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Park C, Kim K, Kim Y, Zhu R, Hain L, Seferovic H, Kim MH, Woo HJ, Hwang H, Lee SH, Kim S, Lee JE, Hinterdorfer P, Ko K, Park S, Oh YJ. Plant-Derived Anti-Human Epidermal Growth Factor Receptor 2 Antibody Suppresses Trastuzumab-Resistant Breast Cancer with Enhanced Nanoscale Binding. ACS NANO 2024; 18:16126-16140. [PMID: 38764224 PMCID: PMC11210341 DOI: 10.1021/acsnano.4c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 05/21/2024]
Abstract
Traditional monoclonal antibodies such as Trastuzumab encounter limitations when treating Human Epidermal Growth Factor Receptor 2 (HER2)-positive breast cancer, particularly in cases that develop resistance. This study introduces plant-derived anti-HER2 variable fragments of camelid heavy chain domain (VHH) fragment crystallizable region (Fc) KEDL(K) antibody as a potent alternative for overcoming these limitations. A variety of biophysical techniques, in vitro assays, and in vivo experiments uncover the antibody's nanoscale binding dynamics with transmembrane HER2 on living cells. Single-molecule force spectroscopy reveals the rapid formation of two robust bonds, exhibiting approximately 50 pN force resistance and bond lifetimes in the second range. The antibody demonstrates a specific affinity for HER2-positive breast cancer cells, including those that are Trastuzumab-resistant. Moreover, in immune-deficient mice, the plant-derived anti-HER2 VHH-FcK antibody exhibits superior antitumor activity, especially against tumors that are resistant to Trastuzumab. These findings underscore the plant-derived antibody's potential as an impactful immunotherapeutic strategy for treating Trastuzumab-resistant HER2-positive breast cancer.
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Affiliation(s)
- Chanyong Park
- School
of Mechanical Engineering, Sungkyunkwan
University, Suwon 16419, Korea
| | - Kibum Kim
- Department
of Medicine, Medical Research Institute, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Yerin Kim
- Department
of Medicine, Medical Research Institute, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Rong Zhu
- Department
of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, 4040 Linz, Austria
| | - Lisa Hain
- Department
of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, 4040 Linz, Austria
| | - Hannah Seferovic
- Department
of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, 4040 Linz, Austria
| | - Min-Hyeok Kim
- School
of Mechanical Engineering, Sungkyunkwan
University, Suwon 16419, Korea
| | - Hyun Joo Woo
- Major
of Nano-Bioengineering, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea
| | - Hyunju Hwang
- Department
of Medicine, Medical Research Institute, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Seung Ho Lee
- Major
of Nano-Bioengineering, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea
| | - Sangmin Kim
- Department
of Breast Cancer Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Jeong Eon Lee
- Division
of Breast Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Peter Hinterdorfer
- Department
of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, 4040 Linz, Austria
| | - Kisung Ko
- Department
of Medicine, Medical Research Institute, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Sungsu Park
- School
of Mechanical Engineering, Sungkyunkwan
University, Suwon 16419, Korea
| | - Yoo Jin Oh
- Department
of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, 4040 Linz, Austria
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Sijmons D, Collett S, Soliman C, Guy AJ, Scott AM, Durrant LG, Elbourne A, Walduck AK, Ramsland PA. Probing the expression and adhesion of glycans involved in Helicobacter pylori infection. Sci Rep 2024; 14:8587. [PMID: 38615147 PMCID: PMC11016089 DOI: 10.1038/s41598-024-59234-w] [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] [Received: 12/19/2023] [Accepted: 04/08/2024] [Indexed: 04/15/2024] Open
Abstract
Helicobacter pylori infects approximately half the human population and has an unusual infective niche of the human stomach. Helicobacter pylori is a major cause of gastritis and has been classified as a group 1 carcinogen by the WHO. Treatment involves triple or quadruple antibiotic therapy, but antibiotic resistance is becoming increasingly prevalent. Helicobacter pylori expresses certain blood group related antigens (Lewis system) as a part of its lipopolysaccharide (LPS), which is thought to assist in immune evasion. Additionally, H. pylori LPS participates in adhesion to host cells alongside several adhesion proteins. This study profiled the carbohydrates of H. pylori reference strains (SS1 and 26695) using monoclonal antibodies (mAbs) and lectins, identifying interactions between two carbohydrate-targeting mAbs and multiple lectins. Atomic force microscopy (AFM) scans were used to probe lectin and antibody interactions with the bacterial surfaces. The selected mAb and lectins displayed an increased adhesive force over the surface of the curved H. pylori rods. Furthermore, this study demonstrates the ability of anti-carbohydrate antibodies to reduce the adhesion of H. pylori 26695 to human gastric adenocarcinoma cells via AFM. Targeting bacterial carbohydrates to disrupt crucial adhesion and immune evasion mechanisms represents a promising strategy for combating H. pylori infection.
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Affiliation(s)
- Daniel Sijmons
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
| | - Simon Collett
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Caroline Soliman
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Andrew J Guy
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
- ZiP Diagnostics, Collingwood, VIC, 3066, Australia
| | - Andrew M Scott
- Olivia Newton-John Cancer Research Institute and School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
- Department of Molecular Imaging and Therapy, Austin Health and Faculty of Medicine, The University of Melbourne, Melbourne, VIC, Australia
| | - Lindy G Durrant
- Scancell Limited, University of Nottingham Biodiscovery Institute, Nottingham, UK
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Aaron Elbourne
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
| | - Anna K Walduck
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia.
- Rural Health Research Institute, Charles Sturt University, Orange, NSW, 2800, Australia.
| | - Paul A Ramsland
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia.
- Department of Immunology, Monash University, Melbourne, VIC, 3004, Australia.
- Department of Surgery, Austin Health, The University of Melbourne, Heidelberg, VIC, 3084, Australia.
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Pan Y, Pohjolainen E, Schmidpeter PAM, Vaiana AC, Nimigean CM, Grubmüller H, Scheuring S. Discrimination between cyclic nucleotides in a cyclic nucleotide-gated ion channel. Nat Struct Mol Biol 2023; 30:512-520. [PMID: 36973509 DOI: 10.1038/s41594-023-00955-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 02/24/2023] [Indexed: 03/29/2023]
Abstract
Cyclic nucleotide-gated ion channels are crucial in many physiological processes such as vision and pacemaking in the heart. SthK is a prokaryotic homolog with high sequence and structure similarities to hyperpolarization-activated and cyclic nucleotide-modulated and cyclic nucleotide-gated channels, especially at the level of the cyclic nucleotide binding domains (CNBDs). Functional measurements showed that cyclic adenosine monophosphate (cAMP) is a channel activator while cyclic guanosine monophosphate (cGMP) barely leads to pore opening. Here, using atomic force microscopy single-molecule force spectroscopy and force probe molecular dynamics simulations, we unravel quantitatively and at the atomic level how CNBDs discriminate between cyclic nucleotides. We find that cAMP binds to the SthK CNBD slightly stronger than cGMP and accesses a deep-bound state that a cGMP-bound CNBD cannot reach. We propose that the deep binding of cAMP is the discriminatory state that is essential for cAMP-dependent channel activation.
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Affiliation(s)
- Yangang Pan
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Emmi Pohjolainen
- Max Planck Institute for Multidisciplinary Sciences, Theoretical and Computational Biophysics Department, Goettingen, Germany
| | | | - Andrea C Vaiana
- Max Planck Institute for Multidisciplinary Sciences, Theoretical and Computational Biophysics Department, Goettingen, Germany
- Institute of Biophysics, National Research Council, Palermo, Italy
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Helmut Grubmüller
- Max Planck Institute for Multidisciplinary Sciences, Theoretical and Computational Biophysics Department, Goettingen, Germany
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
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Mana T, Kundu J, Lahiri H, Bera S, Kolay J, Sinha S, Mukhopadhyay R. Molecularly resolved, label-free nucleic acid sensing at solid-liquid interface using non-ionic DNA analogues. RSC Adv 2022; 12:9263-9274. [PMID: 35424880 PMCID: PMC8985177 DOI: 10.1039/d2ra00386d] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/07/2022] [Indexed: 01/10/2023] Open
Abstract
Nucleic acid-based biosensors, where the capture probe is a nucleic acid, e.g., DNA or its synthetic analogue xeno nucleic acid (XNA), offer interesting ways of eliciting clinically relevant information from hybridization/dehybridization signals. In this respect, the application of XNA probes is attractive since the drawbacks of DNA probes might be overcome. Within the XNA probe repertoire, peptide nucleic acid (PNA) and morpholino (MO) are promising since their backbones are non-ionic. Therefore, in the absence of electrostatic charge repulsion between the capture probe and the target nucleic acid, a stable duplex can be formed. In addition, these are nuclease-resistant probes. Herein, we have tested the molecularly resolved nucleic acid sensing capacity of PNA and MO capture probes using a fluorescent label-free single molecule force spectroscopy approach. As far as single nucleobase mismatch discrimination is concerned, both PNA and MO performed better than DNA, while the performance of the MO probe was the best. We propose that the conformationally more rigid backbone of MO, compared to the conformationally flexible PNA, is an advantage for MO, since the probe orientation can be made more upright on the surface and therefore MO can be more effectively accessed by the target sequences. The performance of the XNA probes has been compared to that of the DNA probe, using fixed nucleobase sequences, so that the effect of backbone variation could be investigated. To our knowledge, this is the first report on molecularly resolved nucleic acid sensing by non-ionic capture probes, here, MO and PNA. Improved nucleic acid sensing in terms of single nucleobase mismatch discrimination, as achieved by the surface-confined non-ionic PNA and MO capture probes, is exemplified by single molecule force spectroscopy.![]()
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Affiliation(s)
- Tanushree Mana
- School of Biological Sciences, Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India +91 33 2473 2805 +91 33 2473 4971 extn 1506
| | - Jayanta Kundu
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India
| | - Hiya Lahiri
- School of Biological Sciences, Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India +91 33 2473 2805 +91 33 2473 4971 extn 1506
| | - Sudipta Bera
- School of Biological Sciences, Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India +91 33 2473 2805 +91 33 2473 4971 extn 1506
| | - Jayeeta Kolay
- School of Biological Sciences, Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India +91 33 2473 2805 +91 33 2473 4971 extn 1506
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India
| | - Rupa Mukhopadhyay
- School of Biological Sciences, Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India +91 33 2473 2805 +91 33 2473 4971 extn 1506
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Lallemang M, Yu L, Cai W, Rischka K, Hartwig A, Haag R, Hugel T, Balzer BN. Multivalent non-covalent interactions lead to strongest polymer adhesion. NANOSCALE 2022; 14:3768-3776. [PMID: 35171194 DOI: 10.1039/d1nr08338d] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Multivalent interactions play a leading role in biological processes such as the inhibition of inflammation or virus internalization. The multivalent interactions show enhanced strength and better selectivity compared to monovalent interactions, but they are much less understood due to their complexity. Here, we detect molecular interactions in the range of a few piconewtons to several nanonewtons and correlate them with the formation and subsequent breaking of one or several bonds and assign these bonds. This becomes possible by performing atomic force microcopy (AFM)-based single molecule force spectroscopy of a multifunctional polymer covalently attached to an AFM cantilever tip on a substrate bound polymer layer of the multifunctional polymer. Varying the pH value and the crosslinking state of the polymer layer, we find that bonds of intermediate strength (non-covalent), like coordination bonds, give the highest multivalent bond strength, even outperforming strong (covalent) bonds. At the same time, covalent bonds enhance the polymer layer density, increasing in particular the number of non-covalent bonds. In summary, we can show that the key for the design of stable and durable polymer coatings is to provide a variety of multivalent interactions and to keep the number of non-covalent interactions at a high level.
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Affiliation(s)
- Max Lallemang
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany.
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Leixiao Yu
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takusstraße 3, 14195 Berlin, Germany
| | - Wanhao Cai
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany.
| | - Klaus Rischka
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials IFAM, Wiener Straße 12, 28359 Bremen, Germany
| | - Andreas Hartwig
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials IFAM, Wiener Straße 12, 28359 Bremen, Germany
- University of Bremen, Department 2 Biology/Chemistry, Leobener Straße 3, 28359 Bremen, Germany
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takusstraße 3, 14195 Berlin, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany.
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Bizan N Balzer
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany.
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
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Sarkar A. Biosensing, Characterization of Biosensors, and Improved Drug Delivery Approaches Using Atomic Force Microscopy: A Review. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2021.798928] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Since its invention, atomic force microscopy (AFM) has come forth as a powerful member of the “scanning probe microscopy” (SPM) family and an unparallel platform for high-resolution imaging and characterization for inorganic and organic samples, especially biomolecules, biosensors, proteins, DNA, and live cells. AFM characterizes any sample by measuring interaction force between the AFM cantilever tip (the probe) and the sample surface, and it is advantageous over other SPM and electron micron microscopy techniques as it can visualize and characterize samples in liquid, ambient air, and vacuum. Therefore, it permits visualization of three-dimensional surface profiles of biological specimens in the near-physiological environment without sacrificing their native structures and functions and without using laborious sample preparation protocols such as freeze-drying, staining, metal coating, staining, or labeling. Biosensors are devices comprising a biological or biologically extracted material (assimilated in a physicochemical transducer) that are utilized to yield electronic signal proportional to the specific analyte concentration. These devices utilize particular biochemical reactions moderated by isolated tissues, enzymes, organelles, and immune system for detecting chemical compounds via thermal, optical, or electrical signals. Other than performing high-resolution imaging and nanomechanical characterization (e.g., determining Young’s modulus, adhesion, and deformation) of biosensors, AFM cantilever (with a ligand functionalized tip) can be transformed into a biosensor (microcantilever-based biosensors) to probe interactions with a particular receptors of choice on live cells at a single-molecule level (using AFM-based single-molecule force spectroscopy techniques) and determine interaction forces and binding kinetics of ligand receptor interactions. Targeted drug delivery systems or vehicles composed of nanoparticles are crucial in novel therapeutics. These systems leverage the idea of targeted delivery of the drug to the desired locations to reduce side effects. AFM is becoming an extremely useful tool in figuring out the topographical and nanomechanical properties of these nanoparticles and other drug delivery carriers. AFM also helps determine binding probabilities and interaction forces of these drug delivery carriers with the targeted receptors and choose the better agent for drug delivery vehicle by introducing competitive binding. In this review, we summarize contributions made by us and other researchers so far that showcase AFM as biosensors, to characterize other sensors, to improve drug delivery approaches, and to discuss future possibilities.
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7
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Two energy barriers and a transient intermediate state determine the unfolding and folding dynamics of cold shock protein. Commun Chem 2021; 4:156. [PMID: 36697724 PMCID: PMC9814876 DOI: 10.1038/s42004-021-00592-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/15/2021] [Indexed: 01/28/2023] Open
Abstract
Cold shock protein (Csp) is a typical two-state folding model protein which has been widely studied by biochemistry and single molecule techniques. Recently two-state property of Csp was confirmed by atomic force microscopy (AFM) through direct pulling measurement, while several long-lifetime intermediate states were found by force-clamp AFM. We systematically studied force-dependent folding and unfolding dynamics of Csp using magnetic tweezers with intrinsic constant force capability. Here we report that Csp mostly folds and unfolds with a single step over force range from 5 pN to 50 pN, and the unfolding rates show different force sensitivities at forces below and above ~8 pN, which determines a free energy landscape with two barriers and a transient intermediate state between them along one transition pathway. Our results provide a new insight on protein folding mechanism of two-state proteins.
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Campbell EA, Ramirez K, Holegadde M, Yeshlur N, Khaja A, Sulchek TA. Tuning Antibody Presentation to Enhance T-Cell Activation for Downstream Cytotoxicity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:4783-4792. [PMID: 33848167 DOI: 10.1021/acs.langmuir.0c03203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cytotoxic effector cells are an integral component of the immune response against pathogens and diseases such as cancer and thus of great interest to researchers who wish to enhance the native immune response. Although researchers routinely use particles to stimulate cytotoxic T cells, few studies have comprehensively investigated: (1) beyond initial activation responses (i.e., proliferation and CD25/CD69 expression) to downstream cancer-killing effects and (2) how to drive cytotoxic T-cell responses by adjusting biomolecular and physical properties of particles. In this study, we designed particles displaying an anti-CD3 antibody to activate cytotoxic T cells and study their downstream cytotoxic effects. We evaluated the effect of antibody immobilization, particle size, molecular surface density of an anti-CD3 antibody, and the inclusion of an anti-CD28 antibody on cytolytic granule release by T cells. We found that immobilizing the anti-CD3 antibody onto smaller nanoparticles elicited increased T-cell activation products for an equivalent delivery of the anti-CD3 antibody. We further established that the mechanism behind increased cancer cell death was associated with the proximity of T cells to cancer cells. Functionalizing particles additionally with the anti-CD28 antibody at an optimized antibody density caused increased T-cell proliferation and T-cell binding but we observed no effective increase in cytotoxicity. Meaningfully, our results are discussed within the context of commercially available and widely used anti-CD3/28 Dynabeads. These results showed that T-cell activation and cytotoxicity can be optimized with a molecular presentation on smaller particles and thus, offer exciting new possibilities to engineer T-cell activation responses for effective outcomes.
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Affiliation(s)
- Elizabeth A Campbell
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
| | - Katily Ramirez
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
| | - Meghana Holegadde
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
| | - Nayana Yeshlur
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
| | - Akram Khaja
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
| | - Todd A Sulchek
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30313, United States
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Francis LW, Yao SN, Powell LC, Griffiths S, Berquand A, Piasecki T, Howe W, Gazze AS, Farach-Carson MC, Constantinou P, Carson D, Margarit L, Gonzalez D, Conlan RS. Highly glycosylated MUC1 mediates high affinity L-selectin binding at the human endometrial surface. J Nanobiotechnology 2021; 19:50. [PMID: 33596915 PMCID: PMC7890821 DOI: 10.1186/s12951-021-00793-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/04/2021] [Indexed: 12/30/2022] Open
Abstract
Background Sialyl-Lewis X/L-selectin high affinity binding interactions between transmembrane O-glycosylated mucins proteins and the embryo have been implicated in implantation processes within the human reproductive system. However, the adhesive properties of these mucins at the endometrial cell surface are difficult to resolve due to known discrepancies between in vivo models and the human reproductive system and a lack of sensitivity in current in vitro models. To overcome these limitations, an in vitro model of the human endometrial epithelial was interrogated with single molecule force spectroscopy (SMFS) to delineate the molecular configurations of mucin proteins that mediate the high affinity L-selectin binding required for human embryo implantation. Results This study reveals that MUC1 contributes to both the intrinsic and extrinsic adhesive properties of the HEC-1 cellular surface. High expression of MUC1 on the cell surface led to a significantly increased intrinsic adhesion force (148 pN vs. 271 pN, p < 0.001), whereas this adhesion force was significantly reduced (271 pN vs. 118 pN, p < 0.001) following siRNA mediated MUC1 ablation. Whilst high expression of MUC1 displaying elevated glycosylation led to strong extrinsic (> 400 pN) L-selectin binding at the cell surface, low expression of MUC1 with reduced glycosylation resulted in significantly less (≤200 pN) binding events. Conclusions An optimal level of MUC1 together with highly glycosylated decoration of the protein is critical for high affinity L-selectin binding. This study demonstrates that MUC1 contributes to cellular adhesive properties which may function to facilitate trophoblast binding to the endometrial cell surface through the L-selectin/sialyl-Lewis x adhesion system subsequent to implantation.![]()
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Affiliation(s)
- Lewis W Francis
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, Wales, UK
| | - Seydou N Yao
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, Wales, UK
| | - Lydia C Powell
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, Wales, UK
| | - Sean Griffiths
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, Wales, UK
| | | | - Thomas Piasecki
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, Wales, UK
| | - William Howe
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, Wales, UK
| | - Andrea S Gazze
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, Wales, UK
| | - Mary C Farach-Carson
- School of Dentistry, The University of Texas Health Science Center, Houston, 77054, Texas, USA
| | - Pamela Constantinou
- Department of Biosciences, Wiess School of Natural Science, Rice University, Houston, Texas, 77251, USA
| | - Daniel Carson
- Department of Biosciences, Wiess School of Natural Science, Rice University, Houston, Texas, 77251, USA
| | - Lavinia Margarit
- Cwm Taf Morgannwg University Health Board, Princess of Wales Hospital, Bridgend, CF31 1RQ, UK
| | - Deya Gonzalez
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, Wales, UK
| | - R Steven Conlan
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, Wales, UK.
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10
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Cibulski SP, de Sales Lima FE, Teixeira TF, Varela APM, Scheffer CM, Mayer FQ, Witt AA, Roehe PM. Detection of multiple viruses in oropharyngeal samples from Brazilian free-tailed bats (Tadarida brasiliensis) using viral metagenomics. Arch Virol 2020; 166:207-212. [PMID: 33047159 PMCID: PMC7549734 DOI: 10.1007/s00705-020-04825-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/26/2020] [Indexed: 12/14/2022]
Abstract
In this study, we analyzed the viral population in oropharyngeal samples from T. brasiliensis using a viral metagenomic approach. Genomes corresponding to members of the families Circoviridae, Genomoviridae, Herpesviridae, Paramyxoviridae, Coronaviridae, and Astroviridae were detected. This study provides the first preliminary understanding of the oropharyngeal virome of T. brasiliensis, which may guide the discovery and isolation of novel viruses in the future and highlights the need for continuing investigations in this regard.
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Affiliation(s)
- Samuel Paulo Cibulski
- Centro de Biotecnologia-CBiotec, Laboratório de Biotecnologia Celular e Molecular, Universidade Federal da Paraíba-UFPB, João Pessoa, Paraíba, Brazil.
| | | | - Thais Fumaco Teixeira
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul-UFRGS-Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Paula Muterle Varela
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul-UFRGS-Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Camila Mengue Scheffer
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul-UFRGS-Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, RS, Brazil
| | - André Alberto Witt
- Secretaria da Agricultura, Pecuária e Irrigação/RS, Divisão de Defesa Sanitária Animal, Porto Alegre, Rio Grande do Sul, Brazil
| | - Paulo Michel Roehe
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul-UFRGS-Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
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11
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Chen MP, Kiduko SA, Saad NS, Canan BD, Kilic A, Mohler PJ, Janssen PML. Stretching single titin molecules from failing human hearts reveals titin's role in blunting cardiac kinetic reserve. Cardiovasc Res 2020; 116:127-137. [PMID: 30778519 DOI: 10.1093/cvr/cvz043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/08/2018] [Accepted: 02/13/2019] [Indexed: 11/15/2022] Open
Abstract
AIMS Heart failure (HF) patients commonly experience symptoms primarily during elevated heart rates, as a result of physical activities or stress. A main determinant of diastolic passive tension, the elastic sarcomeric protein titin, has been shown to be associated with HF, with unresolved involvement regarding its role at different heart rates. To determine whether titin is playing a role in the heart rate (frequency-) dependent acceleration of relaxation (FDAR). W, we studied the FDAR responses in live human left ventricular cardiomyocytes and the corresponding titin-based passive tension (TPT) from failing and non-failing human hearts. METHODS AND RESULTS Using atomic force, we developed a novel single-molecule force spectroscopy approach to detect TPT based on the frequency-modulated cardiac cycle. Mean TPT reduced upon an increased heart rate in non-failing human hearts, while this reduction was significantly blunted in failing human hearts. These mechanical changes in the titin distal Ig domain significantly correlated with the frequency-dependent relaxation kinetics of human cardiomyocytes obtained from the corresponding hearts. Furthermore, the data suggested that the higher the TPT, the faster the cardiomyocytes relaxed, but the lower the potential of myocytes to speed up relaxation at a higher heart rate. Such poorer FDAR response was also associated with a lesser reduction or a bigger increase in TPT upon elevated heart rate. CONCLUSIONS Our study established a novel approach in detecting dynamic heart rate relevant tension changes physiologically on native titin domains. Using this approach, the data suggested that the regulation of kinetic reserve in cardiac relaxation and its pathological changes were associated with the intensity and dynamic changes of passive tension by titin.
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Affiliation(s)
- Mei-Pian Chen
- Department of Physiology and Cell Biology, The Ohio State University, Hamilton Hall 207a, 1645 Neil Avenue, Columbus, OH 43210, USA.,Dorothy M. Davis Heart and Lung Research Institute, 473 W 12th Ave, Columbus, OH 43210 USA
| | - Salome A Kiduko
- Department of Physiology and Cell Biology, The Ohio State University, Hamilton Hall 207a, 1645 Neil Avenue, Columbus, OH 43210, USA.,Dorothy M. Davis Heart and Lung Research Institute, 473 W 12th Ave, Columbus, OH 43210 USA
| | - Nancy S Saad
- Department of Physiology and Cell Biology, The Ohio State University, Hamilton Hall 207a, 1645 Neil Avenue, Columbus, OH 43210, USA.,Dorothy M. Davis Heart and Lung Research Institute, 473 W 12th Ave, Columbus, OH 43210 USA.,Department of Pharmacology and Toxicology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Benjamin D Canan
- Department of Physiology and Cell Biology, The Ohio State University, Hamilton Hall 207a, 1645 Neil Avenue, Columbus, OH 43210, USA.,Dorothy M. Davis Heart and Lung Research Institute, 473 W 12th Ave, Columbus, OH 43210 USA
| | - Ahmet Kilic
- Division of Cardiothoracic Surgery, Department of Surgery, The Ohio State University Wexner Medical Center, 410 W 10th Ave, Columbus, OH 43210, USA
| | - Peter J Mohler
- Department of Physiology and Cell Biology, The Ohio State University, Hamilton Hall 207a, 1645 Neil Avenue, Columbus, OH 43210, USA.,Dorothy M. Davis Heart and Lung Research Institute, 473 W 12th Ave, Columbus, OH 43210 USA.,Department of Internal Medicine, The Ohio State University Wexner Medical Center, 395 W 12th Ave, Columbus, OH 43210, USA
| | - Paul M L Janssen
- Department of Physiology and Cell Biology, The Ohio State University, Hamilton Hall 207a, 1645 Neil Avenue, Columbus, OH 43210, USA.,Dorothy M. Davis Heart and Lung Research Institute, 473 W 12th Ave, Columbus, OH 43210 USA.,Department of Internal Medicine, The Ohio State University Wexner Medical Center, 395 W 12th Ave, Columbus, OH 43210, USA
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12
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Cuellar-Camacho JL, Bhatia S, Reiter-Scherer V, Lauster D, Liese S, Rabe JP, Herrmann A, Haag R. Quantification of Multivalent Interactions between Sialic Acid and Influenza A Virus Spike Proteins by Single-Molecule Force Spectroscopy. J Am Chem Soc 2020; 142:12181-12192. [PMID: 32538085 DOI: 10.1021/jacs.0c02852] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Multivalency is a key principle in reinforcing reversible molecular interactions through the formation of multiple bonds. The influenza A virus deploys this strategy to bind strongly to cell surface receptors. We performed single-molecule force spectroscopy (SMFS) to investigate the rupture force required to break individual and multiple bonds formed between synthetic sialic acid (SA) receptors and the two principal spike proteins of the influenza A virus (H3N2): hemagglutinin (H3) and neuraminidase (N2). Kinetic parameters such as the rupture length (χβ) and dissociation rate (koff) are extracted using the model by Friddle, De Yoreo, and Noy. We found that a monovalent SA receptor binds to N2 with a significantly higher bond lifetime (270 ms) compared to that for H3 (36 ms). By extending the single-bond rupture analysis to a multibond system of n protein-receptor pairs, we provide an unprecedented quantification of the mechanistic features of multivalency between H3 and N2 with SA receptors and show that the stability of the multivalent connection increases with the number of bonds from tens to hundreds of milliseconds. Association rates (kon) are also provided, and an estimation of the dissociation constants (KD) between the SA receptors to both proteins indicate a 17-fold higher binding affinity for the SA-N2 bond with respect to that of SA-H3. An optimal designed multivalent SA receptor showed a higher binding stability to the H3 protein of the influenza A virus than to the monovalent SA receptor. Our study emphasizes the influence of the scaffold on the presentation of receptors during multivalent binding.
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Affiliation(s)
- Jose Luis Cuellar-Camacho
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Sumati Bhatia
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Valentin Reiter-Scherer
- Department of Physics & IRIS Adlershof, Humboldt-Universität zu Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Daniel Lauster
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany.,Institute for Biology & IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115 Berlin, Germany
| | - Susanne Liese
- Department of Mathematics, University of Oslo, Moltke Moes vei 35, 1053 Oslo, Norway
| | - Jürgen P Rabe
- Department of Physics & IRIS Adlershof, Humboldt-Universität zu Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Andreas Herrmann
- Institute for Biology & IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115 Berlin, Germany
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
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13
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Lekka M, Herman K, Zemła J, Bodek Ł, Pyka-Fościak G, Gil D, Dulińska-Litewka J, Ptak A, Laidler P. Probing the recognition specificity of α Vβ 1 integrin and syndecan-4 using force spectroscopy. Micron 2020; 137:102888. [PMID: 32554186 DOI: 10.1016/j.micron.2020.102888] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/20/2020] [Accepted: 05/18/2020] [Indexed: 12/13/2022]
Abstract
The knowledge on how cells interact with microenvironment is particularly important in understanding the interaction of cancer cells with surrounding stroma, which affects cell migration, adhesion, and metastasis. The main cell surface receptors responsible for the interaction with extracellular matrix (ECM) are integrins, however, they are not the only ones. Integrins are accompanied to other molecules such as syndecans. The role of the latter has not yet been fully established. In our study, we would like to answer the question of whether integrins and syndecans, possessing similar functions, share also similar unbinding properties. By using single molecule force spectroscopy (SMFS), we conducted measurements of the unbinding properties of αVβ1 and syndecan-4 in the interaction with vitronectin (VN), which, as each ECM protein, possesses two binding sites specific to integrins and syndecans. The unbinding force and the kinetic off rate constant derived from SMFS describe the stability of single molecular complex. Obtained data show one barrier transition for each complex. The proposed model shows that the unbinding of αVβ1 from VN proceeds before the unbinding of SDC-4. However, despite different unbinding kinetics, the access to both receptors is needed for cell growth and proliferation.
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Affiliation(s)
- Małgorzata Lekka
- Department of Biophysical Microstructures, Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland.
| | - Katarzyna Herman
- Institute of Physics, Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Piotrowo 3, 60-965 Poznań, Poland
| | - Joanna Zemła
- Department of Biophysical Microstructures, Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland
| | - Łukasz Bodek
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland
| | - Grażyna Pyka-Fościak
- Department of Histology, Jagiellonian University Medical College, Kopernika 7, 31-034, Kraków, Poland
| | - Dorota Gil
- Chair of Medical Biochemistry Jagiellonian University Medical College, Kopernika 7, 31-034 Kraków, Poland
| | - Joanna Dulińska-Litewka
- Chair of Medical Biochemistry Jagiellonian University Medical College, Kopernika 7, 31-034 Kraków, Poland
| | - Arkadiusz Ptak
- Institute of Physics, Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Piotrowo 3, 60-965 Poznań, Poland
| | - Piotr Laidler
- Chair of Medical Biochemistry Jagiellonian University Medical College, Kopernika 7, 31-034 Kraków, Poland
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14
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Yang B, Liu Z, Liu H, Nash MA. Next Generation Methods for Single-Molecule Force Spectroscopy on Polyproteins and Receptor-Ligand Complexes. Front Mol Biosci 2020; 7:85. [PMID: 32509800 PMCID: PMC7248566 DOI: 10.3389/fmolb.2020.00085] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/16/2020] [Indexed: 12/31/2022] Open
Abstract
Single-molecule force spectroscopy with the atomic force microscope provides molecular level insights into protein function, allowing researchers to reconstruct energy landscapes and understand functional mechanisms in biology. With steadily advancing methods, this technique has greatly accelerated our understanding of force transduction, mechanical deformation, and mechanostability within single- and multi-domain polyproteins, and receptor-ligand complexes. In this focused review, we summarize the state of the art in terms of methodology and highlight recent methodological improvements for AFM-SMFS experiments, including developments in surface chemistry, considerations for protein engineering, as well as theory and algorithms for data analysis. We hope that by condensing and disseminating these methods, they can assist the community in improving data yield, reliability, and throughput and thereby enhance the information that researchers can extract from such experiments. These leading edge methods for AFM-SMFS will serve as a groundwork for researchers cognizant of its current limitations who seek to improve the technique in the future for in-depth studies of molecular biomechanics.
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Affiliation(s)
- Byeongseon Yang
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Zhaowei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Haipei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michael A. Nash
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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15
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Liu H, Schittny V, Nash MA. Removal of a Conserved Disulfide Bond Does Not Compromise Mechanical Stability of a VHH Antibody Complex. NANO LETTERS 2019; 19:5524-5529. [PMID: 31257893 PMCID: PMC6975629 DOI: 10.1021/acs.nanolett.9b02062] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/28/2019] [Indexed: 05/28/2023]
Abstract
Single-domain VHH antibodies are promising reagents for medical therapy. A conserved disulfide bond within the VHH framework region is known to be critical for thermal stability, however, no prior studies have investigated its influence on the stability of VHH antibody-antigen complexes under mechanical load. Here, we used single-molecule force spectroscopy to test the influence of a VHH domain's conserved disulfide bond on the mechanical strength of the interaction with its antigen mCherry. We found that although removal of the disulfide bond through cysteine-to-alanine mutagenesis significantly lowered VHH domain denaturation temperature, it had no significant impact on the mechanical strength of the VHH:mCherry interaction with complex rupture occurring at ∼60 pN at 103-104 pN/sec regardless of disulfide bond state. These results demonstrate that mechanostable binding interactions can be built on molecular scaffolds that may be thermodynamically compromised at equilibrium.
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Affiliation(s)
- Haipei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Valentin Schittny
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Michael A. Nash
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
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16
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Cross-reactivity between myelin oligodendrocyte glycoprotein and human endogenous retrovirus W protein: nanotechnological evidence for the potential trigger of multiple sclerosis. Micron 2019; 120:66-73. [PMID: 30802755 DOI: 10.1016/j.micron.2019.02.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/17/2019] [Accepted: 02/17/2019] [Indexed: 12/22/2022]
Abstract
Multiple sclerosis (MS) is an autoimmune and inflammatory demyelinating disease of the central nervous system. Experimental evidence supports the reactivity of autoantibodies against components of myelin sheath including the myelin oligodendrocyte glycoprotein (MOG). The MS etiology is still unknown, but some risk factors associated with immune dysregulation, genetic susceptibility, and environmental factors are under investigation. The last consider the hypothesis of molecular mimicry mechanism, which is potentially triggered by viral antigen inducing MS autoimmunity. The Human Endogenous Retroviruses W family (HERV-W) is the subject of studies within this field, based on the detection of HERV-W envelope gene proteins in MS patients' samples. In the biomedical field of diagnosis and therapeutics, nanotechnology is of great use for the detailed study of molecular mechanisms involving specific interactions between biomolecules providing high specificity and sensitivity of response. In view of the significance of etiological aspects for the comprehension of MS mechanisms of action, we applied a nanotechnological approach designed for antibody detection. For this, we analyzed MOG peptide sequences similar to the HERV-W protein. These sequences were subjected to interaction with anti-HERV-W antibodies using atomic force spectroscopy (AFS) and silver nanoparticles (AgNPs) methods to survey the potential occurrence of molecular mimicry. Our results revealed the molecular recognition between the anti-HERV-W antibody and the HERV-W and MOG epitopes by AFS and AgNPs approaches. Specific non-linear shape of force curves and median adhesion force values within the expected range for an antigen-antibody interaction were obtained for HERV-W and MOG peptides, 163 pN and 178 pN, respectively, suggesting the occurrence of cross-reactivity in these systems.
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17
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Zhao J, Su H, Vansuch GE, Liu Z, Salaita K, Dyer RB. Localized Nanoscale Heating Leads to Ultrafast Hydrogel Volume-Phase Transition. ACS NANO 2019; 13:515-525. [PMID: 30574782 PMCID: PMC6467806 DOI: 10.1021/acsnano.8b07150] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The rate of the volume-phase transition for stimuli-responsive hydrogel particles ranging in size from millimeters to nanometers is limited by the rate of water transport, which is proportional to the surface area of the particle. Here, we hypothesized that the rate of volume-phase transition could be accelerated if the stimulus is geometrically controlled from the inside out, thus facilitating outward water ejection. To test this concept, we applied transient absorption spectroscopy, laser temperature-jump spectroscopy, and finite-element analysis modeling to characterize the dynamics of the volume-phase transition of hydrogel particles with a gold nanorod core. Our results demonstrate that the nanoscale heating of the hydrogel particle core led to an ultrafast, 60 ns particle collapse, which is 2-3 orders of magnitude faster than the response generated from conventional heating. This is the fastest recorded response time of a hydrogel material, thus opening potential applications for such stimuli-responsive materials.
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Affiliation(s)
- Jing Zhao
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Hanquan Su
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Gregory E. Vansuch
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Zheng Liu
- Institute for Advanced Studies, Wuhan University, Wuhan, PR China
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Corresponding Authors
| | - R. Brian Dyer
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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18
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Sumbul F, Rico F. Single-Molecule Force Spectroscopy: Experiments, Analysis, and Simulations. Methods Mol Biol 2019; 1886:163-189. [PMID: 30374867 DOI: 10.1007/978-1-4939-8894-5_9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The mechanical properties of cells and of subcellular components are important to obtain a mechanistic molecular understanding of biological processes. The quantification of mechanical resistance of cells and biomolecules using biophysical methods matured thanks to the development of nanotechnologies such as optical and magnetic tweezers, the biomembrane force probe, and atomic force microscopy (AFM). The quantitative nature of force spectroscopy measurements has converted AFM into a valuable tool in biophysics. Force spectroscopy allows the determination of the forces required to unfold protein domains and to disrupt individual receptor/ligand bonds. Molecular simulations as a computational microscope allow investigation of similar biological processes with an atomistic detail. In this chapter, we first provide a step-by-step protocol of force spectroscopy experiments using AFM, including sample preparation, measurements, and analysis and interpretation of the resulting dynamic force spectrum in terms of available theories. Next, we present the background for molecular dynamics (MD) simulations focusing on steered molecular dynamics (SMD) and the importance of bridging computational tools with experimental techniques.
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Affiliation(s)
- Fidan Sumbul
- LAI, Aix-Marseille Université, INSERM UMR_S 1067, CNRS UMR 7333, 163 Avenue de Luminy, Marseille, 13009, France
| | - Felix Rico
- LAI, Aix-Marseille Université, INSERM UMR_S 1067, CNRS UMR 7333, 163 Avenue de Luminy, Marseille, 13009, France.
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19
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Nguyen TH, Greinacher A. Distinct Binding Characteristics of Pathogenic Anti-Platelet Factor-4/Polyanion Antibodies to Antigens Coated on Different Substrates: A Perspective on Clinical Application. ACS NANO 2018; 12:12030-12041. [PMID: 30540167 DOI: 10.1021/acsnano.8b04487] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The polyanion heparin, which is frequently used in patients, complexes with the platelet-derived cationic chemokine platelet factor (PF4, CXCL4). This results in the formation of anti-PF4/heparin antibodies (anti-PF4/H Abs). Anti-PF4/H Abs are classified into three groups: (i) nonpathogenic Abs (group 1) with no clinical relevance; (ii) pathogenic heparin-dependent Abs (group 2), which activate platelets and can cause the severe adverse drug effect heparin-induced thrombocytopenia (HIT); and (iii) pathogenic autoimmune-HIT Abs (group 3), in which group 3 anti-PF4/H Abs causes a HIT-like autoimmune disease in the absence of heparin. Enzyme immunoassays using PF4/H complexes coated on the solid phase for detection of anti-PF4/H Abs cannot differentiate between pathogenic and nonpathogenic anti-PF4/H Abs. By single-molecule force spectroscopy, we identify a specific feature of pathogenic group 2 and group 3 Abs antibodies that (in contrast to nonpathogenic group 1 Abs) their binding forces to PF4/H complexes coated on platelets were significantly higher compared with those of PF4/H complexes immobilized on a solid phase. Only group 3 Abs showed high binding forces to platelets without the addition of PF4. In the presence of 50 μg/mL PF4, group 2 Abs also showed high binding forces to platelets. In contrast, binding forces of group 1 Abs always remained low (<100 pN). Our findings may have major relevance for the development of clinically applicable solid-phase assays, which allow differentiation of pathogenic platelet-activating from nonpathogenic anti-PF4/H Abs. Membrane-based expression of antigens might also increase the specificity of other assays for the detection of pathogenic (auto)-antibodies in clinical medicine.
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Affiliation(s)
- Thi-Huong Nguyen
- Institute for Immunology and Transfusion Medicine , University Medicine Greifswald , 17475 Greifswald , Germany
- ZIK HIKE - Center for Innovation Competence, Humoral Immune Reactions in Cardiovascular Diseases , University of Greifswald , 17489 Greifswald , Germany
| | - Andreas Greinacher
- Institute for Immunology and Transfusion Medicine , University Medicine Greifswald , 17475 Greifswald , Germany
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20
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Li Q, Wei G. Label-free determination of adenosine and mercury ions according to force mapping-based force-to-color variety. Analyst 2018; 143:4400-4407. [PMID: 30137104 DOI: 10.1039/c8an01043a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Single molecule force spectroscopy based on atomic force microscopy (AFM) is a simple and sensitive technique to probe molecular recognition forces. Here we demonstrate that visual color-intensity analysis of single molecule force mapping (SMFM) can be employed as a quick and convenient force-to-color detection towards the presence of various dissolved analytes in very low concentrations. To achieve this aim, analyte-specific single-strand DNA aptamers are first bound to an AFM tip. The measured forces between the functionalized tip and a suitable substrate, namely either a clean surface or a surface functionalized with the complementary DNA oligomer, change when a critical concentration of the analyte is reached. The current SMFM-based visual biosensing shows improved developments like higher sensitivity, lower detection limits, quicker detection, and much simple readout. The color of the obtained force maps reveals the force intensity, which gives a highly selective and immediate visual force-to-color response towards the presence of adenosine (above ∼0.1 nM) and Hg2+ (∼10 pM). The strategies shown in this work will be helpful to design and fabricate aptasensors for biomedical analysis as well as to understand the molecular interactions between DNA hybridization.
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Affiliation(s)
- Qing Li
- Faculty of Production Engineering and Center for Environmental Research and Sustainable Technology (UFT) University of Bremen, D-28359 Bremen, Germany.
| | - Gang Wei
- Faculty of Production Engineering and Center for Environmental Research and Sustainable Technology (UFT) University of Bremen, D-28359 Bremen, Germany.
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21
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Dutta PK, Zhang Y, Blanchard A, Ge C, Rushdi M, Weiss K, Zhu C, Ke Y, Salaita K. Programmable Multivalent DNA-Origami Tension Probes for Reporting Cellular Traction Forces. NANO LETTERS 2018; 18:4803-4811. [PMID: 29911385 PMCID: PMC6087633 DOI: 10.1021/acs.nanolett.8b01374] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mechanical forces are central to most, if not all, biological processes, including cell development, immune recognition, and metastasis. Because the cellular machinery mediating mechano-sensing and force generation is dependent on the nanoscale organization and geometry of protein assemblies, a current need in the field is the development of force-sensing probes that can be customized at the nanometer-length scale. In this work, we describe a DNA origami tension sensor that maps the piconewton (pN) forces generated by living cells. As a proof-of-concept, we engineered a novel library of six-helix-bundle DNA-origami tension probes (DOTPs) with a tailorable number of tension-reporting hairpins (each with their own tunable tension response threshold) and a tunable number of cell-receptor ligands. We used single-molecule force spectroscopy to determine the probes' tension response thresholds and used computational modeling to show that hairpin unfolding is semi-cooperative and orientation-dependent. Finally, we use our DOTP library to map the forces applied by human blood platelets during initial adhesion and activation. We find that the total tension signal exhibited by platelets on DOTP-functionalized surfaces increases with the number of ligands per DOTP, likely due to increased total ligand density, and decreases exponentially with the DOTP's force-response threshold. This work opens the door to applications for understanding and regulating biophysical processes involving cooperativity and multivalency.
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Affiliation(s)
- Palash K. Dutta
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
| | - Yun Zhang
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA
| | - Aaron Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA
| | - Chenghao Ge
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
| | - Muaz Rushdi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
| | - Kristin Weiss
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
| | - Cheng Zhu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
- Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Khalid Salaita
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA
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22
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Johnson KC, Thomas WE. How Do We Know when Single-Molecule Force Spectroscopy Really Tests Single Bonds? Biophys J 2018; 114:2032-2039. [PMID: 29742396 PMCID: PMC5961468 DOI: 10.1016/j.bpj.2018.04.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 03/16/2018] [Accepted: 04/02/2018] [Indexed: 01/04/2023] Open
Abstract
Single-molecule force spectroscopy makes it possible to measure the mechanical strength of single noncovalent receptor-ligand-type bonds. A major challenge in this technique is to ensure that measurements reflect bonds between single biomolecules because the molecules cannot be directly observed. This perspective evaluates different methodologies for identifying and reducing the contribution of multiple molecule interactions to single-molecule measurements to help the reader design experiments or assess publications in the single-molecule force spectroscopy field. We apply our analysis to the large body of literature that purports to measure the strength of single bonds between biotin and streptavidin as a demonstration that measurements are only reproducible when the most reliable methods for ensuring single molecules are used.
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Affiliation(s)
- Keith C Johnson
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Wendy E Thomas
- Department of Bioengineering, University of Washington, Seattle, Washington.
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23
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Ghanti D, Patra S, Chowdhury D. Molecular force spectroscopy of kinetochore-microtubule attachment in silico: Mechanical signatures of an unusual catch bond and collective effects. Phys Rev E 2018; 97:052414. [PMID: 29906871 DOI: 10.1103/physreve.97.052414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Indexed: 06/08/2023]
Abstract
Measurement of the lifetime of attachments formed by a single microtubule (MT) with a single kinetochore (kt) in vitro under force-clamp conditions had earlier revealed a catch-bond-like behavior. In the past, the physical origin of this apparently counterintuitive phenomenon was traced to the nature of the force dependence of the (de)polymerization kinetics of the MTs. Here, first the same model MT-kt attachment is subjected to external tension that increases linearly with time until rupture occurs. In our force-ramp experiments in silico, the model displays the well known "mechanical signatures" of a catch bond probed by molecular force spectroscopy. Exploiting this evidence, we have further strengthened the analogy between MT-kt attachments and common ligand-receptor bonds in spite of the crucial differences in their underlying physical mechanisms. We then extend the formalism to model the stochastic kinetics of an attachment formed by a bundle of multiple parallel microtubules with a single kt considering the effect of rebinding under force-clamp and force-ramp conditions. From numerical studies of the model we predict the trends of variation of the mean lifetime and mean rupture force with the increasing number of MTs in the bundle. Both the mean lifetime and the mean rupture force display nontrivial nonlinear dependence on the maximum number of MTs that can attach simultaneously to the same kt.
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Affiliation(s)
- Dipanwita Ghanti
- Department of Physics, Indian Institute of Technology Kanpur, 208016, India
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24
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Sumbul F, Marchesi A, Rico F. History, rare, and multiple events of mechanical unfolding of repeat proteins. J Chem Phys 2018; 148:123335. [PMID: 29604819 DOI: 10.1063/1.5013259] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mechanical unfolding of proteins consisting of repeat domains is an excellent tool to obtain large statistics. Force spectroscopy experiments using atomic force microscopy on proteins presenting multiple domains have revealed that unfolding forces depend on the number of folded domains (history) and have reported intermediate states and rare events. However, the common use of unspecific attachment approaches to pull the protein of interest holds important limitations to study unfolding history and may lead to discarding rare and multiple probing events due to the presence of unspecific adhesion and uncertainty on the pulling site. Site-specific methods that have recently emerged minimize this uncertainty and would be excellent tools to probe unfolding history and rare events. However, detailed characterization of these approaches is required to identify their advantages and limitations. Here, we characterize a site-specific binding approach based on the ultrastable complex dockerin/cohesin III revealing its advantages and limitations to assess the unfolding history and to investigate rare and multiple events during the unfolding of repeated domains. We show that this approach is more robust, reproducible, and provides larger statistics than conventional unspecific methods. We show that the method is optimal to reveal the history of unfolding from the very first domain and to detect rare events, while being more limited to assess intermediate states. Finally, we quantify the forces required to unfold two molecules pulled in parallel, difficult when using unspecific approaches. The proposed method represents a step forward toward more reproducible measurements to probe protein unfolding history and opens the door to systematic probing of rare and multiple molecule unfolding mechanisms.
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Affiliation(s)
- Fidan Sumbul
- U1006, Aix-Marseille Université and INSERM, 163 Avenue de Luminy, 13009 Marseille, France
| | - Arin Marchesi
- U1006, Aix-Marseille Université and INSERM, 163 Avenue de Luminy, 13009 Marseille, France
| | - Felix Rico
- U1006, Aix-Marseille Université and INSERM, 163 Avenue de Luminy, 13009 Marseille, France
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25
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Stockslager MA, Bagnall JS, Hecht VC, Hu K, Aranda-Michel E, Payer K, Kimmerling RJ, Manalis SR. Microfluidic platform for characterizing TCR-pMHC interactions. BIOMICROFLUIDICS 2017; 11:064103. [PMID: 29204244 PMCID: PMC5685811 DOI: 10.1063/1.5002116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 10/20/2017] [Indexed: 05/03/2023]
Abstract
The physical characteristics of the T cell receptor (TCR)-peptide-major histocompatibility complex (pMHC) interaction are known to play a central role in determining T cell function in the initial stages of the adaptive immune response. State-of-the-art assays can probe the kinetics of this interaction with single-molecular-bond resolution, but this precision typically comes at the cost of low throughput, since the complexity of these measurements largely precludes "scaling up." Here, we explore the feasibility of detecting specific TCR-pMHC interactions by flowing T cells past immobilized pMHC and measuring the reduction in cell speed due to the mechanical force of the receptor-ligand interaction. To test this new fluidic measurement modality, we fabricated a microfluidic device in which pMHC-coated beads are immobilized in hydrodynamic traps along the length of a serpentine channel. As T cells flow past the immobilized beads, their change in speed is tracked via microscopy. We validated this approach using two model systems: primary CD8+ T cells from an OT-1 TCR transgenic mouse with beads conjugated with H-2Kb:SIINFEKL, and Jurkat T cells with beads conjugated with anti-CD3 and anti-CD28 antibodies.
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Affiliation(s)
- Max A Stockslager
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Josephine Shaw Bagnall
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Vivian C Hecht
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Kevin Hu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Edgar Aranda-Michel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Kristofor Payer
- Microsystems Technology Laboratories, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Robert J Kimmerling
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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26
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Srinivasan K, Banerjee S, Parimal S, Sejergaard L, Berkovich R, Barquera B, Garde S, Cramer SM. Single Molecule Force Spectroscopy and Molecular Dynamics Simulations as a Combined Platform for Probing Protein Face-Specific Binding. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:10851-10860. [PMID: 28949551 DOI: 10.1021/acs.langmuir.7b03011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Biomolecular interactions frequently occur in orientation-specific manner. For example, prior nuclear magnetic resonance spectroscopy experiments in our lab have suggested the presence of a group of strongly binding residues on a particular face of the protein ubiquitin for interactions with Capto MMC multimodal ligands ("Capto" ligands) (Srinivasan, K.; et al. Langmuir 2014, 30 (44), 13205-13216). We present a clear confirmation of those studies by performing single-molecule force spectroscopy (SMFS) measurements of unbinding complemented with molecular dynamics (MD) calculations of the adsorption free energy of ubiquitin in two distinct orientations with self-assembled monolayers (SAMs) functionalized with "Capto" ligands. These orientations were maintained in the SMFS experiments by tethering ubiquitin mutants to SAM surfaces through strategically located cysteines, thus exposing the desired faces of the protein. Analogous orientations were maintained in MD simulations using suitable constraining methods. Remarkably, despite differences between the finer details of experimental and simulation methodologies, they confirm a clear preference for the previously hypothesized binding face of ubiquitin. Furthermore, MD simulations provided significant insights into the mechanism of protein binding onto this multimodal surface. Because SMFS and MD simulations both directly probe protein-surface interactions, this work establishes a key link between experiments and simulations at molecular scale through the determination of protein face-specific binding energetics. Our approach may have direct applications in biophysical systems where face- or orientation-specific interactions are important, such as biomaterials, sensors, and biomanufacturing.
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Affiliation(s)
- Kartik Srinivasan
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Suvrajit Banerjee
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Siddharth Parimal
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Lars Sejergaard
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Ronen Berkovich
- Department of Chemical Engineering, Ben-Gurion University , Beer-Sheva 84105, Israel
| | - Blanca Barquera
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Department of Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Shekhar Garde
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Steven M Cramer
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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27
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Newcomb CJ, Qafoku NP, Grate JW, Bailey VL, De Yoreo JJ. Developing a molecular picture of soil organic matter-mineral interactions by quantifying organo-mineral binding. Nat Commun 2017; 8:396. [PMID: 28855506 PMCID: PMC5577185 DOI: 10.1038/s41467-017-00407-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 06/27/2017] [Indexed: 01/13/2023] Open
Abstract
Long residence times of soil organic matter have been attributed to reactive mineral surface sites that sorb organic species and cause inaccessibility due to physical isolation and chemical stabilization at the organic–mineral interface. Instrumentation for probing this interface is limited. As a result, much of the micron- and molecular-scale knowledge about organic–mineral interactions remains largely qualitative. Here we report the use of force spectroscopy to directly measure the binding between organic ligands with known chemical functionalities and soil minerals in aqueous environments. By systematically studying the role of organic functional group chemistry with model minerals, we demonstrate that chemistry of both the organic ligand and mineral contribute to values of binding free energy and that changes in pH and ionic strength produce significant differences in binding energies. These direct measurements of molecular binding provide mechanistic insights into organo–mineral interactions, which could potentially inform land-carbon models that explicitly include mineral-bound C pools. Most molecular scale knowledge on soil organo–mineral interactions remains qualitative due to instrument limitations. Here, the authors use force spectroscopy to directly measure free binding energy between organic ligands and minerals and find that both chemistry and environmental conditions affect binding.
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Affiliation(s)
- C J Newcomb
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington, 99354, USA
| | - N P Qafoku
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington, 99354, USA
| | - J W Grate
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington, 99354, USA
| | - V L Bailey
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington, 99354, USA
| | - J J De Yoreo
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington, 99354, USA. .,Department of Materials Science and Engineering, University of Washington, 302 Roberts Hall, Seattle, Washington, 98195, USA.
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28
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Angely C, Nguyen NM, Andre Dias S, Planus E, Pelle G, Louis B, Filoche M, Chenal A, Ladant D, Isabey D. Exposure to Bordetella pertussis adenylate cyclase toxin affects integrin-mediated adhesion and mechanics in alveolar epithelial cells. Biol Cell 2017; 109:293-311. [PMID: 28597954 DOI: 10.1111/boc.201600082] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND INFORMATION The adenylate cyclase (CyaA) toxin is a major virulent factor of Bordetella pertussis, the causative agent of whooping cough. CyaA toxin is able to invade eukaryotic cells where it produces high levels of cyclic adenosine monophosphate (cAMP) affecting cellular physiology. Whether CyaA toxin can modulate cell matrix adhesion and mechanics of infected cells remains largely unknown. RESULTS In this study, we use a recently proposed multiple bond force spectroscopy (MFS) with an atomic force microscope to assess the early phase of cell adhesion (maximal detachment and local rupture forces) and cell rigidity (Young's modulus) in alveolar epithelial cells (A549) for toxin exposure <1 h. At 30 min of exposure, CyaA toxin has a minimal effect on cell viability (>95%) at CyaA concentration of 0.5 nM, but a significant effect (≈81%) at 10 nM. MFS performed on A549 for three different concentrations (0.5, 5 and 10 nM) demonstrates that CyaA toxin significantly affects both cell adhesion (detachment forces are decreased) and cell mechanics (Young's modulus is increased). CyaA toxin (at 0.5 nM) assessed at three indentation/retraction speeds (2, 5 and 10 μm/s) significantly affects global detachment forces, local rupture events and Young modulus compared with control conditions, while an enzymatically inactive variant CyaAE5 has no effect. These results reveal the loading rate dependence of the multiple bonds newly formed between the cell and integrin-specific coated probe as well as the individual bond kinetics which are only slightly affected by the patho-physiological dose of CyaA toxin. Finally, theory of multiple bond force rupture enables us to deduce the bond number N which is reduced by a factor of 2 upon CyaA exposure (N ≈ 6 versus N ≈ 12 in control conditions). CONCLUSIONS MFS measurements demonstrate that adhesion and mechanical properties of A549 are deeply affected by exposure to the CyaA toxin but not to an enzymatically inactive variant. This indicates that the alteration of cell mechanics triggered by CyaA is a consequence of the increase in intracellular cAMP in these target cells. SIGNIFICANCE These results suggest that mechanical and adhesion properties of the cells appear as pertinent markers of cytotoxicity of CyaA toxin.
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Affiliation(s)
- Christelle Angely
- Inserm, U955, Equipe 13, Biomécanique & Appareil Respiratoire: une approche multi-échelle, Créteil Cedex, 94010, France.,Université Paris Est, UMRS 955, UPEC, Créteil Cedex, 94010, France.,CNRS, ERL 7240, Créteil Cedex, 94010, France
| | - Ngoc-Minh Nguyen
- Inserm, U955, Equipe 13, Biomécanique & Appareil Respiratoire: une approche multi-échelle, Créteil Cedex, 94010, France.,Université Paris Est, UMRS 955, UPEC, Créteil Cedex, 94010, France.,CNRS, ERL 7240, Créteil Cedex, 94010, France
| | - Sofia Andre Dias
- Inserm, U955, Equipe 13, Biomécanique & Appareil Respiratoire: une approche multi-échelle, Créteil Cedex, 94010, France.,Université Paris Est, UMRS 955, UPEC, Créteil Cedex, 94010, France.,CNRS, ERL 7240, Créteil Cedex, 94010, France
| | - Emmanuelle Planus
- Institute for Advanced Biosciences (IAB), Centre de Recherche UGA/Inserm U1209/CNRS UMR 5309, La Tronche 38700, France
| | - Gabriel Pelle
- Inserm, U955, Equipe 13, Biomécanique & Appareil Respiratoire: une approche multi-échelle, Créteil Cedex, 94010, France.,Université Paris Est, UMRS 955, UPEC, Créteil Cedex, 94010, France.,CNRS, ERL 7240, Créteil Cedex, 94010, France.,AP-HP, Groupe Hospitalier H. Mondor - A. Chenevier, Service des Explorations Fonctionnelles, Créteil Cedex, 94010, France
| | - Bruno Louis
- Inserm, U955, Equipe 13, Biomécanique & Appareil Respiratoire: une approche multi-échelle, Créteil Cedex, 94010, France.,Université Paris Est, UMRS 955, UPEC, Créteil Cedex, 94010, France.,CNRS, ERL 7240, Créteil Cedex, 94010, France
| | - Marcel Filoche
- Inserm, U955, Equipe 13, Biomécanique & Appareil Respiratoire: une approche multi-échelle, Créteil Cedex, 94010, France.,Université Paris Est, UMRS 955, UPEC, Créteil Cedex, 94010, France.,CNRS, ERL 7240, Créteil Cedex, 94010, France.,Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, Université Paris Saclay, Palaiseau, 91128, France
| | - Alexandre Chenal
- Unité de Biochimie des Interactions Macromoléculaires (CNRS UMR 3528), Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, 75014, France
| | - Daniel Ladant
- Unité de Biochimie des Interactions Macromoléculaires (CNRS UMR 3528), Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, 75014, France
| | - Daniel Isabey
- Inserm, U955, Equipe 13, Biomécanique & Appareil Respiratoire: une approche multi-échelle, Créteil Cedex, 94010, France.,Université Paris Est, UMRS 955, UPEC, Créteil Cedex, 94010, France.,CNRS, ERL 7240, Créteil Cedex, 94010, France
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Sundar Rajan V, Laurent VM, Verdier C, Duperray A. Unraveling the Receptor-Ligand Interactions between Bladder Cancer Cells and the Endothelium Using AFM. Biophys J 2017; 112:1246-1257. [PMID: 28355551 DOI: 10.1016/j.bpj.2017.01.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/10/2017] [Accepted: 01/23/2017] [Indexed: 01/18/2023] Open
Abstract
Adhesion of cancer cells to endothelial cells is a key step in cancer metastasis; therefore, identifying the key molecules involved during this process promises to aid in efforts to block the metastatic cascade. We have previously shown that intercellular adhesion molecule-1 (ICAM-1) expressed by endothelial cells is involved in the interactions of bladder cancer cells (BCs) with the endothelium. However, the ICAM-1 ligands have never been investigated. In this study, we combined adhesion assays and atomic force microscopy (AFM) to identify the ligands involved and to quantify the forces relevant in such interactions. We report the expression of MUC1 and CD43 on BCs, and demonstrate that these ligands interact with ICAM-1 to mediate cancer cell-endothelial cell adhesion in the case of the more invasive BCs. This was achieved with the use of adhesion assays, which showed a strong decrease in the attachment of BCs to endothelial cells when MUC1 and CD43 were blocked by antibodies. In addition, AFM measurements showed a similar decrease, by up to 70%, in the number of rupture events that occurred when MUC1 and CD43 were blocked. When we applied a Gaussian mixture model to the AFM data, we observed a distinct force range for receptor-ligand bonds, which allowed us to precisely identify the interactions of ICAM-1 with MUC1 or CD43. Furthermore, a detailed analysis of the rupture events suggested that CD43 is strongly connected to the cytoskeleton and that its interaction with ICAM-1 mainly corresponds to force ramps followed by sudden jumps. In contrast, MUC1 seems to be weakly connected to the cytoskeleton, as its interactions with ICAM-1 are mainly associated with the formation of tethers. This analysis is quite promising and may also be applied to other types of cancer cells.
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Affiliation(s)
- Vinoth Sundar Rajan
- INSERM U1209, CNRS UMR5309, IAB, Grenoble, France; University Grenoble Alpes, IAB, Grenoble, France
| | - Valérie M Laurent
- CNRS UMR 5588, LIPhy, Grenoble, France; University Grenoble Alpes, LIPhy, Grenoble, France
| | - Claude Verdier
- CNRS UMR 5588, LIPhy, Grenoble, France; University Grenoble Alpes, LIPhy, Grenoble, France
| | - Alain Duperray
- INSERM U1209, CNRS UMR5309, IAB, Grenoble, France; University Grenoble Alpes, IAB, Grenoble, France.
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30
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Nguyen NM, Angely C, Andre Dias S, Planus E, Filoche M, Pelle G, Louis B, Isabey D. Characterisation of cellular adhesion reinforcement by multiple bond force spectroscopy in alveolar epithelial cells. Biol Cell 2017; 109:255-272. [DOI: 10.1111/boc.201600080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 05/09/2017] [Accepted: 05/11/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Ngoc-Minh Nguyen
- Inserm; U955; Equipe 13; Biomécanique & Appareil Respiratoire; Créteil Cedex F-94010 France
- Université Paris Est; UMR S955, UPEC Créteil Cedex F-94010 France
- CNRS; ERL 7240 Créteil Cedex F-94010 France
| | - Christelle Angely
- Inserm; U955; Equipe 13; Biomécanique & Appareil Respiratoire; Créteil Cedex F-94010 France
- Université Paris Est; UMR S955, UPEC Créteil Cedex F-94010 France
- CNRS; ERL 7240 Créteil Cedex F-94010 France
| | - Sofia Andre Dias
- Inserm; U955; Equipe 13; Biomécanique & Appareil Respiratoire; Créteil Cedex F-94010 France
- Université Paris Est; UMR S955, UPEC Créteil Cedex F-94010 France
- CNRS; ERL 7240 Créteil Cedex F-94010 France
| | - Emmanuelle Planus
- Institute for Advanced Biosciences (IAB); Centre de Recherche UGA/Inserm U1209/CNRS UMR 5309; La Tronche 38700 France
| | - Marcel Filoche
- Inserm; U955; Equipe 13; Biomécanique & Appareil Respiratoire; Créteil Cedex F-94010 France
- Université Paris Est; UMR S955, UPEC Créteil Cedex F-94010 France
- CNRS; ERL 7240 Créteil Cedex F-94010 France
- Laboratoire de Physique de la Matière Condensée; Ecole Polytechnique; CNRS; Université Paris Saclay; Palaiseau 91128 France
| | - Gabriel Pelle
- Inserm; U955; Equipe 13; Biomécanique & Appareil Respiratoire; Créteil Cedex F-94010 France
- Université Paris Est; UMR S955, UPEC Créteil Cedex F-94010 France
- CNRS; ERL 7240 Créteil Cedex F-94010 France
- AP-HP; Groupe Hospitalier H. Mondor - A. Chenevier; Service des Explorations Fonctionnelles; Créteil Cedex F-94010 France
| | - Bruno Louis
- Inserm; U955; Equipe 13; Biomécanique & Appareil Respiratoire; Créteil Cedex F-94010 France
- Université Paris Est; UMR S955, UPEC Créteil Cedex F-94010 France
- CNRS; ERL 7240 Créteil Cedex F-94010 France
| | - Daniel Isabey
- Inserm; U955; Equipe 13; Biomécanique & Appareil Respiratoire; Créteil Cedex F-94010 France
- Université Paris Est; UMR S955, UPEC Créteil Cedex F-94010 France
- CNRS; ERL 7240 Créteil Cedex F-94010 France
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31
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Casillas-Ituarte NN, Cruz CHB, Lins RD, DiBartola AC, Howard J, Liang X, Höök M, Viana IFT, Sierra-Hernández MR, Lower SK. Amino acid polymorphisms in the fibronectin-binding repeats of fibronectin-binding protein A affect bond strength and fibronectin conformation. J Biol Chem 2017; 292:8797-8810. [PMID: 28400484 DOI: 10.1074/jbc.m117.786012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 04/08/2017] [Indexed: 11/06/2022] Open
Abstract
The Staphylococcus aureus cell surface contains cell wall-anchored proteins such as fibronectin-binding protein A (FnBPA) that bind to host ligands (e.g. fibronectin; Fn) present in the extracellular matrix of tissue or coatings on cardiac implants. Recent clinical studies have found a correlation between cardiovascular infections caused by S. aureus and nonsynonymous SNPs in FnBPA. Atomic force microscopy (AFM), surface plasmon resonance (SPR), and molecular simulations were used to investigate interactions between Fn and each of eight 20-mer peptide variants containing amino acids Ala, Asn, Gln, His, Ile, and Lys at positions equivalent to 782 and/or 786 in Fn-binding repeat-9 of FnBPA. Experimentally measured bond lifetimes (1/koff) and dissociation constants (Kd = koff/kon), determined by mechanically dissociating the Fn·peptide complex at loading rates relevant to the cardiovascular system, varied from the lowest-affinity H782A/K786A peptide (0.011 s, 747 μm) to the highest-affinity H782Q/K786N peptide (0.192 s, 15.7 μm). These atomic force microscopy results tracked remarkably well to metadynamics simulations in which peptide detachment was defined solely by the free-energy landscape. Simulations and SPR experiments suggested that an Fn conformational change may enhance the stability of the binding complex for peptides with K786I or H782Q/K786I (Kdapp = 0.2-0.5 μm, as determined by SPR) compared with the lowest-affinity double-alanine peptide (Kdapp = 3.8 μm). Together, these findings demonstrate that amino acid substitutions in Fn-binding repeat-9 can significantly affect bond strength and influence the conformation of Fn upon binding. They provide a mechanistic explanation for the observation of nonsynonymous SNPs in fnbA among clinical isolates of S. aureus that cause endovascular infections.
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Affiliation(s)
| | - Carlos H B Cruz
- the Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE, 50.740-465, Brazil, and
| | - Roberto D Lins
- the Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE, 50.740-465, Brazil, and
| | | | | | - Xiaowen Liang
- the Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas 77030
| | - Magnus Höök
- the Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas 77030
| | - Isabelle F T Viana
- the Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE, 50.740-465, Brazil, and
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Signorelli S, Santini S, Yamada T, Bizzarri AR, Beattie CW, Cannistraro S. Binding of Amphipathic Cell Penetrating Peptide p28 to Wild Type and Mutated p53 as studied by Raman, Atomic Force and Surface Plasmon Resonance spectroscopies. Biochim Biophys Acta Gen Subj 2017; 1861:910-921. [PMID: 28126403 DOI: 10.1016/j.bbagen.2017.01.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 12/21/2016] [Accepted: 01/20/2017] [Indexed: 10/20/2022]
Abstract
BACKGROUND Mutations within the DNA binding domain (DBD) of the tumor suppressor p53 are found in >50% of human cancers and may significantly modify p53 secondary structure impairing its function. p28, an amphipathic cell-penetrating peptide, binds to the DBD through hydrophobic interaction and induces a posttranslational increase in wildtype and mutant p53 restoring functionality. We use mutation analyses to explore which elements of secondary structure may be critical to p28 binding. METHODS Molecular modeling, Raman spectroscopy, Atomic Force Spectroscopy (AFS) and Surface Plasmon Resonance (SPR) were used to identify which secondary structure of site-directed and naturally occurring mutant DBDs are potentially altered by discrete changes in hydrophobicity and the molecular interaction with p28. RESULTS We show that specific point mutations that alter hydrophobicity within non-mutable and mutable regions of the p53 DBD alter specific secondary structures. The affinity of p28 was positively correlated with the β-sheet content of a mutant DBD, and reduced by an increase in unstructured or random coil that resulted from a loss in hydrophobicity and redistribution of surface charge. CONCLUSIONS These results help refine our knowledge of how mutations within p53-DBD alter secondary structure and provide insight on how potential structural alterations in p28 or similar molecules improve their ability to restore p53 function. GENERAL SIGNIFICANCE Raman spectroscopy, AFS, SPR and computational modeling are useful approaches to characterize how mutations within the p53DBD potentially affect secondary structure and identify those structural elements prone to influence the binding affinity of agents designed to increase the functionality of p53.
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Affiliation(s)
- Sara Signorelli
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Viterbo, Italy; Department of Science, University Roma Tre, Rome, Italy
| | - Simona Santini
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Viterbo, Italy
| | - Tohru Yamada
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, USA
| | - Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Viterbo, Italy.
| | - Craig W Beattie
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, USA
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Haider A, Potter D, Sulchek TA. Enhanced stochastic fluctuations to measure steep adhesive energy landscapes. Proc Natl Acad Sci U S A 2016; 113:14213-14218. [PMID: 27911778 PMCID: PMC5167171 DOI: 10.1073/pnas.1608792113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Free-energy landscapes govern the behavior of all interactions in the presence of thermal fluctuations in the fields of physical chemistry, materials sciences, and the biological sciences. From the energy landscape, critical information about an interaction, such as the reaction kinetic rates, bond lifetimes, and the presence of intermediate states, can be determined. Despite the importance of energy landscapes to understanding reaction mechanisms, most experiments do not directly measure energy landscapes, particularly for interactions with steep force gradients that lead to premature jump to contact of the probe and insufficient sampling of transition regions. Here we present an atomic force microscopy (AFM) approach for measuring energy landscapes that increases sampling of strongly adhesive interactions by using white-noise excitation to enhance the cantilever's thermal fluctuations. The enhanced fluctuations enable the recording of subtle deviations from a harmonic potential to accurately reconstruct interfacial energy landscapes with steep gradients. Comparing the measured energy landscape with adhesive force measurements reveals the existence of an optimal excitation voltage that enables the cantilever fluctuations to fully sample the shape and depth of the energy surface.
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Affiliation(s)
- Ahmad Haider
- Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Daniel Potter
- Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Todd A Sulchek
- Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332;
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332
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Baldacchini C, Bizzarri AR, Cannistraro S. Electron transfer, conduction and biorecognition properties of the redox metalloprotein Azurin assembled onto inorganic substrates. Eur Polym J 2016. [DOI: 10.1016/j.eurpolymj.2016.04.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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The Power of Force: Insights into the Protein Folding Process Using Single-Molecule Force Spectroscopy. J Mol Biol 2016; 428:4245-4257. [PMID: 27639437 DOI: 10.1016/j.jmb.2016.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 01/03/2023]
Abstract
One of the major challenges in modern biophysics is observing and understanding conformational changes during complex molecular processes, from the fundamental protein folding to the function of molecular machines. Single-molecule techniques have been one of the major driving forces of the huge progress attained in the last few years. Recent advances in resolution of the experimental setups, aided by theoretical developments and molecular dynamics simulations, have revealed a much higher degree of complexity inside these molecular processes than previously reported using traditional ensemble measurements. This review sums up the evolution of these developments and gives an outlook on prospective discoveries.
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36
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Theory for nonlinear dynamic force spectroscopy. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:225-233. [PMID: 27461369 PMCID: PMC5346443 DOI: 10.1007/s00249-016-1158-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/01/2016] [Accepted: 07/11/2016] [Indexed: 11/25/2022]
Abstract
Dynamic force spectroscopy (DFS) is an experimental technique that is commonly used to assess information on the strength, energy landscape, and lifetime of noncovalent bio-molecular interactions. DFS traditionally requires an applied force that increases linearly with time so that the bio-complex under investigation is exposed to a constant loading rate. However, tethers or polymers can modulate the applied force in a nonlinear manner. For example, bacterial adhesion pili and polymers with worm-like chain properties are structures that show nonlinear force responses. In these situations, the theory for traditional DFS cannot be readily applied. In this work, we expand the theory for DFS to also include nonlinear external forces while still maintaining compatibility with the linear DFS theory. To validate the theory, we modeled a bio-complex expressed on a stiff, an elastic, and a worm-like chain polymer, using Monte Carlo methods, and assessed the corresponding rupture force spectra. It was found that the nonlinear DFS (NLDFS) theory correctly predicted the numerical results. We also present a protocol suggesting an experimental approach and analysis method of the data to estimate the bond length and the thermal off-rate.
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37
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Yen CF, Harischandra DS, Kanthasamy A, Sivasankar S. Copper-induced structural conversion templates prion protein oligomerization and neurotoxicity. SCIENCE ADVANCES 2016; 2:e1600014. [PMID: 27419232 PMCID: PMC4942324 DOI: 10.1126/sciadv.1600014] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 05/27/2016] [Indexed: 05/26/2023]
Abstract
Prion protein (PrP) misfolding and oligomerization are key pathogenic events in prion disease. Copper exposure has been linked to prion pathogenesis; however, its mechanistic basis is unknown. We resolve, with single-molecule precision, the molecular mechanism of Cu(2+)-induced misfolding of PrP under physiological conditions. We also demonstrate that misfolded PrPs serve as seeds for templated formation of aggregates, which mediate inflammation and degeneration of neuronal tissue. Using a single-molecule fluorescence assay, we demonstrate that Cu(2+) induces PrP monomers to misfold before oligomer assembly; the disordered amino-terminal region mediates this structural change. Single-molecule force spectroscopy measurements show that the misfolded monomers have a 900-fold higher binding affinity compared to the native isoform, which promotes their oligomerization. Real-time quaking-induced conversion demonstrates that misfolded PrPs serve as seeds that template amyloid formation. Finally, organotypic slice cultures show that misfolded PrPs mediate inflammation and degeneration of neuronal tissue. Our study establishes a direct link, at the molecular level, between copper exposure and PrP neurotoxicity.
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Affiliation(s)
- Chi-Fu Yen
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA
| | - Dilshan S. Harischandra
- Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Anumantha Kanthasamy
- Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Sanjeevi Sivasankar
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA
- Department of Physics and Astronomy, Iowa State University, Ames, IA 50011, USA
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Ma CD, Acevedo-Vélez C, Wang C, Gellman SH, Abbott NL. Interaction of the Hydrophobic Tip of an Atomic Force Microscope with Oligopeptides Immobilized Using Short and Long Tethers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:2985-2995. [PMID: 26895750 DOI: 10.1021/acs.langmuir.5b04618] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We report an investigation of the adhesive force generated between the hydrophobic tip of an atomic force microscope (AFM) and surfaces presenting oligopeptides immobilized using either short (∼1 nm) or long (∼60 nm) tethers. Specifically, we used either sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SSMCC) or 10 kDa polyethylene glycol (PEG) end-functionalized with maleimide and N-hydroxysuccinimide groups to immobilize helical oligomers of β-amino acids (β-peptides) to mixed monolayers presenting tetraethylene glycol (EG4) and amine-terminated EG4 (EG4N) groups. When SSMCC was used to immobilize the β-peptides, we measured the adhesive interaction between the AFM tip and surface to rupture through a single event with magnitude consistent with the interaction of a single β-peptide with the AFM tip. Surprisingly, this occurred even when, on average, multiple β-peptides were located within the interaction area between the AFM tip and surface. In contrast, when using the long 10 kDa PEG tether, we observed the magnitude of the adhesive interaction as well as the dynamics of the rupture events to unmask the presence of the multiple β-peptides within the interaction area. To provide insight into these observations, we formulated a simple mechanical model of the interaction of the AFM tip with the immobilized β-peptides and used the model to demonstrate that adhesion measurements performed using short tethers (but not long tethers) are dominated by the interaction of single β-peptides because (i) the mechanical properties of the short tether are highly nonlinear, thus causing one β-peptide to dominate the adhesion force at the point of rupture, and (ii) the AFM cantilever is mechanically unstable following the rupture of the adhesive interaction with a single β-peptide. Overall, our study reveals that short tethers offer the basis of an approach that facilitates measurement of adhesive interactions with single molecules presented at surfaces.
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Affiliation(s)
- C Derek Ma
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison , 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Claribel Acevedo-Vélez
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison , 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Chenxuan Wang
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison , 1415 Engineering Drive, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Nicholas L Abbott
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison , 1415 Engineering Drive, Madison, Wisconsin 53706, United States
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Mishra S, Lahiri H, Banerjee S, Mukhopadhyay R. Molecularly resolved label-free sensing of single nucleobase mismatches by interfacial LNA probes. Nucleic Acids Res 2016; 44:3739-49. [PMID: 27025649 PMCID: PMC4856997 DOI: 10.1093/nar/gkw197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/14/2016] [Indexed: 01/29/2023] Open
Abstract
So far, there has been no report on molecularly resolved discrimination of single nucleobase mismatches using surface-confined single stranded locked nucleic acid (ssLNA) probes. Herein, it is exemplified using a label-independent force-sensing approach that an optimal coverage of 12-mer ssLNA sensor probes formed onto gold(111) surface allows recognition of ssDNA targets with twice stronger force sensitivity than 12-mer ssDNA sensor probes. The force distributions are reproducible and the molecule-by-molecule force measurements are largely in agreement with ensemble on-surface melting temperature data. Importantly, the molecularly resolved detection is responsive to the presence of single nucleobase mismatches in target sequences. Since the labelling steps can be eliminated from protocol, and each force-based detection event occurs within milliseconds' time scale, the force-sensing assay is potentially capable of rapid detection. The LNA probe performance is indicative of versatility in terms of substrate choice - be it gold (for basic research and array-based applications) or silicon (for ‘lab-on-a-chip’ type devices). The nucleic acid microarray technologies could therefore be generally benefited by adopting the LNA films, in place of DNA. Since LNA is nuclease-resistant, unlike DNA, and the LNA-based assay is sensitive to single nucleobase mismatches, the possibilities for label-free in vitro rapid diagnostics based on the LNA probes may be explored.
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Affiliation(s)
- Sourav Mishra
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India
| | - Hiya Lahiri
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India
| | - Siddhartha Banerjee
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India
| | - Rupa Mukhopadhyay
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India
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40
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Dumitru AC, Herruzo ET, Rausell E, Ceña V, Garcia R. Unbinding forces and energies between a siRNA molecule and a dendrimer measured by force spectroscopy. NANOSCALE 2015; 7:20267-20276. [PMID: 26580848 DOI: 10.1039/c5nr04906g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We have measured the intermolecular forces between small interference RNA (siRNA) and polyamidoamine dendrimers at the single molecular level. A single molecule force spectroscopy approach has been developed to measure the unbinding forces and energies between a siRNA molecule and polyamidoamine dendrimers deposited on a mica surface in a buffer solution. We report three types of unbinding events which are characterized by forces and free unbinding energies, respectively, of 28 pN, 0.709 eV; 38 pN, 0.722 eV; and 50 pN, 0.724 eV. These events reflect different possible electrostatic interactions between the positive charges of one or two dendrimers and the negatively charged phosphate groups of a single siRNA. We have evidence of a high binding affinity of siRNA towards polyamidoamine dendrimers that leads to a 45% probability of measuring specific unbinding events.
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Affiliation(s)
- Andra C Dumitru
- Instituto de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Ines de la Cruz 3, 28049 Madrid, Spain.
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41
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Marcuello C, de Miguel R, Martínez-Júlvez M, Gómez-Moreno C, Lostao A. Mechanostability of the Single-Electron-Transfer Complexes of Anabaena Ferredoxin-NADP(+) Reductase. Chemphyschem 2015; 16:3161-9. [PMID: 26248023 DOI: 10.1002/cphc.201500534] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Indexed: 01/24/2023]
Abstract
The complexes formed between the flavoenzyme ferredoxin-NADP(+) reductase (FNR; NADP(+) =nicotinamide adenine dinucleotide phosphate) and its redox protein partners, ferredoxin (Fd) and flavodoxin (Fld), have been analysed by using dynamic force spectroscopy through AFM. A strategy is developed to immobilise proteins on a substrate and AFM tip to optimise the recognition ability. The differences in the recognition efficiency regarding a random attachment procedure, together with nanomechanical results, show two binding models for these systems. The interaction of the reductase with the natural electron donor, Fd, is threefold stronger and its lifetime is longer and more specific than that with the substitute under iron-deficient conditions, Fld. The higher bond probability and two possible dissociation pathways in Fld binding to FNR are probably due to the nature of this complex, which is closer to a dynamic ensemble model. This is in contrast with the one-step dissociation kinetics that has been observed and a specific interaction described for the FNR:Fd complex.
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Affiliation(s)
- Carlos Marcuello
- Laboratorio de Microscopías Avanzadas, Instituto de Nanociencia de Aragón, Universidad de Zaragoza, C/Mariano Esquillor, s/n. Ed. I+D+i, 50018, Zaragoza, Spain
| | - Rocío de Miguel
- Laboratorio de Microscopías Avanzadas, Instituto de Nanociencia de Aragón, Universidad de Zaragoza, C/Mariano Esquillor, s/n. Ed. I+D+i, 50018, Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Facultad de Ciencias, C/Pedro Cerbuna, 12, 50009, Zaragoza, Spain
| | - Carlos Gómez-Moreno
- Laboratorio de Microscopías Avanzadas, Instituto de Nanociencia de Aragón, Universidad de Zaragoza, C/Mariano Esquillor, s/n. Ed. I+D+i, 50018, Zaragoza, Spain.,Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Facultad de Ciencias, C/Pedro Cerbuna, 12, 50009, Zaragoza, Spain
| | - Anabel Lostao
- Laboratorio de Microscopías Avanzadas, Instituto de Nanociencia de Aragón, Universidad de Zaragoza, C/Mariano Esquillor, s/n. Ed. I+D+i, 50018, Zaragoza, Spain. .,Fundación ARAID, C/María de Luna, 11. Ed. CEEI Aragón, 50018, Zaragoza, Spain.
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42
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Håti AG, Aachmann FL, Stokke BT, Skjåk-Bræk G, Sletmoen M. Energy Landscape of Alginate-Epimerase Interactions Assessed by Optical Tweezers and Atomic Force Microscopy. PLoS One 2015; 10:e0141237. [PMID: 26496653 PMCID: PMC4619708 DOI: 10.1371/journal.pone.0141237] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/05/2015] [Indexed: 11/28/2022] Open
Abstract
Mannuronan C-5 epimerases are a family of enzymes that catalyze epimerization of alginates at the polymer level. This group of enzymes thus enables the tailor-making of various alginate residue sequences to attain various functional properties, e.g. viscosity, gelation and ion binding. Here, the interactions between epimerases AlgE4 and AlgE6 and alginate substrates as well as epimerization products were determined. The interactions of the various epimerase–polysaccharide pairs were determined over an extended range of force loading rates by the combined use of optical tweezers and atomic force microscopy. When studying systems that in nature are not subjected to external forces the access to observations obtained at low loading rates, as provided by optical tweezers, is a great advantage since the low loading rate region for these systems reflect the properties of the rate limiting energy barrier. The AlgE epimerases have a modular structure comprising both A and R modules, and the role of each of these modules in the epimerization process were examined through studies of the A- module of AlgE6, AlgE6A. Dynamic strength spectra obtained through combination of atomic force microscopy and the optical tweezers revealed the existence of two energy barriers in the alginate-epimerase complexes, of which one was not revealed in previous AFM based studies of these complexes. Furthermore, based on these spectra estimates of the locations of energy transition states (xβ), lifetimes in the absence of external perturbation (τ0) and free energies (ΔG#) were determined for the different epimerase–alginate complexes. This is the first determination of ΔG# for these complexes. The values determined were up to 8 kBT for the outer barrier, and smaller values for the inner barriers. The size of the free energies determined are consistent with the interpretation that the enzyme and substrate are thus not tightly locked at all times but are able to relocate. Together with the observed different affinities determined for AlgE4-polymannuronic acid (poly-M) and AlgE4-polyalternating alginate (poly-MG) macromolecular pairs these data give important contribution to the growing understanding of the mechanisms underlying the processive mode of these enzymes.
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Affiliation(s)
- Armend Gazmeno Håti
- Biophysics and Medical Technology, Dept. of Physics, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
| | - Finn Lillelund Aachmann
- NOBIPOL, Dept. of Biotechnology, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
| | - Bjørn Torger Stokke
- Biophysics and Medical Technology, Dept. of Physics, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
| | - Gudmund Skjåk-Bræk
- NOBIPOL, Dept. of Biotechnology, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
| | - Marit Sletmoen
- NOBIPOL, Dept. of Biotechnology, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
- * E-mail:
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Parreira P, Shi Q, Magalhaes A, Reis CA, Bugaytsova J, Borén T, Leckband D, Martins MCL. Atomic force microscopy measurements reveal multiple bonds between Helicobacter pylori blood group antigen binding adhesin and Lewis b ligand. J R Soc Interface 2015; 11:20141040. [PMID: 25320070 DOI: 10.1098/rsif.2014.1040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The strength of binding between the Helicobacter pylori blood group antigen-binding adhesin (BabA) and its cognate glycan receptor, the Lewis b blood group antigen (Le(b)), was measured by means of atomic force microscopy. High-resolution measurements of rupture forces between single receptor-ligand pairs were performed between the purified BabA and immobilized Le(b) structures on self-assembled monolayers. Dynamic force spectroscopy revealed two similar but statistically different bond populations. These findings suggest that the BabA may form different adhesive attachments to the gastric mucosa in ways that enhance the efficiency and stability of bacterial adhesion.
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Affiliation(s)
- P Parreira
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | - Q Shi
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - A Magalhaes
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - C A Reis
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal Faculdade de Medicina, Universidade do Porto, Porto, Portugal Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - J Bugaytsova
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - T Borén
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - D Leckband
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - M C L Martins
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
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Sirbuly DJ, Friddle RW, Villanueva J, Huang Q. Nanomechanical force transducers for biomolecular and intracellular measurements: is there room to shrink and why do it? REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:024101. [PMID: 25629797 DOI: 10.1088/0034-4885/78/2/024101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Over the past couple of decades there has been a tremendous amount of progress on the development of ultrasensitive nanomechanical instruments, which has enabled scientists to peer for the first time into the mechanical world of biomolecular systems. Currently, work-horse instruments such as the atomic force microscope and optical/magnetic tweezers have provided the resolution necessary to extract quantitative force data from various molecular systems down to the femtonewton range, but it remains difficult to access the intracellular environment with these analytical tools as they have fairly large sizes and complicated feedback systems. This review is focused on highlighting some of the major milestones and discoveries in the field of biomolecular mechanics that have been made possible by the development of advanced atomic force microscope and tweezer techniques as well as on introducing emerging state-of-the-art nanomechanical force transducers that are addressing the size limitations presented by these standard tools. We will first briefly cover the basic setup and operation of these instruments, and then focus heavily on summarizing advances in in vitro force studies at both the molecular and cellular level. The last part of this review will include strategies for shrinking down the size of force transducers and provide insight into why this may be important for gaining a more complete understanding of cellular activity and function.
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Affiliation(s)
- Donald J Sirbuly
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA. Materials Science and Engineering, University of California, San Diego, La Jolla, CA, 92093, USA
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Bacharouche J, Degardin M, Jierry L, Carteret C, Lavalle P, Hemmerlé J, Senger B, Auzély-Velty R, Boulmedais F, Boturyn D, Coche-Guérente L, Schaaf P, Francius G. Multivalency: influence of the residence time and the retraction rate on rupture forces measured by AFM. J Mater Chem B 2015; 3:1801-1812. [DOI: 10.1039/c4tb01261e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular orientation and flexibility of β-CD modulate the contact time and the multivalence effects of specific host–guest interactions.
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46
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Haugstad KE, Stokke BT, Brewer CF, Gerken TA, Sletmoen M. Single molecule study of heterotypic interactions between mucins possessing the Tn cancer antigen. Glycobiology 2014; 25:524-34. [PMID: 25527429 DOI: 10.1093/glycob/cwu183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Mucins are linear, heavily O-glycosylated proteins with physiological roles that include cell signaling, cell adhesion, inflammation, immune response and tumorgenesis. Cancer-associated mucins often differ from normal mucins by presenting truncated carbohydrate chains. Characterization of the binding properties of mucins with truncated carbohydrate side chains could thus prove relevant for understanding their role in cancer mechanisms such as metastasis and recognition by the immune system. In this work, heterotypic interactions of model mucins that possess the Tn (GalNAcαThr/Ser) and T (Galβ1-3GalNAcαThr/Ser) cancer antigens derived from porcine submaxillary mucin (PSM) were studied using atomic force microscopy. PSM possessing only the Tn antigen (Tn-PSM) was found to bind to PSM analogs possessing a combination of T, Tn and STn antigens as well as biosynthetic analogs of the core 1 blood group A tetrasaccharide (GalNAcα1-3[Fucα1-2] Galβ1-3GalNAcαSer/Thr). The rupture forces for the heterotypic interactions ranged from 18- to 31 pN at a force-loading rate of ∼0.5 nN/s. The thermally averaged distance from the bound complex to the transition state (xβ) was estimated to be in the range 0.37-0.87 nm for the first barrier of the Bell Evans analysis and within 0.34-0.64 nm based on a lifetime analysis. These findings reveal that the binding strength and energy landscape for heterotypic interactions of Tn-PSM with the above mucins, resemble homotypic interactions of Tn-PSM. This suggests common carbohydrate epitope interactions for the Tn cancer antigen with the above mucin analogs, a finding that may be important to the role of the Tn antigen in cancer cells.
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Affiliation(s)
- Kristin E Haugstad
- Department of Physics, Biophysics and Medical Technology, The Norwegian University of Science and Technology, Trondheim NO-7491, Norway
| | - Bjørn T Stokke
- Department of Physics, Biophysics and Medical Technology, The Norwegian University of Science and Technology, Trondheim NO-7491, Norway
| | - C Fred Brewer
- Department of Molecular Pharmacology Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Thomas A Gerken
- W.A. Bernbaum Center for Cystic Fibrosis Research, Departments of Pediatrics, Biochemistry and Chemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4948, USA
| | - Marit Sletmoen
- Department of Physics, Biophysics and Medical Technology, The Norwegian University of Science and Technology, Trondheim NO-7491, Norway
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Gupta VK. Effects of cellular viscoelasticity in multiple-bond force spectroscopy. Biomech Model Mechanobiol 2014; 14:615-32. [PMID: 25326875 DOI: 10.1007/s10237-014-0626-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 10/04/2014] [Indexed: 12/17/2022]
Abstract
Receptor-ligand bonds are often subjected to forces that regulate their detachment via modulating off-rates. Though the dynamics of detachment is primarily controlled by the physical chemistry of adhesion molecules cellular features such as cell deformability and microvillus viscoelasticity have been shown to have an effect on it as well. In this work, Monte Carlo simulation of the rupture of multiple receptor-ligand bonds between substrate and a polymorphonuclear leukocyte (PMN) cell suspended in a Newtonian fluid is performed. It is demonstrated via various micromechanical models of the PMN cell adhered to the substrate by multiple receptor-ligand bonds that viscous drag caused by relative motion of cell suspended in a Newtonian fluid and cellular viscoelasticity modulate transmission of an applied external load to receptor-ligand bonds. It is demonstrated that due to cellular viscoelasticity the instantaneous intermolecular bond force is lower than the instantaneous applied force. It is also demonstrated that due to cellular viscoelasticity, the mean intermolecular bond rupture forces are lowered while the mean bond lifetime increases.
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Affiliation(s)
- V K Gupta
- Department of Mechanical Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA,
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Rakshit S, Sivasankar S. Biomechanics of cell adhesion: how force regulates the lifetime of adhesive bonds at the single molecule level. Phys Chem Chem Phys 2014; 16:2211-23. [PMID: 24419646 DOI: 10.1039/c3cp53963f] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cell adhesion proteins play critical roles in positioning cells during development, segregating cells into distinct tissue compartments and in maintaining tissue integrity. The principle function of these proteins is to bind cells together and resist mechanical force. Adhesive proteins also enable migrating cells to adhere and roll on surfaces even in the presence of shear forces exerted by fluid flow. Recently, several experimental and theoretical studies have provided quantitative insights into the physical mechanisms by which adhesion proteins modulate their unbinding kinetics in response to tensile force. This perspective reviews these biophysical investigations. We focus on single molecule studies of cadherins, selectins, integrins, the von Willebrand factor and FimH adhesion proteins; the effect of mechanical force on the lifetime of these interactions has been extensively characterized. We review both theoretical models and experimental investigations and discuss future directions in this exciting area of research.
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Affiliation(s)
- Sabyasachi Rakshit
- Department of Physics and Astronomy, Iowa State University, Ames, IA 50011, USA.
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49
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Bizzarri AR, Cannistraro S. Antigen-antibody biorecognition events as discriminated by noise analysis of force spectroscopy curves. NANOTECHNOLOGY 2014; 25:335102. [PMID: 25073811 DOI: 10.1088/0957-4484/25/33/335102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Atomic force spectroscopy is able to extract kinetic and thermodynamic parameters of biomolecular complexes provided that the registered unbinding force curves could be reliably attributed to the rupture of the specific complex interactions. To this aim, a commonly used strategy is based on the analysis of the stretching features of polymeric linkers which are suitably introduced in the biomolecule-substrate immobilization procedure. Alternatively, we present a method to select force curves corresponding to specific biorecognition events, which relies on a careful analysis of the force fluctuations of the biomolecule-functionalized cantilever tip during its approach to the partner molecules immobilized on a substrate. In the low frequency region, a characteristic 1/f (α) noise with α equal to one (flickering noise) is found to replace white noise in the cantilever fluctuation power spectrum when, and only when, a specific biorecognition process between the partners occurs. The method, which has been validated on a well-characterized antigen-antibody complex, represents a fast, yet reliable alternative to the use of linkers which may involve additional surface chemistry and reproducibility concerns.
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Affiliation(s)
- Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Largo dell'Università, I-01100 Viterbo, Italy
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50
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Boye K, Ligezowska A, Eble JA, Hoffmann B, Klösgen B, Merkel R. Two barriers or not? Dynamic force spectroscopy on the integrin α7β1 invasin complex. Biophys J 2014; 105:2771-80. [PMID: 24359749 DOI: 10.1016/j.bpj.2013.10.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 09/19/2013] [Accepted: 10/28/2013] [Indexed: 11/18/2022] Open
Abstract
Dynamic force spectroscopy was used to test force-induced dissociation of the complex between the integrin α7β1 and the bacterial protein invasin. Both proteins were used in truncated forms comprising the respective binding sites. Using the biomembrane force-probe, the bond system was exposed to 14 different loading rates ranging from 18 pN/s to 5.3 nN/s. At each rate, bond rupture spectra were collected. Median forces ranged from 8 to 72 pN. These showed two linear regimes when plotted against the logarithm of the force-loading rate. However, a statistical analysis of the full rupture force spectra including the detection limits of the setup showed that all measured data are well described by dissociation over a single barrier.
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Affiliation(s)
- Kristian Boye
- MEMPHYS-Center for Biomembrane Physics, Institute of Physics and Chemistry, University of Southern Denmark, Odense, Denmark
| | - Agnieszka Ligezowska
- MEMPHYS-Center for Biomembrane Physics, Institute of Physics and Chemistry, University of Southern Denmark, Odense, Denmark; Department of Physics, Jagiellonian University, Cracow, Poland; Institute of Complex Systems 7: Biomechanics, Forschungszentrum Jülich, Jülich, Germany
| | - Johannes A Eble
- Institute for Physiological Chemistry and Pathobiochemistry, University of Münster, Münster, Germany
| | - Bernd Hoffmann
- Institute of Complex Systems 7: Biomechanics, Forschungszentrum Jülich, Jülich, Germany
| | - Beate Klösgen
- MEMPHYS-Center for Biomembrane Physics, Institute of Physics and Chemistry, University of Southern Denmark, Odense, Denmark
| | - Rudolf Merkel
- Institute of Complex Systems 7: Biomechanics, Forschungszentrum Jülich, Jülich, Germany.
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