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Kogut-Günthel MM, Zara Z, Nicoli A, Steuer A, Lopez-Balastegui M, Selent J, Karanth S, Koehler M, Ciancetta A, Abiko LA, Hagn F, Di Pizio A. The path to the G protein-coupled receptor structural landscape: Major milestones and future directions. Br J Pharmacol 2024. [PMID: 39209310 DOI: 10.1111/bph.17314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 06/14/2024] [Accepted: 06/28/2024] [Indexed: 09/04/2024] Open
Abstract
G protein-coupled receptors (GPCRs) play a crucial role in cell function by transducing signals from the extracellular environment to the inside of the cell. They mediate the effects of various stimuli, including hormones, neurotransmitters, ions, photons, food tastants and odorants, and are renowned drug targets. Advancements in structural biology techniques, including X-ray crystallography and cryo-electron microscopy (cryo-EM), have driven the elucidation of an increasing number of GPCR structures. These structures reveal novel features that shed light on receptor activation, dimerization and oligomerization, dichotomy between orthosteric and allosteric modulation, and the intricate interactions underlying signal transduction, providing insights into diverse ligand-binding modes and signalling pathways. However, a substantial portion of the GPCR repertoire and their activation states remain structurally unexplored. Future efforts should prioritize capturing the full structural diversity of GPCRs across multiple dimensions. To do so, the integration of structural biology with biophysical and computational techniques will be essential. We describe in this review the progress of nuclear magnetic resonance (NMR) to examine GPCR plasticity and conformational dynamics, of atomic force microscopy (AFM) to explore the spatial-temporal dynamics and kinetic aspects of GPCRs, and the recent breakthroughs in artificial intelligence for protein structure prediction to characterize the structures of the entire GPCRome. In summary, the journey through GPCR structural biology provided in this review illustrates how far we have come in decoding these essential proteins architecture and function. Looking ahead, integrating cutting-edge biophysics and computational tools offers a path to navigating the GPCR structural landscape, ultimately advancing GPCR-based applications.
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Affiliation(s)
| | - Zeenat Zara
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Faculty of Science, University of South Bohemia in Ceske Budejovice, České Budějovice, Czech Republic
| | - Alessandro Nicoli
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Professorship for Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
| | - Alexandra Steuer
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Professorship for Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
| | - Marta Lopez-Balastegui
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute & Pompeu Fabra University, Barcelona, Spain
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute & Pompeu Fabra University, Barcelona, Spain
| | - Sanjai Karanth
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Melanie Koehler
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- TUM Junior Fellow at the Chair of Nutritional Systems Biology, Technical University of Munich, Freising, Germany
| | - Antonella Ciancetta
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Layara Akemi Abiko
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
| | - Franz Hagn
- Structural Membrane Biochemistry, Bavarian NMR Center, Dept. Bioscience, School of Natural Sciences, Technical University of Munich, Munich, Germany
- Institute of Structural Biology (STB), Helmholtz Munich, Neuherberg, Germany
| | - Antonella Di Pizio
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Professorship for Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
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2
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Zhang Z, Li S, Wang H, Shan Y. The Effects of the Carrier and Ligand Spatial Conformation on RNA Nanodrug Cell Delivery. Anal Chem 2024. [PMID: 39096242 DOI: 10.1021/acs.analchem.4c02270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
Abstract
Small interfering RNA (siRNA) highlights the immense therapeutic potential for cancer treatment. The major challenge in siRNA therapy is the effective RNA nanodrug delivery system, which is facilitated by the ligand and the carrier. In this study, we analyzed the binding specificity of linear RGD and circular RGD to αVβ3 integrins by mapping the morphology using super-resolution direct stochastic optical reconstruction microscopy. Meanwhile, the binding dynamics was investigated using single-molecule force spectroscopy. Then, the effects of the ligand and carrier on RNA nanodrug cell entry dynamic parameters were evaluated at the single particle level by the force tracing technique. Furthermore, the delivery efficiency of RNA nanodrugs was assessed using AFM-based nanoindentation at the single cell level. This report will provide valuable insights for rational design strategies aiming to achieve improved efficiency for nanodrug delivery systems.
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Affiliation(s)
- Zhuang Zhang
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
| | - Siying Li
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Yuping Shan
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
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3
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Wang C, Paiva TO, Speziale P, Dufrêne YF. Nanomechanics of CCN1-Mediated Staphylococcus aureus Phagocytosis. NANO LETTERS 2024; 24:8567-8574. [PMID: 38959438 DOI: 10.1021/acs.nanolett.4c01533] [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: 07/05/2024]
Abstract
Phagocytosis is an essential mechanism of the human immune system where pathogens are eliminated by immune cells. The CCN1 protein plays an important role in the phagocytosis of Staphylococcus aureus by favoring the bridging of the αVβ3 integrin to the bacterial peptidoglycan (PG), through mechanical forces that remain unknown. Here, we employ single-molecule experiments to unravel the nanomechanics of the PG-CCN1-αVβ3 ternary complex. While CCN1 binds αVβ3 integrins with moderate force (∼60 pN), much higher binding strengths (up to ∼800 pN) are observed between CCN1 and PG. Notably, the strength of both CCN1-αVβ3 and CCN1-PG bonds is dramatically enhanced by tensile loading, favoring a model in which mechanical stress induces the exposure of cryptic integrin binding sites in CCN1 and multivalent binding between CCN1 lectin sites and monosaccharides along the PG glycan chains.
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Affiliation(s)
- Can Wang
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Telmo O Paiva
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Pietro Speziale
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Viale Taramelli 3/b, 27100 Pavia, Italy
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
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4
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Thakur N, Ray AP, Jin B, Afsharian NP, Lyman E, Gao ZG, Jacobson KA, Eddy MT. Membrane mimetic-dependence of GPCR energy landscapes. Structure 2024; 32:523-535.e5. [PMID: 38401537 PMCID: PMC11069452 DOI: 10.1016/j.str.2024.01.013] [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: 10/16/2023] [Revised: 01/03/2024] [Accepted: 01/30/2024] [Indexed: 02/26/2024]
Abstract
We leveraged variable-temperature 19F-NMR spectroscopy to compare the conformational equilibria of the human A2A adenosine receptor (A2AAR), a class A G protein-coupled receptor (GPCR), across a range of temperatures ranging from lower temperatures typically employed in 19F-NMR experiments to physiological temperature. A2AAR complexes with partial agonists and full agonists showed large increases in the population of a fully active conformation with increasing temperature. NMR data measured at physiological temperature were more in line with functional data. This was pronounced for complexes with partial agonists, where the population of active A2AAR was nearly undetectable at lower temperature but became evident at physiological temperature. Temperature-dependent behavior of complexes with either full or partial agonists exhibited a pronounced sensitivity to the specific membrane mimetic employed. Cellular signaling experiments correlated with the temperature-dependent conformational equilibria of A2AAR in lipid nanodiscs but not in some detergents, underscoring the importance of the membrane environment in studies of GPCR function.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Arka Prabha Ray
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Beining Jin
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | | | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, DE, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew T Eddy
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA.
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5
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Zhang W, Fan Y, Chi J. The synergistic effect of multiple organic macromolecules on the formation of calcium oxalate raphides of Musa spp. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2470-2480. [PMID: 38243384 DOI: 10.1093/jxb/erae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
Needle-like calcium oxalate crystals called raphides are unique structures in the plant kingdom. Multiple biomacromolecules work together in the regulatory and transportation pathways to form raphides; however, the mechanism by which this occurs remains unknown. Using banana (Musa spp.), this study combined in vivo methods including confocal microscopy, transmission electron microscopy, and Q Exactive mass spectrometry to identify the main biomolecules, such as vesicles, together with the compositions of lipids and proteins in the crystal chamber, which is the membrane compartment that surrounds each raphide during its formation. Simulations of the vesicle transportation process and the synthesis of elongated calcium oxalate crystals in vitro were then conducted, and the results suggested that the vesicles carrying amorphous calcium oxalate and proteins embedded in raphides are transported along actin filaments. These vesicles subsequently fuse with the crystal chamber, utilizing the proteins embedded in the raphides as a template for the final formation of the structure. Our findings contribute to the fundamental understanding of the regulation of the diverse biomacromolecules that are crucial for raphide formation. Moreover, the implications of these findings extend to other fields such as materials science, and particularly the synthesis of functionalized materials.
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Affiliation(s)
- Wenjun Zhang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuke Fan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jialin Chi
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
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6
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Sun H, Liao F, Tian Y, Lei Y, Fu Y, Wang J. Molecular-Scale Investigations Reveal the Effect of Natural Polyphenols on BAX/Bcl-2 Interactions. Int J Mol Sci 2024; 25:2474. [PMID: 38473728 DOI: 10.3390/ijms25052474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
Apoptosis signaling controls the cell cycle through the protein-protein interactions (PPIs) of its major B-cell lymphoma 2-associated x protein (BAX) and B-cell lymphoma 2 protein (Bcl-2). Due to the antagonistic function of both proteins, apoptosis depends on a properly tuned balance of the kinetics of BAX and Bcl-2 activities. The utilization of natural polyphenols to regulate the binding process of PPIs is feasible. However, the mechanism of this modulation has not been studied in detail. Here, we utilized atomic force microscopy (AFM) to evaluate the effects of polyphenols (kaempferol, quercetin, dihydromyricetin, baicalin, curcumin, rutin, epigallocatechin gallate, and gossypol) on the BAX/Bcl-2 binding mechanism. We demonstrated at the molecular scale that polyphenols quantitatively affect the interaction forces, kinetics, thermodynamics, and structural properties of BAX/Bcl-2 complex formation. We observed that rutin, epigallocatechin gallate, and baicalin reduced the binding affinity of BAX/Bcl-2 by an order of magnitude. Combined with surface free energy and molecular docking, the results revealed that polyphenols are driven by multiple forces that affect the orientation freedom of PPIs, with hydrogen bonding, hydrophobic interactions, and van der Waals forces being the major contributors. Overall, our work provides valuable insights into how molecules tune PPIs to modulate their function.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Fenghui Liao
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yichen Tian
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yongrong Lei
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yuna Fu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
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7
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Thakur N, Ray AP, Lyman E, Gao ZG, Jacobson KA, Eddy MT. Membrane Mimetic-Dependence of GPCR Energy Landscapes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562552. [PMID: 37905159 PMCID: PMC10614885 DOI: 10.1101/2023.10.16.562552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Protein function strongly depends on temperature, which is related to temperature-dependent changes in the equilibria of protein conformational states. We leveraged variable-temperature 19F-NMR spectroscopy to interrogate the temperature dependence of the conformational landscape of the human A2A adenosine receptor (A2AAR), a class A GPCR. Temperature-induced changes in the conformational equilibria of A2AAR in lipid nanodiscs were markedly dependent on the efficacy of bound drugs. While antagonist complexes displayed only modest changes as the temperature rose, both full and partial agonist complexes exhibited substantial increases in the active state population. Importantly, the temperature-dependent response of complexes with both full and partial agonists exhibited a pronounced sensitivity to the specific membrane mimetic employed. In striking contrast to observations within lipid nanodiscs, in detergent micelles the active state population exhibited different behavior for A2AAR complexes with both full and partial agonists. This underscores the importance of the protein environment in understanding the thermodynamics of GPCR activation.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Arka Prabha Ray
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew T Eddy
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
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8
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Fernandez M, Shkumatov AV, Liu Y, Stulemeijer C, Derclaye S, Efremov R, Hallet B, Alsteens D. AFM-based force spectroscopy unravels stepwise formation of the DNA transposition complex in the widespread Tn3 family mobile genetic elements. Nucleic Acids Res 2023; 51:4929-4941. [PMID: 37026471 PMCID: PMC10250215 DOI: 10.1093/nar/gkad241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/03/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Transposon Tn4430 belongs to a widespread family of bacterial transposons, the Tn3 family, which plays a prevalent role in the dissemination of antibiotic resistance among pathogens. Despite recent data on the structural architecture of the transposition complex, the molecular mechanisms underlying the replicative transposition of these elements are still poorly understood. Here, we use force-distance curve-based atomic force microscopy to probe the binding of the TnpA transposase of Tn4430 to DNA molecules containing one or two transposon ends and to extract the thermodynamic and kinetic parameters of transposition complex assembly. Comparing wild-type TnpA with previously isolated deregulated TnpA mutants supports a stepwise pathway for transposition complex formation and activation during which TnpA first binds as a dimer to a single transposon end and then undergoes a structural transition that enables it to bind the second end cooperatively and to become activated for transposition catalysis, the latter step occurring at a much faster rate for the TnpA mutants. Our study thus provides an unprecedented approach to probe the dynamic of a complex DNA processing machinery at the single-particle level.
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Affiliation(s)
- Maricruz Fernandez
- NanoBioPhysics lab, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
- Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Alexander V Shkumatov
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yun Liu
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Claire Stulemeijer
- Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Sylvie Derclaye
- NanoBioPhysics lab, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Rouslan G Efremov
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bernard Hallet
- Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - David Alsteens
- NanoBioPhysics lab, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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9
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Qi G, Zhang M, Tang J, Jin Y. Molecular/Nanomechanical Insights into Electrostimulation-Inhibited Energy Metabolism Mechanisms and Cytoskeleton Damage of Cancer Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207165. [PMID: 37029462 DOI: 10.1002/advs.202207165] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/20/2023] [Indexed: 06/04/2023]
Abstract
Inhibiting energy metabolism of cancer cells is an effective way to treat cancer but remains a great challenge. Herein, electrostimulation (ES) is applied to effectively suppress energy metabolism of cancer cells to induce rapid cell death, and deeply reveal the underlying mechanisms at the molecular and nanomechanical levels by combined use of fluorescence imaging and atomic force microscopy. Cancer cells are found significantly less tolerant to ES than normal cells; and ES causes "domino effect" to induce mitochondrial dysfunction to impede electron transport chain (ETC) and tricarboxylic acid (TCA) cycle pathways, leading to fatal energy-supply crisis and death of cancer cells. From the perspective of cell mechanics, the Young's modulus decreases and cytoskeleton destruction of MCF-7 cell membranes caused by F-actin depolymerization occurs, along with down-regulation and sporadic distribution of glucose transporter 1 (GLUT1) after ES. Such a double whammy renders ES highly effective and promising for potential clinical cancer treatments.
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Affiliation(s)
- Guohua Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Miaomiao Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Jilin Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Yongdong Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
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10
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Pan W, Han Z, Chang Y, Yan X, Zhou F, Shen S, Duan X. Rational design of multivalent biosensor surfaces to enhance viral particle capture. J Mater Chem B 2023; 11:4511-4522. [PMID: 37161578 DOI: 10.1039/d2tb02828j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Viral particles bind to receptors through multivalent protein interactions. Such high avidity interactions on sensor surfaces are less studied. In this work, three polyelectrolytes that can form biosensing surfaces with different interfacial characteristics in probe density and spatial arrangement were designed. Quartz crystal microbalance, interferometry and atomic force microscopy were used to study their surface density and binding behaviors with proteins and virus particles. A multivalent adsorption kinetic model was developed to estimate the number of bonds from the viral particles bound to the polyelectrolyte surfaces. Experimental results show that the heterogeneous 3D surface with jagged forest-like structure enhances the virus capture ability by maximizing the multivalent interactions. As a proof of concept, specific coronavirus detection was achieved in spiked swab samples. These results indicate the importance of both probe density and their spatial arrangement on the sensing performance, which could be used as a guideline for rational biosensing surface design.
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Affiliation(s)
- Wenwei Pan
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
- College of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
- Department of Chemistry, School of Science, Tianjin University, Tianjin 300072, China
| | - Ziyu Han
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
- College of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Ye Chang
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
- College of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Xu Yan
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
- College of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Feng Zhou
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
- College of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Sihong Shen
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
- College of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Xuexin Duan
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
- College of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
- Department of Chemistry, School of Science, Tianjin University, Tianjin 300072, China
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11
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Guo X, Zhang M, Qin J, Li Z, Rankl C, Jiang X, Zhang B, Wang D, Tang J. Revealing the Effect of Photothermal Therapy on Human Breast Cancer Cells: A Combined Study from Mechanical Properties to Membrane HSP70. ACS APPLIED MATERIALS & INTERFACES 2023; 15:21965-21973. [PMID: 37127843 DOI: 10.1021/acsami.3c02964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Hyperthermia-induced overexpression of heat shock protein 70 (HSP70) leads to the thermoresistance of cancer cells and reduces the efficiency of photothermal therapy (PTT). In contrast, cancer cell-specific membrane-associated HSP70 has been proven to activate antitumor immune responses. The dual effect of HSP70 on cancer cells inspires us that in-depth research of membrane HSP70 (mHSP70) during PTT treatment is essential. In this work, a PTT treatment platform for human breast cancer cells (MCF-7 cells) based on a mPEG-NH2-modified polydopamine (PDA)-coated gold nanorod core-shell structure (GNR@PDA-PEG) is developed. Using the force-distance curve-based atomic force microscopy (FD-based AFM), we gain insight into the PTT-induced changes in the morphology, mechanical properties, and mHSP70 expression and distribution of individual MCF-7 cells with high-resolution at the single-cell level. PTT treatment causes pseudopod contraction of MCF-7 cells and generates a high level of intracellular reactive oxygen species, which severely disrupt the cytoskeleton, leading to a decrease in cellular mechanical properties. The adhesion maps, which are recorded by aptamer A8 functional probes using FD-based AFM, reveal that PTT treatment causes a significant upregulation of mHSP70 expression and it starts to exhibit a partial aggregation distribution on the MCF-7 cell surface. This work not only exemplifies that AFM can be a powerful tool for detecting changes in cancer cells during PTT treatment but also provides a better view for targeting mHSP70 for cancer therapy.
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Affiliation(s)
- Xinyue Guo
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Science and Technology of China, Hefei 230026, P.R. China
| | - Miaomiao Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Juan Qin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Science and Technology of China, Hefei 230026, P.R. China
| | - Zongjia Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Science and Technology of China, Hefei 230026, P.R. China
| | - Christian Rankl
- Research Center for Non-Destructive Testing GmbH, Science Park 2/2, OG, Altenberger Straße 69, A-4040 Linz, Austria
| | - Xiue Jiang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Science and Technology of China, Hefei 230026, P.R. China
| | - Bailin Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Dapeng Wang
- University of Science and Technology of China, Hefei 230026, P.R. China
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Jilin Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Science and Technology of China, Hefei 230026, P.R. China
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12
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Dumitru AC, Koehler M. Recent advances in the application of atomic force microscopy to structural biology. J Struct Biol 2023; 215:107963. [PMID: 37044358 DOI: 10.1016/j.jsb.2023.107963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/21/2023] [Accepted: 04/07/2023] [Indexed: 04/14/2023]
Abstract
The application of atomic force microscopy (AFM) for (functional) imaging and manipulating biomolecules at all levels of organization has enabled great progress in the structural biology field over the last decades, contributing to the discovery of novel structural entities of biological significance across many disciplines ranging from biochemistry, biomedicine and biophysics to molecular and cell biology, up to food systems and beyond. AFM has the capability to generate high-resolution topographic images spanning from the submolecular to the (sub)cellular range and can probe biochemical and biophysical sample properties in close to native conditions with excellent temporal resolution. Instrumental developments in the past decade enable dynamical structural and conformational studies of single biomolecules and new techniques for structural and chemical modification of the AFM probe have converted the cantilever into a versatile tool to study different biological phenomena, such as the mechanical stability of biomolecular complexes or the force induced dynamic changes of mechanically stressed proteins at the nanoscopic level. To improve the functionality of AFM and approach dynamic processes of complex biological systems ex vivo, AFM is combined with complementary microscopy, nanoscopy and spectroscopy tools. These multimethodological approaches provide unprecedented possibilities of probing physical, chemical and biological properties of complex cellular systems with high spatio-temporal resolution, leading to novel applications that correlate structural results with functional biochemical, biophysical, immunological, or genetic data on the system under study.
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Affiliation(s)
- Andra C Dumitru
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain.
| | - Melanie Koehler
- Leibniz Institute for Food Systems Biology at the Technical University Munich, Freising, Germany.
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13
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Sun H, Wang J. Novel perspective for protein-drug interaction analysis: atomic force microscope. Analyst 2023; 148:454-474. [PMID: 36398684 DOI: 10.1039/d2an01591a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Proteins are major drug targets, and drug-target interaction identification and analysis are important factors for drug discovery. Atomic force microscopy (AFM) is a powerful tool making it possible to image proteins with nanometric resolution and probe intermolecular forces under physiological conditions. We review recent studies conducted in the field of target protein drug discovery using AFM-based analysis technology, including drug-driven changes in nanomechanical properties of protein morphology and interactions. Underlying mechanisms (including thermodynamic and kinetic parameters) of the drug-target interaction and drug-modulating protein-protein interaction (PPI) on the surfaces of models or living cells are discussed. Furthermore, challenges and the outlook for the field are likewise discussed. Overall, this insight into the mechanical properties of protein-drug interactions provides an unprecedented information framework for rational drug discovery in the pharmaceutical field.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
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14
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Li Q, Yin G, Wang J, Li L, Liang Q, Zhao X, Chen Y, Zheng X, Zhao X. An emerging paradigm to develop analytical methods based on immobilized transmembrane proteins and its applications in drug discovery. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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15
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Petitjean SJL, Chen W, Koehler M, Jimmidi R, Yang J, Mohammed D, Juniku B, Stanifer ML, Boulant S, Vincent SP, Alsteens D. Multivalent 9-O-Acetylated-sialic acid glycoclusters as potent inhibitors for SARS-CoV-2 infection. Nat Commun 2022; 13:2564. [PMID: 35538121 PMCID: PMC9091252 DOI: 10.1038/s41467-022-30313-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/25/2022] [Indexed: 01/08/2023] Open
Abstract
The recent emergence of highly transmissible SARS-CoV-2 variants illustrates the urgent need to better understand the molecular details of the virus binding to its host cell and to develop anti-viral strategies. While many studies focused on the role of the angiotensin-converting enzyme 2 receptor in the infection, others suggest the important role of cell attachment factors such as glycans. Here, we use atomic force microscopy to study these early binding events with the focus on the role of sialic acids (SA). We show that SARS-CoV-2 binds specifically to 9-O-acetylated-SA with a moderate affinity, supporting its role as an attachment factor during virus landing to cell host surfaces. For therapeutic purposes and based on this finding, we have designed novel blocking molecules with various topologies and carrying a controlled number of SA residues, enhancing affinity through a multivalent effect. Inhibition assays show that the AcSA-derived glycoclusters are potent inhibitors of cell binding and infectivity, offering new perspectives in the treatment of SARS-CoV-2 infection. Cell surface attachment factors, such as glycans, play an important role in viral infection. Here, Petitjean et al. show that SARS-CoV-2 specifically binds to 9-Oacetylated sialic acid and have designed novel inhibitors based on multivalent derivatives.
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Affiliation(s)
- Simon J L Petitjean
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Wenzhang Chen
- Laboratory of Bio-Organic Chemistry (NARILIS), UNamur, Namur, Belgium
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Ravikumar Jimmidi
- Laboratory of Bio-Organic Chemistry (NARILIS), UNamur, Namur, Belgium
| | - Jinsung Yang
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Danahe Mohammed
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Blinera Juniku
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Megan L Stanifer
- Dept. of Infectious Diseases, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120, Heidelberg, Germany.,Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, USA
| | - Steeve Boulant
- Dept. of Infectious Diseases, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120, Heidelberg, Germany.,Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, USA
| | | | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium. .,Walloon Excellence in Life sciences and Biotechnology (WELBIO), Wavre, Belgium.
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16
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Pu J, Putnis CV, Wang L. AFM imaging and single-molecule recognition of plant cell walls. TRENDS IN PLANT SCIENCE 2022; 27:412-413. [PMID: 34916130 DOI: 10.1016/j.tplants.2021.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Junbao Pu
- 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 Sciences, Curtin University, Perth 6845, Australia
| | - Lijun Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
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17
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Wang YF, Zhang Q, Tian F, Wang H, Wang Y, Ma X, Huang Q, Cai M, Ji Y, Wu X, Gan Y, Yan Y, Dawson KA, Guo S, Zhang J, Shi X, Shan Y, Liang XJ. Spatiotemporal Tracing of the Cellular Internalization Process of Rod-Shaped Nanostructures. ACS NANO 2022; 16:4059-4071. [PMID: 35191668 DOI: 10.1021/acsnano.1c09684] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Endocytosis, as one of the main ways for nanostructures enter cells, is affected by several aspects, and shape is an especially critical aspect during the endocytosis of nanostructures. However, it has remained challenging to capture the dynamic internalization behaviors of rod-shaped nanostructures while also probing the mechanical aspects of the internalization. Here, using the atomic force microscopy-based force tracing technique, transmission electron microscopy, and molecular dynamic simulation, we mapped the detailed internalization behaviors of rod-shaped nanostructures with different aspect ratios at the single-particle level. We found that the gold nanorod is endocytosed in a noncontinuous and force-rebound rotation manner, herein named "intermittent rotation". The force tracing test indicated that the internalization force (∼81 pN, ∼108 pN, and ∼157 pN) and time (∼0.56 s, ∼0.66 s, and ∼1.14 s for a 12.10 nm × 11.96 nm gold nanosphere and 26.15 nm × 13.05 nm and 48.71 nm × 12.45 nm gold nanorods, respectively) are positively correlated with the aspect ratios. However, internalization speed is negatively correlated with internalization time, irrespective of the aspect ratio. Further, the energy analysis suggested that intermittent rotation from the horizontal to vertical direction can reduce energy dissipation during the internalization process. Thus, to overcome the energy barrier of internalization, the number and angle of rotation increases with aspect ratios. Our findings provide critical missing evidence of rod-shaped nanostructure's internalization, which is essential for fundamentally understanding the internalization mechanism in living cells.
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Affiliation(s)
- Yi-Feng Wang
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Qingrong Zhang
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, P.R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Falin Tian
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Nanosystem and Hierarchy Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Yufei Wang
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xiaowei Ma
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
| | - Qianqian Huang
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Mingjun Cai
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Yinglu Ji
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
| | - Xiaochun Wu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
| | - Yaling Gan
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
| | - Yan Yan
- Centre for BioNano Interactions, School of Chemistry, School of Biomolecular and Biomedical Science, University College Dublin, Dublin D04 V1W8, Ireland
| | - Kenneth A Dawson
- Centre for BioNano Interactions, School of Chemistry, School of Biomolecular and Biomedical Science, University College Dublin, Dublin D04 V1W8, Ireland
- Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumor Microenvironment, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, P.R. China
| | - Shutao Guo
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology and Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P.R. China
| | - Jinchao Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, P.R China
| | - Xinghua Shi
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Nanosystem and Hierarchy Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
| | - Yuping Shan
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, P.R. China
| | - Xing-Jie Liang
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
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18
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Alhalhooly L, Confeld MI, Woo SO, Mamnoon B, Jacobson R, Ghosh S, Kim J, Mallik S, Choi Y. Single-Molecule Force Probing of RGD-Binding Integrins on Pancreatic Cancer Cells. ACS APPLIED MATERIALS & INTERFACES 2022; 14:7671-7679. [PMID: 35113515 PMCID: PMC8890904 DOI: 10.1021/acsami.1c23361] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Integrin-targeting arginine-glycine-aspartic acid (RGD)-based nanocarriers have been widely used for tumor imaging, monitoring of tumor development, and delivery of anticancer drugs. However, the thermodynamics of an RGD-integrin formation and dissociation associated with binding dynamics, affinity, and stability remains unclear. Here, we probed the binding strength of the binary complex to live pancreatic cancer cells using single-molecule binding force spectroscopy methods, in which RGD peptides were functionalized on a force probe tip through poly(ethylene glycol) (PEG)-based bifunctional linker molecules. While the density of integrin αV receptors on the cell surface varies more than twofold from cell line to cell line, the individual RGD-integrin complexes exhibited a cell type-independent, monovalent bond strength. The load-dependent bond strength of multivalent RGD-integrin interactions scaled sublinearly with increasing bond number, consistent with the noncooperative, parallel bond model. Furthermore, the multivalent bonds ruptured sequentially either by one or in multiples, and the force strength was comparable to the synchronous rupture force. Comparison of energy landscapes of the bond number revealed a substantial decrease of kinetic off-rates for multivalent bonds, along with the increased width of the potential well and the increased potential barrier height between bound and unbound states, enhancing the stability of the multivalent bonds between them.
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Affiliation(s)
- Lina Alhalhooly
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, United State
| | - Matthew I. Confeld
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota 58108, United State
| | - Sung Oh Woo
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, United State
| | - Babak Mamnoon
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota 58108, United State
| | - Reed Jacobson
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota 58108, United State
| | - Shrinwanti Ghosh
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota 58108, United State
| | - Jiha Kim
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota 58108, United State
- Molecular and Cellular Biology Program, North Dakota State University, Fargo, North Dakota 58108, United State
| | - Sanku Mallik
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota 58108, United State
| | - Yongki Choi
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, United State
- Molecular and Cellular Biology Program, North Dakota State University, Fargo, North Dakota 58108, United State
- Materials and Nanotechnology Program, North Dakota State University, Fargo, North Dakota 58108, United State
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19
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Shim WC, Woo S, Park JW. Nanoscale Force-Mapping-Based Quantification of Low-Abundance Methylated DNA. NANO LETTERS 2022; 22:1324-1330. [PMID: 35080393 DOI: 10.1021/acs.nanolett.1c04637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Methylation changes at cytosine-guanine dinucleotide (CpG) sites in genes are closely related to cancer development. Thus, detection and quantification of low-abundance methylated DNA is critical for early diagnosis. Here, we report an atomic force microscopy (AFM)-based quantification method for DNA that contains methyl-CpG at a specific site, without any treatment to the target DNA such as chemical labeling, fluorescence tagging, or amplification. We employed AFM-tip-tethered methyl-CpG-binding proteins to probe surface-captured methylated DNA. We observed a linear correlation (R2 = 0.982) between the input copy number and detected copy number, in the low copy number regime (10 or fewer; subattomolar concentrations). For a mixture of methylated and nonmethylated DNA that resembles clinical samples, we were still able to quantify the methylated DNA. These results highlight the potential of our force-mapping-based quantification method for wide applications in early detection of diseases associated with methylated DNA.
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Affiliation(s)
- Woo Cheol Shim
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Sungwook Woo
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
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20
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Fang B, Zhao L, Du X, Liu Q, Yang H, Li F, Sheng Y, Zhao W, Zhong H. Studying the
Rhodopsin‐Like
G Protein Coupled Receptors by Atomic Force Microscopy. Cytoskeleton (Hoboken) 2022; 78:400-416. [DOI: 10.1002/cm.21692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Bin Fang
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
| | - Li Zhao
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
| | - Xiaowei Du
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
| | - Qiyuan Liu
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
- School of Basic Medicine Gannan Medical University Ganzhou People's Republic of China
| | - Hui Yang
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
| | - Fangzuo Li
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
| | - Yaohuan Sheng
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
| | - Weidong Zhao
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
| | - Haijian Zhong
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
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21
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Lipke PN, Rauceo JM, Viljoen A. Cell-Cell Mating Interactions: Overview and Potential of Single-Cell Force Spectroscopy. Int J Mol Sci 2022; 23:ijms23031110. [PMID: 35163034 PMCID: PMC8835621 DOI: 10.3390/ijms23031110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/08/2022] [Accepted: 01/14/2022] [Indexed: 02/01/2023] Open
Abstract
It is an understatement that mating and DNA transfer are key events for living organisms. Among the traits needed to facilitate mating, cell adhesion between gametes is a universal requirement. Thus, there should be specific properties for the adhesion proteins involved in mating. Biochemical and biophysical studies have revealed structural information about mating adhesins, as well as their specificities and affinities, leading to some ideas about these specialized adhesion proteins. Recently, single-cell force spectroscopy (SCFS) has added important findings. In SCFS, mating cells are brought into contact in an atomic force microscope (AFM), and the adhesive forces are monitored through the course of mating. The results have shown some remarkable characteristics of mating adhesins and add knowledge about the design and evolution of mating adhesins.
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Affiliation(s)
- Peter N. Lipke
- Biology Department, Brooklyn College of the City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Correspondence: (P.N.L.); (A.V.)
| | - Jason M. Rauceo
- Department of Sciences, John Jay College of the City University of New York, New York, NY 10019, USA;
| | - Albertus Viljoen
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4–5, bte L7.07.07, 1348 Louvain-la-Neuve, Belgium
- Correspondence: (P.N.L.); (A.V.)
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22
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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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23
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Cheng H, Yu J, Wang Z, Ma P, Guo C, Wang B, Zhong W, Xu B. Details of Single-Molecule Force Spectroscopy Data Decoded by a Network-Based Automatic Clustering Algorithm. J Phys Chem B 2021; 125:9660-9667. [PMID: 34425052 DOI: 10.1021/acs.jpcb.1c03552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomic force microscopy-single-molecule force spectroscopy (AFM-SMFS) is a powerful methodology to probe intermolecular and intramolecular interactions in biological systems because of its operability in physiological conditions, facile and rapid sample preparation, versatile molecular manipulation, and combined functionality with high-resolution imaging. Since a huge number of AFM-SMFS force-distance curves are collected to avoid human bias and errors and to save time, numerous algorithms have been developed to analyze the AFM-SMFS curves. Nevertheless, there is still a need to develop new algorithms for the analysis of AFM-SMFS data since the current algorithms cannot specify an unbinding force to a corresponding/each binding site due to the lack of networking functionality to model the relationship between the unbinding forces. To address this challenge, herein, we develop an unsupervised method, i.e., a network-based automatic clustering algorithm (NASA), to decode the details of specific molecules, e.g., the unbinding force of each binding site, given the input of AFM-SMFS curves. Using the interaction of heparan sulfate (HS)-antithrombin (AT) on different endothelial cell surfaces as a model system, we demonstrate that NASA is able to automatically detect the peak and calculate the unbinding force. More importantly, NASA successfully identifies three unbinding force clusters, which could belong to three different binding sites, for both Ext1f/f and Ndst1f/f cell lines. NASA has great potential to be applied either readily or slightly modified to other AFM-based SMFS measurements that result in "saw-tooth"-shaped force-distance curves showing jumps related to the force unbinding, such as antibody-antigen interaction and DNA-protein interaction.
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Affiliation(s)
- Huimin Cheng
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Jun Yu
- School of Mathematics and Statistics, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Zhen Wang
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Ping Ma
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Cunlan Guo
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.,Single Molecule Study Laboratory, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Bin Wang
- Single Molecule Study Laboratory, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Wenxuan Zhong
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Bingqian Xu
- Single Molecule Study Laboratory, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
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24
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Bian K, Gerber C, Heinrich AJ, Müller DJ, Scheuring S, Jiang Y. Scanning probe microscopy. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00033-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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25
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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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26
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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: 9] [Impact Index Per Article: 3.0] [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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27
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Fake It 'Till You Make It-The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics. Int J Mol Sci 2020; 22:ijms22010050. [PMID: 33374526 PMCID: PMC7793082 DOI: 10.3390/ijms22010050] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.
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28
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Dumitru AC, Deepak RNVK, Liu H, Koehler M, Zhang C, Fan H, Alsteens D. Submolecular probing of the complement C5a receptor-ligand binding reveals a cooperative two-site binding mechanism. Commun Biol 2020; 3:786. [PMID: 33339958 PMCID: PMC7749166 DOI: 10.1038/s42003-020-01518-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/20/2020] [Indexed: 01/10/2023] Open
Abstract
A current challenge to produce effective therapeutics is to accurately determine the location of the ligand-biding site and to characterize its properties. So far, the mechanisms underlying the functional activation of cell surface receptors by ligands with a complex binding mechanism remain poorly understood due to a lack of suitable nanoscopic methods to study them in their native environment. Here, we elucidated the ligand-binding mechanism of the human G protein-coupled C5a receptor (C5aR). We discovered for the first time a cooperativity between the two orthosteric binding sites. We found that the N-terminus C5aR serves as a kinetic trap, while the transmembrane domain acts as the functional site and both contributes to the overall high-affinity interaction. In particular, Asp282 plays a key role in ligand binding thermodynamics, as revealed by atomic force microscopy and steered molecular dynamics simulation. Our findings provide a new structural basis for the functional and mechanistic understanding of the GPCR family that binds large macromolecular ligands.
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Affiliation(s)
- Andra C Dumitru
- Université catholique de Louvain, Louvain Institute of Biomolecular Science and Technology, 1348, Louvain-la-Neuve, Belgium
| | - R N V Krishna Deepak
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Heng Liu
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Melanie Koehler
- Université catholique de Louvain, Louvain Institute of Biomolecular Science and Technology, 1348, Louvain-la-Neuve, Belgium
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Hao Fan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - David Alsteens
- Université catholique de Louvain, Louvain Institute of Biomolecular Science and Technology, 1348, Louvain-la-Neuve, Belgium.
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29
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New small molecule fluorescent probes for G protein-coupled receptors: valuable tools for drug discovery. Future Med Chem 2020; 13:63-90. [PMID: 33319586 DOI: 10.4155/fmc-2019-0327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are essential signaling proteins and tractable therapeutic targets. To develop new drug candidates, GPCR drug discovery programs require versatile, sensitive pharmacological tools for ligand binding and compound screening. With the availability of new imaging modalities and proximity-based ligand binding technologies, fluorescent ligands offer many advantages and are increasingly being used, yet labeling small molecules remains considerably more challenging relative to peptides. Focusing on recent fluorescent small molecule studies for family A GPCRs, this review addresses some of the key challenges, synthesis approaches and structure-activity relationship considerations, and discusses advantages of using high-resolution GPCR structures to inform conjugation strategies. While no single approach guarantees successful labeling without loss of affinity or selectivity, the choice of fluorophore, linker type and site of attachment have proved to be critical factors that can significantly affect their utility in drug discovery programs, and as discussed, can sometimes lead to very unexpected results.
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30
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Müller DJ, Dumitru AC, Lo Giudice C, Gaub HE, Hinterdorfer P, Hummer G, De Yoreo JJ, Dufrêne YF, Alsteens D. Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems. Chem Rev 2020; 121:11701-11725. [PMID: 33166471 DOI: 10.1021/acs.chemrev.0c00617] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During the last three decades, a series of key technological improvements turned atomic force microscopy (AFM) into a nanoscopic laboratory to directly observe and chemically characterize molecular and cell biological systems under physiological conditions. Here, we review key technological improvements that have established AFM as an analytical tool to observe and quantify native biological systems from the micro- to the nanoscale. Native biological systems include living tissues, cells, and cellular components such as single or complexed proteins, nucleic acids, lipids, or sugars. We showcase the procedures to customize nanoscopic chemical laboratories by functionalizing AFM tips and outline the advantages and limitations in applying different AFM modes to chemically image, sense, and manipulate biosystems at (sub)nanometer spatial and millisecond temporal resolution. We further discuss theoretical approaches to extract the kinetic and thermodynamic parameters of specific biomolecular interactions detected by AFM for single bonds and extend the discussion to multiple bonds. Finally, we highlight the potential of combining AFM with optical microscopy and spectroscopy to address the full complexity of biological systems and to tackle fundamental challenges in life sciences.
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Affiliation(s)
- Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 28, 4056 Basel, Switzerland
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Cristina Lo Giudice
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Hermann E Gaub
- Applied Physics, Ludwig-Maximilians-Universität Munich, Amalienstrasse 54, 80799 München, Germany
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics and Department of Physics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.,Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
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31
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Yang J, Petitjean SJL, Koehler M, Zhang Q, Dumitru AC, Chen W, Derclaye S, Vincent SP, Soumillion P, Alsteens D. Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor. Nat Commun 2020; 11:4541. [PMID: 32917884 PMCID: PMC7486399 DOI: 10.1038/s41467-020-18319-6] [Citation(s) in RCA: 407] [Impact Index Per Article: 101.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/18/2020] [Indexed: 12/15/2022] Open
Abstract
Study of the interactions established between the viral glycoproteins and their host receptors is of critical importance for a better understanding of virus entry into cells. The novel coronavirus SARS-CoV-2 entry into host cells is mediated by its spike glycoprotein (S-glycoprotein), and the angiotensin-converting enzyme 2 (ACE2) has been identified as a cellular receptor. Here, we use atomic force microscopy to investigate the mechanisms by which the S-glycoprotein binds to the ACE2 receptor. We demonstrate, both on model surfaces and on living cells, that the receptor binding domain (RBD) serves as the binding interface within the S-glycoprotein with the ACE2 receptor and extract the kinetic and thermodynamic properties of this binding pocket. Altogether, these results provide a picture of the established interaction on living cells. Finally, we test several binding inhibitor peptides targeting the virus early attachment stages, offering new perspectives in the treatment of the SARS-CoV-2 infection. SARS-CoV-2 spike protein binds host ACE2 for virus entry. Here, the authors determine kinetic and thermodynamic properties of this interaction using atomic force microscopy, develop peptides that inhibit binding and suggest existence of additional attachment factors.
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Affiliation(s)
- Jinsung Yang
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Simon J L Petitjean
- 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
| | - Qingrong Zhang
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Wenzhang Chen
- Départment de Chimie, Laboratoire de Chimie Bio-Organique, University of Namur, Namur, Belgium
| | - Sylvie Derclaye
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Stéphane P Vincent
- Départment de Chimie, Laboratoire de Chimie Bio-Organique, University of Namur, Namur, Belgium
| | - Patrice Soumillion
- 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. .,Walloon Excellence in Life sciences and Biotechnology (WELBIO), 1300, Wavre, Belgium.
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32
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Zanetti C, Krause DS. "Caught in the net": the extracellular matrix of the bone marrow in normal hematopoiesis and leukemia. Exp Hematol 2020; 89:13-25. [PMID: 32755619 DOI: 10.1016/j.exphem.2020.07.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022]
Abstract
The influence of the bone marrow microenvironment on normal hematopoiesis, but also leukemia, has largely been accepted. However, the focus has been predominantly on the role of various cell types or cytokines maintaining hematopoietic stem cells or protecting leukemia stem cells from different therapies. A frequently overlooked component of the bone marrow microenvironment is the extracellular matrix, which not only provides a mechanical scaffold, but also serves as a source of growth factors. We discuss here how extracellular matrix proteins directly or indirectly modulate hematopoietic stem cell physiology and influence leukemia progression. It is hoped that existing and future studies on this topic may propel forward the possibility of augmenting normal hematopoiesis and improving therapies for leukemia, for instance, by targeting of the extracellular matrix in the bone marrow.
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Affiliation(s)
- Costanza Zanetti
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Daniela S Krause
- German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Germany; Frankfurt Cancer Institute, Frankfurt, Germany; Faculty of Medicine, Johann Wolfgang Goethe University, Frankfurt, Germany.
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33
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Mathelié-Guinlet M, Chantraine C, Viela F, Pietrocola G, Speziale P, Dufrêne YF. Nanomechanics of the molecular complex between staphylococcal adhesin SpsD and elastin. NANOSCALE 2020; 12:13996-14003. [PMID: 32578656 DOI: 10.1039/d0nr02745f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Staphylococcus pseudintermedius surface protein SpsD binds to extracellular matrix proteins to invade canine epithelial cells. Using single-molecule experiments, we show that SpsD engages in two modes of interaction with elastin that are tightly controlled by physical stress. Binding is weak (∼100 pN) at low tensile force (i.e. loading rate), but is dramatically enhanced (up to ∼1500 pN) by mechanical tension. Consistent with a "dock, lock, and latch" (DLL) mechanism, this force represents among the highest mechanical strengths known for a non-covalent biological interaction. The transition from weak to strong binding correlates with an increase in molecular stiffness but, surprisingly, with a decrease in molecular extension. This unanticipated mechanical behavior indicates that the adhesin is engaged in two distinct interaction mechanisms. Our results emphasize the crucial role of protein nanomechanics in the adhesion of staphylococci, and illustrate their wide diversity of force-dependent ligand-binding activities. These single-molecule mechanical experiments may contribute to the development of antiadhesion approaches to treat infections caused by S. pseudintermedius and other bacterial pathogens engaged in DLL interactions.
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Affiliation(s)
- Marion Mathelié-Guinlet
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium.
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34
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Garcia R. Nanomechanical mapping of soft materials with the atomic force microscope: methods, theory and applications. Chem Soc Rev 2020; 49:5850-5884. [PMID: 32662499 DOI: 10.1039/d0cs00318b] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Fast, high-resolution, non-destructive and quantitative characterization methods are needed to develop materials with tailored properties at the nanoscale or to understand the relationship between mechanical properties and cell physiology. This review introduces the state-of-the-art force microscope-based methods to map at high-spatial resolution the elastic and viscoelastic properties of soft materials. The experimental methods are explained in terms of the theories that enable the transformation of observables into material properties. Several applications in materials science, molecular biology and mechanobiology illustrate the scope, impact and potential of nanomechanical mapping methods.
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Affiliation(s)
- Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain.
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35
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Lo Giudice C, Zhang H, Wu B, Alsteens D. Mechanochemical Activation of Class-B G-Protein-Coupled Receptor upon Peptide-Ligand Binding. NANO LETTERS 2020; 20:5575-5582. [PMID: 32578992 DOI: 10.1021/acs.nanolett.0c02333] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Glucagon binding to the class-B G-protein-coupled glucagon receptor (GCGR) triggers the release of glucose from the liver during fasting. Recently, GCGR crystal structures have highlighted the conformation and molecular details of inactive and active receptor states. However, the dynamics of the conformational changes accompanying GCGR activation remains unclear. Here, we use multiplex force-distance curve-based atomic force microscopy (FD-based AFM) to probe in situ glucagon binding to individual GCGRs and monitor dynamically the transition to the active conformer. After a "dock" step, in which glucagon is partially bound to the GCGR extracellular domain, further interactions of the N-terminus with the transmembrane domain trigger an increase in the stiffness of the complex, adopting a highly stable and rigid "lock" conformer. This mechanotransduction is key for G-protein recruitment.
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Affiliation(s)
- Cristina Lo Giudice
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Haonan Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Beili Wu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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36
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Zhang Q, Tian F, Wang F, Guo Z, Cai M, Xu H, Wang H, Yang G, Shi X, Shan Y, Cui Z. Entry Dynamics of Single Ebola Virus Revealed by Force Tracing. ACS NANO 2020; 14:7046-7054. [PMID: 32383590 DOI: 10.1021/acsnano.0c01739] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Infections by the Ebola virus (EBOV) rapidly cause fatal hemorrhagic fever in humans. Viral entry into host cells is the most critical step in infection and an attractive target for therapeutic intervention. Herein, the invagination behavior and entry dynamics of filamentous Ebola virus-like particles (EBO-VLPs) were investigated using a force tracing technique based on atomic force microscopy and single-particle fluorescence tracking in real time. The filamentous EBOV-VLPs might enter cells in both horizontal and vertical modes, and the virus-receptor interactions during endocytic uptake were analyzed. In addition, molecular dynamics simulations and engulfment energy analysis further depicted EBO-VLP entry in the horizontal and vertical directions and suggested that internalization in the vertical direction requires a larger force and more time. This report provides useful information for further revealing the mechanism of viral infection, which is important for understanding viral pathogenesis.
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Affiliation(s)
- Qingrong Zhang
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, P.R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Falin Tian
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Nanosystem and Hierarchy Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Fei Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Zhengyuan Guo
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Mingjun Cai
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Haijiao Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Guocheng Yang
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, P.R. China
| | - Xinghua Shi
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Nanosystem and Hierarchy Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Yuping Shan
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, P.R. China
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
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37
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Zhang M, Liu Y, Cui F, Rankl C, Qin J, Guan Y, Guo X, Zhang B, Tang J. Interaction of vascular endothelial growth factor and heparin quantified by single molecule force spectroscopy. NANOSCALE 2020; 12:11927-11935. [PMID: 32458960 DOI: 10.1039/d0nr01570a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Heparin, as an effective anticoagulant, has been increasingly used in clinical practice, but the binding characteristics and influence of exogenous heparin on heparin-affinity proteins in the body are still unclear. Vascular endothelial growth factor A (VEGF-A) is a kind of protein with heparin affinity involved in the pathogenesis and progression of many angiogenesis-dependent diseases including cancer. As an important step in the angiogenesis-related cascade, it is necessary to clarify the interaction between VEGF165 (the major form of VEGF-A) and heparin. In this work, we investigated this interaction based on single molecule force spectroscopy (SMFS) and molecular dynamics (MD) simulation. From the SMFS study, binding forces between VEGF165 and heparin at different loading rates were quantified under near-physiological conditions. Meanwhile, the kinetic and thermodynamic parameters of the VEGF165/heparin complex dissociation process were also obtained. Results of MD simulation visually displayed the most likely binding conformation of VEGF165/heparin* complex, indicating that hydrogen bonding and hydrophobic interaction play a positive role in the binding between the two molecules. This work provides a new insight into the binding between VEGF165 and heparin and offers a research framework to study the interaction between heparin and multiple heparin affinity proteins, which is helpful for guiding the safe application of heparin in the clinic.
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Affiliation(s)
- Miaomiao Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China. and University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Ying Liu
- College of Humanities & Information Changchun University of Technology, Changchun, 130122, P. R. China
| | - Fengchao Cui
- Key Laboratory of High-Performance Rubber and Its Composite Materials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Christian Rankl
- Research Center for Non Destructive Testing GmbH, Science Park 2/2. OG, Altenberger Straße 69, A-4040 Linz, Austria
| | - Juan Qin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China. and University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Yanxue Guan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China. and University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Xinyue Guo
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China. and University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Bailin Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China. and University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Jilin Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China. and University of Science and Technology of China, Hefei, 230026, P. R. China
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38
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Viljoen A, Alsteens D, Dufrêne Y. Mechanical Forces between Mycobacterial Antigen 85 Complex and Fibronectin. Cells 2020; 9:cells9030716. [PMID: 32183296 PMCID: PMC7140604 DOI: 10.3390/cells9030716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/09/2020] [Accepted: 03/13/2020] [Indexed: 12/27/2022] Open
Abstract
Adhesion to extracellular matrix proteins is an important first step in host invasion, employed by many bacterial pathogens. In mycobacteria, the secreted Ag85 complex proteins, involved in the synthesis of the cell envelope, are known to bind to fibronectin (Fn) through molecular forces that are currently unknown. In this study, single-molecule force spectroscopy is used to study the strength, kinetics and thermodynamics of the Ag85-Fn interaction, focusing on the multidrug-resistant Mycobacterium abscessus species. Single Ag85 proteins bind Fn with a strength of ~75 pN under moderate tensile loading, which compares well with the forces reported for other Fn-binding proteins. The binding specificity is demonstrated by using free Ag85 and Fn peptides with active binding sequences. The Ag85-Fn rupture force increases with mechanical stress (i.e., loading rate) according to the Friddle–Noy–de Yoreo theory. From this model, we extract thermodynamic parameters that are in good agreement with previous affinity determinations by surface plasmon resonance. Strong bonds (up to ~500 pN) are observed under high tensile loading, which may favor strong mycobacterial attachment in the lung where cells are exposed to high shear stress or during hematogenous spread which leads to a disseminated infection. Our results provide new insight into the pleiotropic functions of an important mycobacterial virulence factor that acts as a stress-sensitive adhesin.
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Affiliation(s)
- Albertus Viljoen
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium; (A.V.); (D.A.)
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium; (A.V.); (D.A.)
- Walloon Excellence in Life sciences and Biotechnology (WELBIO), 1300 Wavre, Belgium
| | - Yves Dufrêne
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium; (A.V.); (D.A.)
- Walloon Excellence in Life sciences and Biotechnology (WELBIO), 1300 Wavre, Belgium
- Correspondence:
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39
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Feng L, Torun H. Miniaturized magnetic bead-actuators for force-clamp spectroscopy-based single-molecule measurements. Ultramicroscopy 2019; 209:112888. [PMID: 31734437 DOI: 10.1016/j.ultramic.2019.112888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 10/27/2019] [Accepted: 11/09/2019] [Indexed: 10/25/2022]
Abstract
Force-clamp spectroscopy can mimic the physiological conditions for the proteins under investigation. In addition, it is a direct way of observing the relationship between bond lifetime and molecular forces. However, traditional force-clamp methods rely on active feedback controllers that can introduce artefacts. In this work, we introduce a new method to enable force-clamp spectroscopy without a need for an active feedback. The method is based on miniaturized magnetic beads offering improved stability. As a case study, we performed force-clamp experiments using biotin-streptavidin molecule pairs with and without active feedback. Our results demonstrate the feasibility of force-clamp experiments without feedback and illustrate the advantages of our method.
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Affiliation(s)
- L Feng
- Faculty of Engineering and Environment, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom
| | - H Torun
- Faculty of Engineering and Environment, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom.
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40
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Michaelis M, Fayyaz A, Parambath M, Koeppen S, Ciacchi LC, Hanley QS, Perry CC. Platform for Screening Abiotic/Biotic Interactions Using Indicator Displacement Assays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14230-14237. [PMID: 31609123 DOI: 10.1021/acs.langmuir.9b03085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This paper describes novel adaptations of optically sectioned planar format assays to screen compounds for their affinities to materials surfaces. The novel platform, which we name optically sectioned indicator displacement assays (O-IDA), makes use of displaceable dyes in a format adaptable to high-throughput multiwell plate technologies. We describe two approaches: the first being where the dye exhibits fluorescence in both the surface bound and unbound state and the second, where fluorescence is lost upon displacement of the dye from the surface. Half maximal inhibitory concentration (IC50), binding affinity (Ki), and binding free energy (ΔGads) values can be extracted from the raw data. Representative biomolecules were tested for interactions with silica in an aqueous environment and ZnO(0001)-Zn and (10-10) facets in a nonaqueous environment. We provide the first experimental values for both the binding of small molecules to silica and the facet-dependent ZnO binding affinity of key amino acids associated with ZnO-specific oligopeptides. The specific data will be invaluable to those studying interactions at interfaces both experimentally and computationally. O-IDA provides a general framework for the high-throughput screening of molecule binding to materials surfaces, which has important applications in drug delivery, (bio-) catalysis, biosensing, and biomaterial engineering.
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Affiliation(s)
- Monika Michaelis
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Material Science (BCCMS), Center for Environmental Research and Sustainable Technology (UFT) and MAPEX Centre for Materials and Processes , University of Bremen , D-28359 Bremen , Germany
| | | | | | - Susan Koeppen
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Material Science (BCCMS), Center for Environmental Research and Sustainable Technology (UFT) and MAPEX Centre for Materials and Processes , University of Bremen , D-28359 Bremen , Germany
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Material Science (BCCMS), Center for Environmental Research and Sustainable Technology (UFT) and MAPEX Centre for Materials and Processes , University of Bremen , D-28359 Bremen , Germany
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41
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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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42
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Krainer G, Keller S, Schlierf M. Structural dynamics of membrane-protein folding from single-molecule FRET. Curr Opin Struct Biol 2019; 58:124-137. [DOI: 10.1016/j.sbi.2019.05.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
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43
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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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44
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Conformational Plasticity of Human Protease-Activated Receptor 1 upon Antagonist- and Agonist-Binding. Structure 2019; 27:1517-1526.e3. [PMID: 31422910 DOI: 10.1016/j.str.2019.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/07/2019] [Accepted: 07/23/2019] [Indexed: 01/14/2023]
Abstract
G protein-coupled receptors (GPCRs) show complex relationships between functional states and conformational plasticity that can be qualitatively and quantitatively described by contouring their free energy landscape. However, how ligands modulate the free energy landscape to direct conformation and function of GPCRs is not entirely understood. Here, we employ single-molecule force spectroscopy to parametrize the free energy landscape of the human protease-activated receptor 1 (PAR1), and delineate the mechanical, kinetic, and energetic properties of PAR1 being set into different functional states. Whereas in the inactive unliganded state PAR1 adopts mechanically rigid and stiff conformations, upon agonist or antagonist binding the receptor mechanically softens, while increasing its conformational flexibility, and kinetic and energetic stability. By mapping the free energy landscape to the PAR1 structure, we observe key structural regions putting this conformational plasticity into effect. Our insight, complemented with previously acquired knowledge on other GPCRs, outlines a more general framework to understand how GPCRs stabilize certain functional states.
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45
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Lo Giudice C, Dumitru AC, Alsteens D. Probing ligand-receptor bonds in physiologically relevant conditions using AFM. Anal Bioanal Chem 2019; 411:6549-6559. [PMID: 31410537 DOI: 10.1007/s00216-019-02077-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 12/16/2022]
Abstract
Cell surface receptors, often called transmembrane receptors, are key cellular components as they control and mediate cell communication and signalling, converting extracellular signals into intracellular signals. Elucidating the molecular details of ligand binding (cytokine, growth factors, hormones, pathogens,...) to cell surface receptors and how this binding triggers conformational changes that initiate intracellular signalling is needed to improve our understanding of cellular processes and for rational drug design. Unfortunately, the molecular complexity and high hydrophobicity of membrane proteins significantly hamper their structural and functional characterization in conditions mimicking their native environment. With its piconewton force sensitivity and (sub)nanometer spatial resolution, together with the capability of operating in liquid environment and at physiological temperature, atomic force microscopy (AFM) has proven to be one of the most powerful tools to image and quantify receptor-ligand bonds in situ under physiologically relevant conditions. In this article, a brief overview of the rapid evolution of AFM towards quantitative biological mapping will be given, followed by selected examples highlighting the main advances that AFM-based ligand-receptor studies have brought to the fields of cell biology, immunology, microbiology, and virology, along with future prospects and challenges. Graphical abstract.
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Affiliation(s)
- Cristina Lo Giudice
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du sud 4-5, 1348, Louvain-la-Neuve, Belgium.
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46
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Fibrinogen binding is affected by amino acid substitutions in C-terminal repeat region of fibronectin binding protein A. Sci Rep 2019; 9:11619. [PMID: 31406152 PMCID: PMC6690874 DOI: 10.1038/s41598-019-48031-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 07/29/2019] [Indexed: 11/14/2022] Open
Abstract
Fibronectin-binding protein A (FnBPA), a protein displayed on the outer surface of Staphylococcus aureus, has a structured A-domain that binds fibrinogen (Fg) and a disordered repeat-region that binds fibronectin (Fn). Amino acid substitutions in Fn-binding repeats (FnBRs) have previously been linked to cardiovascular infection in humans. Here we used microtiter and atomic force microscopy (AFM) to investigate adhesion by variants of full-length FnBPA covalently anchored in the outer cell wall of Lactococcus lactis, a Gram-positive surrogate that otherwise lacks adhesins to mammalian ligands. Fn adhesion increased in five of seven FnBPA variants under static conditions. The bond targeting Fn increased its strength with load under mechanical dissociation. Substitutions extended bond lifetime (1/koff) up to 2.1 times for FnBPA-Fn. Weaker adhesion was observed for Fg in all FnBPA variants tested with microtiter. However, mechanical dissociation with AFM showed significantly increased tensile strength for Fg interacting with the E652D/H782Q variant. This is consistent with a force-induced mechanism and suggests that the dock, lock, and latch (DLL) mechanism is favored for Fg-binding under mechanical stress. Collectively, these experiments reveal that FnBPA exhibits bimodal, ligand-dependent adhesive behavior. Amino acid substitutions in the repeat-region of FnBPA impact binding to both ligands. This was unexpected for Fg since all variants have the same A-domain sequence, and the Fg-binding site is distant from the repeat region. This indicates that FnBRs may fold back on the A-domain in a way that impacts the DLL binding mechanism for Fg.
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47
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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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48
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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 2019; 57:25-32. [PMID: 30412846 PMCID: PMC6472649 DOI: 10.1016/j.ceb.2018.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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) 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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49
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Yang Q, Ma Q, Herum KM, Wang C, Patel N, Lee J, Wang S, Yen TM, Wang J, Tang H, Lo YH, Head BP, Azam F, Xu S, Cauwenberghs G, McCulloch AD, John S, Liu Z, Lal R. Array atomic force microscopy for real-time multiparametric analysis. Proc Natl Acad Sci U S A 2019; 116:5872-5877. [PMID: 30850523 PMCID: PMC6442637 DOI: 10.1073/pnas.1813518116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Nanoscale multipoint structure-function analysis is essential for deciphering the complexity of multiscale biological and physical systems. Atomic force microscopy (AFM) allows nanoscale structure-function imaging in various operating environments and can be integrated seamlessly with disparate probe-based sensing and manipulation technologies. Conventional AFMs only permit sequential single-point analysis; widespread adoption of array AFMs for simultaneous multipoint study is challenging owing to the intrinsic limitations of existing technological approaches. Here, we describe a prototype dispersive optics-based array AFM capable of simultaneously monitoring multiple probe-sample interactions. A single supercontinuum laser beam is utilized to spatially and spectrally map multiple cantilevers, to isolate and record beam deflection from individual cantilevers using distinct wavelength selection. This design provides a remarkably simplified yet effective solution to overcome the optical cross-talk while maintaining subnanometer sensitivity and compatibility with probe-based sensors. We demonstrate the versatility and robustness of our system on parallel multiparametric imaging at multiscale levels ranging from surface morphology to hydrophobicity and electric potential mapping in both air and liquid, mechanical wave propagation in polymeric films, and the dynamics of living cells. This multiparametric, multiscale approach provides opportunities for studying the emergent properties of atomic-scale mechanical and physicochemical interactions in a wide range of physical and biological networks.
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Affiliation(s)
- Qingqing Yang
- Materials Science and Engineering, University of California, San Diego, La Jolla, CA 92093
| | - Qian Ma
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA 92093
| | - Kate M Herum
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Chonghe Wang
- Department of Nanoengineering, University of California, San Diego, La Jolla, CA 92093
| | - Nirav Patel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Joon Lee
- Materials Science and Engineering, University of California, San Diego, La Jolla, CA 92093
| | - Shanshan Wang
- Department of Anesthesiology, University of California, San Diego, La Jolla, CA 92093
- Department of Anesthesia, Veterans Affairs San Diego Healthcare System, San Diego, CA 92161
| | - Tony M Yen
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Jun Wang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Hanmei Tang
- Department of Nanoengineering, University of California, San Diego, La Jolla, CA 92093
| | - Yu-Hwa Lo
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA 92093
| | - Brian P Head
- Department of Anesthesiology, University of California, San Diego, La Jolla, CA 92093
- Department of Anesthesia, Veterans Affairs San Diego Healthcare System, San Diego, CA 92161
| | - Farooq Azam
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Sheng Xu
- Materials Science and Engineering, University of California, San Diego, La Jolla, CA 92093
- Department of Nanoengineering, University of California, San Diego, La Jolla, CA 92093
| | - Gert Cauwenberghs
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Andrew D McCulloch
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Scott John
- Cardiovascular Research Laboratory, University of California, Los Angeles, CA 90095
| | - Zhaowei Liu
- Materials Science and Engineering, University of California, San Diego, La Jolla, CA 92093;
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA 92093
| | - Ratnesh Lal
- Materials Science and Engineering, University of California, San Diego, La Jolla, CA 92093;
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093
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