for ligand binding and an experimental approach using single-molecule force spectroscopy to determine binding energies, selectivity, and allostery of nucleic acids and peptides in a model-independent fashion. A similar approach could be used for proteins. This work extends the use of fluctuation theorems beyond unimolecular folding reactions, bridging the thermodynamics of small systems and the basic laws of chemical equilibrium.
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Affiliation(s)
- Joan Camunas-Soler
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, Spain
| | - Anna Alemany
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, Spain
| | - Felix Ritort
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Barcelona, Spain. .,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, Spain
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25
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Walder R, LeBlanc MA, Van Patten WJ, Edwards DT, Greenberg JA, Adhikari A, Okoniewski SR, Sullan RMA, Rabuka D, Sousa MC, Perkins TT. Rapid Characterization of a Mechanically Labile α-Helical Protein Enabled by Efficient Site-Specific Bioconjugation. J Am Chem Soc 2017; 139:9867-9875. [PMID: 28677396 DOI: 10.1021/jacs.7b02958] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is a powerful yet accessible means to characterize mechanical properties of biomolecules. Historically, accessibility relies upon the nonspecific adhesion of biomolecules to a surface and a cantilever and, for proteins, the integration of the target protein into a polyprotein. However, this assay results in a low yield of high-quality data, defined as the complete unfolding of the polyprotein. Additionally, nonspecific surface adhesion hinders studies of α-helical proteins, which unfold at low forces and low extensions. Here, we overcame these limitations by merging two developments: (i) a polyprotein with versatile, genetically encoded short peptide tags functionalized via a mechanically robust Hydrazino-Pictet-Spengler ligation and (ii) the efficient site-specific conjugation of biomolecules to PEG-coated surfaces. Heterobifunctional anchoring of this polyprotein construct and DNA via copper-free click chemistry to PEG-coated substrates and a strong but reversible streptavidin-biotin linkage to PEG-coated AFM tips enhanced data quality and throughput. For example, we achieved a 75-fold increase in the yield of high-quality data and repeatedly probed the same individual polyprotein to deduce its dynamic force spectrum in just 2 h. The broader utility of this polyprotein was demonstrated by measuring three diverse target proteins: an α-helical protein (calmodulin), a protein with internal cysteines (rubredoxin), and a computationally designed three-helix bundle (α3D). Indeed, at low loading rates, α3D represents the most mechanically labile protein yet characterized by AFM. Such efficient SMFS studies on a commercial AFM enable the rapid characterization of macromolecular folding over a broader range of proteins and a wider array of experimental conditions (pH, temperature, denaturants). Further, by integrating these enhancements with optical traps, we demonstrate how efficient bioconjugation to otherwise nonstick surfaces can benefit diverse single-molecule studies.
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Affiliation(s)
- Robert Walder
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder, Colorado 80309, United States
| | | | - William J Van Patten
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder, Colorado 80309, United States
| | - Devin T Edwards
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder, Colorado 80309, United States
| | | | - Ayush Adhikari
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder, Colorado 80309, United States
| | - Stephen R Okoniewski
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder, Colorado 80309, United States
| | - Ruby May A Sullan
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder, Colorado 80309, United States
| | - David Rabuka
- Catalent Biologics-West , Emeryville, California 94608, United States
| | | | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder, Colorado 80309, United States
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26
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Abstract
Advancements in single-molecule force spectroscopy techniques such as atomic force microscopy and magnetic tweezers allow investigation of how domain folding under force can play a physiological role. Combining these techniques with protein engineering and HaloTag covalent attachment, we investigate similarities and differences between four model proteins: I10 and I91-two immunoglobulin-like domains from the muscle protein titin, and two α + β fold proteins-ubiquitin and protein L. These proteins show a different mechanical response and have unique extensions under force. Remarkably, when normalized to their contour length, the size of the unfolding and refolding steps as a function of force reduces to a single master curve. This curve can be described using standard models of polymer elasticity, explaining the entropic nature of the measured steps. We further validate our measurements with a simple energy landscape model, which combines protein folding with polymer physics and accounts for the complex nature of tandem domains under force. This model can become a useful tool to help in deciphering the complexity of multidomain proteins operating under force.
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Affiliation(s)
- Jessica Valle-Orero
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
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27
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Ramírez MP, Rivera M, Quiroga-Roger D, Bustamante A, Vega M, Baez M, Puchner EM, Wilson CAM. Single molecule force spectroscopy reveals the effect of BiP chaperone on protein folding. Protein Sci 2017; 26:1404-1412. [PMID: 28176394 DOI: 10.1002/pro.3137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/18/2017] [Accepted: 02/03/2017] [Indexed: 11/10/2022]
Abstract
BiP (Immunoglobulin Binding Protein) is a member of the Hsp70 chaperones that participates in protein folding in the endoplasmic reticulum. The function of BiP relies on cycles of ATP hydrolysis driving the binding and release of its substrate proteins. It still remains unknown how BiP affects the protein folding pathway and there has been no direct demonstration showing which folding state of the substrate protein is bound by BiP, as previous work has used only peptides. Here, we employ optical tweezers for single molecule force spectroscopy experiments to investigate how BiP affects the folding mechanism of a complete protein and how this effect depends on nucleotides. Using the protein MJ0366 as the substrate for BiP, we performed pulling and relaxing cycles at constant velocity to unfold and refold the substrate. In the absence of BiP, MJ0366 unfolded and refolded in every cycle. However, when BiP was added, the frequency of folding events of MJ0366 significantly decreased, and the loss of folding always occurred after a successful unfolding event. This process was dependent on ATP and ADP, since when either ATP was decreased or ADP was added, the duration of periods without folding events increased. Our results show that the affinity of BiP for the substrate protein increased in these conditions, which correlates with previous studies in bulk. Therefore, we conclude that BiP binds to the unfolded state of MJ0366 and prevents its refolding, and that this effect is dependent on both the type and concentration of nucleotides.
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Affiliation(s)
- María Paz Ramírez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile.,Laboratory of Cellular and Molecular Biophysics, School of Physics & Astronomy, University of Minnesota, Twin Cities, Minnesota
| | - Maira Rivera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Diego Quiroga-Roger
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Andrés Bustamante
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Marcela Vega
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Elias M Puchner
- Laboratory of Cellular and Molecular Biophysics, School of Physics & Astronomy, University of Minnesota, Twin Cities, Minnesota
| | - Christian A M Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
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28
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Edwards DT, Perkins TT. Optimizing force spectroscopy by modifying commercial cantilevers: Improved stability, precision, and temporal resolution. J Struct Biol 2017; 197:13-25. [DOI: 10.1016/j.jsb.2016.01.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/13/2016] [Accepted: 01/18/2016] [Indexed: 11/24/2022]
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29
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Lei H, He C, Hu C, Li J, Hu X, Hu X, Li H. Single-Molecule Force Spectroscopy Trajectories of a Single Protein and Its Polyproteins Are Equivalent: A Direct Experimental Validation Based on A Small Protein NuG2. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610648] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hai Lei
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Chengzhi He
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Chunguang Hu
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Jinliang Li
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
| | - Xiaodong Hu
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Xiaotang Hu
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Hongbin Li
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
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30
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Lei H, He C, Hu C, Li J, Hu X, Hu X, Li H. Single-Molecule Force Spectroscopy Trajectories of a Single Protein and Its Polyproteins Are Equivalent: A Direct Experimental Validation Based on A Small Protein NuG2. Angew Chem Int Ed Engl 2016; 56:6117-6121. [DOI: 10.1002/anie.201610648] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Hai Lei
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Chengzhi He
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Chunguang Hu
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Jinliang Li
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
| | - Xiaodong Hu
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Xiaotang Hu
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Hongbin Li
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
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31
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Popa I, Rivas-Pardo JA, Eckels EC, Echelman DJ, Badilla CL, Valle-Orero J, Fernández JM. A HaloTag Anchored Ruler for Week-Long Studies of Protein Dynamics. J Am Chem Soc 2016; 138:10546-53. [PMID: 27409974 PMCID: PMC5510598 DOI: 10.1021/jacs.6b05429] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Under physiological conditions, protein oxidation and misfolding occur with very low probability and on long times scales. Single-molecule techniques provide the ability to distinguish between properly folded and damaged proteins that are otherwise masked in ensemble measurements. However, at physiological conditions these rare events occur with a time constant of several hours, inaccessible to current single-molecule approaches. Here we present a magnetic-tweezers-based technique that allows, for the first time, the study of folding of single proteins during week-long experiments. This technique combines HaloTag anchoring, sub-micrometer positioning of magnets, and an active correction of the focal drift. Using this technique and protein L as a molecular template, we generate a magnet law by correlating the distance between the magnet and the measuring paramagnetic bead with unfolding/folding steps. We demonstrate that, using this magnet law, we can accurately measure the dynamics of proteins over a wide range of forces, with minimal dispersion from bead to bead. We also show that the force calibration remains invariant over week-long experiments applied to the same single proteins. The approach demonstrated in this Article opens new, exciting ways to examine proteins on the "human" time scale and establishes magnetic tweezers as a valuable technique to study low-probability events that occur during protein folding under force.
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Affiliation(s)
- Ionel Popa
- Department of Biological Sciences, Columbia University , 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Jaime Andrés Rivas-Pardo
- Department of Biological Sciences, Columbia University , 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Edward C Eckels
- Department of Biological Sciences, Columbia University , 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Daniel J Echelman
- Department of Biological Sciences, Columbia University , 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Carmen L Badilla
- Department of Biological Sciences, Columbia University , 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Jessica Valle-Orero
- Department of Biological Sciences, Columbia University , 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Julio M Fernández
- Department of Biological Sciences, Columbia University , 1212 Amsterdam Avenue, New York, New York 10027, United States
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32
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Effects of ligand binding on the mechanical stability of protein GB1 studied by steered molecular dynamics simulation. J Mol Model 2016; 22:188. [DOI: 10.1007/s00894-016-3052-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 06/28/2016] [Indexed: 10/21/2022]
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33
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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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34
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Teixeira SR, Lloyd C, Yao S, Whitaker IS, Francis L, Conlan RS, Azzopardi E. Polyaniline-graphene based α-amylase biosensor with a linear dynamic range in excess of 6 orders of magnitude. Biosens Bioelectron 2016; 85:395-402. [PMID: 27196256 DOI: 10.1016/j.bios.2016.05.034] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/21/2016] [Accepted: 05/08/2016] [Indexed: 11/19/2022]
Abstract
α-amylase is an established marker for diagnosis of pancreatic and salivary disease, and recent research has seen a substantial expansion of its use in therapeutic and diagnostic applications for infection, cancer and wound healing. The lack of bedside monitoring devices for α-amylase detection has hitherto restricted the clinical progress of such applications. We have developed a highly sensitive α-amylase immunosensor platform, produced via in situ electropolymerization of aniline onto a screen-printed graphene support (SPE). Covalently binding an α-amylase specific antibody to a polyaniline (PANI) layer and controlling device assembly using electrochemical impedance spectroscopy (EIS), we have achieved a highly linear response against α-amylase concentration. Each stage of the assembly was characterized using a suite of high-resolution topographical, chemical and mechanical techniques. Quantitative, highly sensitive detection was demonstrated using an artificially spiked human blood plasma samples. The device has a remarkably wide limit of quantification (0.025-1000IU/L) compared to α-amylase assays in current clinical use. With potential for simple scale up to volume manufacturing though standard semiconductor production techniques and subsequently clinical application, this biosensor will enable clinical benefit through early disease detection, and better informed administration of correct therapeutic dose of drugs used to treat α-amylase related diseases.
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Affiliation(s)
- Sofia Rodrigues Teixeira
- College of Engineering, Swansea University, Bay Campus, Swansea SA1 8QQ, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea SA2 8PP, UK.
| | - Catherine Lloyd
- College of Engineering, Swansea University, Bay Campus, Swansea SA1 8QQ, UK; Swansea University Medical School, Singleton Park, Swansea SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea SA2 8PP, UK
| | - Seydou Yao
- Swansea University Medical School, Singleton Park, Swansea SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea SA2 8PP, UK
| | - Iain S Whitaker
- Swansea University Medical School, Singleton Park, Swansea SA2 8PP, UK; The Welsh Centre for Burns and Plastic Surgery, Morriston Hospital, Swansea SA66NL, UK
| | - Lewis Francis
- Swansea University Medical School, Singleton Park, Swansea SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea SA2 8PP, UK
| | - R Steven Conlan
- Swansea University Medical School, Singleton Park, Swansea SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea SA2 8PP, UK
| | - Ernest Azzopardi
- Swansea University Medical School, Singleton Park, Swansea SA2 8PP, UK; The Welsh Centre for Burns and Plastic Surgery, Morriston Hospital, Swansea SA66NL, UK
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35
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Stigler J, Rief M. Ligand-induced changes of the apparent transition-state position in mechanical protein unfolding. Biophys J 2016. [PMID: 26200872 DOI: 10.1016/j.bpj.2015.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Force-spectroscopic measurements of ligand-receptor systems and the unfolding/folding of nucleic acids or proteins reveal information on the underlying energy landscape along the pulling coordinate. The slope Δx(‡) of the force-dependent unfolding/unbinding rates is interpreted as the distance from the folded/bound state to the transition state for unfolding/unbinding and, hence, often related to the mechanical compliance of the sample molecule. Here we show that in ligand-binding proteins, the experimentally inferred Δx(‡) can depend on the ligand concentration, unrelated to changes in mechanical compliance. We describe the effect in single-molecule, force-spectroscopy experiments of the calcium-binding protein calmodulin and explain it in a simple model where mechanical unfolding and ligand binding occur on orthogonal reaction coordinates. This model predicts changes in the experimentally inferred Δx(‡), depending on ligand concentration and the associated shift of the dominant barrier between the two reaction coordinates. We demonstrate quantitative agreement between experiments and simulations using a realistic six-state kinetic scheme using literature values for calcium-binding kinetics and affinities. Our results have important consequences for the interpretation of force-spectroscopic data of ligand-binding proteins.
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Affiliation(s)
- Johannes Stigler
- Physik Department E22, Technische Universität München, Garching, Germany.
| | - Matthias Rief
- Physik Department E22, Technische Universität München, Garching, Germany; Munich Center for Integrated Protein Science, München, Germany
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36
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Gou X, Wang R, Lam SSY, Hou J, Leung AYH, Sun D. Cell adhesion manipulation through single cell assembly for characterization of initial cell-to-cell interaction. Biomed Eng Online 2015; 14:114. [PMID: 26652601 PMCID: PMC4676142 DOI: 10.1186/s12938-015-0109-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 11/28/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cell-to-cell interactions are complex processes that involve physical interactions, chemical binding, and biological signaling pathways. Identification of the functions of special signaling pathway in cell-to-cell interaction from the very first contact will help characterize the mechanism underlying the interaction and advance new drug discovery. METHODS This paper reported a case study of characterizing initial interaction between leukemia cancer cells and bone marrow stromal cells, through the use of an optical tweezers-based cell manipulation tool. Optical traps were used to assemble leukemia cells at different positions of the stromal cell layer and enable their interactions by applying a small trapping force to maintain the cell contact for a few minutes. Specific drug was used to inhibit the binding of molecules during receptor-ligand-mediated adhesion. RESULTS AND CONCLUSIONS Our results showed that the amount of adhesion molecule could affect cell adhesion during the first few minutes contact. We also found that leukemia cancer cells could migrate on the stromal cell layer, which was dependent on the adhesion state and activation triggered by specific chemokine. The reported approaches provided a new opportunity to investigate cell-to-cell interaction through single cell adhesion manipulation.
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Affiliation(s)
- Xue Gou
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong, China.
| | - Ran Wang
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong, China.
| | - Stephen S Y Lam
- Department of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Jundi Hou
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong, China.
| | - Anskar Y H Leung
- Department of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Dong Sun
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong, China.
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37
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Rivas-Pardo JA, Alegre-Cebollada J, Ramírez-Sarmiento CA, Fernandez JM, Guixé V. Identifying sequential substrate binding at the single-molecule level by enzyme mechanical stabilization. ACS NANO 2015; 9:3996-4005. [PMID: 25840594 PMCID: PMC4467879 DOI: 10.1021/nn507480v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Enzyme-substrate binding is a dynamic process intimately coupled to protein structural changes, which in turn changes the unfolding energy landscape. By the use of single-molecule force spectroscopy (SMFS), we characterize the open-to-closed conformational transition experienced by the hyperthermophilic adenine diphosphate (ADP)-dependent glucokinase from Thermococcus litoralis triggered by the sequential binding of substrates. In the absence of substrates, the mechanical unfolding of TlGK shows an intermediate 1, which is stabilized in the presence of Mg·ADP(-), the first substrate to bind to the enzyme. However, in the presence of this substrate, an additional unfolding event is observed, intermediate 1*. Finally, in the presence of both substrates, the unfolding force of intermediates 1 and 1* increases as a consequence of the domain closure. These results show that SMFS can be used as a powerful experimental tool to investigate binding mechanisms of different enzymes with more than one ligand, expanding the repertoire of protocols traditionally used in enzymology.
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Affiliation(s)
- Jaime Andrés Rivas-Pardo
- Department of Biological Sciences, Columbia University, Northwest Corner Building, 550 West 120 Street, New York, New York 10027, USA
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Jorge Alegre-Cebollada
- Department of Biological Sciences, Columbia University, Northwest Corner Building, 550 West 120 Street, New York, New York 10027, USA
| | - César A. Ramírez-Sarmiento
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Julio M. Fernandez
- Department of Biological Sciences, Columbia University, Northwest Corner Building, 550 West 120 Street, New York, New York 10027, USA
| | - Victoria Guixé
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
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38
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Tych KM, Hughes ML, Bourke J, Taniguchi Y, Kawakami M, Brockwell DJ, Dougan L. Optimizing the calculation of energy landscape parameters from single-molecule protein unfolding experiments. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:012710. [PMID: 25679645 DOI: 10.1103/physreve.91.012710] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Indexed: 06/04/2023]
Abstract
Single-molecule force spectroscopy using an atomic force microscope (AFM) can be used to measure the average unfolding force of proteins in a constant velocity experiment. In combination with Monte Carlo simulations and through the application of the Zhurkov-Bell model, information about the parameters describing the underlying unfolding energy landscape of the protein can be obtained. Using this approach, we have completed protein unfolding experiments on the polyprotein (I27)(5) over a range of pulling velocities. In agreement with previous work, we find that the observed number of protein unfolding events observed in each approach-retract cycle varies between one and five, due to the nature of the interactions between the polyprotein, the AFM tip, and the substrate, and there is an unequal unfolding probability distribution. We have developed a Monte Carlo simulation that incorporates the impact of this unequal unfolding probability distribution on the median unfolding force and the calculation of the protein unfolding energy landscape parameters. These results show that while there is a significant, unequal unfolding probability distribution, the unfolding energy landscape parameters obtained from use of the Zhurkov-Bell model are not greatly affected. This result is important because it demonstrates that the minimum acceptance criteria typically used in force extension experiments are justified and do not skew the calculation of the unfolding energy landscape parameters. We further validate this approach by determining the error in the energy landscape parameters for two extreme cases, and we provide suggestions for methods that can be employed to increase the level of accuracy in single-molecule experiments using polyproteins.
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Affiliation(s)
- Katarzyna M Tych
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Megan L Hughes
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - James Bourke
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yukinori Taniguchi
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Masaru Kawakami
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lorna Dougan
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
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39
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Single-molecule force spectroscopy reveals force-enhanced binding of calcium ions by gelsolin. Nat Commun 2014; 5:4623. [PMID: 25100107 PMCID: PMC4143929 DOI: 10.1038/ncomms5623] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 07/08/2014] [Indexed: 01/30/2023] Open
Abstract
Force is increasingly recognized as an important element in controlling biological processes. Forces can deform native protein conformations leading to protein-specific effects. Protein–protein binding affinities may be decreased, or novel protein–protein interaction sites may be revealed, on mechanically stressing one or more components. Here we demonstrate that the calcium-binding affinity of the sixth domain of the actin-binding protein gelsolin (G6) can be enhanced by mechanical force. Our kinetic model suggests that the calcium-binding affinity of G6 increases exponentially with force, up to the point of G6 unfolding. This implies that gelsolin may be activated at lower calcium ion levels when subjected to tensile forces. The demonstration that cation–protein binding affinities can be force-dependent provides a new understanding of the complex behaviour of cation-regulated proteins in stressful cellular environments, such as those found in the cytoskeleton-rich leading edge and at cell adhesions. The application of force can influence biological processes such as ligand and protein–protein binding, with mechanical stress typically hindering such interactions. Here, the authors use atomic force microscopy to show that the binding of calcium to gelsolin can be improved under stress.
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40
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Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains. Proc Natl Acad Sci U S A 2014; 111:10550-5. [PMID: 25002491 DOI: 10.1073/pnas.1402768111] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ligand binding modulates the energy landscape of proteins, thus altering their folding and allosteric conformational dynamics. To investigate such interplay, calmodulin has been a model protein. Despite much attention, fully resolved mechanisms of calmodulin folding/binding have not been elucidated. Here, by constructing a computational model that can integrate folding, binding, and allosteric motions, we studied in-depth folding of isolated calmodulin domains coupled with binding of two calcium ions and associated allosteric conformational changes. First, mechanically pulled simulations revealed coexistence of three distinct conformational states: the unfolded, the closed, and the open states, which is in accord with and augments structural understanding of recent single-molecule experiments. Second, near the denaturation temperature, we found the same three conformational states as well as three distinct binding states: zero, one, and two calcium ion bound states, leading to as many as nine states. Third, in terms of the nine-state representation, we found multiroute folding/binding pathways and shifts in their probabilities with the calcium concentration. At a lower calcium concentration, "combined spontaneous folding and induced fit" occurs, whereas at a higher concentration, "binding-induced folding" dominates. Even without calcium binding, we observed that the folding pathway of calmodulin domains can be modulated by the presence of metastable states. Finally, full-length calmodulin also exhibited an intriguing coupling between two domains when applying tension.
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41
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Bull MS, Sullan RMA, Li H, Perkins TT. Improved single molecule force spectroscopy using micromachined cantilevers. ACS NANO 2014; 8:4984-95. [PMID: 24670198 DOI: 10.1021/nn5010588] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Enhancing the short-term force precision of atomic force microscopy (AFM) while maintaining excellent long-term force stability would result in improved performance across multiple AFM modalities, including single molecule force spectroscopy (SMFS). SMFS is a powerful method to probe the nanometer-scale dynamics and energetics of biomolecules (DNA, RNA, and proteins). The folding and unfolding rates of such macromolecules are sensitive to sub-pN changes in force. Recently, we demonstrated sub-pN stability over a broad bandwidth (Δf = 0.01-16 Hz) by removing the gold coating from a 100 μm long cantilever. However, this stability came at the cost of increased short-term force noise, decreased temporal response, and poor sensitivity. Here, we avoided these compromises while retaining excellent force stability by modifying a short (L = 40 μm) cantilever with a focused ion beam. Our process led to a ∼10-fold reduction in both a cantilever's stiffness and its hydrodynamic drag near a surface. We also preserved the benefits of a highly reflective cantilever while mitigating gold-coating induced long-term drift. As a result, we extended AFM's sub-pN bandwidth by a factor of ∼50 to span five decades of bandwidth (Δf ≈ 0.01-1000 Hz). Measurements of mechanically stretching individual proteins showed improved force precision coupled with state-of-the-art force stability and no significant loss in temporal resolution compared to the stiffer, unmodified cantilever. Finally, these cantilevers were robust and were reused for SFMS over multiple days. Hence, we expect these responsive, yet stable, cantilevers to broadly benefit diverse AFM-based studies.
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Affiliation(s)
- Matthew S Bull
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder, Colorado 80309, United States
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42
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Hu X, Li H. Force spectroscopy studies on protein-ligand interactions: a single protein mechanics perspective. FEBS Lett 2014; 588:3613-20. [PMID: 24747422 DOI: 10.1016/j.febslet.2014.04.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 01/04/2023]
Abstract
Protein-ligand interactions are ubiquitous and play important roles in almost every biological process. The direct elucidation of the thermodynamic, structural and functional consequences of protein-ligand interactions is thus of critical importance to decipher the mechanism underlying these biological processes. A toolbox containing a variety of powerful techniques has been developed to quantitatively study protein-ligand interactions in vitro as well as in living systems. The development of atomic force microscopy-based single molecule force spectroscopy techniques has expanded this toolbox and made it possible to directly probe the mechanical consequence of ligand binding on proteins. Many recent experiments have revealed how ligand binding affects the mechanical stability and mechanical unfolding dynamics of proteins, and provided mechanistic understanding on these effects. The enhancement effect of mechanical stability by ligand binding has been used to help tune the mechanical stability of proteins in a rational manner and develop novel functional binding assays for protein-ligand interactions. Single molecule force spectroscopy studies have started to shed new lights on the structural and functional consequence of ligand binding on proteins that bear force under their biological settings.
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Affiliation(s)
- Xiaotang Hu
- State Key Laboratory of Precision Measurements Technology and Instruments, School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin 300072, PR China
| | - Hongbin Li
- State Key Laboratory of Precision Measurements Technology and Instruments, School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin 300072, PR China; Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
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43
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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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44
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Scholl ZN, Li Q, Marszalek PE. Single molecule mechanical manipulation for studying biological properties of proteins,
DNA
, and sugars. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2013; 6:211-29. [DOI: 10.1002/wnan.1253] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/10/2013] [Accepted: 10/17/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Zackary N. Scholl
- Department of Computational Biology and Bioinformatics Duke University Durham NC USA
| | - Qing Li
- Department of Mechanical Engineering and Materials Science Duke University Durham NC USA
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials Science, Center for Biologically Inspired Materials and Material Systems Duke University Durham NC USA
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45
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Lv C, Zou D, Qin M, Meng W, Cao Y, Wang W. Hydrodynamic force depends not only on the viscosity of solution but also on the molecular weights of viscogens. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:10624-10629. [PMID: 23944228 DOI: 10.1021/la4023689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Many cellular processes, such as the diffusion of biomacromolecules, the movement of molecular motors, and the conformational dynamics of proteins, are subjected to hydrodynamic forces because of the high viscosities of cellular environments. However, it is still unknown how hydrodynamic forces are related to the physical properties of different viscogens. Here, using the atomic force microscope-based force spectroscopy technique, we directly measured the hydrodynamic forces acting on a moving cantilever in various viscogen solutions. We found that the hydrodynamic force is not only dependent on the viscosity but also related to the molecular weight of viscogens. Counterintuitively, at the same macroscopic viscosity, the hydrodynamic force rises with the increasing molecular weight of viscogens, although the local microscopic viscosity of the solution decreases. This finding provides insights into the origin of hydrodynamic forces in biomolecule solutions and could inspire many force-spectroscopy-based techniques to measure the molecular weight and conformational changes of biomacromolecules in biological settings directly.
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Affiliation(s)
- Chunmei Lv
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiangsu, 210093 PR China
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46
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Mashaghi A, Kramer G, Bechtluft P, Zachmann-Brand B, Driessen AJM, Bukau B, Tans SJ. Reshaping of the conformational search of a protein by the chaperone trigger factor. Nature 2013; 500:98-101. [DOI: 10.1038/nature12293] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 05/14/2013] [Indexed: 12/20/2022]
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Bujalowski PJ, Oberhauser AF. Tracking unfolding and refolding reactions of single proteins using atomic force microscopy methods. Methods 2013; 60:151-60. [PMID: 23523554 DOI: 10.1016/j.ymeth.2013.03.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/07/2013] [Accepted: 03/11/2013] [Indexed: 11/26/2022] Open
Abstract
During the last two decades single-molecule manipulation techniques such as atomic force microscopy (AFM) has risen to prominence through their unique capacity to provide fundamental information on the structure and function of biomolecules. Here we describe the use of single-molecule AFM to track protein unfolding and refolding pathways, enzymatic catalysis and the effects of osmolytes and chaperones on protein stability and folding. We will outline the principles of operation for two different AFM pulling techniques: length clamp and force-clamp and discuss prominent applications. We provide protocols for the construction of polyproteins which are amenable for AFM experiments, the preparation of different coverslips, choice and calibration of AFM cantilevers. We also discuss the selection criteria for AFM recordings, the calibration of AFM cantilevers, protein sample preparations and analysis of the obtained data.
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Affiliation(s)
- Paul J Bujalowski
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, TX 77555, USA
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Settanni G, Serquera D, Marszalek PE, Paci E, Itzhaki LS. Effects of ligand binding on the mechanical properties of ankyrin repeat protein gankyrin. PLoS Comput Biol 2013; 9:e1002864. [PMID: 23341763 PMCID: PMC3547791 DOI: 10.1371/journal.pcbi.1002864] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 11/11/2012] [Indexed: 11/30/2022] Open
Abstract
Ankyrin repeat proteins are elastic materials that unfold and refold sequentially, repeat by repeat, under force. Herein we use atomistic molecular dynamics to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with its binding partner S6-C. We show that the bound S6-C greatly increases the resistance of Gankyrin to mechanical stress. The effect is specific to those repeats of Gankyrin directly in contact with S6-C, and the mechanical ‘hot spots’ of the interaction map to the same repeats as the thermodynamic hot spots. A consequence of stepwise nature of unfolding and the localized nature of ligand binding is that it impacts on all aspects of the protein's mechanical behavior, including the order of repeat unfolding, the diversity of unfolding pathways accessed, the nature of partially unfolded intermediates, the forces required and the work transferred to the system to unfold the whole protein and its parts. Stepwise unfolding thus provides the means to buffer repeat proteins and their binding partners from mechanical stress in the cell. Our results illustrate how ligand binding can control the mechanical response of proteins. The data also point to a cellular mechano-switching mechanism whereby binding between two partner macromolecules is regulated by mechanical stress. Here we use molecular dynamics simulation to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with binding partner S6-C. Tandem repeat proteins like Gankyrin comprise tandem arrays of small structural motifs that pack linearly to produce elongated architectures. They are elastic, mechanically weak molecules and they unfold and refold repeat by repeat under force. We show that S6-C binding greatly increases the resistance of Gankyrin to mechanical stress. The enhanced mechanical stability is specific to those ankyrin repeats in contact with S6-C, and the localized nature of the effect results in fundamental changes in the way the protein responds to force. Thus, the forced unfolding of isolated Gankryin involves a diverse set of pathways with a preference for a C- to N-terminus unfolding mechanism whereas this diversity is reduced upon complex formation with the central repeats, which are those most tightly bound to the ligand, tending to unfold last. Our study shows how stepwise unfolding can buffer repeat proteins and their binding partners from mechanical stress in the cell. It also points to a mechano-switching mechanism whereby binding between two partner macromolecules is regulated by mechanical stress.
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Affiliation(s)
- Giovanni Settanni
- Physics Department, Johannes Gutenberg University, Mainz, Germany
- * E-mail: (GS); (EP); (LSI)
| | - David Serquera
- MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, United States of America
| | - Emanuele Paci
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- * E-mail: (GS); (EP); (LSI)
| | - Laura S. Itzhaki
- University of Cambridge Department of Chemistry, Cambridge, United Kingdom
- * E-mail: (GS); (EP); (LSI)
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Heidarsson PO, Naqvi MM, Sonar P, Valpapuram I, Cecconi C. Conformational Dynamics of Single Protein Molecules Studied by Direct Mechanical Manipulation. DYNAMICS OF PROTEINS AND NUCLEIC ACIDS 2013; 92:93-133. [DOI: 10.1016/b978-0-12-411636-8.00003-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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50
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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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