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Zhong BL, Lee CE, Vachharajani VT, Bauer MS, Südhof TC, Dunn AR. Piconewton Forces Mediate GAIN Domain Dissociation of the Latrophilin-3 Adhesion GPCR. NANO LETTERS 2023; 23:9187-9194. [PMID: 37831891 DOI: 10.1021/acs.nanolett.3c03171] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Latrophilins are adhesion G-protein coupled receptors (aGPCRs) that control excitatory synapse formation. Most aGPCRs, including latrophilins, are autoproteolytically cleaved at their GPCR-autoproteolysis inducing (GAIN) domain, but the two resulting fragments remain noncovalently associated on the cell surface. Force-mediated dissociation of the fragments is thought to activate G-protein signaling, but how this mechanosensitivity arises is poorly understood. Here, we use magnetic tweezer assays to show that physiologically relevant forces in the 1-10 pN range lead to dissociation of the latrophilin-3 GAIN domain on the seconds-to-minutes time scale, compared to days in the absence of force. In addition, we find that the GAIN domain undergoes large changes in length in response to increasing mechanical load. These data are consistent with a model in which a force-sensitive equilibrium between compact and extended GAIN domain states precedes dissociation, suggesting a mechanism by which latrophilins and other aGPCRs may mediate mechanically induced signal transduction.
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Affiliation(s)
- Brian L Zhong
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Christina E Lee
- Graduate Program in Biophysics, Stanford University, Stanford, California 94305, United States
| | - Vipul T Vachharajani
- Graduate Program in Biophysics, Stanford University, Stanford, California 94305, United States
| | - Magnus S Bauer
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
| | - Alexander R Dunn
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
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2
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Chu J, Romero A, Taulbee J, Aran K. Development of Single Molecule Techniques for Sensing and Manipulation of CRISPR and Polymerase Enzymes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300328. [PMID: 37226388 PMCID: PMC10524706 DOI: 10.1002/smll.202300328] [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: 01/11/2023] [Revised: 03/20/2023] [Indexed: 05/26/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and polymerases are powerful enzymes and their diverse applications in genomics, proteomics, and transcriptomics have revolutionized the biotechnology industry today. CRISPR has been widely adopted for genomic editing applications and Polymerases can efficiently amplify genomic transcripts via polymerase chain reaction (PCR). Further investigations into these enzymes can reveal specific details about their mechanisms that greatly expand their use. Single-molecule techniques are an effective way to probe enzymatic mechanisms because they may resolve intermediary conformations and states with greater detail than ensemble or bulk biosensing techniques. This review discusses various techniques for sensing and manipulation of single biomolecules that can help facilitate and expedite these discoveries. Each platform is categorized as optical, mechanical, or electronic. The methods, operating principles, outputs, and utility of each technique are briefly introduced, followed by a discussion of their applications to monitor and control CRISPR and Polymerases at the single molecule level, and closing with a brief overview of their limitations and future prospects.
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Affiliation(s)
- Josephine Chu
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Andres Romero
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Jeffrey Taulbee
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Kiana Aran
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
- Cardea, San Diego, CA, 92121, USA
- University of California Berkeley, Berkeley, CA, 94720, USA
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3
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Guo Y, Ao Y, Ye C, Xia R, Mi J, Shan Z, Shi M, Xie L, Chen Z. Nanotopographic micro-nano forces finely tune the conformation of macrophage mechanosensitive membrane protein integrin β 2 to manipulate inflammatory responses. NANO RESEARCH 2023; 16:1-15. [PMID: 37359074 PMCID: PMC9986042 DOI: 10.1007/s12274-023-5550-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 06/28/2023]
Abstract
Finely tuning mechanosensitive membrane proteins holds great potential in precisely controlling inflammatory responses. In addition to macroscopic force, mechanosensitive membrane proteins are reported to be sensitive to micro-nano forces. Integrin β2, for example, might undergo a piconewton scale stretching force in the activation state. High-aspect-ratio nanotopographic structures were found to generate nN-scale biomechanical force. Together with the advantages of uniform and precisely tunable structural parameters, it is fascinating to develop low-aspect-ratio nanotopographic structures to generate micro-nano forces for finely modulating their conformations and the subsequent mechanoimmiune responses. In this study, low-aspect-ratio nanotopographic structures were developed to finely manipulate the conformation of integrin β2. The direct interaction of forces and the model molecule integrin αXβ2 was first performed. It was demonstrated that pressing force could successfully induce conformational compression and deactivation of integrin αXβ2, and approximately 270 to 720 pN may be required to inhibit its conformational extension and activation. Three low-aspect-ratio nanotopographic surfaces (nanohemispheres, nanorods, and nanoholes) with various structural parameters were specially designed to generate the micro-nano forces. It was found that the nanorods and nanohemispheres surfaces induce greater contact pressure at the contact interface between macrophages and nanotopographic structures, particularly after cell adhesion. These higher contact pressures successfully inhibited the conformational extension and activation of integrin β2, suppressing focal adhesion activity and the downstream PI3K-Akt signaling pathway, reducing NF-κB signaling and macrophage inflammatory responses. Our findings suggest that nanotopographic structures can be used to finely tune mechanosensitive membrane protein conformation changes, providing an effective strategy for precisely modulating inflammatory responses. Electronic Supplementary Material Supplementary material (primer sequences of target genes in RT-qPCR assay; the results of solvent accessible surface area during equilibrium simulation, the ligplut results of hydrogen bonds, and hydrophobic interactions; the density of different nanotopographic structures; interaction analysis of the downregulated leading genes of "focal adhesion" signaling pathway in nanohemispheres and nanorods groups; and the GSEA results of "Rap 1 signaling pathway" and "regulation of actin cytoskeleton" in different groups) is available in the online version of this article at 10.1007/s12274-023-5550-0.
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Affiliation(s)
- Yuanlong Guo
- Hospital of Stomatology, Sun Yat-sen University and Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, 510055 China
| | - Yong Ao
- Hospital of Stomatology, Sun Yat-sen University and Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, 510055 China
| | - Chen Ye
- Hospital of Stomatology, Sun Yat-sen University and Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, 510055 China
| | - Ruidi Xia
- Hospital of Stomatology, Sun Yat-sen University and Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, 510055 China
| | - Jiaomei Mi
- Hospital of Stomatology, Sun Yat-sen University and Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, 510055 China
| | - Zhengjie Shan
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
| | - Mengru Shi
- Hospital of Stomatology, Sun Yat-sen University and Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, 510055 China
| | - Lv Xie
- Hospital of Stomatology, Sun Yat-sen University and Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, 510055 China
| | - Zetao Chen
- Hospital of Stomatology, Sun Yat-sen University and Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, 510055 China
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4
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Monroe L, Kihara D. Using steered molecular dynamic tension for assessing quality of computational protein structure models. J Comput Chem 2022; 43:1140-1150. [PMID: 35475517 DOI: 10.1002/jcc.26876] [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: 10/21/2021] [Revised: 02/16/2022] [Accepted: 04/15/2022] [Indexed: 11/12/2022]
Abstract
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their biological function can be properly carried out. Experimentally, the stability of a protein can be measured by several means, among which the pulling experiment using the atomic force microscope (AFM) stands as a unique method. AFM directly measures the resistance from unfolding, which can be quantified from the observed force-extension profile. It has been shown that key features observed in an AFM pulling experiment can be well reproduced by computational molecular dynamics simulations. Here, we applied computational pulling for estimating the accuracy of computational protein structure models under the hypothesis that the structural stability would positively correlated with the accuracy, i.e. the closeness to the native, of a model. We used in total 4929 structure models for 24 target proteins from the Critical Assessment of Techniques of Structure Prediction (CASP) and investigated if the magnitude of the break force, that is, the force required to rearrange the model's structure, from the force profile was sufficient information for selecting near-native models. We found that near-native models can be successfully selected by examining their break forces suggesting that high break force indeed indicates high stability of models. On the other hand, there were also near-native models that had relatively low peak forces. The mechanisms of the stability exhibited by the break forces were explored and discussed.
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Affiliation(s)
- Lyman Monroe
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Department of Computer Science, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
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5
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Guzowski J, Buda RJ, Costantini M, Ćwiklińska M, Garstecki P, Stone HA. From dynamic self-organization to avalanching instabilities in soft-granular threads. SOFT MATTER 2022; 18:1801-1818. [PMID: 35166293 PMCID: PMC8889560 DOI: 10.1039/d1sm01350e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
We study the dynamics of threads of monodisperse droplets, including droplet chains and multi-chains, in which the droplets are interconnected by capillary bridges of another immiscible liquid phase. This system represents wet soft-granular matter - a class of granular materials in which the grains are soft and wetted by thin fluid films-with other examples including wet granular hydrogels or foams. In contrast to wet granular matter with rigid grains (e.g., wet sand), studied previously, the deformability of the grains raises the number of available metastable states and facilitates rearrangements which allow for reorganization and self-assembly of the system under external drive, e.g., applied via viscous forces. We use a co-flow configuration to generate a variety of unique low-dimensional regular granular patterns, intermediate between 1D and 2D, ranging from linear chains and chains with periodically occurring folds to multi-chains and segmented structures including chains of finite length. In particular, we observe that the partially folded chains self-organize via limit cycle of displacements and rearrangements occurring at a frequency self-adapted to the rate of build-up of compressive strain in the chain induced by the viscous forces. Upon weakening of the capillary arrest of the droplets, we observe spontaneous fluidization of the quasi-solid structures and avalanches of rearrangements. We identify two types of fluidization-induced instabilities and rationalize them in terms of a competition between advection and propagation. While we use aqueous droplets as the grains we demonstrate that the reported mechanisms of adaptive self-assembly apply to other types of soft granular systems including foams and microgels. We discuss possible application of the reported quasi-1D compartmentalized structures in tissue engineering, bioprinting and materials science.
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Affiliation(s)
- J Guzowski
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - R J Buda
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - M Costantini
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - M Ćwiklińska
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - P Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - H A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, 08544 NJ, USA
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6
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Laskowski PR, Pluhackova K, Haase M, Lang BM, Nagler G, Kuhn A, Müller DJ. Monitoring the binding and insertion of a single transmembrane protein by an insertase. Nat Commun 2021; 12:7082. [PMID: 34873152 PMCID: PMC8648943 DOI: 10.1038/s41467-021-27315-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 11/11/2021] [Indexed: 11/27/2022] Open
Abstract
Cells employ highly conserved families of insertases and translocases to insert and fold proteins into membranes. How insertases insert and fold membrane proteins is not fully known. To investigate how the bacterial insertase YidC facilitates this process, we here combine single-molecule force spectroscopy and fluorescence spectroscopy approaches, and molecular dynamics simulations. We observe that within 2 ms, the cytoplasmic α-helical hairpin of YidC binds the polypeptide of the membrane protein Pf3 at high conformational variability and kinetic stability. Within 52 ms, YidC strengthens its binding to the substrate and uses the cytoplasmic α-helical hairpin domain and hydrophilic groove to transfer Pf3 to the membrane-inserted, folded state. In this inserted state, Pf3 exposes low conformational variability such as typical for transmembrane α-helical proteins. The presence of YidC homologues in all domains of life gives our mechanistic insight into insertase-mediated membrane protein binding and insertion general relevance for membrane protein biogenesis.
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Affiliation(s)
- Pawel R. Laskowski
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Kristyna Pluhackova
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Maximilian Haase
- grid.9464.f0000 0001 2290 1502Molecular Microbiology, Biology Institute, Universität Hohenheim, 70599 Stuttgart, Germany
| | - Brian M. Lang
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Gisela Nagler
- grid.9464.f0000 0001 2290 1502Molecular Microbiology, Biology Institute, Universität Hohenheim, 70599 Stuttgart, Germany
| | - Andreas Kuhn
- grid.9464.f0000 0001 2290 1502Molecular Microbiology, Biology Institute, Universität Hohenheim, 70599 Stuttgart, Germany
| | - Daniel J. Müller
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
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7
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Sinelnikova A, Mandl T, Östlin C, Grånäs O, Brodmerkel MN, Marklund EG, Caleman C. Reproducibility in the unfolding process of protein induced by an external electric field. Chem Sci 2020; 12:2030-2038. [PMID: 34163965 PMCID: PMC8179335 DOI: 10.1039/d0sc06008a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The dynamics of proteins are crucial for their function. However, commonly used techniques for studying protein structures are limited in monitoring time-resolved dynamics at high resolution. Combining electric fields with existing techniques to study gas-phase proteins, such as single particle imaging using free-electron lasers and gas-phase small angle X-ray scattering, has the potential to open up a new era in time-resolved studies of gas-phase protein dynamics. Using molecular dynamics simulations, we identify well-defined unfolding pathways of a protein, induced by experimentally achievable external electric fields. Our simulations show that strong electric fields in conjunction with short-pulsed X-ray sources such as free-electron lasers can be a new path for imaging dynamics of gas-phase proteins at high spatial and temporal resolution.
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Affiliation(s)
- Anna Sinelnikova
- Department of Physics and Astronomy, Uppsala University Box 516 SE-751 20 Uppsala Sweden
| | - Thomas Mandl
- Department of Physics and Astronomy, Uppsala University Box 516 SE-751 20 Uppsala Sweden .,University of Applied Sciences Technikum Wien Höchstädtplatz 6 A-1200 Wien Austria
| | - Christofer Östlin
- Department of Physics and Astronomy, Uppsala University Box 516 SE-751 20 Uppsala Sweden
| | - Oscar Grånäs
- Department of Physics and Astronomy, Uppsala University Box 516 SE-751 20 Uppsala Sweden
| | - Maxim N Brodmerkel
- Department of Chemistry - BMC, Uppsala University Box 576 SE-751 23 Uppsala Sweden
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University Box 576 SE-751 23 Uppsala Sweden
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University Box 516 SE-751 20 Uppsala Sweden .,Center for Free-Electron Laser Science, DESY Notkestrasse 85 DE-22607 Hamburg Germany
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8
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A Region of UNC-89 (Obscurin) Lying between Two Protein Kinase Domains Is a Highly Elastic Spring Required for Proper Sarcomere Organization. J Mol Biol 2020; 432:4799-4814. [PMID: 32645312 DOI: 10.1016/j.jmb.2020.06.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/07/2020] [Accepted: 06/25/2020] [Indexed: 12/17/2022]
Abstract
In Caenorhabditis elegans, unc-89 encodes a set of giant multi-domain proteins (up 8081 residues) localized to the M-lines of muscle sarcomeres and required for normal sarcomere organization and whole-animal locomotion. Multiple UNC-89 isoforms contain two protein kinase domains. There is conservation in arrangement of domains between UNC-89 and its two mammalian homologs, obscurin and SPEG: kinase, a non-domain region of 647-742 residues, Ig domain, Fn3 domain and a second kinase domain. In all three proteins, this non-domain "interkinase region" has low sequence complexity, has high proline content, and lacks predicted secondary structure. We report that a major portion of this interkinase (571 residues out of 647 residues) when examined by single molecule force spectroscopy in vitro displays the properties of a random coil and acts as an entropic spring. We used CRISPR/Cas9 to create nematodes carrying an in-frame deletion of the same 571-residue portion of the interkinase. These animals display severe disorganization of all portions of the sarcomere in body wall muscle. Super-resolution microscopy reveals extra, short-A-bands lying close to the outer muscle cell membrane and between normally spaced A-bands. Nematodes with this in-frame deletion show defective locomotion and muscle force generation. We designed our CRISPR-generatedin-frame deletion to contain an HA tag at the N terminus of the large UNC-89 isoforms. This HA tag results in normal organization of body wall muscle, but approximately half the normal levels of the giant UNC-89 isoforms, dis-organization of pharyngeal muscle, small body size, and reduced muscle force, likely due to poor nutritional uptake.
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9
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Li M, Xi N, Wang Y, Liu L. Atomic Force Microscopy as a Powerful Multifunctional Tool for Probing the Behaviors of Single Proteins. IEEE Trans Nanobioscience 2020; 19:78-99. [DOI: 10.1109/tnb.2019.2954099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Liang X, Nakajima K. Investigating the Dynamic Viscoelasticity of Single Polymer Chains using Atomic Force Microscopy. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/polb.24908] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Xiaobin Liang
- Department of Chemical Science and EngineeringSchool of Materials and Chemical Technology, Tokyo Institute of Technology, Ookayama 2‐12‐1, Meguro‐ku Tokyo 152‐8552 Japan
| | - Ken Nakajima
- Department of Chemical Science and EngineeringSchool of Materials and Chemical Technology, Tokyo Institute of Technology, Ookayama 2‐12‐1, Meguro‐ku Tokyo 152‐8552 Japan
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11
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Xu W, Zhang W, Guang C, Zhang T, Mu W. A close look on the effect of polyethylene glycol on the levansucrase thermostability: a case study of Brenneria sp. levansucrase. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:6315-6323. [PMID: 31260112 DOI: 10.1002/jsfa.9908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/26/2019] [Accepted: 06/27/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND To increase the low residual activity of levansucrase during long-time processing, an enhancement of its weak thermostability is needed. Here, the effect of metal ions and polyethylene glycol (PEG) on the thermostability of levansucrase from Brenneria sp. EniD312 were studied and evaluated. The residual activity was determined and the protein structure was evaluated by circular dichroism spectrum, fluorescence intensity (FI), and surface hydrophobicity (S0 ). RESULTS As a result of incubation with 10% (w/v) PEG 4000, the enzyme activity was increased by 1.24-fold. After incubation with 5% PEG 4000 for 6 h, the residual activity at 35 and 45 °C was decreased to 55% and 60% of the initial activity, with an increase of 1.2- and 3.3-fold than the wild-type enzyme. Furthermore, the random coil content of enzyme was decreased from 53% of the wild-type enzyme to 33.9% of the PEG pre-incubated enzyme. Additionally, the FI was maximally increased and the S0 was decreased from 117 to 69. CONCLUSION All of these results suggested that after incubation with PEG 4000, the secondary and tertiary structure of wild-type enzyme could be greatly maintained and then its thermostability could be increased. This study was the first report on the enhancement of levansucrase thermostability by PEG incubation and might be a good guideline to other researches on levansucrase. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Wei Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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12
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J B, M M B, Chanda K. Evolutionary approaches in protein engineering towards biomaterial construction. RSC Adv 2019; 9:34720-34734. [PMID: 35530663 PMCID: PMC9074691 DOI: 10.1039/c9ra06807d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/01/2019] [Indexed: 11/29/2022] Open
Abstract
The tailoring of proteins for specific applications by evolutionary methods is a highly active area of research. Rational design and directed evolution are the two main strategies to reengineer proteins or create chimeric structures. Rational engineering is often limited by insufficient knowledge about proteins' structure-function relationships; directed evolution overcomes this restriction but poses challenges in the screening of candidates. A combination of these protein engineering approaches will allow us to create protein variants with a wide range of desired properties. Herein, we focus on the application of these approaches towards the generation of protein biomaterials that are known for biodegradability, biocompatibility and biofunctionality, from combinations of natural, synthetic, or engineered proteins and protein domains. Potential applications depend on the enhancement of biofunctional, mechanical, or other desired properties. Examples include scaffolds for tissue engineering, thermostable enzymes for industrial biocatalysis, and other therapeutic applications.
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Affiliation(s)
- Brindha J
- Department of Chemistry, School of Advanced Science, Vellore Institute of Technology, Chennai Campus Vandalur-Kelambakkam Road Chennai-600 127 Tamil Nadu India
| | - Balamurali M M
- Department of Chemistry, School of Advanced Science, Vellore Institute of Technology, Chennai Campus Vandalur-Kelambakkam Road Chennai-600 127 Tamil Nadu India
| | - Kaushik Chanda
- Department of Chemistry, School of Advanced Science, Vellore Institute of Technology Vellore-632014 Tamil Nadu India
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13
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Mechanical unfolding of spectrin reveals a super-exponential dependence of unfolding rate on force. Sci Rep 2019; 9:11101. [PMID: 31366931 PMCID: PMC6668576 DOI: 10.1038/s41598-019-46525-w] [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: 09/11/2018] [Accepted: 06/18/2019] [Indexed: 11/12/2022] Open
Abstract
We investigated the mechanical unfolding of single spectrin molecules over a broad range of loading rates and thus unfolding forces by combining magnetic tweezers with atomic force microscopy. We find that the mean unfolding force increases logarithmically with loading rate at low loading rates, but the increase slows at loading rates above 1pN/s. This behavior indicates an unfolding rate that increases exponentially with the applied force at low forces, as expected on the basis of one-dimensional models of protein unfolding. At higher forces, however, the increase of the unfolding rate with the force becomes faster than exponential, which may indicate anti-Hammond behavior where the structures of the folded and transition states become more different as their free energies become more similar. Such behavior is rarely observed and can be explained by either a change in the unfolding pathway or as a reflection of a multidimensional energy landscape of proteins under force.
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14
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Harris MC, Cislo D, Lenz JS, Umbach C, Lindau M. AFM/TIRF force clamp measurements of neurosecretory vesicle tethers reveal characteristic unfolding steps. PLoS One 2017; 12:e0173993. [PMID: 28323853 PMCID: PMC5360256 DOI: 10.1371/journal.pone.0173993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/01/2017] [Indexed: 12/31/2022] Open
Abstract
Although several proteins have been implicated in secretory vesicle tethering, the identity and mechanical properties of the components forming the physical vesicle-plasma membrane link remain unknown. Here we present the first experimental measurements of nanomechanical properties of secretory vesicle-plasma membrane tethers using combined AFM force clamp and TIRF microscopy on membrane sheets from PC12 cells expressing the vesicle marker ANF-eGFP. Application of pulling forces generated tether extensions composed of multiple steps with variable length. The frequency of short (<10 nm) tether extension events was markedly higher when a fluorescent vesicle was present at the cantilever tip and increased in the presence of GTPγS, indicating that these events reflect specifically the properties of vesicle-plasma membrane tethers. The magnitude of the short tether extension events is consistent with extension lengths expected from progressive unfolding of individual helices of the exocyst complex, supporting its direct role in forming the physical vesicle-plasma membrane link.
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Affiliation(s)
- Mark C. Harris
- School of Applied and Engineering Physics, Engineering, Cornell University, Ithaca, NY, United States of America
| | - Dillon Cislo
- School of Applied and Engineering Physics, Engineering, Cornell University, Ithaca, NY, United States of America
| | - Joan S. Lenz
- School of Applied and Engineering Physics, Engineering, Cornell University, Ithaca, NY, United States of America
| | - Christopher Umbach
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, United States of America
| | - Manfred Lindau
- School of Applied and Engineering Physics, Engineering, Cornell University, Ithaca, NY, United States of America
- Laboratory for Nanoscale Cell Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
- * E-mail:
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Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy. SENSORS 2017; 17:s17010200. [PMID: 28117741 PMCID: PMC5298773 DOI: 10.3390/s17010200] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 01/12/2017] [Accepted: 01/16/2017] [Indexed: 12/23/2022]
Abstract
The advent of atomic force microscopy (AFM) has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface) was summarized. The challenges and future directions were also discussed.
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16
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Fonin AV, Uversky VN, Kuznetsova IM, Turoverov KK. Protein folding and stability in the presence of osmolytes. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916020056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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17
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Diao M, Nguyen TA, Taran E, Mahler SM, Nguyen AV. Effect of energy source, salt concentration and loading force on colloidal interactions between Acidithiobacillus ferrooxidans cells and mineral surfaces. Colloids Surf B Biointerfaces 2015; 132:271-80. [DOI: 10.1016/j.colsurfb.2015.05.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 05/11/2015] [Accepted: 05/14/2015] [Indexed: 11/28/2022]
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18
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Nanoscale monitoring of drug actions on cell membrane using atomic force microscopy. Acta Pharmacol Sin 2015; 36:769-82. [PMID: 26027658 DOI: 10.1038/aps.2015.28] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 03/13/2015] [Indexed: 02/06/2023] Open
Abstract
Knowledge of the nanoscale changes that take place in individual cells in response to a drug is useful for understanding the drug action. However, due to the lack of adequate techniques, such knowledge was scarce until the advent of atomic force microscopy (AFM), which is a multifunctional tool for investigating cellular behavior with nanometer resolution under near-physiological conditions. In the past decade, researchers have applied AFM to monitor the morphological and mechanical dynamics of individual cells following drug stimulation, yielding considerable novel insight into how the drug molecules affect an individual cell at the nanoscale. In this article we summarize the representative applications of AFM in characterization of drug actions on cell membrane, including topographic imaging, elasticity measurements, molecular interaction quantification, native membrane protein imaging and manipulation, etc. The challenges that are hampering the further development of AFM for studies of cellular activities are aslo discussed.
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Dickinson ER, Jurneczko E, Pacholarz KJ, Clarke DJ, Reeves M, Ball KL, Hupp T, Campopiano D, Nikolova PV, Barran PE. Insights into the conformations of three structurally diverse proteins: cytochrome c, p53, and MDM2, provided by variable-temperature ion mobility mass spectrometry. Anal Chem 2015; 87:3231-8. [PMID: 25629302 DOI: 10.1021/ac503720v] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Thermally induced conformational transitions of three proteins of increasing intrinsic disorder-cytochrome c, the tumor suppressor protein p53 DNA binding domain (p53 DBD), and the N-terminus of the oncoprotein murine double minute 2 (NT-MDM2)-have been studied by native mass spectrometry and variable-temperature drift time ion mobility mass spectrometry (VT-DT-IM-MS). Ion mobility measurements were carried out at temperatures ranging from 200 to 571 K. Multiple conformations are observable over several charge states for all three monomeric proteins, and for cytochrome c, dimers of significant intensity are also observed. Cytochrome c [M + 5H](5+) ions present in one conformer of CCS ∼1200 Å(2), undergoing compaction in line with the reported Tmelt = 360.15 K before slight unfolding at 571 K. The more extended [M + 7H](7+) cytochrome c monomer presents as two conformers undergoing similar compaction and structural rearrangements, prior to thermally induced unfolding. The [D + 11H](11+) dimer presents as two conformers, which undergo slight structural compaction or annealing before dissociation. p53 DBD follows a trend of structural collapse before an increase in the observed collision cross section (CCS), akin to that observed for cytochrome c but proceeding more smoothly. At 300 K, the monomeric charge states present in two conformational families, which compact to one conformer of CCS ∼1750 Å(2) at 365 K, in line with the low solution Tmelt = 315-317 K. The protein then extends to produce either a broad unresolved CCS distribution or, for z > 9, two conformers. NT-MDM2 exhibits a greater number of structural rearrangements, displaying charge-state-dependent unfolding pathways. DT-IM-MS experiments at 200 K resolve multiple conformers. Low charge state species of NT-MDM2 present as a single compact conformational family centered on CCS ∼1250 Å(2) at 300 K. This undergoes conformational tightening in line with the solution Tmelt = 348 K before unfolding at the highest temperatures. The more extended charge states present in two or more conformers at room temperature, undergoing thermally induced unfolding before significant structural collapse or annealing at high temperatures. Variable-temperature IM-MS is here shown to be an exciting approach to discern protein unfolding pathways for conformationally diverse proteins.
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Affiliation(s)
- Eleanor R Dickinson
- †Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Ewa Jurneczko
- ‡School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Kamila J Pacholarz
- †Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
| | - David J Clarke
- ‡School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Matthew Reeves
- ‡School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Kathryn L Ball
- §Institute of Genetics and Molecular Medicine, CRUK Cancer Research Centre, University of Edinburgh, Edinburgh EH4 2XR, United Kingdom
| | - Ted Hupp
- §Institute of Genetics and Molecular Medicine, CRUK Cancer Research Centre, University of Edinburgh, Edinburgh EH4 2XR, United Kingdom
| | - Dominic Campopiano
- ‡School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Penka V Nikolova
- ∥School of Biomedical Science, Institute of Pharmaceutical Sciences, King's College London, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Perdita E Barran
- †Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
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Abstract
Recent progress in surface science, nanotechnology and biophysics has cast new light on the correlation between the physicochemical properties of biomaterials and the resulting biological response. One experimental tool that promises to generate an increasingly more sophisticated knowledge of how proteins, cells and bacteria interact with nanostructured surfaces is the atomic force microscope (AFM). This unique instrument permits to close in on interfacial events at the scale at which they occur, the nanoscale. This perspective covers recent developments in the exploitation of the AFM, and suggests insights on future opportunities that can arise from the exploitation of this powerful technique.
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Affiliation(s)
- Fabio Variola
- Faculty of Engineering, Department of Mechanical Engineering, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
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21
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Rodríguez-Zamora P, Yin F, Palmer RE. Enhanced immobilization of gold nanoclusters on graphite. J Phys Chem A 2014; 118:8182-7. [PMID: 24802164 DOI: 10.1021/jp500914x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The immobilization of individual biological molecules by metal nanoparticles requires that the particles themselves be immobilized. We introduce a new technique for immobilization of gold clusters based on their binding to small tunnels in a graphite support, themselves created by the implantation of small clusters. These tunnels are shown to perform as more effective cluster immobilization sites than point defects on the surface of graphite. The method is tested with atomic force microscopy (AFM) (both contact and noncontact mode) scanning. Size-selected clusters with 923, 561, 309, and 147 atoms have been immobilized and imaged with high-resolution, noncontact AFM.
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Affiliation(s)
- P Rodríguez-Zamora
- Nanoscale Physics Research Laboratory, School of Physics and Astronomy, University of Birmingham , Birmingham B15 2TT, United Kingdom
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22
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Wu L, Liu H, Zhao W, Wang L, Hou C, Liu Q, Lu Z. Electrically facilitated translocation of protein through solid nanopore. NANOSCALE RESEARCH LETTERS 2014; 9:140. [PMID: 24661490 PMCID: PMC3976542 DOI: 10.1186/1556-276x-9-140] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 03/14/2014] [Indexed: 06/01/2023]
Abstract
Nanopores have been proven as versatile single-molecule sensors for individual unlabeled biopolymer detection and characterization. In the present work, a relative large nanopore with a diameter of about 60 nm has been used to detect protein translocation driven by a series of applied voltages. Compared with previous studied small nanopores, a distinct profile of protein translocation through a larger nanopore has been characterized. First, a higher threshold voltage is required to drive proteins into the large nanopore. With the increase of voltages, the capture frequency of protein into the nanopore has been markedly enhanced. And the distribution of current blockage events is characterized as a function of biased voltages. Due to the large dimension of the nanopore, the adsorption and desorption phenomenon of proteins observed with a prolonged dwell time has been weakened in our work. Nevertheless, the protein can still be stretched into an unfolded state by increased electric forces at high voltages. In consideration of the high throughput of the large nanopore, a couple of proteins passing through the nanopore simultaneously occur at high voltage. As a new feature, the feasibility and specificity of a nanopore with distinct geometry have been demonstrated for sensing protein translocation, which broadly expand the application of nanopore devices.
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Affiliation(s)
- Lingzhi Wu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210046, China
| | - Hang Liu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Wenyuan Zhao
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Lei Wang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Chuanrong Hou
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
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Wang C, Yadavalli VK. Investigating biomolecular recognition at the cell surface using atomic force microscopy. Micron 2014; 60:5-17. [PMID: 24602267 DOI: 10.1016/j.micron.2014.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/07/2014] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
Probing the interaction forces that drive biomolecular recognition on cell surfaces is essential for understanding diverse biological processes. Force spectroscopy has been a widely used dynamic analytical technique, allowing measurement of such interactions at the molecular and cellular level. The capabilities of working under near physiological environments, combined with excellent force and lateral resolution make atomic force microscopy (AFM)-based force spectroscopy a powerful approach to measure biomolecular interaction forces not only on non-biological substrates, but also on soft, dynamic cell surfaces. Over the last few years, AFM-based force spectroscopy has provided biophysical insight into how biomolecules on cell surfaces interact with each other and induce relevant biological processes. In this review, we focus on describing the technique of force spectroscopy using the AFM, specifically in the context of probing cell surfaces. We summarize recent progress in understanding the recognition and interactions between macromolecules that may be found at cell surfaces from a force spectroscopy perspective. We further discuss the challenges and future prospects of the application of this versatile technique.
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Affiliation(s)
- Congzhou Wang
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Vamsi K Yadavalli
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA.
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