1
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Zhang H, Li X, Qu Z, Zhang W, Wang Q, Cao D, Wang Y, Wang X, Wang Y, Yu L, Ding J. Effects of serum proteins on corrosion rates and product bioabsorbability of biodegradable metals. Regen Biomater 2023; 11:rbad112. [PMID: 38173765 PMCID: PMC10761199 DOI: 10.1093/rb/rbad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/03/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
Corrodible metals are the newest kind of biodegradable materials and raise a new problem of the corrosion products. However, the removal of the precipitated products has been unclear and even largely ignored in publications. Herein, we find that albumin, an abundant macromolecule in serum, enhances the solubility of corrosion products of iron in blood mimetic Hank's solution significantly. This is universal for other main biodegradable metals such as magnesium, zinc and polyester-coated iron. Albumin also influences corrosion rates in diverse trends in Hank's solution and normal saline. Based on quantitative study theoretically and experimentally, both the effects on corrosion rates and soluble fractions are interpreted by a unified mechanism, and the key factor leading to different corrosion behaviors in corrosion media is the interference of albumin to the Ca/P passivation layer on the metal surface. This work has illustrated that the interactions between metals and media macromolecules should be taken into consideration in the design of the next-generation metal-based biodegradable medical devices in the formulism of precision medicine. The improved Hank's solution in the presence of albumin and with a higher content of initial calcium salt is suggested to access biodegradable metals potentially for cardiovascular medical devices, where the content of calcium salt is calculated after consideration of chelating of calcium ions by albumin, resulting in the physiological concentration of free calcium ions.
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Affiliation(s)
- Hongjie Zhang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Xin Li
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Zehua Qu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Wanqian Zhang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Qunsong Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Dinglingge Cao
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Yaoben Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Xin Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Yang Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Lin Yu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Jiandong Ding
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
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2
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Blaimschein N, Parameswaran H, Nagler G, Manioglu S, Helenius J, Ardelean C, Kuhn A, Guan L, Müller DJ. The insertase YidC chaperones the polytopic membrane protein MelB inserting and folding simultaneously from both termini. Structure 2023; 31:1419-1430.e5. [PMID: 37708891 PMCID: PMC10840855 DOI: 10.1016/j.str.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/22/2023] [Accepted: 08/18/2023] [Indexed: 09/16/2023]
Abstract
The insertion and folding of proteins into membranes is crucial for cell viability. Yet, the detailed contributions of insertases remain elusive. Here, we monitor how the insertase YidC guides the folding of the polytopic melibiose permease MelB into membranes. In vivo experiments using conditionally depleted E. coli strains show that MelB can insert in the absence of SecYEG if YidC resides in the cytoplasmic membrane. In vitro single-molecule force spectroscopy reveals that the MelB substrate itself forms two folding cores from which structural segments insert stepwise into the membrane. However, misfolding dominates, particularly in structural regions that interface the pseudo-symmetric α-helical domains of MelB. Here, YidC takes an important role in accelerating and chaperoning the stepwise insertion and folding process of both MelB folding cores. Our findings reveal a great flexibility of the chaperoning and insertase activity of YidC in the multifaceted folding processes of complex polytopic membrane proteins.
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Affiliation(s)
- Nina Blaimschein
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | - Hariharan Parameswaran
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Gisela Nagler
- Institute of Biology, University of Hohenheim, 70599 Stuttgart, Baden-Württemberg, Germany
| | - Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | - Jonne Helenius
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | | | - Andreas Kuhn
- Institute of Biology, University of Hohenheim, 70599 Stuttgart, Baden-Württemberg, Germany
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland.
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3
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Feng Y, Liu M, Li X, Li M, Xing X, Liu L. Nanomechanical Signatures of Extracellular Vesicles from Hematologic Cancer Patients Unraveled by Atomic Force Microscopy for Liquid Biopsy. NANO LETTERS 2023; 23:1591-1599. [PMID: 36723485 DOI: 10.1021/acs.nanolett.3c00093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Cells release extracellular vesicles (EVs) as the carriers for intercellular communications to regulate life activities. Particularly, it is increasingly apparent that mechanical forces play an essential role in biological systems. The nanomechanical properties of EVs and their dynamics in cancer development are still not fully understood. Herein, with the use of atomic force microscopy (AFM), the nanomechanical signatures of EVs from the liquid biopsies of hematologic cancer patients were unraveled. Single native EVs were probed by AFM under aqueous conditions. The elastic and viscous properties of EVs were measured and visualized to correlate EV mechanics with EV geometry. Experimental results remarkably reveal the significant differences in EV mechanics among multiple myeloma patients, lymphoma patients, and healthy volunteers. The study unveils the unique nanomechanical signatures of EVs in hematologic cancers, which will benefit the studies of liquid biopsies for cancer diagnosis and prognosis with translational significance.
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Affiliation(s)
- Yaqi Feng
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Meichen Liu
- Cancer Hospital of China Medical University, Shenyang 110042, People's Republic of China
- Liaoning Cancer Hospital & Institute, Shenyang 110042, People's Republic of China
| | - Xinxin Li
- Cancer Hospital of China Medical University, Shenyang 110042, People's Republic of China
- Liaoning Cancer Hospital & Institute, Shenyang 110042, People's Republic of China
| | - Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xiaojing Xing
- Cancer Hospital of China Medical University, Shenyang 110042, People's Republic of China
- Liaoning Cancer Hospital & Institute, Shenyang 110042, People's Republic of China
| | - Lianqing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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4
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Blaimschein N, Hariharan P, Manioglu S, Guan L, Müller DJ. Substrate-binding guides individual melibiose permeases MelB to structurally soften and to destabilize cytoplasmic middle-loop C3. Structure 2023; 31:58-67.e4. [PMID: 36525976 PMCID: PMC9825662 DOI: 10.1016/j.str.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/06/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
The melibiose permease MelB is a well-studied Na+-coupled transporter of the major facilitator superfamily. However, the symport mechanism of galactosides and cations is still not fully understood, especially at structural levels. Here, we use single-molecule force spectroscopy to investigate substrate-induced structural changes of MelB from Salmonella typhimurium. In the absence of substrate, MelB equally populates two different states, from which one shows higher mechanical structural stability with additional stabilization of the cytoplasmic middle-loop C3. In the presence of either melibiose or a coupling Na+-cation, however, MelB increasingly populates the mechanically less stable state, which shows a destabilized middle-loop C3. In the presence of both substrate and co-substrate, this mechanically less stable state of MelB is predominant. Our findings describe how both substrates guide MelB transporters to populate two different mechanically stabilized states, and contribute mechanistic insights to the alternating-access action for the galactoside/cation symport catalyzed by MelB.
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Affiliation(s)
- Nina Blaimschein
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland.
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5
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Covalent organic framework membranes for efficient separation of monovalent cations. Nat Commun 2022; 13:7123. [DOI: 10.1038/s41467-022-34849-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/09/2022] [Indexed: 11/21/2022] Open
Abstract
AbstractCovalent organic frameworks (COF), with rigid, highly ordered and tunable structures, can actively manipulate the synergy of entropic selectivity and enthalpic selectivity, holding great potential as next-generation membrane materials for ion separations. Here, we demonstrated the efficient separation of monovalent cations by COF membrane. The channels of COF membrane are decorated with three different kinds of acid groups. A concept of confined cascade separation was proposed to elucidate the separation process. The channels of COF membrane comprised two kinds of domains, acid-domains and acid-free-domains. The acid-domains serve as confined stages, rendering high selectivity, while the acid-free-domains preserve the pristine channel size, rendering high permeation flux. A set of descriptors of stage properties were designed to elucidate their effect on selective ion transport behavior. The resulting COF membrane acquired high ion separation performances, with an actual selectivity of 4.2–4.7 for K+/Li+ binary mixtures and an ideal selectivity of ~13.7 for K+/Li+.
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6
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Manioglu S, Modaresi SM, Ritzmann N, Thoma J, Overall SA, Harms A, Upert G, Luther A, Barnes AB, Obrecht D, Müller DJ, Hiller S. Antibiotic polymyxin arranges lipopolysaccharide into crystalline structures to solidify the bacterial membrane. Nat Commun 2022; 13:6195. [PMID: 36271003 PMCID: PMC9587031 DOI: 10.1038/s41467-022-33838-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 10/04/2022] [Indexed: 12/24/2022] Open
Abstract
Polymyxins are last-resort antibiotics with potent activity against multi-drug resistant pathogens. They interact with lipopolysaccharide (LPS) in bacterial membranes, but mechanistic details at the molecular level remain unclear. Here, we characterize the interaction of polymyxins with native, LPS-containing outer membrane patches of Escherichia coli by high-resolution atomic force microscopy imaging, along with structural and biochemical assays. We find that polymyxins arrange LPS into hexagonal assemblies to form crystalline structures. Formation of the crystalline structures is correlated with the antibiotic activity, and absent in polymyxin-resistant strains. Crystal lattice parameters alter with variations of the LPS and polymyxin molecules. Quantitative measurements show that the crystalline structures decrease membrane thickness and increase membrane area as well as stiffness. Together, these findings suggest the formation of rigid LPS-polymyxin crystals and subsequent membrane disruption as the mechanism of polymyxin action and provide a benchmark for optimization and de novo design of LPS-targeting antimicrobials.
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Affiliation(s)
- Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 26, Basel, Switzerland
| | | | - Noah Ritzmann
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 26, Basel, Switzerland
| | - Johannes Thoma
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Sarah A Overall
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Alexander Harms
- Biozentrum, University of Basel, Spitalstrasse 41, Basel, Switzerland
| | | | | | | | | | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 26, Basel, Switzerland.
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, Basel, Switzerland.
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7
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Lactoferrin network with MC3T3-E1 cell proliferation, auxiliary mineralization, antibacterial functions: A multifunctional coating for biofunctionalization of implant surfaces. Colloids Surf B Biointerfaces 2022; 216:112598. [PMID: 35636326 DOI: 10.1016/j.colsurfb.2022.112598] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/27/2022] [Accepted: 05/22/2022] [Indexed: 12/24/2022]
Abstract
Developing biocompatible, low-immunoreactive, and antibacterial implants are challenging yet fundamental to osteosynthesis. In this study, mineralization-stimulative and antibacterial networking nanostructures are assembled via amyloid-like aggregation of lactoferrin (LF) triggered by reducing the intramolecular disulfide bonds. Due to the adhesive property of their rich β-sheet architecture, the LF networks are amenable to the deposition upon the surface of various implant materials, functionalizing the implants with cell-proliferative, mineralization-stimulative, and antibacterial properties. Specifically, the abundant functional groups and amino acids exposed on the surface of LF networks provide abundant functional microdomains for subsequent mineralization of different forms of calcium ions and promote the formation of hydroxyapatite (HAp) crystals in simulated body fluids. We further demonstrate that the LF network inherits the innate antibacterial properties of LF and exerts a synergistic antibacterial ability with surface-enriched positively charged and hydrophobic amino acid residues, disrupting bacterial biofilm formation, enhancing microbial cell wall perturbation, and ultimately leading to microbial death. The results underscore the feasibility of the LF network as a multifunctional coating on bioscaffold surfaces, which may provide insight into its future applications in next-generation artificial bone implants with bacterial/biofilm clearance and bone tissue remodeling capabilities.
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8
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Rahman M, Islam KR, Islam MR, Islam MJ, Kaysir MR, Akter M, Rahman MA, Alam SMM. A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices. MICROMACHINES 2022; 13:968. [PMID: 35744582 PMCID: PMC9229244 DOI: 10.3390/mi13060968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023]
Abstract
Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.
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Affiliation(s)
- Mahmudur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Kazi Rafiqul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Rashedul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Jahirul Islam
- Department of Electrical and Electronic Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh;
| | - Md. Rejvi Kaysir
- Department of Electrical and Computer Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada;
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Masuma Akter
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Arifur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - S. M. Mahfuz Alam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
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9
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Mari SA, Pluhackova K, Pipercevic J, Leipner M, Hiller S, Engel A, Müller DJ. Gasdermin-A3 pore formation propagates along variable pathways. Nat Commun 2022; 13:2609. [PMID: 35545613 PMCID: PMC9095878 DOI: 10.1038/s41467-022-30232-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 04/22/2022] [Indexed: 12/31/2022] Open
Abstract
Gasdermins are main effectors of pyroptosis, an inflammatory form of cell death. Released by proteolysis, the N-terminal gasdermin domain assembles large oligomers to punch lytic pores into the cell membrane. While the endpoint of this reaction, the fully formed pore, has been well characterized, the assembly and pore-forming mechanisms remain largely unknown. To resolve these mechanisms, we characterize mouse gasdermin-A3 by high-resolution time-lapse atomic force microscopy. We find that gasdermin-A3 oligomers assemble on the membrane surface where they remain attached and mobile. Once inserted into the membrane gasdermin-A3 grows variable oligomeric stoichiometries and shapes, each able to open transmembrane pores. Molecular dynamics simulations resolve how the membrane-inserted amphiphilic β-hairpins and the structurally adapting hydrophilic head domains stabilize variable oligomeric conformations and open the pore. The results show that without a vertical collapse gasdermin pore formation propagates along a set of multiple parallel but connected reaction pathways to ensure a robust cellular response.
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Affiliation(s)
- Stefania A Mari
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland
| | - Kristyna Pluhackova
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland.
| | | | - Matthew Leipner
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland
| | | | - Andreas Engel
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland.
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10
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Review on the applications of atomic force microscopy imaging in proteins. Micron 2022; 159:103293. [DOI: 10.1016/j.micron.2022.103293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/22/2022] [Accepted: 05/06/2022] [Indexed: 11/19/2022]
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11
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Supramolecular systems chemistry through advanced analytical techniques. Anal Bioanal Chem 2022; 414:5105-5119. [DOI: 10.1007/s00216-021-03824-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 11/01/2022]
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12
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Ritzmann N, Manioglu S, Hiller S, Müller DJ. Monitoring the antibiotic darobactin modulating the β-barrel assembly factor BamA. Structure 2021; 30:350-359.e3. [PMID: 34875215 DOI: 10.1016/j.str.2021.11.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/30/2021] [Accepted: 11/11/2021] [Indexed: 12/15/2022]
Abstract
The β-barrel assembly machinery (BAM) complex is an essential component of Escherichia coli that inserts and folds outer membrane proteins (OMPs). The natural antibiotic compound darobactin inhibits BamA, the central unit of BAM. Here, we employ dynamic single-molecule force spectroscopy (SMFS) to better understand the structure-function relationship of BamA and its inhibition by darobactin. The five N-terminal polypeptide transport (POTRA) domains show low mechanical, kinetic, and energetic stabilities. In contrast, the structural region linking the POTRA domains to the transmembrane β-barrel exposes the highest mechanical stiffness and lowest kinetic stability within BamA, thus indicating a mechano-functional role. Within the β-barrel, the four N-terminal β-hairpins H1-H4 expose the highest mechanical stabilities and stiffnesses, while the four C-terminal β-hairpins H5-H6 show lower stabilities and higher flexibilities. This asymmetry within the β-barrel suggests that substrates funneling into the lateral gate formed by β-hairpins H1 and H8 can force the flexible C-terminal β-hairpins to change conformations.
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Affiliation(s)
- Noah Ritzmann
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.
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13
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Park JH, Kwak MJ, Hwang C, Kang KN, Liu N, Jang JH, Grzybowski BA. Self-Assembling Films of Covalent Organic Frameworks Enable Long-Term, Efficient Cycling of Zinc-Ion Batteries. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2101726. [PMID: 34288151 DOI: 10.1002/adma.202101726] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/19/2021] [Indexed: 06/13/2023]
Abstract
Despite their safety, nontoxicity, and cost-effectiveness, zinc aqueous batteries still suffer from limited rechargeability and poor cycle life, largely due to spontaneous surface corrosion and formation of large Zn dendrites by irregular and uneven plating and stripping. In this work, these untoward effects are minimized by covering Zn electrodes with ultrathin layers of covalent organic frameworks, COFs. These nanoporous and mechanically flexible films form by self-assembly-via the straightforward and scalable dip-coating technique-and permit efficient mass and charge transport while suppressing surface corrosion and growth of large Zn dendrites. The batteries demonstrated have excellent capacity retention and stable polarization voltage for over 420 h of cycling at 1 mA cm-2 . The COF films essential for these improvements can be readily deposited over large areas and curvilinear supports, enabling, for example, foldable wire-type batteries.
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Affiliation(s)
- Jun Heuk Park
- Center for Soft and Living Matter, Institute for Basic Science, UNIST-gil 50, Ulsan, 44919, South Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, South Korea
| | - Myung-Jun Kwak
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, South Korea
| | - Chihyun Hwang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, South Korea
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Kyeong-Nam Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, South Korea
| | - Nian Liu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Ji-Hyun Jang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, South Korea
| | - Bartosz A Grzybowski
- Center for Soft and Living Matter, Institute for Basic Science, UNIST-gil 50, Ulsan, 44919, South Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, South Korea
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14
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Wang D, Stuart JD, Jones AA, Snow CD, Kipper MJ. Measuring interactions of DNA with nanoporous protein crystals by atomic force microscopy. NANOSCALE 2021; 13:10871-10881. [PMID: 34124715 DOI: 10.1039/d1nr01703a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Crosslinked porous protein crystals are a new biomaterial that can be engineered to encapsulate, stabilize, and organize guest molecules, nanoparticles, and biological moieties. In this study, for the first time, the combined interactions of DNA strands with porous protein crystals are quantitatively measured by high-resolution atomic force microscopy (AFM) and chemical force microscopy. The surface structure of protein crystals with unusually large pores was observed in liquid via high-resolution AFM. Force-distance (F-D) curves were also obtained using AFM tips modified to present or capture DNA. The modification of AFM tips allowed the tips to covalently bind DNA that was pre-loaded in the protein crystal nanopores. The modified tips enabled the interactions of DNA molecules with protein crystals to be quantitatively studied while revealing the morphology of the buffer-immersed protein crystal surface in detail, thereby preserving the structure and properties of protein crystals that could be disrupted or destroyed by drying. The hexagonal space group was manifest at the crystal surface, as were the strong interactions between DNA and the porous protein crystals in question. In sum, this study furthered our understanding of how a new protein-based biomaterial can be used to bind guest DNA assemblies.
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Affiliation(s)
- Dafu Wang
- School of Advanced Materials Discovery, Colorado State University, 1617 Campus Delivery, Fort Collins, CO 80523, USA and Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO 80523, USA.
| | - Julius D Stuart
- Department of Chemistry, Colorado State University, 1872 Campus Delivery, Fort Collins, CO 80523, USA
| | - Alec A Jones
- School of Biomedical Engineering, Colorado State University, 1301 Campus Delivery, Fort Collins, CO 80523, USA
| | - Christopher D Snow
- School of Advanced Materials Discovery, Colorado State University, 1617 Campus Delivery, Fort Collins, CO 80523, USA and Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO 80523, USA. and Department of Chemistry, Colorado State University, 1872 Campus Delivery, Fort Collins, CO 80523, USA and School of Biomedical Engineering, Colorado State University, 1301 Campus Delivery, Fort Collins, CO 80523, USA
| | - Matt J Kipper
- School of Advanced Materials Discovery, Colorado State University, 1617 Campus Delivery, Fort Collins, CO 80523, USA and Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO 80523, USA. and School of Biomedical Engineering, Colorado State University, 1301 Campus Delivery, Fort Collins, CO 80523, USA
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15
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Li M, Xi N, Liu L. Peak force tapping atomic force microscopy for advancing cell and molecular biology. NANOSCALE 2021; 13:8358-8375. [PMID: 33913463 DOI: 10.1039/d1nr01303c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The advent of atomic force microscopy (AFM) provides an exciting tool to detect molecular and cellular behaviors under aqueous conditions. AFM is able to not only visualize the surface topography of the specimens, but also can quantify the mechanical properties of the specimens by force spectroscopy assay. Nevertheless, integrating AFM topographic imaging with force spectroscopy assay has long been limited due to the low spatiotemporal resolution. In recent years, the appearance of a new AFM imaging mode called peak force tapping (PFT) has shattered this limit. PFT allows AFM to simultaneously acquire the topography and mechanical properties of biological samples with unprecedented spatiotemporal resolution. The practical applications of PFT in the field of life sciences in the past decade have demonstrated the excellent capabilities of PFT in characterizing the fine structures and mechanics of living biological systems in their native states, offering novel possibilities to reveal the underlying mechanisms guiding physiological/pathological activities. In this paper, the recent progress in cell and molecular biology that has been made with the utilization of PFT is summarized, and future perspectives for further progression and biomedical applications of PFT are provided.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China and Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China and University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ning Xi
- Department of Industrial and Manufacturing Systems Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Lianqing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China and Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China and University of Chinese Academy of Sciences, Beijing 100049, China.
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16
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Pu J, Wang L, Zhang W, Ma J, Zhang X, Putnis CV. Organically-bound silicon enhances resistance to enzymatic degradation and nanomechanical properties of rice plant cell walls. Carbohydr Polym 2021; 266:118057. [PMID: 34044915 DOI: 10.1016/j.carbpol.2021.118057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 12/31/2022]
Abstract
Plant cell walls exhibit excellent mechanical properties, which form the structural basis for sustainable bioresources and multifunctional nanocelluloses. The wall nanomechanical properties of living cells through covalent modifications of hybrid inorganic elements, such as silicon, may confer significant influence on local mechano-response and enzymatic degradation. Here, we present a combination of ex situ measurements of enzyme-released oligosaccharide fragments using MALDI-TOF MS and in situ atomic force microscopy (AFM) imaging through PeakForce quantitative nanomechanical mapping of tip-functionalized single-molecule enzyme-polysaccharide substrate recognition and the nanoscale dissolution kinetics of individual cellulose microfibrils of living rice (Oryza sativa) cells following silicate cross-linking of cell wall xyloglucan. We find that xyloglucan-bound silicon enhances the resistance to degradation by cellulase and improves the wall nanomechanical properties in the elastic modulus at the single-cell level. The findings establish a direct link between an inorganic element of silicon and the nanoscale architecture of plant cell wall materials for sustainable utilization.
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Affiliation(s)
- Junbao Pu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lijun Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Wenjun Zhang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jie Ma
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiuqing Zhang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Christine V Putnis
- Institut für Mineralogie, University of Münster, 48149, Münster, Germany; School of Molecular and Life Science, Curtin University, 6845, Perth, Australia
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17
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Vilhena JG, Ortega M, Uhlig MR, Garcia R, Pérez R. Practical Guide to Single-Protein AFM Nanomechanical Spectroscopy Mapping: Insights and Pitfalls As Unraveled by All-Atom MD Simulations on Immunoglobulin G. ACS Sens 2021; 6:553-564. [PMID: 33503368 DOI: 10.1021/acssensors.0c02241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Atomic force microscopy is an invaluable characterization tool in almost every biophysics laboratory. However, obtaining atomic/sub-nanometer resolution on single proteins has thus far remained elusive-a feat long achieved on hard substrates. In this regard, nanomechanical spectroscopy mapping may provide a viable approach to overcome this limitation. By complementing topography with mechanical properties measured locally, one may thus enhance spatial resolution at the single-protein level. In this work, we perform all-atom molecular dynamics simulations of the indentation process on a single immunoglobulin G (IgG) adsorbed on a graphene slab. Our simulations reveal three different stages as a function of strain: a noncontact regime-where the mechanical response is linked to the presence of the water environment- followed by an elastic response and a final plastic deformation regime. In the noncontact regime, we are able to identify hydrophobic/hydrophilic patches over the protein. This regime provides the most local mechanical information that allows one to discern different regions with similar height/topography and leads to the best spatial resolution. In the elastic regime, we conclude that the Young modulus is a well-defined property only within mechanically decoupled domains. This is caused by the fact that the elastic deformation is associated with a global reorganization of the domain. Differences in the mechanical response are large enough to clearly resolve domains within a single protein, such as the three subunits forming the IgG. Two events, unfolding or protein slipping, are observed in the plastic regime. Our simulations allow us to characterize these two processes and to provide a strategy to identify them in the force curves. Finally, we elaborate on possible challenges that could hamper the interpretation of such experiments/simulations and how to overcome them. All in all, our simulations provide a detailed picture of nanomechanical spectroscopy mapping on single proteins, showing its potential and the challenges that need to be overcome to unlock its full potential.
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Affiliation(s)
- J. G. Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Maria Ortega
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Manuel R. Uhlig
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, 28049 Madrid, Spain
| | - Ricardo Garcia
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, 28049 Madrid, Spain
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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18
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Vorselen D, Piontek MC, Roos WH, Wuite GJL. Mechanical Characterization of Liposomes and Extracellular Vesicles, a Protocol. Front Mol Biosci 2020; 7:139. [PMID: 32850949 PMCID: PMC7396484 DOI: 10.3389/fmolb.2020.00139] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/09/2020] [Indexed: 12/26/2022] Open
Abstract
Both natural as well as artificial vesicles are of tremendous interest in biology and nanomedicine. Small vesicles (<200 nm) perform essential functions in cell biology and artificial vesicles (liposomes) are used as drug delivery vehicles. Atomic Force Microscopy (AFM) is a powerful technique to study the structural properties of these vesicles. AFM is a well-established technique for imaging at nanometer resolution and for mechanical measurements under physiological conditions. Here, we describe the procedure of AFM imaging and force spectroscopy on small vesicles. We discuss how to image vesicles with minimal structural disturbance, and how to analyze the data for accurate size and shape measurements. In addition, we describe the procedure for performing nanoindentations on vesicles and the subsequent data analysis including mechanical models used for data interpretation.
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Affiliation(s)
- Daan Vorselen
- Fysica Van Levende Systemen and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Melissa C. Piontek
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | - Gijs J. L. Wuite
- Fysica Van Levende Systemen and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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19
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Li M, Xi N, Wang Y, Liu L. In Situ High-Resolution AFM Imaging and Force Probing of Cell Culture Medium-Forming Nanogranular Surfaces for Cell Growth. IEEE Trans Nanobioscience 2020; 19:385-393. [DOI: 10.1109/tnb.2020.2982164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Chen S, Xu J, Liu M, Rao ALN, Zandi R, Gill SS, Mohideen U. Investigation of HIV-1 Gag binding with RNAs and lipids using Atomic Force Microscopy. PLoS One 2020; 15:e0228036. [PMID: 32015565 PMCID: PMC6996966 DOI: 10.1371/journal.pone.0228036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/06/2020] [Indexed: 11/22/2022] Open
Abstract
Atomic Force Microscopy was utilized to study the morphology of Gag, ΨRNA, and their binding complexes with lipids in a solution environment with 0.1Å vertical and 1nm lateral resolution. TARpolyA RNA was used as a RNA control. The lipid used was phospha-tidylinositol-(4,5)-bisphosphate (PI(4,5)P2). The morphology of specific complexes Gag-ΨRNA, Gag-TARpolyA RNA, Gag-PI(4,5)P2 and PI(4,5)P2-ΨRNA-Gag were studied. They were imaged on either positively or negatively charged mica substrates depending on the net charges carried. Gag and its complexes consist of monomers, dimers and tetramers, which was confirmed by gel electrophoresis. The addition of specific ΨRNA to Gag is found to increase Gag multimerization. Non-specific TARpolyA RNA was found not to lead to an increase in Gag multimerization. The addition PI(4,5)P2 to Gag increases Gag multimerization, but to a lesser extent than ΨRNA. When both ΨRNA and PI(4,5)P2 are present Gag undergoes comformational changes and an even higher degree of multimerization.
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Affiliation(s)
- Shaolong Chen
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - Jun Xu
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - Mingyue Liu
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - A. L. N. Rao
- Department of Plant Pathology & Microbiology, University of California, Riverside, California, United States of America
| | - Roya Zandi
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - Sarjeet S. Gill
- Department of Cell Biology & Neuroscience, University of California, Riverside, California, United States of America
| | - Umar Mohideen
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
- * E-mail:
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21
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Li M, Xi N, Wang Y, Liu L. Atomic Force Microscopy as a Powerful Multifunctional Tool for Probing the Behaviors of Single Proteins. IEEE Trans Nanobioscience 2020; 19:78-99. [DOI: 10.1109/tnb.2019.2954099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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22
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Liu W, Guo Y, Wang K, Zhou X, Wang Y, Lü J, Shao Z, Hu J, Czajkowsky DM, Li B. Atomic force microscopy-based single-molecule force spectroscopy detects DNA base mismatches. NANOSCALE 2019; 11:17206-17210. [PMID: 31535117 DOI: 10.1039/c9nr05234h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Atomic force microscopy-based single-molecule-force spectroscopy is limited by low throughput. We introduce addressable DNA origami to study multiple target molecules. Six target DNAs that differed by only a single base-pair mismatch were clearly differentiated a rupture force of only 4 pN.
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Affiliation(s)
- Wenjing Liu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yourong Guo
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Kaizhe Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingfei Zhou
- School of Science, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Ying Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Junhong Lü
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Jun Hu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China and School of Physical Science and Technology, Shanghai Tech University, Shanghai 201204, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Bin Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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23
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Mulvihill E, Pfreundschuh M, Thoma J, Ritzmann N, Müller DJ. High-Resolution Imaging of Maltoporin LamB while Quantifying the Free-Energy Landscape and Asymmetry of Sugar Binding. NANO LETTERS 2019; 19:6442-6453. [PMID: 31385710 DOI: 10.1021/acs.nanolett.9b02674] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Maltoporins are a family of membrane proteins that facilitate the diffusion of hydrophilic molecules and maltosaccharides across the outer membrane of Gram-negative bacteria. Two contradicting models propose the sugar binding, uptake, and transport by maltoporins to be either symmetric or asymmetric. Here, we address this contradiction and introduce force-distance-based atomic force microscopy to image single maltoporin LamB trimers in the membrane at sub-nanometer resolution and simultaneously quantify the binding of different malto-oligosaccharides. We assay subtle differences of the binding free-energy landscape of maltotriose, maltotetraose, and maltopentaose, which quantifies how binding strength and affinity increase with the malto-oligosaccharide chain length. The ligand-binding parameters change considerably by mutating the extracellular loop 3, which folds into and constricts the transmembrane pore of LamB. By recording LamB topographs and structurally mapping binding events at sub-nanometer resolution, we observe LamB to preferentially bind maltodextrin from the periplasmic side, which shows sugar binding and uptake to be asymmetric. The study introduces atomic force microscopy as an analytical nanoscopic tool that can differentiate among the factors modulating and models describing the binding and uptake of substrates by membrane proteins.
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Affiliation(s)
- Estefania Mulvihill
- Department of Biosystems Science and Engineering , Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Moritz Pfreundschuh
- Department of Biosystems Science and Engineering , Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Johannes Thoma
- Department of Biosystems Science and Engineering , Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Noah Ritzmann
- Department of Biosystems Science and Engineering , Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering , Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26 , 4058 Basel , Switzerland
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24
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Das G, Sharma SK, Prakasam T, Gándara F, Mathew R, Alkhatib N, Saleh N, Pasricha R, Olsen JC, Baias M, Kirmizialtin S, Jagannathan R, Trabolsi A. A polyrotaxanated covalent organic network based on viologen and cucurbit[7]uril. Commun Chem 2019. [DOI: 10.1038/s42004-019-0207-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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25
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Solidifying framework nucleic acids with silica. Nat Protoc 2019; 14:2416-2436. [PMID: 31270509 DOI: 10.1038/s41596-019-0184-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/18/2019] [Indexed: 11/08/2022]
Abstract
Soft matter can serve as a template to guide the growth of inorganic components with well-controlled structural features. However, the limited design space of conventional organic and biomolecular templates restricts the complexity and accuracy of templated growth. In past decades, the blossoming of structural DNA nanotechnology has provided us with a large reservoir of delicate-framework nucleic acids with design precision down to a single base. Here, we describe a DNA origami silicification (DOS) approach for generating complex silica composite nanomaterials. By utilizing modified silica sol-gel chemistry, pre-hydrolyzed silica precursor clusters can be uniformly coated onto the surface of DNA frameworks; thus, user-defined DNA-silica hybrid materials with ~3-nm precision can be achieved. More importantly, this method is applicable to various 1D, 2D and 3D DNA frameworks that range from 10 to >1,000 nm. Compared to pure DNA scaffolds, a tenfold increase in the Young's modulus (E modulus) of these composites was observed, owing to their soft inner core and solid silica shell. We further demonstrate the use of solidified DNA frameworks to create 3D metal plasmonic devices. This protocol provides a platform for synthesizing inorganic materials with unprecedented complexity and tailored structural properties. The whole protocol takes ~10 d to complete.
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26
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Senapati S, Poma AB, Cieplak M, Filipek S, Park PSH. Differentiating between Inactive and Active States of Rhodopsin by Atomic Force Microscopy in Native Membranes. Anal Chem 2019; 91:7226-7235. [PMID: 31074606 DOI: 10.1021/acs.analchem.9b00546] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Membrane proteins, including G protein-coupled receptors (GPCRs), present a challenge in studying their structural properties under physiological conditions. Moreover, to better understand the activity of proteins requires examination of single molecule behaviors rather than ensemble averaged behaviors. Force-distance curve-based AFM (FD-AFM) was utilized to directly probe and localize the conformational states of a GPCR within the membrane at nanoscale resolution based on the mechanical properties of the receptor. FD-AFM was applied to rhodopsin, the light receptor and a prototypical GPCR, embedded in native rod outer segment disc membranes from photoreceptor cells of the retina in mice. Both FD-AFM and computational studies on coarse-grained models of rhodopsin revealed that the active state of the receptor has a higher Young's modulus compared to the inactive state of the receptor. Thus, the inactive and active states of rhodopsin could be differentiated based on the stiffness of the receptor. Differentiating the states based on the Young's modulus allowed for the mapping of the different states within the membrane. Quantifying the active states present in the membrane containing the constitutively active G90D rhodopsin mutant or apoprotein opsin revealed that most receptors adopt an active state. Traditionally, constitutive activity of GPCRs has been described in terms of two-state models where the receptor can achieve only a single active state. FD-AFM data are inconsistent with a two-state model but instead require models that incorporate multiple active states.
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Affiliation(s)
- Subhadip Senapati
- Department of Ophthalmology and Visual Sciences , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Adolfo B Poma
- Institute of Fundamental Technological Research , Polish Academy of Sciences , Pawińskiego 5B , 02-106 Warsaw , Poland.,Institute of Physics , Polish Academy of Sciences , Aleja Lotników 32/46 , 02-668 Warsaw , Poland
| | - Marek Cieplak
- Institute of Physics , Polish Academy of Sciences , Aleja Lotników 32/46 , 02-668 Warsaw , Poland
| | - Sławomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre , University of Warsaw , 02-093 Warsaw , Poland
| | - Paul S H Park
- Department of Ophthalmology and Visual Sciences , Case Western Reserve University , Cleveland , Ohio 44106 , United States
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27
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Wang N, Zhang M, Chen X, Ma X, Li C, Zhang Z, Tang J. Mapping the interaction sites of Mucin 1 and DNA aptamer by atomic force microscopy. Analyst 2018; 142:3800-3804. [PMID: 28930315 DOI: 10.1039/c7an01119a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mucin 1 (MUC1) is an attractive tumor marker for cancer diagnosis. An advanced atomic force microscopy (AFM) mode, peak-force tapping AFM with an aptamer functionalized tip, was introduced to map the specific interaction sites of an aptamer and MUC1. Single molecular force spectroscopy (SMFS) was used to investigate dynamic parameters of the aptamer-MUC1.
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Affiliation(s)
- Nan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China.
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28
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Barinov NA, Vlasova II, Sokolov AV, Kostevich VA, Dubrovin EV, Klinov DV. High-resolution atomic force microscopy visualization of metalloproteins and their complexes. Biochim Biophys Acta Gen Subj 2018; 1862:2862-2868. [DOI: 10.1016/j.bbagen.2018.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/17/2018] [Accepted: 09/11/2018] [Indexed: 12/19/2022]
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29
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Benaglia S, Gisbert VG, Perrino AP, Amo CA, Garcia R. Fast and high-resolution mapping of elastic properties of biomolecules and polymers with bimodal AFM. Nat Protoc 2018; 13:2890-2907. [DOI: 10.1038/s41596-018-0070-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Sapra KT, Spoerri PM, Engel A, Alsteens D, Müller DJ. Seeing and sensing single G protein-coupled receptors by atomic force microscopy. Curr Opin Cell Biol 2018; 57:25-32. [PMID: 30412846 PMCID: PMC6472649 DOI: 10.1016/j.ceb.2018.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 12/21/2022]
Abstract
G protein-coupled receptors (GPCRs) regulate key physiological processes and are therefore important drug targets. Complementary approaches are required to obtain mechanistic insight into the structure-function relationship of GPCRs. AFM-based approaches allow various properties of GPCRs to be directly observed and quantified in physiological conditions. FD-based AFM can image single GPCRs at high-resolution and quantify the free-energy landscape of ligand-binding. AFM-based force spectroscopy interrogates the physical and chemical properties of GPCRs.
G protein-coupled receptors (GPCRs) relay extracellular information across cell membranes through a continuum of conformations that are not always captured in structures. Hence, complementary approaches are required to quantify the physical and chemical properties of the dynamic conformations linking to GPCR function. Atomic force microscopy (AFM)-based high-resolution imaging and force spectroscopy are unique methods to scrutinize GPCRs and to sense their interactions. Here, we exemplify recent AFM-based applications to directly observe the supramolecular assembly of GPCRs in native membranes, to measure the ligand-binding free-energy landscape, and how interactions modulate the structural properties of GPCRs. Common trends in GPCR function are beginning to emerge. We envision that technical developments in combining AFM with superresolution fluorescence imaging will provide insights into how cellular states modulate GPCRs and vice versa.
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Affiliation(s)
- K Tanuj Sapra
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Patrizia M Spoerri
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Andreas Engel
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.07., B-1348 Louvain-la-Neuve, Belgium
| | - Daniel J Müller
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland.
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31
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Ruggeri FS, Charmet J, Kartanas T, Peter Q, Chia S, Habchi J, Dobson CM, Vendruscolo M, Knowles TPJ. Microfluidic deposition for resolving single-molecule protein architecture and heterogeneity. Nat Commun 2018; 9:3890. [PMID: 30250131 PMCID: PMC6155325 DOI: 10.1038/s41467-018-06345-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 07/31/2018] [Indexed: 11/10/2022] Open
Abstract
Scanning probe microscopy provides a unique window into the morphology, mechanics, and structure of proteins and their complexes on the nanoscale. Such measurements require, however, deposition of samples onto substrates. This process can affect conformations and assembly states of the molecular species under investigation and can bias the molecular populations observed in heterogeneous samples through differential adsorption. Here, we show that these limitations can be overcome with a single-step microfluidic spray deposition platform. This method transfers biological solutions to substrates as microdroplets with subpicoliter volume, drying in milliseconds, a timescale that is shorter than typical diffusion times of proteins on liquid–solid interfaces, thus avoiding surface mass transport and change to the assembly state. Finally, the single-step deposition ensures the attachment of the full molecular content of the sample to the substrate, allowing quantitative measurements of different molecular populations within heterogeneous systems, including protein aggregates. Manual sample deposition on a substrate can introduce artifacts in quantitative AFM measurements. Here the authors present a microfluidic spray device for reliable deposition of subpicoliter droplets which dry out in milliseconds after landing on the surface, thereby avoiding protein self-assembly.
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Affiliation(s)
| | - Jerome Charmet
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,WMG, University of Warwick, Coventry, CV4 7AL, UK
| | - Tadas Kartanas
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Quentin Peter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sean Chia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Johnny Habchi
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. .,Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK.
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32
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Syed N, Zavabeti A, Ou JZ, Mohiuddin M, Pillai N, Carey BJ, Zhang BY, Datta RS, Jannat A, Haque F, Messalea KA, Xu C, Russo SP, McConville CF, Daeneke T, Kalantar-Zadeh K. Printing two-dimensional gallium phosphate out of liquid metal. Nat Commun 2018; 9:3618. [PMID: 30190463 PMCID: PMC6127148 DOI: 10.1038/s41467-018-06124-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/20/2018] [Indexed: 12/29/2022] Open
Abstract
Two-dimensional piezotronics will benefit from the emergence of new crystals featuring high piezoelectric coefficients. Gallium phosphate (GaPO4) is an archetypal piezoelectric material, which does not naturally crystallise in a stratified structure and hence cannot be exfoliated using conventional methods. Here, we report a low-temperature liquid metal-based two-dimensional printing and synthesis strategy to achieve this goal. We exfoliate and surface print the interfacial oxide layer of liquid gallium, followed by a vapour phase reaction. The method offers access to large-area, wide bandgap two-dimensional (2D) GaPO4 nanosheets of unit cell thickness, while featuring lateral dimensions reaching centimetres. The unit cell thick nanosheets present a large effective out-of-plane piezoelectric coefficient of 7.5 ± 0.8 pm V-1. The developed printing process is also suitable for the synthesis of free standing GaPO4 nanosheets. The low temperature synthesis method is compatible with a variety of electronic device fabrication procedures, providing a route for the development of future 2D piezoelectric materials.
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Affiliation(s)
- Nitu Syed
- School of Engineering, RMIT University, Melbourne, VIC, 3001, Australia
| | - Ali Zavabeti
- School of Engineering, RMIT University, Melbourne, VIC, 3001, Australia
| | - Jian Zhen Ou
- School of Engineering, RMIT University, Melbourne, VIC, 3001, Australia
| | - Md Mohiuddin
- School of Engineering, RMIT University, Melbourne, VIC, 3001, Australia
| | - Naresh Pillai
- School of Engineering, RMIT University, Melbourne, VIC, 3001, Australia
| | - Benjamin J Carey
- Institute of Physics and Center for Nanotechnology, University of Münster, Münster, 48149, Germany
| | - Bao Yue Zhang
- School of Engineering, RMIT University, Melbourne, VIC, 3001, Australia
| | - Robi S Datta
- School of Engineering, RMIT University, Melbourne, VIC, 3001, Australia
| | - Azmira Jannat
- School of Engineering, RMIT University, Melbourne, VIC, 3001, Australia
| | - Farjana Haque
- School of Engineering, RMIT University, Melbourne, VIC, 3001, Australia
| | - Kibret A Messalea
- School of Engineering, RMIT University, Melbourne, VIC, 3001, Australia
| | - Chenglong Xu
- School of Engineering, RMIT University, Melbourne, VIC, 3001, Australia
| | - Salvy P Russo
- Chemical and Quantum Physics Group, ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, VIC, 3001, Australia
| | | | - Torben Daeneke
- School of Engineering, RMIT University, Melbourne, VIC, 3001, Australia.
| | - Kourosh Kalantar-Zadeh
- School of Engineering, RMIT University, Melbourne, VIC, 3001, Australia. .,School of Chemical Engineering, University of New South Wales, Kensington, NSW, 2033, Australia.
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Puiggalí-Jou A, Pawlowski J, del Valle LJ, Michaux C, Perpète EA, Sek S, Alemán C. Properties of Omp2a-Based Supported Lipid Bilayers: Comparison with Polymeric Bioinspired Membranes. ACS OMEGA 2018; 3:9003-9019. [PMID: 31459033 PMCID: PMC6645002 DOI: 10.1021/acsomega.8b00913] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 07/19/2018] [Indexed: 05/31/2023]
Abstract
Omp2a β-barrel outer membrane protein has been reconstituted into supported lipid bilayers (SLBs) to compare the nanomechanical properties (elastic modulus, adhesion forces, and deformation) and functionality of the resulting bioinspired system with those of Omp2a-based polymeric nanomembranes (NMs). Protein reconstitution into lipid bilayers has been performed using different strategies, the most successful one consisting of a detergent-mediated process into preformed liposomes. The elastic modulus obtained for the lipid bilayer and Omp2a are ∼19 and 10.5 ± 1.7 MPa, respectively. Accordingly, the protein is softer than the lipid bilayer, whereas the latter exhibits less mechanical strength than polymeric NMs. Besides, the function of Omp2a in the SLB is similar to that observed for Omp2a-based polymeric NMs. Results open the door to hybrid bioinspired substrates based on the integration of Omp2a-proteoliposomes and nanoperforated polymeric freestanding NMs.
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Affiliation(s)
- Anna Puiggalí-Jou
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, 08019 Barcelona, Spain
| | - Jan Pawlowski
- Biological
and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Luis J. del Valle
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, 08019 Barcelona, Spain
| | - Catherine Michaux
- Laboratoire
de Chimie Physique des Biomolécules, University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Eric A. Perpète
- Laboratoire
de Chimie Physique des Biomolécules, University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Slawomir Sek
- Biological
and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Carlos Alemán
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, 08019 Barcelona, Spain
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34
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Imaging in Biologically-Relevant Environments with AFM Using Stiff qPlus Sensors. Sci Rep 2018; 8:9330. [PMID: 29921947 PMCID: PMC6008343 DOI: 10.1038/s41598-018-27608-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/04/2018] [Indexed: 11/08/2022] Open
Abstract
High-resolution imaging of soft biological samples with atomic force microscopy (AFM) is challenging because they must be imaged with small forces to prevent deformation. Typically, AFM of those samples is performed with soft silicon cantilevers (k ≈ 0.1-10 N/m) and optical detection in a liquid environment. We set up a new microscope that uses a stiff qPlus sensor (k ≥ 1 kN/m). Several complex biologically-relevant solutions are non-transparent, and even change their optical properties over time, such as the cell culture medium we used. While this would be problematic for AFM setups with optical detection, it is no problem for our qPlus setup which uses electrical detection. The high stiffness of the qPlus sensor allows us to use small amplitudes in frequency-modulation mode and obtain high Q factors even in liquid. The samples are immersed in solution in a liquid cell and long tips are used, with only the tip apex submerged. We discuss the noise terms and compare the minimal detectable signal to that of soft cantilevers. Atomic resolution of muscovite mica was achieved in various liquids: H2O, Tris buffer and a cell culture medium. We show images of lipid membranes in which the individual head groups are resolved.
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35
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Mulvihill E, Sborgi L, Mari SA, Pfreundschuh M, Hiller S, Müller DJ. Mechanism of membrane pore formation by human gasdermin-D. EMBO J 2018; 37:embj.201798321. [PMID: 29898893 PMCID: PMC6043855 DOI: 10.15252/embj.201798321] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 05/02/2018] [Accepted: 05/07/2018] [Indexed: 11/09/2022] Open
Abstract
Gasdermin‐D (GSDMD), a member of the gasdermin protein family, mediates pyroptosis in human and murine cells. Cleaved by inflammatory caspases, GSDMD inserts its N‐terminal domain (GSDMDNterm) into cellular membranes and assembles large oligomeric complexes permeabilizing the membrane. So far, the mechanisms of GSDMDNterm insertion, oligomerization, and pore formation are poorly understood. Here, we apply high‐resolution (≤ 2 nm) atomic force microscopy (AFM) to describe how GSDMDNterm inserts and assembles in membranes. We observe GSDMDNterm inserting into a variety of lipid compositions, among which phosphatidylinositide (PI(4,5)P2) increases and cholesterol reduces insertion. Once inserted, GSDMDNterm assembles arc‐, slit‐, and ring‐shaped oligomers, each of which being able to form transmembrane pores. This assembly and pore formation process is independent on whether GSDMD has been cleaved by caspase‐1, caspase‐4, or caspase‐5. Using time‐lapse AFM, we monitor how GSDMDNterm assembles into arc‐shaped oligomers that can transform into larger slit‐shaped and finally into stable ring‐shaped oligomers. Our observations translate into a mechanistic model of GSDMDNterm transmembrane pore assembly, which is likely shared within the gasdermin protein family.
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Affiliation(s)
- Estefania Mulvihill
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | | | - Stefania A Mari
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - Moritz Pfreundschuh
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | | | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
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36
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Protein-enriched outer membrane vesicles as a native platform for outer membrane protein studies. Commun Biol 2018; 1:23. [PMID: 30271910 PMCID: PMC6123736 DOI: 10.1038/s42003-018-0027-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 02/20/2018] [Indexed: 01/15/2023] Open
Abstract
Most studies characterizing the folding, structure, and function of membrane proteins rely on solubilized or reconstituted samples. Whereas solubilized membrane proteins lack the functionally important lipid membrane, reconstitution embeds them into artificial lipid bilayers, which lack characteristic features of cellular membranes including lipid diversity, composition and asymmetry. Here, we utilize outer membrane vesicles (OMVs) released from Escherichia coli to study outer membrane proteins (Omps) in the native membrane environment. Enriched in the native membrane of the OMV we characterize the assembly, folding, and structure of OmpG, FhuA, Tsx, and BamA. Comparing Omps in OMVs to those reconstituted into artificial lipid membranes, we observe different unfolding pathways for some Omps. This observation highlights the importance of the native membrane environment to maintain the native structure and function relationship of Omps. Our fast and easy approach paves the way for functional and structural studies of Omps in the native membrane. Johannes Thoma et al. overexpress outer membrane proteins (Omps) in Escherichia coli and collect the expelled outer membrane vesicles (OMVs) to study Omp assembly, folding and structure. They find that Omps in OMVs show different unfolding pathways compared to Omps reconstituted in artificial lipid membranes.
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37
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Knoops B, Becker S, Poncin MA, Glibert J, Derclaye S, Clippe A, Alsteens D. Specific Interactions Measured by AFM on Living Cells between Peroxiredoxin-5 and TLR4: Relevance for Mechanisms of Innate Immunity. Cell Chem Biol 2018; 25:550-559.e3. [PMID: 29551349 DOI: 10.1016/j.chembiol.2018.02.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/08/2018] [Accepted: 02/07/2018] [Indexed: 12/14/2022]
Abstract
Inflammation is a pathophysiological response of innate immunity to infection or tissue damage. This response is among others triggered by factors released by damaged or dying cells, termed damage-associated molecular pattern (DAMP) molecules that act as danger signals. DAMPs interact with pattern recognition receptors (PRRs) to contribute to the induction of inflammation. However, how released peroxiredoxins (PRDXs) are able to activate PRRs, such as Toll-like receptors (TLRs), remains elusive. Here, we used force-distance curve-based atomic force microscopy to investigate the molecular mechanisms by which extracellular human PRDX5 can activate a proinflammatory response. Single-molecule experiments demonstrated that PRDX5 binds to purified TLR4 receptors, on macrophage-differentiated THP-1 cells, and on human TLR4-transfected CHO cells. These findings suggest that extracellular PRDX5 can specifically trigger a proinflammatory response. Moreover, our work also revealed that PRDX5 binding induces a cellular mechanoresponse. Collectively, this study provides insights into the role of extracellular PRDX5 in innate immunity.
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Affiliation(s)
- Bernard Knoops
- Université catholique de Louvain, Institut des Sciences de la Vie (ISV), 1348 Louvain-la-Neuve, Belgium.
| | - Sarah Becker
- Université catholique de Louvain, Institut des Sciences de la Vie (ISV), 1348 Louvain-la-Neuve, Belgium
| | - Mégane Anne Poncin
- Université catholique de Louvain, Institut des Sciences de la Vie (ISV), 1348 Louvain-la-Neuve, Belgium
| | - Julien Glibert
- Université catholique de Louvain, Institut des Sciences de la Vie (ISV), 1348 Louvain-la-Neuve, Belgium
| | - Sylvie Derclaye
- Université catholique de Louvain, Institut des Sciences de la Vie (ISV), 1348 Louvain-la-Neuve, Belgium
| | - André Clippe
- Université catholique de Louvain, Institut des Sciences de la Vie (ISV), 1348 Louvain-la-Neuve, Belgium
| | - David Alsteens
- Université catholique de Louvain, Institut des Sciences de la Vie (ISV), 1348 Louvain-la-Neuve, Belgium.
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38
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Seo MH, Ko JH, Lee JO, Ko SD, Mun JH, Cho BJ, Kim YH, Yoon JB. >1000-Fold Lifetime Extension of a Nickel Electromechanical Contact Device via Graphene. ACS APPLIED MATERIALS & INTERFACES 2018; 10:9085-9093. [PMID: 29461033 DOI: 10.1021/acsami.7b15772] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Micro-/nano-electromechanical (M/NEM) switches have received significant attention as promising switching devices for a wide range of applications such as computing, radio frequency communication, and power gating devices. However, M/NEM switches still suffer from unacceptably low reliability because of irreversible degradation at the contacting interfaces, hindering adoption in practical applications and further development. Here, we evaluate and verify graphene as a contact material for reliability-enhanced M/NEM switching devices. Atomic force microscopy experiments and quantum mechanics calculations reveal that energy-efficient mechanical contact-separation characteristics are achieved when a few layers of graphene are used as a contact material on a nickel surface, reducing the energy dissipation by 96.6% relative to that of a bare nickel surface. Importantly, graphene displays almost elastic contact-separation, indicating that little atomic-scale wear, including plastic deformation, fracture, and atomic attrition, is generated. We also develop a feasible fabrication method to demonstrate a MEM switch, which has high-quality graphene as the contact material, and verify that the devices with graphene show mechanically stable and elastic-like contact properties, consistent with our nanoscale contact experiment. The graphene coating extends the switch lifetime >103 times under hot switching conditions.
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39
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Nautiyal P, Alam F, Balani K, Agarwal A. The Role of Nanomechanics in Healthcare. Adv Healthc Mater 2018; 7. [PMID: 29193838 DOI: 10.1002/adhm.201700793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/18/2017] [Indexed: 12/21/2022]
Abstract
Nanomechanics has played a vital role in pushing our capability to detect, probe, and manipulate the biological species, such as proteins, cells, and tissues, paving way to a deeper knowledge and superior strategies for healthcare. Nanomechanical characterization techniques, such as atomic force microscopy, nanoindentation, nanotribology, optical tweezers, and other hybrid techniques have been utilized to understand the mechanics and kinetics of biospecies. Investigation of the mechanics of cells and tissues has provided critical information about mechanical characteristics of host body environments. This information has been utilized for developing biomimetic materials and structures for tissue engineering and artificial implants. This review summarizes nanomechanical characterization techniques and their potential applications in healthcare research. The principles and examples of label-free detection of cancers and myocardial infarction by nanomechanical cantilevers are discussed. The vital importance of nanomechanics in regenerative medicine is highlighted from the perspective of material selection and design for developing biocompatible scaffolds. This review interconnects the advancements made in fundamental materials science research and biomedical technology, and therefore provides scientific insight that is of common interest to the researchers working in different disciplines of healthcare science and technology.
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Affiliation(s)
- Pranjal Nautiyal
- Nanomechanics and Nanotribology Laboratory Florida International University 10555 West Flagler Street Miami FL 33174 USA
| | - Fahad Alam
- Biomaterials Processing and Characterization Laboratory Department of Materials Science and Engineering Indian Institute of Technology Kanpur Kanpur 208016 India
| | - Kantesh Balani
- Biomaterials Processing and Characterization Laboratory Department of Materials Science and Engineering Indian Institute of Technology Kanpur Kanpur 208016 India
| | - Arvind Agarwal
- Nanomechanics and Nanotribology Laboratory Florida International University 10555 West Flagler Street Miami FL 33174 USA
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40
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Li Y, Mehra N, Ji T, Yang X, Mu L, Gu J, Zhu J. The stiffness-thermal conduction relationship at the composite interface: the effect of particle alignment on the long-range confinement of polymer chains monitored by scanning thermal microscopy. NANOSCALE 2018; 10:1695-1703. [PMID: 29308501 DOI: 10.1039/c7nr06780a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The polymer/filler interface is usually considered as a thermal barrier in composites due to the mismatch of the phonon frequency across the interface. How the interface plays its role in thermal conduction has not yet been fully understood. In this work, scanning thermal microscopy is used to map the probe current across the composite interface and force-displacement curves are obtained to assess the polymer stiffness. The microscale stiffness-thermal conduction relationship is investigated at the composite interface in three representative cases: a single aggregated particle domain, two neighboring particle domains and two parallelly aligned particle chains. In the studied poly(vinyl alcohol) (PVA)/Fe3O4 composites, it is revealed that the interface property dominates the thermal conduction behavior rather than particle percolation. The long range order of polymer chains surrounding the particle domains is responsible for the enhanced crystallinity and thermal conductivity of the composites. With magnetic alignment of Fe3O4 particles, PVA crystallinity and thermal conductivity can be further enhanced. The macroscopic thermal conductivity measurement is highly consistent with the microscale observation. Specifically, with only 2.3 vol% loading of Fe3O4 in PVA, the thermal conductivity can be increased by 56% to 0.42 W m-1 K-1. By the magnetic alignment of the particles at the same loading, 133% enhancement of thermal conductivity (∼0.63 W m-1 K-1) can be achieved. This work presents an experimental study on the exploration of the interface property-thermal conductivity relationship in differently structured micro-domains and reveals the positive role of the composite interface in thermal conduction.
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Affiliation(s)
- Yifan Li
- Intelligent Composites Laboratory, Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, USA.
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41
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Delguste M, Koehler M, Alsteens D. Probing Single Virus Binding Sites on Living Mammalian Cells Using AFM. Methods Mol Biol 2018; 1814:483-514. [PMID: 29956251 DOI: 10.1007/978-1-4939-8591-3_29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the last years, atomic force microscopy (AFM)-based approaches have evolved into a powerful multiparametric tool that allows biological samples ranging from single receptors to membranes and tissues to be probed. Force-distance curve-based AFM (FD-based AFM) nowadays enables to image living cells at high resolution and simultaneously localize and characterize specific ligand-receptor binding events. In this chapter, we present how FD-based AFM permits to investigate virus binding to living mammalian cells and quantify the kinetic and thermodynamic parameters that describe the free-energy landscape of the single virus-receptor-mediated binding. Using a model virus, we probed the specific interaction with cells expressing its cognate receptor and measured the affinity of the interaction. Furthermore, we observed that the virus rapidly established specific multivalent interactions and found that each bond formed in sequence strengthens the attachment of the virus to the cell.
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Affiliation(s)
- Martin Delguste
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
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42
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Li M, Dang D, Xi N, Wang Y, Liu L. Nanoscale imaging and force probing of biomolecular systems using atomic force microscopy: from single molecules to living cells. NANOSCALE 2017; 9:17643-17666. [PMID: 29135007 DOI: 10.1039/c7nr07023c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Due to the lack of adequate tools for observation, native molecular behaviors at the nanoscale have been poorly understood. The advent of atomic force microscopy (AFM) provides an exciting instrument for investigating physiological processes on individual living cells with molecular resolution, which attracts the attention of worldwide researchers. In the past few decades, AFM has been widely utilized to investigate molecular activities on diverse biological interfaces, and the performances and functions of AFM have also been continuously improved, greatly improving our understanding of the behaviors of single molecules in action and demonstrating the important role of AFM in addressing biological issues with unprecedented spatiotemporal resolution. In this article, we review the related techniques and recent progress about applying AFM to characterize biomolecular systems in situ from single molecules to living cells. The challenges and future directions are also discussed.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
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43
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Wu Z, Chun J, Chatterjee S, Li D. Fabrication of oriented crystals as force measurement tips via focused ion beam and microlithography methods. SURF INTERFACE ANAL 2017. [DOI: 10.1002/sia.6346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhigang Wu
- School of Science; North University of China; Shanxi 030051 China
| | - Jaehun Chun
- Physical and Computational Sciences Directorate; Pacific Northwest National Laboratory; WA USA
| | - Sayandev Chatterjee
- Energy and Environment Directorate, Pacific Northwest National Laboratory; WA USA
| | - Dongsheng Li
- Physical and Computational Sciences Directorate; Pacific Northwest National Laboratory; WA USA
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44
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Bae YI, Hwang I, Kim I, Kim K, Park JW. Force Measurement for the Interaction between Cucurbit[7]uril and Mica and Self-Assembled Monolayer in the Presence of Zn 2+ Studied with Atomic Force Microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:11884-11892. [PMID: 28946747 DOI: 10.1021/acs.langmuir.7b02168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Force spectroscopy with atomic force microscopy (AFM) revealed that cucurbit[7]uril (CB[7]) strongly binds to a mica surface in the presence of cations. Indeed, Zn2+ was observed to facilitate the self-assembly of CB[7] on the mica surface, whereas monocations, such as Na+, were less effective. The progression of the process and the cation-mediated self-assembled monolayer were characterized using AFM, and the observed height of the layer agrees well with the calculated CB[7] value (9.1 Å). We utilized force-based AFM to further study the interaction of CB[7] with guest molecules. To this end, CB[7] was immobilized on a glass substrate, and aminomethylferrocene (am-Fc) was conjugated onto an AFM tip. The single-molecule interaction between CB[7] and am-Fc was monitored by collecting the unbinding force curves. The force histogram showed single ruptures and a unimodal distribution, and the most probable unbinding force value was 101 pN in deionized water and 86 pN in phosphate-buffered saline buffer. The results indicate that the unbinding force was larger than that of streptavidin-biotin measured under the same conditions, whereas the dissociation constant was smaller by 1 order of magnitude (0.012 s-1 vs 0.13 s-1). Furthermore, a high-resolution adhesion force map showed a part of the CB[7] cavities on the surface.
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Affiliation(s)
- Young-In Bae
- Department of Chemistry, ‡Center for Self-Assembly and Complexity (CSC), Institute for Basic Science (IBS), and §Division of Advanced Materials Science, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Ilha Hwang
- Department of Chemistry, ‡Center for Self-Assembly and Complexity (CSC), Institute for Basic Science (IBS), and §Division of Advanced Materials Science, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Ikjin Kim
- Department of Chemistry, ‡Center for Self-Assembly and Complexity (CSC), Institute for Basic Science (IBS), and §Division of Advanced Materials Science, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Kimoon Kim
- Department of Chemistry, ‡Center for Self-Assembly and Complexity (CSC), Institute for Basic Science (IBS), and §Division of Advanced Materials Science, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Joon Won Park
- Department of Chemistry, ‡Center for Self-Assembly and Complexity (CSC), Institute for Basic Science (IBS), and §Division of Advanced Materials Science, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
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Combining confocal and atomic force microscopy to quantify single-virus binding to mammalian cell surfaces. Nat Protoc 2017; 12:2275-2292. [PMID: 28981124 DOI: 10.1038/nprot.2017.112] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Over the past five years, atomic force microscopy (AFM)-based approaches have evolved into a powerful multiparametric tool set capable of imaging the surfaces of biological samples ranging from single receptors to membranes and tissues. One of these approaches, force-distance curve-based AFM (FD-based AFM), uses a probing tip functionalized with a ligand to image living cells at high-resolution and simultaneously localize and characterize specific ligand-receptor binding events. Analyzing data from FD-based AFM experiments using appropriate probabilistic models allows quantification of the kinetic and thermodynamic parameters that describe the free-energy landscape of the ligand-receptor bond. We have recently developed an FD-based AFM approach to quantify the binding events of single enveloped viruses to surface receptors of living animal cells while simultaneously observing them by fluorescence microscopy. This approach has provided insights into the early stages of the interaction between a virus and a cell. Applied to a model virus, we probed the specific interaction with cells expressing viral cognate receptors and measured the affinity of the interaction. Furthermore, we observed that the virus rapidly established specific multivalent interactions and found that each bond formed in sequence strengthened the attachment of the virus to the cell. Here we describe detailed procedures for probing the specific interactions of viruses with living cells; these procedures cover tip preparation, cell sample preparation, step-by-step FD-based AFM imaging and data analysis. Experienced microscopists should be able to master the entire set of protocols in 1 month.
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Zhang S, Geryak R, Geldmeier J, Kim S, Tsukruk VV. Synthesis, Assembly, and Applications of Hybrid Nanostructures for Biosensing. Chem Rev 2017; 117:12942-13038. [DOI: 10.1021/acs.chemrev.7b00088] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shuaidi Zhang
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Ren Geryak
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Jeffrey Geldmeier
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Sunghan Kim
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Vladimir V. Tsukruk
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
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Schön P. Atomic force microscopy of RNA: State of the art and recent advancements. Semin Cell Dev Biol 2017; 73:209-219. [PMID: 28843977 DOI: 10.1016/j.semcdb.2017.08.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/26/2022]
Abstract
The atomic force microscope (AFM) has become a powerful tool for the visualization, probing and manipulation of RNA at the single molecule level. AFM measurements can be carried out in buffer solution in a physiological medium, which is crucial to study the structure and function of biomolecules, also allowing studying them at work. Imaging the specimen in its native state is a great advantage compared to other high resolution methods such as electron microscopy and X-ray diffraction. There is no need to stain, freeze or crystallize biological samples. Moreover, compared to NMR spectroscopy for instance, for AFM studies the size of the biomolecules is not limiting. Consequently the AFM allows one also to investigate larger RNA molecules. In particular, structural studies of nucleic acids and assemblies thereof, have been carried out by AFM routinely including ssRNA, dsRNA and nucleoprotein complexes thereof, as well as RNA aggregates and 2D RNA assemblies. These are becoming increasingly important as novel unique building blocks in the emerging field of RNA nanotechnology. In particular by AFM unique information can be obtained on these RNA based assemblies. Moreover, the AFM is of fundamental relevance to study biological relevant RNA interactions and dynamics. In this short review a brief overview will be given on structural studies that have been done related to AFM topographic imaging of RNA, RNA assemblies and aggregates. Finally, an overview on AFM beyond imaging will be provided. This includes force spectroscopy of RNA under physiological conditions in aqueous buffer to probe RNA interaction with proteins and ligands as well as other AFM tip based RNA probing. Important applications include the detection and quantification of RNA in biological samples. A selection of recent highlights and breakthroughs will be provided related to structural and functional studies by AFM. The main intention of this short review to provide the reader with a flavor of what AFM is able to contribute to RNA research and engineering.
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Affiliation(s)
- Peter Schön
- NanoBioInterface Research Group, Research Center Design and Technology, Saxion University of Applied Sciences, 7500 KB Enschede, The Netherlands; Materials Science and Technology of Polymers, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands.
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Laskowski PR, Pfreundschuh M, Stauffer M, Ucurum Z, Fotiadis D, Müller DJ. High-Resolution Imaging and Multiparametric Characterization of Native Membranes by Combining Confocal Microscopy and an Atomic Force Microscopy-Based Toolbox. ACS NANO 2017; 11:8292-8301. [PMID: 28745869 DOI: 10.1021/acsnano.7b03456] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To understand how membrane proteins function requires characterizing their structure, assembly, and inter- and intramolecular interactions in physiologically relevant conditions. Conventionally, such multiparametric insight is revealed by applying different biophysical methods. Here we introduce the combination of confocal microscopy, force-distance curve-based (FD-based) atomic force microscopy (AFM), and single-molecule force spectroscopy (SMFS) for the identification of native membranes and the subsequent multiparametric analysis of their membrane proteins. As a well-studied model system, we use native purple membrane from Halobacterium salinarum, whose membrane protein bacteriorhodopsin was His-tagged to bind nitrilotriacetate (NTA) ligands. First, by confocal microscopy we localize the extracellular and cytoplasmic surfaces of purple membrane. Then, we apply AFM to image single bacteriorhodopsins approaching sub-nanometer resolution. Afterwards, the binding of NTA ligands to bacteriorhodopsins is localized and quantified by FD-based AFM. Finally, we apply AFM-based SMFS to characterize the (un)folding of the membrane protein and to structurally map inter- and intramolecular interactions. The multimethodological approach is generally applicable to characterize biological membranes and membrane proteins at physiologically relevant conditions.
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Affiliation(s)
- Pawel R Laskowski
- Department of Biosystems Science and Engineering, ETH Zurich , 4058 Basel, Switzerland
| | - Moritz Pfreundschuh
- Department of Biosystems Science and Engineering, ETH Zurich , 4058 Basel, Switzerland
| | - Mirko Stauffer
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zurich , 4058 Basel, Switzerland
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Thoma J, Ritzmann N, Wolf D, Mulvihill E, Hiller S, Müller DJ. Maltoporin LamB Unfolds β Hairpins along Mechanical Stress-Dependent Unfolding Pathways. Structure 2017. [DOI: 10.1016/j.str.2017.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Li M, Wang L, Putnis CV. Energetic Basis for Inhibition of Calcium Phosphate Biomineralization by Osteopontin. J Phys Chem B 2017; 121:5968-5976. [DOI: 10.1021/acs.jpcb.7b04163] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Meng Li
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijun Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Christine V. Putnis
- Institut
für Mineralogie, University of Münster, 48149 Münster, Germany
- Department of Chemistry, Curtin University, Perth, Western Australia 6845, Australia
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