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Boulos I, Jabbour J, Khoury S, Mikhael N, Tishkova V, Candoni N, Ghadieh HE, Veesler S, Bassim Y, Azar S, Harb F. Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics. Molecules 2023; 28:7176. [PMID: 37894653 PMCID: PMC10608922 DOI: 10.3390/molecules28207176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/13/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories: intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome (30% of which is devoted to encoding them). Hydrophobic interactions inside the membrane serve to stabilize integral proteins, which span the lipid bilayer. This review investigates a number of computational and experimental methods used to study membrane proteins. It encompasses a variety of technologies, including electrophoresis, X-ray crystallography, cryogenic electron microscopy (cryo-EM), nuclear magnetic resonance spectroscopy (NMR), biophysical methods, computational methods, and artificial intelligence. The link between structure and function of membrane proteins has been better understood thanks to these approaches, which also hold great promise for future study in the field. The significance of fusing artificial intelligence with experimental data to improve our comprehension of membrane protein biology is also covered in this paper. This effort aims to shed light on the complexity of membrane protein biology by investigating a variety of experimental and computational methods. Overall, the goal of this review is to emphasize how crucial it is to understand the functions of membrane proteins in eukaryotic cells. It gives a general review of the numerous methods used to look into these crucial elements and highlights the demand for multidisciplinary approaches to advance our understanding.
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Affiliation(s)
- Imad Boulos
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Joy Jabbour
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Serena Khoury
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Nehme Mikhael
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Victoria Tishkova
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Nadine Candoni
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Hilda E. Ghadieh
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Stéphane Veesler
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Youssef Bassim
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Sami Azar
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Frédéric Harb
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
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Wijesinghe WCB, Min D. Single-Molecule Force Spectroscopy of Membrane Protein Folding. J Mol Biol 2023; 435:167975. [PMID: 37330286 DOI: 10.1016/j.jmb.2023.167975] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 06/19/2023]
Abstract
Single-molecule force spectroscopy is a unique method that can probe the structural changes of single proteins at a high spatiotemporal resolution while mechanically manipulating them over a wide force range. Here, we review the current understanding of membrane protein folding learned by using the force spectroscopy approach. Membrane protein folding in lipid bilayers is one of the most complex biological processes in which diverse lipid molecules and chaperone proteins are intricately involved. The approach of single protein forced unfolding in lipid bilayers has produced important findings and insights into membrane protein folding. This review provides an overview of the forced unfolding approach, including recent achievements and technical advances. Progress in the methods can reveal more interesting cases of membrane protein folding and clarify general mechanisms and principles.
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Affiliation(s)
- W C Bhashini Wijesinghe
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Center for Wave Energy Materials, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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Chen J, Peng Q, Peng X, Zhang H, Zeng H. Probing and Manipulating Noncovalent Interactions in Functional Polymeric Systems. Chem Rev 2022; 122:14594-14678. [PMID: 36054924 DOI: 10.1021/acs.chemrev.2c00215] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Noncovalent interactions, which usually feature tunable strength, reversibility, and environmental adaptability, have been recognized as driving forces in a variety of biological and chemical processes, contributing to the recognition between molecules, the formation of molecule clusters, and the establishment of complex structures of macromolecules. The marriage of noncovalent interactions and conventional covalent polymers offers the systems novel mechanical, physicochemical, and biological properties, which are highly dependent on the binding mechanisms of the noncovalent interactions that can be illuminated via quantification. This review systematically discusses the nanomechanical characterization of typical noncovalent interactions in polymeric systems, mainly through direct force measurements at microscopic, nanoscopic, and molecular levels, which provide quantitative information (e.g., ranges, strengths, and dynamics) on the binding behaviors. The fundamental understandings of intermolecular and interfacial interactions are then correlated to the macroscopic performances of a series of noncovalently bonded polymers, whose functions (e.g., stimuli-responsiveness, self-healing capacity, universal adhesiveness) can be customized through the manipulation of the noncovalent interactions, providing insights into the rational design of advanced materials with applications in biomedical, energy, environmental, and other engineering fields.
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Affiliation(s)
- Jingsi Chen
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Qiongyao Peng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Xuwen Peng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Hao Zhang
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Hongbo Zeng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
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Shukla AK, Alam J, Alhoshan M. Recent Advancements in Polyphenylsulfone Membrane Modification Methods for Separation Applications. MEMBRANES 2022; 12:247. [PMID: 35207168 PMCID: PMC8876851 DOI: 10.3390/membranes12020247] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 02/04/2023]
Abstract
Polyphenylsulfone (PPSU) membranes are of fundamental importance for many applications such as water treatment, gas separation, energy, electronics, and biomedicine, due to their low cost, controlled crystallinity, chemical, thermal, and mechanical stability. Numerous research studies have shown that modifying surface properties of PPSU membranes influences their stability and functionality. Therefore, the modification of the PPSU membrane surface is a pressing issue for both research and industrial communities. In this review, various surface modification methods and processes along with their mechanisms and performance are considered starting from 2002. There are three main approaches to the modification of PPSU membranes. The first one is bulk modifications, and it includes functional groups inclusion via sulfonation, amination, and chloromethylation. The second is blending with polymer (for instance, blending nanomaterials and biopolymers). Finally, the third one deals with physical and chemical surface modifications. Obviously, each method has its own limitations and advantages that are outlined below. Generally speaking, modified PPSU membranes demonstrate improved physical and chemical properties and enhanced performance. The advancements in PPSU modification have opened the door for the advance of membrane technology and multiple prospective applications.
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Affiliation(s)
- Arun Kumar Shukla
- King Abdullah Institute for Nanotechnology, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - Javed Alam
- King Abdullah Institute for Nanotechnology, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - Mansour Alhoshan
- King Abdullah Institute for Nanotechnology, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
- Department of Chemical Engineering, College of Engineering, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
- K.A. CARE Energy Research and Innovation Center at Riyadh, P.O. Box 2022, Riyadh 11451, Saudi Arabia
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Asgari M, Latifi N, Giovanniello F, Espinosa HD, Amabili M. Revealing Layer‐Specific Ultrastructure and Nanomechanics of Fibrillar Collagen in Human Aorta via Atomic Force Microscopy Testing: Implications on Tissue Mechanics at Macroscopic Scale. ADVANCED NANOBIOMED RESEARCH 2022. [DOI: 10.1002/anbr.202100159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Meisam Asgari
- Department of Mechanical Engineering McGill University 817 Sherbrooke Street West Montreal QC H3A 0C3 Canada
- Theoretical and Applied Mechanics Program Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Neda Latifi
- Department of Mechanical and Industrial Engineering University of Toronto 5 King's College Road Toronto ON M5S 3G8 Canada
| | - Francesco Giovanniello
- Department of Mechanical Engineering McGill University 817 Sherbrooke Street West Montreal QC H3A 0C3 Canada
| | - Horacio D. Espinosa
- Theoretical and Applied Mechanics Program Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Marco Amabili
- Department of Mechanical Engineering McGill University 817 Sherbrooke Street West Montreal QC H3A 0C3 Canada
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Sun W, Gao X, Lei H, Wang W, Cao Y. Biophysical Approaches for Applying and Measuring Biological Forces. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105254. [PMID: 34923777 PMCID: PMC8844594 DOI: 10.1002/advs.202105254] [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] [Received: 11/15/2021] [Indexed: 05/13/2023]
Abstract
Over the past decades, increasing evidence has indicated that mechanical loads can regulate the morphogenesis, proliferation, migration, and apoptosis of living cells. Investigations of how cells sense mechanical stimuli or the mechanotransduction mechanism is an active field of biomaterials and biophysics. Gaining a further understanding of mechanical regulation and depicting the mechanotransduction network inside cells require advanced experimental techniques and new theories. In this review, the fundamental principles of various experimental approaches that have been developed to characterize various types and magnitudes of forces experienced at the cellular and subcellular levels are summarized. The broad applications of these techniques are introduced with an emphasis on the difficulties in implementing these techniques in special biological systems. The advantages and disadvantages of each technique are discussed, which can guide readers to choose the most suitable technique for their questions. A perspective on future directions in this field is also provided. It is anticipated that technical advancement can be a driving force for the development of mechanobiology.
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Affiliation(s)
- Wenxu Sun
- School of SciencesNantong UniversityNantong226019P. R. China
| | - Xiang Gao
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
| | - Hai Lei
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
- Chemistry and Biomedicine Innovation CenterNanjing UniversityNanjing210023P. R. China
| | - Wei Wang
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
| | - Yi Cao
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
- MOE Key Laboratory of High Performance Polymer Materials and TechnologyDepartment of Polymer Science & EngineeringCollege of Chemistry & Chemical EngineeringNanjing UniversityNanjing210023P. R. China
- Chemistry and Biomedicine Innovation CenterNanjing UniversityNanjing210023P. R. China
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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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Yasunaga A, Murad Y, Li ITS. Quantifying molecular tension-classifications, interpretations and limitations of force sensors. Phys Biol 2019; 17:011001. [PMID: 31387091 DOI: 10.1088/1478-3975/ab38ff] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Molecular force sensors (MFSs) have grown to become an important tool to study the mechanobiology of cells and tissues. They provide a minimally invasive means to optically report mechanical interactions at the molecular level. One of the challenges in molecular force sensor studies is the interpretation of the fluorescence readout. In this review, we divide existing MFSs into three classes based on the force-sensing mechanism (reversibility) and the signal output (analog/digital). From single-molecule force spectroscopy (SMFS) perspectives, we provided a critical discussion on how the sensors respond to force and how the different sensor designs affect the interpretation of their fluorescence readout. Lastly, the review focuses on the limitations and attention one must pay in designing MFSs and biological experiments using them; in terms of their tunability, signal-to-noise ratio (SNR), and perturbation of the biological system under investigation.
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Affiliation(s)
- Adam Yasunaga
- These authors contributed equally to the manuscript (co-first author)
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Nanomechanical Analysis of Extracellular Matrix and Cells in Multicellular Spheroids. Cell Mol Bioeng 2019; 12:203-214. [PMID: 31719910 DOI: 10.1007/s12195-019-00577-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/20/2019] [Indexed: 01/09/2023] Open
Abstract
Introduction Over the last decade, atomic force microscopy (AFM) has played an important role in understanding nanomechanical properties of various cancer cell lines. This study is focused on Lewis lung carcinoma cell tumours as 3D multicellular spheroid (MS). Not much is know about the mechanical properties of the cells and the surrounding extracellular matrix (ECM) in rapidly growing tumours. Methods Depth-dependent indentation measurements were conducted with the AFM. Force-vs.-indentation curves were used to create stiffness profiles as a function of depth. Here studies were focused on the outer most layer, i.e., proliferation zone of the spheroid. Results Both surface and sub-surface stiffness profiles of MS were created. This study revealed three nanomechanical topographies, Type A-high modulus due to collagen fibers, Type B-high stiffness at cell membrane and ECM interface and Type C-increased modulus due to cell lying deep inside matrix at a depth of 1.35 μm. Both Type and Type-B topographies result from collagen-based structures in ECM. Conclusion This study has first time revealed mechanical constitution of an MS. Depth-dependent indentation studies have the revealed role of various molecular and cellular components responsible for providing mechanical stability to MS. Nanomechanical heterogeneities revealed in this investigation can shed new light in developing correct dosage regime for collagenase treatment of tumours and designing better controlled artificial extracellular matrix systems for replicating tissue growth in-vitro.
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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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Wang N, Zhang M, Chen X, Ma X, Li C, Zhang Z, Tang J. Mapping the interaction sites of Mucin 1 and DNA aptamer by atomic force microscopy. Analyst 2018; 142:3800-3804. [PMID: 28930315 DOI: 10.1039/c7an01119a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mucin 1 (MUC1) is an attractive tumor marker for cancer diagnosis. An advanced atomic force microscopy (AFM) mode, peak-force tapping AFM with an aptamer functionalized tip, was introduced to map the specific interaction sites of an aptamer and MUC1. Single molecular force spectroscopy (SMFS) was used to investigate dynamic parameters of the aptamer-MUC1.
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Affiliation(s)
- Nan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China.
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Garcia PD, Garcia R. Determination of the viscoelastic properties of a single cell cultured on a rigid support by force microscopy. NANOSCALE 2018; 10:19799-19809. [PMID: 30334057 DOI: 10.1039/c8nr05899g] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Understanding the relationship between the mechanical properties of living cells and physiology is a central issue in mechanobiology. Mechanical properties are used as fingerprints of the pathological state of a single cell. The force exerted on a cell is influenced by the stiffness of the solid support needed to culture it. This effect is a consequence of the cell's boundary conditions. It causes a cell to appear with mechanical properties different from their real values. Here we develop a bottom effect viscoelastic theory to determine the viscoelastic response of a cell. The theory transforms a force-distance curve into the cell's Young's modulus, loss modulus, relaxation time or viscosity coefficient with independence of the stiffness of the rigid support. The theory predicts that, for a given indentation, the force exerted on the cell's periphery will be larger than on a perinuclear region. Results based on the use of semi-infinite contact mechanics models introduce large numerical errors in the determination of the mechanical properties. Finite element simulations confirm the theory and define its range of applicability.
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Affiliation(s)
- Pablo D Garcia
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Ines de la Cruz 3, 28049 Madrid, Spain.
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Puiggalí-Jou A, Pawlowski J, del Valle LJ, Michaux C, Perpète EA, Sek S, Alemán C. Properties of Omp2a-Based Supported Lipid Bilayers: Comparison with Polymeric Bioinspired Membranes. ACS OMEGA 2018; 3:9003-9019. [PMID: 31459033 PMCID: PMC6645002 DOI: 10.1021/acsomega.8b00913] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 07/19/2018] [Indexed: 05/31/2023]
Abstract
Omp2a β-barrel outer membrane protein has been reconstituted into supported lipid bilayers (SLBs) to compare the nanomechanical properties (elastic modulus, adhesion forces, and deformation) and functionality of the resulting bioinspired system with those of Omp2a-based polymeric nanomembranes (NMs). Protein reconstitution into lipid bilayers has been performed using different strategies, the most successful one consisting of a detergent-mediated process into preformed liposomes. The elastic modulus obtained for the lipid bilayer and Omp2a are ∼19 and 10.5 ± 1.7 MPa, respectively. Accordingly, the protein is softer than the lipid bilayer, whereas the latter exhibits less mechanical strength than polymeric NMs. Besides, the function of Omp2a in the SLB is similar to that observed for Omp2a-based polymeric NMs. Results open the door to hybrid bioinspired substrates based on the integration of Omp2a-proteoliposomes and nanoperforated polymeric freestanding NMs.
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Affiliation(s)
- Anna Puiggalí-Jou
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, 08019 Barcelona, Spain
| | - Jan Pawlowski
- Biological
and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Luis J. del Valle
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, 08019 Barcelona, Spain
| | - Catherine Michaux
- Laboratoire
de Chimie Physique des Biomolécules, University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Eric A. Perpète
- Laboratoire
de Chimie Physique des Biomolécules, University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Slawomir Sek
- Biological
and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Carlos Alemán
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, 08019 Barcelona, Spain
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Shih HJ, Dai CL, Shih PJ. Tip Pressure on Semicircular Specimens in Tapping Mode Atomic Force Microscopy in Viscous Fluid Environments. SENSORS (BASEL, SWITZERLAND) 2017; 17:E2182. [PMID: 28937607 PMCID: PMC5676617 DOI: 10.3390/s17102182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/21/2017] [Accepted: 09/21/2017] [Indexed: 11/18/2022]
Abstract
Tapping mode (TM) atomic force microscopy (AFM) in a liquid environment is widely used to measure the contours of biological specimens. The TM triggers the AFM probe approximately at the resonant frequencies and controls the tip such that it periodically touches the specimen along the scanning path. The AFM probe and its tip produce a hydrodynamic pressure on the probe itself and press the specimen. The tip to specimen size ratio is known to affect the measurement accuracy of AFM, however, few studies have focused on the hydrodynamic pressure caused by the effects of specimen size. Such pressure affects the contour distortion of the biological specimen. In this study, a semi-analytical method is employed for a semicircular specimen to analyze the vorticity and pressure distributions for specimens of various sizes and at various tip locations. Changes in pressure distribution, fluid spin motion, and specimen deformation are identified as the tip approaches the specimen. The results indicate the following: the specimen surface experiences the highest pressure when the specimen diameter equals the tip width; the vorticity between tip and specimen is complex when the tip is close to the specimen center line; and the specimen inflates when the tip is aligned with the specimen center line.
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Affiliation(s)
- Hua-Ju Shih
- Institute of Applied Mechanics, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan.
| | - Ching-Liang Dai
- Department of Mechanical Engineering, National Chung Hsing University, No. 145, Xingda Rd. South Dist., Taichung 40227, Taiwan.
| | - Po-Jen Shih
- Department of Civil and Environmental Engineering, National University of Kaohsiung, No. 700, Kaohsiung University Rd., Nanzih District, Kaohsiung 81148, Taiwan.
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15
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Chiodini S, Reinares-Fisac D, Espinosa FM, Gutiérrez-Puebla E, Monge A, Gándara F, Garcia R. Angstrom-Resolved Metal-Organic Framework-Liquid Interfaces. Sci Rep 2017; 7:11088. [PMID: 28894192 PMCID: PMC5593909 DOI: 10.1038/s41598-017-11479-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/23/2017] [Indexed: 11/19/2022] Open
Abstract
Metal-organic frameworks (MOFs) are a class of crystalline materials with a variety of applications in gas storage, catalysis, drug delivery or light harvesting. The optimization of those applications requires the characterization of MOF structure in the relevant environment. Dynamic force microscopy has been applied to follow dynamic processes of metal-organic-framework material. We provide images with spatial and time resolutions, respectively, of angstrom and seconds that show that Ce-RPF-8 surfaces immersed in water and glycerol experience a surface reconstruction process that is characterized by the diffusion of the molecular species along the step edges of the open terraces. The rate of the surface reconstruction process depends on the liquid. In water it happens spontaneously while in glycerol is triggered by applying an external force.
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Affiliation(s)
- Stefano Chiodini
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid, CSIC, c/ Sor Juana Inés de la Cruz 3, 28049, Madrid, Spain
| | - Daniel Reinares-Fisac
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid, CSIC, c/ Sor Juana Inés de la Cruz 3, 28049, Madrid, Spain
| | - Francisco M Espinosa
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid, CSIC, c/ Sor Juana Inés de la Cruz 3, 28049, Madrid, Spain
| | - Enrique Gutiérrez-Puebla
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid, CSIC, c/ Sor Juana Inés de la Cruz 3, 28049, Madrid, Spain
| | - Angeles Monge
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid, CSIC, c/ Sor Juana Inés de la Cruz 3, 28049, Madrid, Spain
| | - Felipe Gándara
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid, CSIC, c/ Sor Juana Inés de la Cruz 3, 28049, Madrid, Spain.
| | - Ricardo Garcia
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid, CSIC, c/ Sor Juana Inés de la Cruz 3, 28049, Madrid, Spain.
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16
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Laskowski PR, Pfreundschuh M, Stauffer M, Ucurum Z, Fotiadis D, Müller DJ. High-Resolution Imaging and Multiparametric Characterization of Native Membranes by Combining Confocal Microscopy and an Atomic Force Microscopy-Based Toolbox. ACS NANO 2017; 11:8292-8301. [PMID: 28745869 DOI: 10.1021/acsnano.7b03456] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To understand how membrane proteins function requires characterizing their structure, assembly, and inter- and intramolecular interactions in physiologically relevant conditions. Conventionally, such multiparametric insight is revealed by applying different biophysical methods. Here we introduce the combination of confocal microscopy, force-distance curve-based (FD-based) atomic force microscopy (AFM), and single-molecule force spectroscopy (SMFS) for the identification of native membranes and the subsequent multiparametric analysis of their membrane proteins. As a well-studied model system, we use native purple membrane from Halobacterium salinarum, whose membrane protein bacteriorhodopsin was His-tagged to bind nitrilotriacetate (NTA) ligands. First, by confocal microscopy we localize the extracellular and cytoplasmic surfaces of purple membrane. Then, we apply AFM to image single bacteriorhodopsins approaching sub-nanometer resolution. Afterwards, the binding of NTA ligands to bacteriorhodopsins is localized and quantified by FD-based AFM. Finally, we apply AFM-based SMFS to characterize the (un)folding of the membrane protein and to structurally map inter- and intramolecular interactions. The multimethodological approach is generally applicable to characterize biological membranes and membrane proteins at physiologically relevant conditions.
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Affiliation(s)
- Pawel R Laskowski
- Department of Biosystems Science and Engineering, ETH Zurich , 4058 Basel, Switzerland
| | - Moritz Pfreundschuh
- Department of Biosystems Science and Engineering, ETH Zurich , 4058 Basel, Switzerland
| | - Mirko Stauffer
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zurich , 4058 Basel, Switzerland
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17
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Li M, Liu L, Xi N, Wang Y. Atomic force microscopy studies on cellular elastic and viscoelastic properties. SCIENCE CHINA-LIFE SCIENCES 2017; 61:57-67. [DOI: 10.1007/s11427-016-9041-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 04/07/2017] [Indexed: 01/03/2023]
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18
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Pfreundschuh M, Harder D, Ucurum Z, Fotiadis D, Müller DJ. Detecting Ligand-Binding Events and Free Energy Landscape while Imaging Membrane Receptors at Subnanometer Resolution. NANO LETTERS 2017; 17:3261-3269. [PMID: 28361535 DOI: 10.1021/acs.nanolett.7b00941] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Force-distance curve-based atomic force microscopy has emerged into a sophisticated technique for imaging cellular membranes and for detecting specific ligand-binding events of native membrane receptors. However, so far the resolution achieved has been insufficient to structurally map ligand-binding sites onto membrane proteins. Here, we introduce experimental and theoretical approaches for overcoming this limitation. To establish a structurally and functionally well-defined reference sample, we engineer a ligand-binding site to the light-driven proton pump bacteriorhodopsin of purple membrane. Functionalizing the AFM stylus with an appropriate linker-system tethering the ligand and optimizing the AFM conditions allows for imaging the engineered bacteriorhodopsin at subnanometer resolution while structurally mapping the specific ligand-receptor binding events. Improved data analysis allows reconstructing the ligand-binding free energy landscape from the experimental data, thus providing thermodynamic and kinetic insight into the ligand-binding process. The nanoscopic method introduced is generally applicable for imaging receptors in native membranes at subnanometer resolution and for systematically mapping and quantifying the free energy landscape of ligand binding.
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Affiliation(s)
- Moritz Pfreundschuh
- Department of Biosystems Science and Engineering, ETH Zürich , 4058 Basel, Switzerland
| | - Daniel Harder
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich , 4058 Basel, Switzerland
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19
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Dufrêne YF, Ando T, Garcia R, Alsteens D, Martinez-Martin D, Engel A, Gerber C, Müller DJ. Imaging modes of atomic force microscopy for application in molecular and cell biology. NATURE NANOTECHNOLOGY 2017; 12:295-307. [PMID: 28383040 DOI: 10.1038/nnano.2017.45] [Citation(s) in RCA: 482] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 02/23/2017] [Indexed: 05/22/2023]
Abstract
Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM imaging in biology, various technological developments would be required to address certain limitations of the method. This has led to the creation of a range of new imaging modes, which continue to push the capabilities of the technique today. Here, we review the basic principles, advantages and limitations of the most common AFM bioimaging modes, including the popular contact and dynamic modes, as well as recently developed modes such as multiparametric, molecular recognition, multifrequency and high-speed imaging. For each of these modes, we discuss recent experiments that highlight their unique capabilities.
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Affiliation(s)
- Yves F Dufrêne
- Institute of Life Sciences and Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Université catholique de Louvain, Croix du Sud 4-5, bte L7.07.06., B-1348 Louvain-la-Neuve, Belgium
| | - Toshio Ando
- Department of Physics, Kanazawa University, Kanazawa 920-1192, Japan
| | - Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid, CSIC, Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
| | - David Alsteens
- Institute of Life Sciences and Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Université catholique de Louvain, Croix du Sud 4-5, bte L7.07.06., B-1348 Louvain-la-Neuve, Belgium
| | - David Martinez-Martin
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 28, 4056 Basel, Switzerland
| | - Andreas Engel
- Department of BioNanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Christoph Gerber
- Swiss Nanoscience Institute, University of Basel, Klingelbergstrasse 80, 4057 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 28, 4056 Basel, Switzerland
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20
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Rodriguez-Ramos J, Perrino AP, Garcia R. Dependence of the volume of an antibody on the force applied in a force microscopy experiment in liquid. Ultramicroscopy 2016; 171:153-157. [PMID: 27686276 DOI: 10.1016/j.ultramic.2016.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/16/2016] [Indexed: 11/26/2022]
Abstract
The volume of a protein can be estimated from its molecular weight. This approach has also been applied in force microscopy experiments. Two factors contribute to the determination of the volume from a force microscope image, the applied force and the tip radius. Those factors act in opposite directions. Here, we demonstrate that in the optimum conditions to image a protein, the apparent volume deduced from an AFM image overestimates the real protein volume. The lateral broadening due to the tip finite size, makes the simulated volume to exceed the real protein volume value, while the force applied by the tip tends to decrease the measured volume. The measured volume could coincide with the real volume for either a point-size tip at zero force or when the compression exerted by the tip compensates its dilation effects. The interplay between the above factors make unsuitable to apply the molecular weight method to determine the volume of a protein from AFM data.
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Affiliation(s)
- Jorge Rodriguez-Ramos
- Centro de Estudios Avanzados de Cuba, Carretera de San Antonio de los Baños, km 1 1/2, Valle Grande, La Habana, Cuba.
| | - Alma P Perrino
- Instituto de Ciencia de Materiales de Madrid, Sor Juana Inés de la Cruz 3, Cantoblanco, 28049 Madrid, Spain
| | - Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid, Sor Juana Inés de la Cruz 3, Cantoblanco, 28049 Madrid, Spain
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21
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Amo C, Garcia R. Fundamental High-Speed Limits in Single-Molecule, Single-Cell, and Nanoscale Force Spectroscopies. ACS NANO 2016; 10:7117-7124. [PMID: 27359243 PMCID: PMC5042359 DOI: 10.1021/acsnano.6b03262] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 06/30/2016] [Indexed: 05/30/2023]
Abstract
Force spectroscopy is enhancing our understanding of single-biomolecule, single-cell, and nanoscale mechanics. Force spectroscopy postulates the proportionality between the interaction force and the instantaneous probe deflection. By studying the probe dynamics, we demonstrate that the total force acting on the probe has three different components: the interaction, the hydrodynamic, and the inertial. The amplitudes of those components depend on the ratio between the resonant frequency and the frequency at which the data are measured. A force-distance curve provides a faithful measurement of the interaction force between two molecules when the inertial and hydrodynamic components are negligible. Otherwise, force spectroscopy measurements will underestimate the value of unbinding forces. Neglecting the above force components requires the use of frequency ratios in the 50-500 range. These ratios will limit the use of high-speed methods in force spectroscopy. The theory is supported by numerical simulations.
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22
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Perrino AP, Garcia R. How soft is a single protein? The stress-strain curve of antibody pentamers with 5 pN and 50 pm resolutions. NANOSCALE 2016; 8:9151-8. [PMID: 26732032 DOI: 10.1039/c5nr07957h] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Understanding the mechanical functionalities of complex biological systems requires the measurement of the mechanical compliance of their smallest components. Here, we develop a force microscopy method to quantify the softness of a single antibody pentamer by measuring the stress-strain curve with force and deformation resolutions, respectively, of 5 pN and 50 pm. The curve shows three distinctive regions. For ultrasmall compressive forces (5-75 pN), the protein's central region shows that the strain and stress are proportional (elastic regime). This region has an average Young's modulus of 2.5 MPa. For forces between 80 and 220 pN, the stress is roughly proportional to the strain with a Young's modulus of 9 MPa. Higher forces lead to irreversible deformations (plastic regime). Full elastic recovery could reach deformations amounting to 40% of the protein height. The existence of two different elastic regions is explained in terms of the structure of the antibody central region. The stress-strain curve explains the capability of the antibody to sustain multiple collisions without any loss of biological functionality.
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Affiliation(s)
- Alma P Perrino
- Instituto de Ciencia de Materiales de Madrid (CSIC), c/ Sor Juana Ines de la Cruz 3, 28049 Madrid, Spain.
| | - Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid (CSIC), c/ Sor Juana Ines de la Cruz 3, 28049 Madrid, Spain.
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23
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Dumitru AC, Herruzo ET, Rausell E, Ceña V, Garcia R. Unbinding forces and energies between a siRNA molecule and a dendrimer measured by force spectroscopy. NANOSCALE 2015; 7:20267-20276. [PMID: 26580848 DOI: 10.1039/c5nr04906g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We have measured the intermolecular forces between small interference RNA (siRNA) and polyamidoamine dendrimers at the single molecular level. A single molecule force spectroscopy approach has been developed to measure the unbinding forces and energies between a siRNA molecule and polyamidoamine dendrimers deposited on a mica surface in a buffer solution. We report three types of unbinding events which are characterized by forces and free unbinding energies, respectively, of 28 pN, 0.709 eV; 38 pN, 0.722 eV; and 50 pN, 0.724 eV. These events reflect different possible electrostatic interactions between the positive charges of one or two dendrimers and the negatively charged phosphate groups of a single siRNA. We have evidence of a high binding affinity of siRNA towards polyamidoamine dendrimers that leads to a 45% probability of measuring specific unbinding events.
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Affiliation(s)
- Andra C Dumitru
- Instituto de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Ines de la Cruz 3, 28049 Madrid, Spain.
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24
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Shih HJ, Shih PJ. Tip Effect of the Tapping Mode of Atomic Force Microscope in Viscous Fluid Environments. SENSORS 2015; 15:18381-401. [PMID: 26225979 PMCID: PMC4570326 DOI: 10.3390/s150818381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 07/02/2015] [Accepted: 07/14/2015] [Indexed: 11/16/2022]
Abstract
Atomic force microscope with applicable types of operation in a liquid environment is widely used to scan the contours of biological specimens. The contact mode of operation allows a tip to touch a specimen directly but sometimes it damages the specimen; thus, a tapping mode of operation may replace the contact mode. The tapping mode triggers the cantilever of the microscope approximately at resonance frequencies, and so the tip periodically knocks the specimen. It is well known that the cantilever induces extra liquid pressure that leads to drift in the resonance frequency. Studies have noted that the heights of protein surfaces measured via the tapping mode of an atomic force microscope are ~25% smaller than those measured by other methods. This discrepancy may be attributable to the induced superficial hydrodynamic pressure, which is worth investigating. In this paper, we introduce a semi-analytical method to analyze the pressure distribution of various tip geometries. According to our analysis, the maximum hydrodynamic pressure on the specimen caused by a cone-shaped tip is ~0.5 Pa, which can, for example, pre-deform a cell by several nanometers in compression before the tip taps it. Moreover, the pressure calculated on the surface of the specimen is 20 times larger than the pressure without considering the tip effect; these results have not been motioned in other papers. Dominating factors, such as surface heights of protein surface, mechanical stiffness of protein increasing with loading velocity, and radius of tip affecting the local pressure of specimen, are also addressed in this study.
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Affiliation(s)
- Hua-Ju Shih
- Department of Civil and Environmental Engineering, National University of Kaohsiung, No. 700, Kaohsiung University Rd., Nanzih District, 81148 Kaohsiung, Taiwan.
| | - Po-Jen Shih
- Department of Civil and Environmental Engineering, National University of Kaohsiung, No. 700, Kaohsiung University Rd., Nanzih District, 81148 Kaohsiung, Taiwan.
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25
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Babahosseini H, Carmichael B, Strobl JS, Mahmoodi SN, Agah M. Sub-cellular force microscopy in single normal and cancer cells. Biochem Biophys Res Commun 2015; 463:587-92. [PMID: 26036579 DOI: 10.1016/j.bbrc.2015.05.100] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 05/28/2015] [Indexed: 01/26/2023]
Abstract
This work investigates the biomechanical properties of sub-cellular structures of breast cells using atomic force microscopy (AFM). The cells are modeled as a triple-layered structure where the Generalized Maxwell model is applied to experimental data from AFM stress-relaxation tests to extract the elastic modulus, the apparent viscosity, and the relaxation time of sub-cellular structures. The triple-layered modeling results allow for determination and comparison of the biomechanical properties of the three major sub-cellular structures between normal and cancerous cells: the up plasma membrane/actin cortex, the mid cytoplasm/nucleus, and the low nuclear/integrin sub-domains. The results reveal that the sub-domains become stiffer and significantly more viscous with depth, regardless of cell type. In addition, there is a decreasing trend in the average elastic modulus and apparent viscosity of the all corresponding sub-cellular structures from normal to cancerous cells, which becomes most remarkable in the deeper sub-domain. The presented modeling in this work constitutes a unique AFM-based experimental framework to study the biomechanics of sub-cellular structures.
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Affiliation(s)
- H Babahosseini
- VT MEMS Laboratory, The Bradley Department of Electrical and Computer Engineering, Blacksburg, VA 24061, USA
| | - B Carmichael
- Nonlinear Intelligent Structures Laboratory, Department of Mechanical Engineering, University of Alabama, Tuscaloosa, AL 35487-0276, USA
| | - J S Strobl
- VT MEMS Laboratory, The Bradley Department of Electrical and Computer Engineering, Blacksburg, VA 24061, USA
| | - S N Mahmoodi
- Nonlinear Intelligent Structures Laboratory, Department of Mechanical Engineering, University of Alabama, Tuscaloosa, AL 35487-0276, USA.
| | - M Agah
- VT MEMS Laboratory, The Bradley Department of Electrical and Computer Engineering, Blacksburg, VA 24061, USA.
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26
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Casalini S, Dumitru AC, Leonardi F, Bortolotti CA, Herruzo ET, Campana A, de Oliveira RF, Cramer T, Garcia R, Biscarini F. Multiscale sensing of antibody-antigen interactions by organic transistors and single-molecule force spectroscopy. ACS NANO 2015; 9:5051-62. [PMID: 25868724 DOI: 10.1021/acsnano.5b00136] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Antibody-antigen (Ab-Ag) recognition is the primary event at the basis of many biosensing platforms. In label-free biosensors, these events occurring at solid-liquid interfaces are complex and often difficult to control technologically across the smallest length scales down to the molecular scale. Here a molecular-scale technique, such as single-molecule force spectroscopy, is performed across areas of a real electrode functionalized for the immunodetection of an inflammatory cytokine, viz. interleukin-4 (IL4). The statistical analysis of force-distance curves allows us to quantify the probability, the characteristic length scales, the adhesion energy, and the time scales of specific recognition. These results enable us to rationalize the response of an electrolyte-gated organic field-effect transistor (EGOFET) operated as an IL4 immunosensor. Two different strategies for the immobilization of IL4 antibodies on the Au gate electrode have been compared: antibodies are bound to (i) a smooth film of His-tagged protein G (PG)/Au; (ii) a 6-aminohexanethiol (HSC6NH2) self-assembled monolayer on Au through glutaraldehyde. The most sensitive EGOFET (concentration minimum detection level down to 5 nM of IL4) is obtained with the first functionalization strategy. This result is correlated to the highest probability (30%) of specific binding events detected by force spectroscopy on Ab/PG/Au electrodes, compared to 10% probability on electrodes with the second functionalization. Specifically, this demonstrates that Ab/PG/Au yields the largest areal density of oriented antibodies available for recognition. More in general, this work shows that specific recognition events in multiscale biosensors can be assessed, quantified, and optimized by means of a nanoscale technique.
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Affiliation(s)
- Stefano Casalini
- †Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Andra C Dumitru
- ‡Instituto de Ciencia de Materiales de Madrid (CSIC), 28049 Madrid, Spain
| | | | - Carlo A Bortolotti
- †Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Elena T Herruzo
- ‡Instituto de Ciencia de Materiales de Madrid (CSIC), 28049 Madrid, Spain
| | - Alessandra Campana
- ⊥"Alma Mater Studiorum", Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Rafael F de Oliveira
- †Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
- #Unesp, Postgraduate Program in Materials Science and Technology, São Paulo State University, 17033-360, Bauru, SP Brazil
| | - Tobias Cramer
- ∞"Alma Mater Studiorum", Dipartimento di Fisica e Astronomia, Università di Bologna, Viale Berti Pichat 6/2, 40127 Bologna, Italy
| | - Ricardo Garcia
- ‡Instituto de Ciencia de Materiales de Madrid (CSIC), 28049 Madrid, Spain
| | - Fabio Biscarini
- †Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
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27
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Li M, Liu L, Xi N, Wang Y. Research progress in quantifying the mechanical properties of single living cells using atomic force microscopy. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11434-014-0581-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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28
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Pfreundschuh M, Alsteens D, Hilbert M, Steinmetz MO, Müller DJ. Localizing chemical groups while imaging single native proteins by high-resolution atomic force microscopy. NANO LETTERS 2014; 14:2957-2964. [PMID: 24766578 DOI: 10.1021/nl5012905] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Simultaneous high-resolution imaging and localization of chemical interaction sites on single native proteins is a pertinent biophysical, biochemical, and nanotechnological challenge. Such structural mapping and characterization of binding sites is of importance in understanding how proteins interact with their environment and in manipulating such interactions in a plethora of biotechnological applications. Thus far, this challenge remains to be tackled. Here, we introduce force-distance curve-based atomic force microscopy (FD-based AFM) for the high-resolution imaging of SAS-6, a protein that self-assembles into cartwheel-like structures. Using functionalized AFM tips bearing Ni(2+)-N-nitrilotriacetate groups, we locate specific interaction sites on SAS-6 at nanometer resolution and quantify the binding strength of the Ni(2+)-NTA groups to histidine residues. The FD-based AFM approach can readily be applied to image any other native protein and to locate and structurally map histidine residues. Moreover, the surface chemistry used to functionalize the AFM tip can be modified to map other chemical interaction sites.
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Affiliation(s)
- Moritz Pfreundschuh
- Department of Biosystems Science and Engineering, ETH Zurich , Mattenstrasse 26, 4058 Basel, Switzerland
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29
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Pfreundschuh M, Martinez-Martin D, Mulvihill E, Wegmann S, Muller DJ. Multiparametric high-resolution imaging of native proteins by force-distance curve–based AFM. Nat Protoc 2014; 9:1113-30. [DOI: 10.1038/nprot.2014.070] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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30
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Suárez-Germà C, Domènech Ò, Montero MT, Hernández-Borrell J. Effect of lactose permease presence on the structure and nanomechanics of two-component supported lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:842-52. [DOI: 10.1016/j.bbamem.2013.11.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 11/20/2013] [Accepted: 11/22/2013] [Indexed: 01/24/2023]
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31
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Herruzo ET, Perrino AP, Garcia R. Fast nanomechanical spectroscopy of soft matter. Nat Commun 2014; 5:3126. [DOI: 10.1038/ncomms4126] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 12/16/2013] [Indexed: 12/23/2022] Open
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32
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Cohen SR, Kalfon-Cohen E. Dynamic nanoindentation by instrumented nanoindentation and force microscopy: a comparative review. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2013; 4:815-33. [PMID: 24367751 PMCID: PMC3869246 DOI: 10.3762/bjnano.4.93] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 10/25/2013] [Indexed: 05/21/2023]
Abstract
Viscoelasticity is a complex yet important phenomenon that drives material response at different scales of time and space. Burgeoning interest in nanoscale dynamic material mechanics has driven, and been driven by two key techniques: instrumented nanoindentation and atomic force microscopy. This review provides an overview of fundamental principles in nanoindentation, and compares and contrasts these two techniques as they are used for characterization of viscoelastic processes at the nanoscale.
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Affiliation(s)
- Sidney R Cohen
- Department of Chemical Research Support, Weizmann Institute of Science, POB 26, Rehovot, ISRAEL 76100
| | - Estelle Kalfon-Cohen
- Department of Chemical Research Support, Weizmann Institute of Science, POB 26, Rehovot, ISRAEL 76100
- School of Engineering and Applied Science, Harvard University, Cambridge, MA 02138, USA
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Pfreundschuh M, Hensen U, Müller DJ. Quantitative imaging of the electrostatic field and potential generated by a transmembrane protein pore at subnanometer resolution. NANO LETTERS 2013; 13:5585-5593. [PMID: 24079830 DOI: 10.1021/nl403232z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Elucidating the mechanisms by which proteins translocate small molecules and ions through transmembrane pores and channels is of great interest in biology, medicine, and nanotechnology. However, the characterization of pore forming proteins in their native state lacks suitable methods that are capable of high-resolution imaging (~1 nm) while simultaneously mapping physical and chemical properties. Here we report how force-distance (FD) curve-based atomic force microscopy (AFM) imaging can be applied to image the native pore forming outer membrane protein F (OmpF) at subnanometer resolution and to quantify the electrostatic field and potential generated by the transmembrane pore. We further observe the electrostatic field and potential of the OmpF pore switching "on" and "off" in dependence of the electrolyte concentration. Because electrostatic field and potential select for charged molecules and ions and guide them to the transmembrane pore the insights are of fundamental importance to understand the pore function. These experimental results establish FD-based AFM as a unique tool to image biological systems to subnanometer resolution and to quantify their electrostatic properties.
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Affiliation(s)
- Moritz Pfreundschuh
- Department of Biosystems Science and Engineering, ETH Zurich , CH-4058 Basel, Switzerland
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Dufrêne YF, Martínez-Martín D, Medalsy I, Alsteens D, Müller DJ. Multiparametric imaging of biological systems by force-distance curve–based AFM. Nat Methods 2013; 10:847-54. [DOI: 10.1038/nmeth.2602] [Citation(s) in RCA: 326] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 07/14/2013] [Indexed: 12/23/2022]
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Li M, Liu L, Xi N, Wang Y, Xiao X, Zhang W. Imaging and measuring the biophysical properties of Fc gamma receptors on single macrophages using atomic force microscopy. Biochem Biophys Res Commun 2013; 438:709-14. [PMID: 23916706 DOI: 10.1016/j.bbrc.2013.07.114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 07/28/2013] [Indexed: 12/22/2022]
Abstract
Fc gamma receptors (FcγR), widely expressed on effector cells (e.g., NK cells, macrophages), play an important role in clinical cancer immunotherapy. The binding of FcγRs to the Fc portions of antibodies that are attached to the target cells can activate the antibody-dependent cell-mediated cytotoxicity (ADCC) killing mechanism which leads to the lysis of target cells. In this work, we used atomic force microscopy (AFM) to observe the cellular ultra-structures and measure the biophysical properties (affinity and distribution) of FcγRs on single macrophages in aqueous environments. AFM imaging was used to obtain the topographies of macrophages, revealing the nanoscale cellular fine structures. For molecular interaction recognition, antibody molecules were attached onto AFM tips via a heterobifunctional polyethylene glycol (PEG) crosslinker. With AFM single-molecule force spectroscopy, the binding affinities of FcγRs were quantitatively measured on single macrophages. Adhesion force mapping method was used to localize the FcγRs, revealing the nanoscale distribution of FcγRs on local areas of macrophages. The experimental results can improve our understanding of FcγRs on macrophages; the established approach will facilitate further research on physiological activities involved in antibody-based immunotherapy.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
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