1
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Shang P, Dos Santos Natividade R, Taylor GM, Ray A, Welsh OL, Fiske KL, Sutherland DM, Alsteens D, Dermody TS. NRP1 is a receptor for mammalian orthoreovirus engaged by distinct capsid subunits. Cell Host Microbe 2024; 32:980-995.e9. [PMID: 38729153 PMCID: PMC11176008 DOI: 10.1016/j.chom.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/27/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024]
Abstract
Mammalian orthoreovirus (reovirus) is a nonenveloped virus that establishes primary infection in the intestine and disseminates to sites of secondary infection, including the CNS. Reovirus entry involves multiple engagement factors, but how the virus disseminates systemically and targets neurons remains unclear. In this study, we identified murine neuropilin 1 (mNRP1) as a receptor for reovirus. mNRP1 binds reovirus with nanomolar affinity using a unique mechanism of virus-receptor interaction, which is coordinated by multiple interactions between distinct reovirus capsid subunits and multiple NRP1 extracellular domains. By exchanging essential capsid protein-encoding gene segments, we determined that the multivalent interaction is mediated by outer-capsid protein σ3 and capsid turret protein λ2. Using capsid mutants incapable of binding NRP1, we found that NRP1 contributes to reovirus dissemination and neurovirulence in mice. Collectively, our results demonstrate that NRP1 is an entry receptor for reovirus and uncover mechanisms by which NRPs promote viral entry and pathogenesis.
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Affiliation(s)
- Pengcheng Shang
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Rita Dos Santos Natividade
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Gwen M Taylor
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Ankita Ray
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Olivia L Welsh
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Kay L Fiske
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Danica M Sutherland
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium; WELBIO department, WEL Research Institute, Wavre, Belgium
| | - Terence S Dermody
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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2
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Ray A, Minh Tran TT, Santos Natividade RD, Moreira RA, Simpson JD, Mohammed D, Koehler M, L Petitjean SJ, Zhang Q, Bureau F, Gillet L, Poma AB, Alsteens D. Single-Molecule Investigation of the Binding Interface Stability of SARS-CoV-2 Variants with ACE2. ACS NANOSCIENCE AU 2024; 4:136-145. [PMID: 38644967 PMCID: PMC11027127 DOI: 10.1021/acsnanoscienceau.3c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 04/23/2024]
Abstract
The SARS-CoV-2 pandemic spurred numerous research endeavors to comprehend the virus and mitigate its global severity. Understanding the binding interface between the virus and human receptors is pivotal to these efforts and paramount to curbing infection and transmission. Here we employ atomic force microscopy and steered molecular dynamics simulation to explore SARS-CoV-2 receptor binding domain (RBD) variants and angiotensin-converting enzyme 2 (ACE2), examining the impact of mutations at key residues upon binding affinity. Our results show that the Omicron and Delta variants possess strengthened binding affinity in comparison to the Mu variant. Further, using sera from individuals either vaccinated or with acquired immunity following Delta strain infection, we assess the impact of immunity upon variant RBD/ACE2 complex formation. Single-molecule force spectroscopy analysis suggests that vaccination before infection may provide stronger protection across variants. These results underscore the need to monitor antigenic changes in order to continue developing innovative and effective SARS-CoV-2 abrogation strategies.
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Affiliation(s)
- Ankita Ray
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Thu Thi Minh Tran
- Faculty
of Materials Science and Technology, University
of Science—VNU HCM, 227 Nguyen Van Cu Street, District 5, 700000 Ho Chi Minh City, Vietnam
- Vietnam
National University, 700000 Ho Chi Minh City, Vietnam
| | - Rita dos Santos Natividade
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Rodrigo A. Moreira
- Basque
Center for Applied Mathematics, Mazarredo 14, 48009 Bilbao, Spain
| | - Joshua D. Simpson
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Danahe Mohammed
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Melanie Koehler
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Simon J. L Petitjean
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Qingrong Zhang
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Fabrice Bureau
- Laboratory
of Cellular and Molecular Immunology, GIGA Institute, Liège University, 4000 Liège, Belgium
| | - Laurent Gillet
- Immunology-Vaccinology
Lab of the Faculty of Veterinary Medicine, Liège University, 4000 Liège, Belgium
| | - Adolfo B. Poma
- Institute
of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
| | - David Alsteens
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
- WELBIO
department, WEL Research Institute, 1300 Wavre, Belgium
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3
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Petitjean SJL, Eeckhout S, Delguste M, Zhang Q, Durlet K, Alsteens D. Heparin-Induced Allosteric Changes in SARS-CoV-2 Spike Protein Facilitate ACE2 Binding and Viral Entry. NANO LETTERS 2023; 23:11678-11684. [PMID: 38055954 DOI: 10.1021/acs.nanolett.3c03550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Understanding the entry of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) into host cells is crucial in the battle against COVID-19. Using atomic force microscopy (AFM), we probed the interaction between the virus's spike protein and heparan sulfate (HS) as a potential attachment factor. Our AFM studies revealed a moderate-affinity interaction between the spike protein and HS on both model surfaces and living cells, highlighting HS's role in early viral attachment. Remarkably, we observed an interplay between HS and the host cell receptor angiotensin-converting enzyme 2 (ACE2), with HS engagement resulting in enhanced ACE2 binding and subsequent viral entry. Our research furthers our understanding of SARS-CoV-2 infection mechanisms and reveals potential interventions targeting viral entry. These insights are valuable as we navigate the evolving landscape of viral threats and seek effective strategies to combat emerging infectious diseases.
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Affiliation(s)
- Simon J L Petitjean
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Savannah Eeckhout
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Martin Delguste
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Qingrong Zhang
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Kimberley Durlet
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Walloon Brabant 1300, Belgium
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4
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Hou D, Cao W, Kim S, Cui X, Ziarnik M, Im W, Zhang XF. Biophysical investigation of interactions between SARS-CoV-2 spike protein and neuropilin-1. Protein Sci 2023; 32:e4773. [PMID: 37656811 PMCID: PMC10510470 DOI: 10.1002/pro.4773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/19/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
Recent studies have suggested that neuropilin-1 (NRP1) may serve as a potential receptor in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, the biophysical characteristics of interactions between NRP1 and SARS-CoV-2 remain unclear. In this study, we examined the interactions between NRP1 and various SARS-CoV-2 spike (S) fragments, including the receptor-binding domain (RBD) and the S protein trimer in a soluble form or expressed on pseudovirions, using atomic force microscopy and structural modeling. Our measurements shows that NRP1 interacts with the RBD and trimer at a higher binding frequency (BF) compared to ACE2. This NRP1-RBD interaction has also been predicted and simulated via AlphaFold2 and molecular dynamics simulations, and the results indicate that their binding patterns are very similar to RBD-ACE2 interactions. Additionally, under similar loading rates, the most probable unbinding forces between NRP1 and S trimer (both soluble form and on pseudovirions) are larger than the forces between NRP1 and RBD and between trimer and ACE2. Further analysis indicates that NRP1 has a stronger binding affinity to the SARS-CoV-2 S trimer with a dissociation rate of 0.87 s-1 , four times lower than the dissociation rate of 3.65 s-1 between NRP1 and RBD. Moreover, additional experiments show that RBD-neutralizing antibodies can significantly reduce the BF for both ACE2 and NRP1. Together, the study suggests that NRP1 can be an alternative receptor for SARS-CoV-2 attachment to human cells, and the neutralizing antibodies targeting SARS-CoV-2 RBD can reduce the binding between SARS-CoV-2 and NRP1.
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Affiliation(s)
- Decheng Hou
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Department of Biomedical EngineeringUniversity of Massachusetts AmherstAmherstMassachusettsUSA
| | - Wenpeng Cao
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Seonghan Kim
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Xinyu Cui
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Department of Biomedical EngineeringUniversity of Massachusetts AmherstAmherstMassachusettsUSA
| | - Matthew Ziarnik
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Wonpil Im
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Departments of Biological Sciences, Chemistry, and Computer Science and EngineeringLehigh UniversityBethlehemUSA
| | - X. Frank Zhang
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Department of Biomedical EngineeringUniversity of Massachusetts AmherstAmherstMassachusettsUSA
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5
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dos Santos Natividade R, Koehler M, Gomes PSFC, Simpson JD, Smith SC, Gomes DEB, de Lhoneux J, Yang J, Ray A, Dermody TS, Bernardi RC, Ogden KM, Alsteens D. Deciphering molecular mechanisms stabilizing the reovirus-binding complex. Proc Natl Acad Sci U S A 2023; 120:e2220741120. [PMID: 37186838 PMCID: PMC10214207 DOI: 10.1073/pnas.2220741120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
Mammalian orthoreoviruses (reoviruses) serve as potential triggers of celiac disease and have oncolytic properties, making these viruses potential cancer therapeutics. Primary attachment of reovirus to host cells is mainly mediated by the trimeric viral protein, σ1, which engages cell-surface glycans, followed by high-affinity binding to junctional adhesion molecule-A (JAM-A). This multistep process is thought to be accompanied by major conformational changes in σ1, but direct evidence is lacking. By combining biophysical, molecular, and simulation approaches, we define how viral capsid protein mechanics influence virus-binding capacity and infectivity. Single-virus force spectroscopy experiments corroborated by in silico simulations show that GM2 increases the affinity of σ1 for JAM-A by providing a more stable contact interface. We demonstrate that conformational changes in σ1 that lead to an extended rigid conformation also significantly increase avidity for JAM-A. Although its associated lower flexibility impairs multivalent cell attachment, our findings suggest that diminished σ1 flexibility enhances infectivity, indicating that fine-tuning of σ1 conformational changes is required to successfully initiate infection. Understanding properties underlying the nanomechanics of viral attachment proteins offers perspectives in the development of antiviral drugs and improved oncolytic vectors.
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Affiliation(s)
- Rita dos Santos Natividade
- Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354Freising, Germany
| | | | - Joshua D. Simpson
- Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
| | - Sydni Caet Smith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 37232Nashville, TN
| | | | - Juliette de Lhoneux
- Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
| | - Jinsung Yang
- Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
| | - Ankita Ray
- Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
| | - Terence S. Dermody
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
- Institute of Infection, Inflammation, and Immunity, University of Pittsburgh Medical Center, Children’s Hospital of Pittsburgh, Pittsburgh, PA15213
| | | | - Kristen M. Ogden
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 37232Nashville, TN
- Department of Pediatrics, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN37232
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
- Walloon Excellence in Life sciences and Biotechnology, Walloon Excellence Research Institute, 1300Wavre, Belgium
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6
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Shang P, Simpson JD, Taylor GM, Sutherland DM, Welsh OL, Aravamudhan P, Natividade RDS, Schwab K, Michel JJ, Poholek AC, Wu Y, Rajasundaram D, Koehler M, Alsteens D, Dermody TS. Paired immunoglobulin-like receptor B is an entry receptor for mammalian orthoreovirus. Nat Commun 2023; 14:2615. [PMID: 37147336 PMCID: PMC10163058 DOI: 10.1038/s41467-023-38327-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/25/2023] [Indexed: 05/07/2023] Open
Abstract
Mammalian orthoreovirus (reovirus) infects most mammals and is associated with celiac disease in humans. In mice, reovirus infects the intestine and disseminates systemically to cause serotype-specific patterns of disease in the brain. To identify receptors conferring reovirus serotype-dependent neuropathogenesis, we conducted a genome-wide CRISPRa screen and identified paired immunoglobulin-like receptor B (PirB) as a receptor candidate. Ectopic expression of PirB allowed reovirus binding and infection. PirB extracelluar D3D4 region is required for reovirus attachment and infectivity. Reovirus binds to PirB with nM affinity as determined by single molecule force spectroscopy. Efficient reovirus endocytosis requires PirB signaling motifs. In inoculated mice, PirB is required for maximal replication in the brain and full neuropathogenicity of neurotropic serotype 3 (T3) reovirus. In primary cortical neurons, PirB expression contributes to T3 reovirus infectivity. Thus, PirB is an entry receptor for reovirus and contributes to T3 reovirus replication and pathogenesis in the murine brain.
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Affiliation(s)
- Pengcheng Shang
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Joshua D Simpson
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Gwen M Taylor
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Danica M Sutherland
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Olivia L Welsh
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Pavithra Aravamudhan
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Rita Dos Santos Natividade
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Kristina Schwab
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joshua J Michel
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amanda C Poholek
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yijen Wu
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Melanie Koehler
- Leibniz Institute for Food Systems Biology at the Technical University Munich, Freising, Germany
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Terence S Dermody
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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7
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Petitjean SJL, Chen W, Koehler M, Jimmidi R, Yang J, Mohammed D, Juniku B, Stanifer ML, Boulant S, Vincent SP, Alsteens D. Multivalent 9-O-Acetylated-sialic acid glycoclusters as potent inhibitors for SARS-CoV-2 infection. Nat Commun 2022; 13:2564. [PMID: 35538121 PMCID: PMC9091252 DOI: 10.1038/s41467-022-30313-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/25/2022] [Indexed: 01/08/2023] Open
Abstract
The recent emergence of highly transmissible SARS-CoV-2 variants illustrates the urgent need to better understand the molecular details of the virus binding to its host cell and to develop anti-viral strategies. While many studies focused on the role of the angiotensin-converting enzyme 2 receptor in the infection, others suggest the important role of cell attachment factors such as glycans. Here, we use atomic force microscopy to study these early binding events with the focus on the role of sialic acids (SA). We show that SARS-CoV-2 binds specifically to 9-O-acetylated-SA with a moderate affinity, supporting its role as an attachment factor during virus landing to cell host surfaces. For therapeutic purposes and based on this finding, we have designed novel blocking molecules with various topologies and carrying a controlled number of SA residues, enhancing affinity through a multivalent effect. Inhibition assays show that the AcSA-derived glycoclusters are potent inhibitors of cell binding and infectivity, offering new perspectives in the treatment of SARS-CoV-2 infection. Cell surface attachment factors, such as glycans, play an important role in viral infection. Here, Petitjean et al. show that SARS-CoV-2 specifically binds to 9-Oacetylated sialic acid and have designed novel inhibitors based on multivalent derivatives.
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Affiliation(s)
- Simon J L Petitjean
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Wenzhang Chen
- Laboratory of Bio-Organic Chemistry (NARILIS), UNamur, Namur, Belgium
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Ravikumar Jimmidi
- Laboratory of Bio-Organic Chemistry (NARILIS), UNamur, Namur, Belgium
| | - Jinsung Yang
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Danahe Mohammed
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Blinera Juniku
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Megan L Stanifer
- Dept. of Infectious Diseases, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120, Heidelberg, Germany.,Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, USA
| | - Steeve Boulant
- Dept. of Infectious Diseases, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120, Heidelberg, Germany.,Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, USA
| | | | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium. .,Walloon Excellence in Life sciences and Biotechnology (WELBIO), Wavre, Belgium.
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8
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Simpson JD, Ray A, Koehler M, Mohammed D, Alsteens D. Atomic force microscopy applied to interrogate nanoscale cellular chemistry and supramolecular bond dynamics for biomedical applications. Chem Commun (Camb) 2022; 58:5072-5087. [PMID: 35315846 DOI: 10.1039/d1cc07200e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding biological interactions at a molecular level grants valuable information relevant to improving medical treatments and outcomes. Among the suite of technologies available, Atomic Force Microscopy (AFM) is unique in its ability to quantitatively probe forces and receptor-ligand interactions in real-time. The ability to assess the formation of supramolecular bonds and intermediates in real-time on surfaces and living cells generates important information relevant to understanding biological phenomena. Combining AFM with fluorescence-based techniques allows for an unprecedented level of insight not only concerning the formation and rupture of bonds, but understanding medically relevant interactions at a molecular level. As the ability of AFM to probe cells and more complex models improves, being able to assess binding kinetics, chemical topographies, and garner spectroscopic information will likely become key to developing further improvements in fields such as cancer, nanomaterials, and virology. The rapid response to the COVID-19 crisis, producing information regarding not just receptor affinities, but also strain-dependent efficacy of neutralizing nanobodies, demonstrates just how viable and integral to the pre-clinical development of information AFM techniques are in this era of medicine.
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Affiliation(s)
- Joshua D Simpson
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium.
| | - Ankita Ray
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium.
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium.
| | - Danahe Mohammed
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium.
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium.
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9
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Scheim DE. A Deadly Embrace: Hemagglutination Mediated by SARS-CoV-2 Spike Protein at Its 22 N-Glycosylation Sites, Red Blood Cell Surface Sialoglycoproteins, and Antibody. Int J Mol Sci 2022; 23:2558. [PMID: 35269703 PMCID: PMC8910562 DOI: 10.3390/ijms23052558] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/11/2022] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
Rouleaux (stacked clumps) of red blood cells (RBCs) observed in the blood of COVID-19 patients in three studies call attention to the properties of several enveloped virus strains dating back to seminal findings of the 1940s. For COVID-19, key such properties are: (1) SARS-CoV-2 binds to RBCs in vitro and also in the blood of COVID-19 patients; (2) although ACE2 is its target for viral fusion and replication, SARS-CoV-2 initially attaches to sialic acid (SA) terminal moieties on host cell membranes via glycans on its spike protein; (3) certain enveloped viruses express hemagglutinin esterase (HE), an enzyme that releases these glycan-mediated bindings to host cells, which is expressed among betacoronaviruses in the common cold strains but not the virulent strains, SARS-CoV, SARS-CoV-2 and MERS. The arrangement and chemical composition of the glycans at the 22 N-glycosylation sites of SARS-CoV-2 spike protein and those at the sialoglycoprotein coating of RBCs allow exploration of specifics as to how virally induced RBC clumping may form. The in vitro and clinical testing of these possibilities can be sharpened by the incorporation of an existing anti-COVID-19 therapeutic that has been found in silico to competitively bind to multiple glycans on SARS-CoV-2 spike protein.
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Affiliation(s)
- David E Scheim
- US Public Health Service, Commissioned Officer, Inactive Reserve, Blacksburg, VA 24060, USA
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10
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Lipke PN, Rauceo JM, Viljoen A. Cell-Cell Mating Interactions: Overview and Potential of Single-Cell Force Spectroscopy. Int J Mol Sci 2022; 23:ijms23031110. [PMID: 35163034 PMCID: PMC8835621 DOI: 10.3390/ijms23031110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/08/2022] [Accepted: 01/14/2022] [Indexed: 02/01/2023] Open
Abstract
It is an understatement that mating and DNA transfer are key events for living organisms. Among the traits needed to facilitate mating, cell adhesion between gametes is a universal requirement. Thus, there should be specific properties for the adhesion proteins involved in mating. Biochemical and biophysical studies have revealed structural information about mating adhesins, as well as their specificities and affinities, leading to some ideas about these specialized adhesion proteins. Recently, single-cell force spectroscopy (SCFS) has added important findings. In SCFS, mating cells are brought into contact in an atomic force microscope (AFM), and the adhesive forces are monitored through the course of mating. The results have shown some remarkable characteristics of mating adhesins and add knowledge about the design and evolution of mating adhesins.
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Affiliation(s)
- Peter N. Lipke
- Biology Department, Brooklyn College of the City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Correspondence: (P.N.L.); (A.V.)
| | - Jason M. Rauceo
- Department of Sciences, John Jay College of the City University of New York, New York, NY 10019, USA;
| | - Albertus Viljoen
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4–5, bte L7.07.07, 1348 Louvain-la-Neuve, Belgium
- Correspondence: (P.N.L.); (A.V.)
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11
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Liashkovich I, Rosso G, Shahin V. Atomic Force Microscopy for Structural and Biophysical Investigations on Nuclear Pore Complexes. Methods Mol Biol 2022; 2502:299-310. [PMID: 35412247 DOI: 10.1007/978-1-0716-2337-4_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Atomic force microscopy (AFM) enables simultaneous generation of topographical and biophysical maps of surfaces of biological samples at nanoresolution in physiologically relevant environments. Here, we describe the application of AFM to study nuclear pore complexes from structural and biophysical aspects.
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Affiliation(s)
- Ivan Liashkovich
- Institute of Physiology II, University of Münster, Münster, Germany
| | - Gonzalo Rosso
- Institute of Physiology II, University of Münster, Münster, Germany
| | - Victor Shahin
- Institute of Physiology II, University of Münster, Münster, Germany.
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12
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Pan J, Kmieciak T, Liu YT, Wildenradt M, Chen YS, Zhao Y. Quantifying molecular- to cellular-level forces in living cells. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2021; 54:483001. [PMID: 34866655 PMCID: PMC8635116 DOI: 10.1088/1361-6463/ac2170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mechanical cues have been suggested to play an important role in cell functions and cell fate determination, however, such physical quantities are challenging to directly measure in living cells with single molecule sensitivity and resolution. In this review, we focus on two main technologies that are promising in probing forces at the single molecule level. We review their theoretical fundamentals, recent technical advancements, and future directions, tailored specifically for interrogating mechanosensitive molecules in live cells.
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Affiliation(s)
- Jason Pan
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Tommy Kmieciak
- Department of Engineering Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Yen-Ting Liu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Matthew Wildenradt
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Yun-Sheng Chen
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Yang Zhao
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, 208 N. Wright Street, Urbana, IL 61801, United States of America
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13
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Koehler M, Ray A, Moreira RA, Juniku B, Poma AB, Alsteens D. Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. Nat Commun 2021; 12:6977. [PMID: 34848718 PMCID: PMC8633007 DOI: 10.1038/s41467-021-27325-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022] Open
Abstract
Despite an unprecedented global gain in knowledge since the emergence of SARS-CoV-2, almost all mechanistic knowledge related to the molecular and cellular details of viral replication, pathology and virulence has been generated using early prototypic isolates of SARS-CoV-2. Here, using atomic force microscopy and molecular dynamics, we investigated how these mutations quantitatively affected the kinetic, thermodynamic and structural properties of RBD-ACE2 complex formation. We observed for several variants of concern a significant increase in the RBD-ACE2 complex stability. While the N501Y and E484Q mutations are particularly important for the greater stability, the N501Y mutation is unlikely to significantly affect antibody neutralization. This work provides unprecedented atomistic detail on the binding of SARS-CoV-2 variants and provides insight into the impact of viral mutations on infection-induced immunity.
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Affiliation(s)
- Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Ankita Ray
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Rodrigo A Moreira
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106, Warsaw, Poland
| | - Blinera Juniku
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Adolfo B Poma
- International Center for Research on Innovative Biobased Materials (ICRI-BioM)-International Research Agenda, Lodz University of Technology, Żeromskiego 116, 90-924, Lodz, Poland.
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
- Walloon Excellence in Life sciences and Biotechnology (WELBIO), 1300, Wavre, Belgium.
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14
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Cheng H, Yu J, Wang Z, Ma P, Guo C, Wang B, Zhong W, Xu B. Details of Single-Molecule Force Spectroscopy Data Decoded by a Network-Based Automatic Clustering Algorithm. J Phys Chem B 2021; 125:9660-9667. [PMID: 34425052 DOI: 10.1021/acs.jpcb.1c03552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomic force microscopy-single-molecule force spectroscopy (AFM-SMFS) is a powerful methodology to probe intermolecular and intramolecular interactions in biological systems because of its operability in physiological conditions, facile and rapid sample preparation, versatile molecular manipulation, and combined functionality with high-resolution imaging. Since a huge number of AFM-SMFS force-distance curves are collected to avoid human bias and errors and to save time, numerous algorithms have been developed to analyze the AFM-SMFS curves. Nevertheless, there is still a need to develop new algorithms for the analysis of AFM-SMFS data since the current algorithms cannot specify an unbinding force to a corresponding/each binding site due to the lack of networking functionality to model the relationship between the unbinding forces. To address this challenge, herein, we develop an unsupervised method, i.e., a network-based automatic clustering algorithm (NASA), to decode the details of specific molecules, e.g., the unbinding force of each binding site, given the input of AFM-SMFS curves. Using the interaction of heparan sulfate (HS)-antithrombin (AT) on different endothelial cell surfaces as a model system, we demonstrate that NASA is able to automatically detect the peak and calculate the unbinding force. More importantly, NASA successfully identifies three unbinding force clusters, which could belong to three different binding sites, for both Ext1f/f and Ndst1f/f cell lines. NASA has great potential to be applied either readily or slightly modified to other AFM-based SMFS measurements that result in "saw-tooth"-shaped force-distance curves showing jumps related to the force unbinding, such as antibody-antigen interaction and DNA-protein interaction.
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Affiliation(s)
- Huimin Cheng
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Jun Yu
- School of Mathematics and Statistics, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Zhen Wang
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Ping Ma
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Cunlan Guo
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.,Single Molecule Study Laboratory, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Bin Wang
- Single Molecule Study Laboratory, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Wenxuan Zhong
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Bingqian Xu
- Single Molecule Study Laboratory, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
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15
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Beloglazova Y, Nikitiuk A, Voronina A, Gagarskikh O, Bayandin Y, Naimark O, Grishko V. Label-Free Single Cell Viability Assay Using Laser Interference Microscopy. BIOLOGY 2021; 10:590. [PMID: 34206974 PMCID: PMC8301067 DOI: 10.3390/biology10070590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 12/20/2022]
Abstract
Laser interference microscopy (LIM) is a promising label-free method for single-cell research applicable to cell viability assessment in the studies of mammalian cells. This paper describes the development of a sensitive and reproducible method for assessing cell viability using LIM. The method, based on associated signal processing techniques, has been developed as a result of real-time investigation in phase thickness fluctuations of viable and non-viable MCF-7 cells, reflecting the presence and absence of their metabolic activity. As evinced by the values of the variable vc, this variable determines the viability of a cell only in the attached state (vc exceeds 20 nm2 for viable attached cells). The critical value of the power spectrum slope βc of the phase thickness fluctuations equals 1.00 for attached MCF-7 cells and 0.71 for suspended cells. The slope of the phase fluctuations' power spectrum for MCF-7 cells was determined to exceed the threshold value of βc for a living cell, otherwise the cell is dead. The results evince the power spectrum slope as the most appropriate indicator of cell viability, while the integrated evaluation criterion (vc and βc values) can be used to assay the viability of attached cells.
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Affiliation(s)
- Yulia Beloglazova
- Perm Federal Scientific Centre, Institute of Technical Chemistry UB RAS, Academician Korolev St. 3, 614013 Perm, Russia; (Y.B.); (A.V.); (O.G.)
| | - Aleksandr Nikitiuk
- Perm Federal Scientific Centre, Institute of Continuous Media Mechanics UB RAS, Academician Korolev St. 1, 614013 Perm, Russia; (A.N.); (Y.B.); (O.N.)
| | - Anna Voronina
- Perm Federal Scientific Centre, Institute of Technical Chemistry UB RAS, Academician Korolev St. 3, 614013 Perm, Russia; (Y.B.); (A.V.); (O.G.)
| | - Olga Gagarskikh
- Perm Federal Scientific Centre, Institute of Technical Chemistry UB RAS, Academician Korolev St. 3, 614013 Perm, Russia; (Y.B.); (A.V.); (O.G.)
| | - Yuriy Bayandin
- Perm Federal Scientific Centre, Institute of Continuous Media Mechanics UB RAS, Academician Korolev St. 1, 614013 Perm, Russia; (A.N.); (Y.B.); (O.N.)
| | - Oleg Naimark
- Perm Federal Scientific Centre, Institute of Continuous Media Mechanics UB RAS, Academician Korolev St. 1, 614013 Perm, Russia; (A.N.); (Y.B.); (O.N.)
| | - Victoria Grishko
- Perm Federal Scientific Centre, Institute of Technical Chemistry UB RAS, Academician Korolev St. 3, 614013 Perm, Russia; (Y.B.); (A.V.); (O.G.)
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16
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Akhmetova AI, Yaminsky IV. High resolution imaging of viruses: Scanning probe microscopy and related techniques. Methods 2021; 197:30-38. [PMID: 34157416 DOI: 10.1016/j.ymeth.2021.06.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 05/26/2021] [Accepted: 06/17/2021] [Indexed: 11/19/2022] Open
Abstract
Scanning probe microscopy is a group of measurements that provides 3D visualization of viruses in different environmental conditions including liquids and air. Besides 3D topography it is possible to measure the properties like mechanical rigidity and stability, adhesion, tendency to crystallization, surface charge, etc. Choosing the right substrate and scanning parameters makes it much easier to obtain reliable data. Rational interpretation of experimental results should take into account possible artifacts, proper filtering and data presentation using specially designed software packages. Animal and human virus characterization is in the focus of many intensive studies because of their potential harm to higher organisms. The article focuses on high-resolution visualization of plant viruses. Tobacco mosaic virus, potato viruses X and B and others are not dangerous for the human being and are widely used in different applications such as vaccine preparation, construction of building units in nanotechnology and material science applications, nanoparticle production and delivery, and even metrology. The methods of virus's deposition, visualization, and consequent image processing and interpretation are described in details. Specific examples of viruses imaging are illustrated using the FemtoScan Online software, which has typical and all the necessary built-in functions for constructing three-dimensional images, their processing and analysis. Despite visible progress in visualizing the viruses using probe microscopy, many unresolved problems still remain. At present time the probe microscopy data on viruses is not systemized. There is no descriptive atlas of the images and morphology as revealed by this type of high resolution microscopy. It is worth emphasizing that new virus investigation methods will appear due to the progress of science.
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Affiliation(s)
- Assel I Akhmetova
- Lomonosov Moscow State University, 1, Leninskie Gory, Moscow, 119991, GSP-1, Russia; Advanced Technologies Center, 4-5-47, Stroitelei str., Moscow, 119311, Russia
| | - Igor V Yaminsky
- Lomonosov Moscow State University, 1, Leninskie Gory, Moscow, 119991, GSP-1, Russia; Advanced Technologies Center, 4-5-47, Stroitelei str., Moscow, 119311, Russia.
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17
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Abstract
The precise measurement of thermodynamic and kinetic properties for biomolecules provides the detailed information for a multitude of applications in biochemistry, biosensing, and health care. However, sensitivity in characterizing the thermodynamic binding affinity down to a single molecule, such as the Gibbs free energy ([Formula: see text]), enthalpy ([Formula: see text]), and entropy ([Formula: see text]), has not materialized. Here, we develop a nanoparticle-based technique to probe the energetic contributions of single-molecule binding events, which introduces a focused laser of optical tweezer to an optical path of plasmonic imaging to accumulate and monitor the transient local heating. This single-molecule calorimeter uncovers the complex nature of molecular interactions and binding characterizations, which can be employed to identify the thermodynamic equilibrium state and determine the energetic components and complete thermodynamic profile of the free energy landscape. This sensing platform promises a breakthrough in measuring thermal effect at the single-molecule level and provides a thorough description of biomolecular specific interactions.
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18
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Bhat SV, Price JDW, Dahms TES. AFM-Based Correlative Microscopy Illuminates Human Pathogens. Front Cell Infect Microbiol 2021; 11:655501. [PMID: 34026660 PMCID: PMC8138568 DOI: 10.3389/fcimb.2021.655501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/08/2021] [Indexed: 12/25/2022] Open
Abstract
Microbes have an arsenal of virulence factors that contribute to their pathogenicity. A number of challenges remain to fully understand disease transmission, fitness landscape, antimicrobial resistance and host heterogeneity. A variety of tools have been used to address diverse aspects of pathogenicity, from molecular host-pathogen interactions to the mechanisms of disease acquisition and transmission. Current gaps in our knowledge include a more direct understanding of host-pathogen interactions, including signaling at interfaces, and direct phenotypic confirmation of pathogenicity. Correlative microscopy has been gaining traction to address the many challenges currently faced in biomedicine, in particular the combination of optical and atomic force microscopy (AFM). AFM, generates high-resolution surface topographical images, and quantifies mechanical properties at the pN scale under physiologically relevant conditions. When combined with optical microscopy, AFM probes pathogen surfaces and their physical and molecular interaction with host cells, while the various modes of optical microscopy view internal cellular responses of the pathogen and host. Here we review the most recent advances in our understanding of pathogens, recent applications of AFM to the field, how correlative AFM-optical microspectroscopy and microscopy have been used to illuminate pathogenicity and how these methods can reach their full potential for studying host-pathogen interactions.
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Affiliation(s)
- Supriya V Bhat
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada
| | - Jared D W Price
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada
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19
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Koehler M, Petitjean SJL, Yang J, Aravamudhan P, Somoulay X, Lo Giudice C, Poncin MA, Dumitru AC, Dermody TS, Alsteens D. Reovirus directly engages integrin to recruit clathrin for entry into host cells. Nat Commun 2021; 12:2149. [PMID: 33846319 PMCID: PMC8041799 DOI: 10.1038/s41467-021-22380-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/09/2021] [Indexed: 02/01/2023] Open
Abstract
Reovirus infection requires the concerted action of viral and host factors to promote cell entry. After interaction of reovirus attachment protein σ1 with cell-surface carbohydrates and proteinaceous receptors, additional host factors mediate virus internalization. In particular, β1 integrin is required for endocytosis of reovirus virions following junctional adhesion molecule A (JAM-A) binding. While integrin-binding motifs in the surface-exposed region of reovirus capsid protein λ2 are thought to mediate integrin interaction, evidence for direct β1 integrin-reovirus interactions and knowledge of how integrins function to mediate reovirus entry is lacking. Here, we use single-virus force spectroscopy and confocal microscopy to discover a direct interaction between reovirus and β1 integrins. Comparison of interactions between reovirus disassembly intermediates as well as mutants and β1 integrin show that λ2 is the integrin ligand. Finally, using fluidic force microscopy, we demonstrate a functional role for β1 integrin interaction in promoting clathrin recruitment to cell-bound reovirus. Our study demonstrates a direct interaction between reovirus and β1 integrins and offers insights into the mechanism of reovirus cell entry. These results provide new perspectives for the development of efficacious antiviral therapeutics and the engineering of improved viral gene delivery and oncolytic vectors.
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Affiliation(s)
- Melanie Koehler
- grid.7942.80000 0001 2294 713XLouvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Simon J. L. Petitjean
- grid.7942.80000 0001 2294 713XLouvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Jinsung Yang
- grid.7942.80000 0001 2294 713XLouvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Pavithra Aravamudhan
- grid.21925.3d0000 0004 1936 9000Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA USA ,grid.239553.b0000 0000 9753 0008Institute of Infection, Inflammation and Immunity, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA USA
| | - Xayathed Somoulay
- grid.21925.3d0000 0004 1936 9000Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA USA ,grid.239553.b0000 0000 9753 0008Institute of Infection, Inflammation and Immunity, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA USA
| | - Cristina Lo Giudice
- grid.7942.80000 0001 2294 713XLouvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Mégane A. Poncin
- grid.7942.80000 0001 2294 713XLouvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Andra C. Dumitru
- grid.7942.80000 0001 2294 713XLouvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Terence S. Dermody
- grid.21925.3d0000 0004 1936 9000Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA USA ,grid.239553.b0000 0000 9753 0008Institute of Infection, Inflammation and Immunity, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA USA ,grid.21925.3d0000 0004 1936 9000Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - David Alsteens
- grid.7942.80000 0001 2294 713XLouvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium ,grid.509491.0Walloon Excellence in Life sciences and Biotechnology (WELBIO), Wavre, Belgium
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20
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Lavrenyuk K, Conway D, Dahl KN. Imaging methods in mechanosensing: a historical perspective and visions for the future. Mol Biol Cell 2021; 32:842-854. [PMID: 33788578 PMCID: PMC8108522 DOI: 10.1091/mbc.e20-10-0671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Over the past three decades, as mechanobiology has become a distinct area of study, researchers have developed novel imaging tools to discover the pathways of biomechanical signaling. Early work with substrate engineering and particle tracking demonstrated the importance of cell–extracellular matrix interactions on the cell cycle as well as the mechanical flux of the intracellular environment. Most recently, tension sensor approaches allowed directly measuring tension in cell–cell and cell–substrate interactions. We retrospectively analyze how these various optical techniques progressed the field and suggest our vision forward for a unified theory of cell mechanics, mapping cellular mechanosensing, and novel biomedical applications for mechanobiology.
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Affiliation(s)
- Kirill Lavrenyuk
- Carnegie Mellon University, College of Engineering, Pittsburgh, PA 15213
| | - Daniel Conway
- Virginia Commonwealth University, College of Engineering, Richmond, VA 23284
| | - Kris Noel Dahl
- Carnegie Mellon University, College of Engineering, Pittsburgh, PA 15213
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21
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Evans CT, Baldock SJ, Hardy JG, Payton O, Picco L, Allen MJ. A Non-Destructive, Tuneable Method to Isolate Live Cells for High-Speed AFM Analysis. Microorganisms 2021; 9:microorganisms9040680. [PMID: 33806176 PMCID: PMC8066395 DOI: 10.3390/microorganisms9040680] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 11/24/2022] Open
Abstract
Suitable immobilisation of microorganisms and single cells is key for high-resolution topographical imaging and study of mechanical properties with atomic force microscopy (AFM) under physiologically relevant conditions. Sample preparation techniques must be able to withstand the forces exerted by the Z range-limited cantilever tip, and not negatively affect the sample surface for data acquisition. Here, we describe an inherently flexible methodology, utilising the high-resolution three-dimensional based printing technique of multiphoton polymerisation to rapidly generate bespoke arrays for cellular AFM analysis. As an example, we present data collected from live Emiliania huxleyi cells, unicellular microalgae, imaged by contact mode High-Speed Atomic Force Microscopy (HS-AFM), including one cell that was imaged continuously for over 90 min.
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Affiliation(s)
- Christopher T. Evans
- Plymouth Marine Laboratory, Plymouth PL1 3DH, UK;
- Interface Analysis Centre, Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK;
| | - Sara J. Baldock
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, UK; (S.J.B.); (J.G.H.)
| | - John G. Hardy
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, UK; (S.J.B.); (J.G.H.)
- Materials Science Institute, Lancaster University, Lancaster LA1 4YB, UK
| | - Oliver Payton
- Interface Analysis Centre, Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK;
| | - Loren Picco
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Michael J. Allen
- Plymouth Marine Laboratory, Plymouth PL1 3DH, UK;
- Department of Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road EX4 4QD, UK
- Correspondence: ; Tel.: +44-(0)-1752-633100
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22
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Li M, Xi N, Wang YC, Liu LQ. Atomic force microscopy for revealing micro/nanoscale mechanics in tumor metastasis: from single cells to microenvironmental cues. Acta Pharmacol Sin 2021; 42:323-339. [PMID: 32807839 PMCID: PMC8027022 DOI: 10.1038/s41401-020-0494-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/27/2020] [Indexed: 02/06/2023] Open
Abstract
Mechanics are intrinsic properties which appears throughout the formation, development, and aging processes of biological systems. Mechanics have been shown to play important roles in regulating the development and metastasis of tumors, and understanding tumor mechanics has emerged as a promising way to reveal the underlying mechanisms guiding tumor behaviors. In particular, tumors are highly complex diseases associated with multifaceted factors, including alterations in cancerous cells, tissues, and organs as well as microenvironmental cues, indicating that investigating tumor mechanics on multiple levels is significantly helpful for comprehensively understanding the effects of mechanics on tumor progression. Recently, diverse techniques have been developed for probing the mechanics of tumors, among which atomic force microscopy (AFM) has appeared as an excellent platform enabling simultaneously characterizing the structures and mechanical properties of living biological systems ranging from individual molecules and cells to tissue samples with unprecedented spatiotemporal resolution, offering novel possibilities for understanding tumor physics and contributing much to the studies of cancer. In this review, we survey the recent progress that has been achieved with the use of AFM for revealing micro/nanoscale mechanics in tumor development and metastasis. Challenges and future progress are also discussed.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China.
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, 110169, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ning Xi
- Department of Industrial and Manufacturing Systems Engineering, The University of Hong Kong, Hong Kong, China
| | - Yue-Chao Wang
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, 110169, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lian-Qing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China.
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, 110169, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
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23
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Investigating virus-host cell interactions: Comparative binding forces between hepatitis C virus-like particles and host cell receptors in 2D and 3D cell culture models. J Colloid Interface Sci 2021; 592:371-384. [PMID: 33677197 DOI: 10.1016/j.jcis.2021.02.067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 12/25/2022]
Abstract
Cell cultures have been successfully used to study hepatitis C virus (HCV) for many years. However, most work has been done using traditional, 2-dimensional (2D) cell cultures (cells grown as a monolayer in growth flasks or dishes). Studies have shown that when cells are grown suspended in an extra-cellular-matrix-like material, they develop into spherical, 'organoid' arrangements of cells (3D growth) that display distinct differences in morphological and functional characteristics compared to 2D cell cultures. In liver organoids, one key difference is the development of clearly differentiated apical and basolateral surfaces separated and maintained by cellular tight junctions. This phenomenon, termed polarity, is vital to normal barrier function of hepatocytes in vivo. It has also been shown that viruses, and virus-like particles, interact very differently with cells derived from 2D as compared to 3D cell cultures, bringing into question the usefulness of 2D cell cultures to study virus-host cell interactions. Here, we investigate differences in cellular architecture as a function of cell culture system, using confocal scanning laser microscopy, and determine differences in binding interactions between HCV virus-like particles (VLPs) and their cognate receptors in the different cell culture systems using atomic force microscopy (AFM). We generated organoid cultures that were polarized, as determined by localization of key apical and basolateral markers. We found that, while uptake of HCV VLPs by both 2D and 3D Huh7 cells was observed by flow cytometry, binding interactions between HCV VLPs and cells were measurable by AFM only on polarized cells. The work presented here adds to the growing body of research suggesting that polarized cell systems are more suitable for the study of HCV infection and dynamics than non-polarized systems.
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24
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Berquand A, Wahart A, Henry A, Gorisse L, Maurice P, Blaise S, Romier-Crouzet B, Pietrement C, Bennasroune A, Sartelet H, Jaisson S, Gillery P, Martiny L, Touré F, Duca L, Molinari M. Revealing the elasticity of an individual aortic fiber during ageing at nanoscale by in situ atomic force microscopy. NANOSCALE 2021; 13:1124-1133. [PMID: 33399602 DOI: 10.1039/d0nr06753a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Arterial stiffness is a complex process affecting the aortic tree that significantly contributes to cardiovascular diseases (systolic hypertension, coronary artery disease, heart failure or stroke). This process involves a large extracellular matrix remodeling mainly associated with elastin content decrease and collagen content increase. Additionally, various chemical modifications that accumulate with ageing have been shown to affect long-lived assemblies, such as elastic fibers, that could affect their elasticity. To precisely characterize the fiber changes and the evolution of its elasticity with ageing, high resolution and multimodal techniques are needed for precise insight into the behavior of a single fiber and its surrounding medium. In this study, the latest developments in atomic force microscopy and the related nanomechanical modes are used to investigate the evolution and in a near-physiological environment, the morphology and elasticity of aorta cross sections obtained from mice of different ages with an unprecedented resolution. In correlation with more classical approaches such as pulse wave velocity and fluorescence imaging, we demonstrate that the relative Young's moduli of elastic fibers, as well as those of the surrounding areas, significantly increase with ageing. This nanoscale characterization presents a new view on the stiffness process, showing that, besides the elastin and collagen content changes, elasticity is impaired at the molecular level, allowing a deeper understanding of the ageing process. Such nanomechanical AFM measurements of mouse tissue could easily be applied to studies of diseases in which elastic fibers suffer pathologies such as atherosclerosis and diabetes, where the precise quantification of fiber elasticity could better follow the fiber remodeling and predict plaque rupture.
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Affiliation(s)
- Alexandre Berquand
- Laboratoire de Recherche en Nanosciences, LRN EA4682, University of Reims Champagne-Ardenne, 51685 Reims, France
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25
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Delguste M, Brun GL, Cotin F, Machiels B, Gillet L, Alsteens D. Single-Virus Force Spectroscopy Discriminates the Intrinsic Role of Two Viral Glycoproteins upon Cell Surface Attachment. NANO LETTERS 2021; 21:847-853. [PMID: 33373240 DOI: 10.1021/acs.nanolett.0c04609] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Viruses are one of the most efficient pathogenic entities on earth, resulting from millions of years of evolution. Each virus particle carries the minimum number of genes and proteins to ensure their reproduction within host cells, hijacking some host replication machinery. However, the role of some viral proteins is not yet unraveled, with some appearing even redundant. For example, murid herpesvirus 4, the current model for human gammaherpesvirus infection, can bind to cell surface glycosaminoglycans using both glycoproteins gp70 and gH/gL. Here, using atomic force microscopy, we discriminate their relative contribution during virus binding to cell surface glycosaminoglycans. Single-virus force spectroscopy experiments demonstrate that gH/gL is the main actor in glycosaminoglycan binding, engaging more numerous and more stable interactions. We also demonstrated that Fab antibody fragments targeting gH/gL or gp70 appear to be a promising treatment to prevent the attachment of virions to cell surfaces.
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Affiliation(s)
- Martin Delguste
- Université Catholique de Louvain, Louvain Institute of Biomolecular Science and Technology, Louvain-la-Neuve 1348, Belgium
| | - Grégoire Le Brun
- Université Catholique de Louvain, Louvain Institute of Biomolecular Science and Technology, Louvain-la-Neuve 1348, Belgium
| | - Florian Cotin
- Université Catholique de Louvain, Louvain Institute of Biomolecular Science and Technology, Louvain-la-Neuve 1348, Belgium
| | | | - Laurent Gillet
- University of Liège, Immunology-Vaccinology, FARAH, Liège 4000, Belgium
| | - David Alsteens
- Université Catholique de Louvain, Louvain Institute of Biomolecular Science and Technology, Louvain-la-Neuve 1348, Belgium
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26
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Cieśluk M, Deptuła P, Piktel E, Fiedoruk K, Suprewicz Ł, Paprocka P, Kot P, Pogoda K, Bucki R. Physics Comes to the Aid of Medicine-Clinically-Relevant Microorganisms through the Eyes of Atomic Force Microscope. Pathogens 2020; 9:pathogens9110969. [PMID: 33233696 PMCID: PMC7699805 DOI: 10.3390/pathogens9110969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 12/01/2022] Open
Abstract
Despite the hope that was raised with the implementation of antibiotics to the treatment of infections in medical practice, the initial enthusiasm has substantially faded due to increasing drug resistance in pathogenic microorganisms. Therefore, there is a need for novel analytical and diagnostic methods in order to extend our knowledge regarding the mode of action of the conventional and novel antimicrobial agents from a perspective of single microbial cells as well as their communities growing in infected sites, i.e., biofilms. In recent years, atomic force microscopy (AFM) has been mostly used to study different aspects of the pathophysiology of noninfectious conditions with attempts to characterize morphological and rheological properties of tissues, individual mammalian cells as well as their organelles and extracellular matrix, and cells’ mechanical changes upon exposure to different stimuli. At the same time, an ever-growing number of studies have demonstrated AFM as a valuable approach in studying microorganisms in regard to changes in their morphology and nanomechanical properties, e.g., stiffness in response to antimicrobial treatment or interaction with a substrate as well as the mechanisms behind their virulence. This review summarizes recent developments and the authors’ point of view on AFM-based evaluation of microorganisms’ response to applied antimicrobial treatment within a group of selected bacteria, fungi, and viruses. The AFM potential in development of modern diagnostic and therapeutic methods for combating of infections caused by drug-resistant bacterial strains is also discussed.
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Affiliation(s)
- Mateusz Cieśluk
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Bialystok, Poland; (M.C.); (P.D.); (E.P.); (K.F.); (Ł.S.)
| | - Piotr Deptuła
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Bialystok, Poland; (M.C.); (P.D.); (E.P.); (K.F.); (Ł.S.)
| | - Ewelina Piktel
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Bialystok, Poland; (M.C.); (P.D.); (E.P.); (K.F.); (Ł.S.)
| | - Krzysztof Fiedoruk
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Bialystok, Poland; (M.C.); (P.D.); (E.P.); (K.F.); (Ł.S.)
| | - Łukasz Suprewicz
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Bialystok, Poland; (M.C.); (P.D.); (E.P.); (K.F.); (Ł.S.)
| | - Paulina Paprocka
- Department of Microbiology and Immunology, Institute of Medical Science, Collegium Medicum, Jan Kochanowski University in Kielce, PL-25317 Kielce, Poland; (P.P.); (P.K.)
| | - Patrycja Kot
- Department of Microbiology and Immunology, Institute of Medical Science, Collegium Medicum, Jan Kochanowski University in Kielce, PL-25317 Kielce, Poland; (P.P.); (P.K.)
| | - Katarzyna Pogoda
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland;
| | - Robert Bucki
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Bialystok, Poland; (M.C.); (P.D.); (E.P.); (K.F.); (Ł.S.)
- Correspondence:
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27
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Müller DJ, Dumitru AC, Lo Giudice C, Gaub HE, Hinterdorfer P, Hummer G, De Yoreo JJ, Dufrêne YF, Alsteens D. Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems. Chem Rev 2020; 121:11701-11725. [PMID: 33166471 DOI: 10.1021/acs.chemrev.0c00617] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During the last three decades, a series of key technological improvements turned atomic force microscopy (AFM) into a nanoscopic laboratory to directly observe and chemically characterize molecular and cell biological systems under physiological conditions. Here, we review key technological improvements that have established AFM as an analytical tool to observe and quantify native biological systems from the micro- to the nanoscale. Native biological systems include living tissues, cells, and cellular components such as single or complexed proteins, nucleic acids, lipids, or sugars. We showcase the procedures to customize nanoscopic chemical laboratories by functionalizing AFM tips and outline the advantages and limitations in applying different AFM modes to chemically image, sense, and manipulate biosystems at (sub)nanometer spatial and millisecond temporal resolution. We further discuss theoretical approaches to extract the kinetic and thermodynamic parameters of specific biomolecular interactions detected by AFM for single bonds and extend the discussion to multiple bonds. Finally, we highlight the potential of combining AFM with optical microscopy and spectroscopy to address the full complexity of biological systems and to tackle fundamental challenges in life sciences.
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Affiliation(s)
- Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 28, 4056 Basel, Switzerland
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Cristina Lo Giudice
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Hermann E Gaub
- Applied Physics, Ludwig-Maximilians-Universität Munich, Amalienstrasse 54, 80799 München, Germany
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics and Department of Physics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.,Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
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28
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Reovirus σ1 Conformational Flexibility Modulates the Efficiency of Host Cell Attachment. J Virol 2020; 94:JVI.01163-20. [PMID: 32938765 DOI: 10.1128/jvi.01163-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/09/2020] [Indexed: 02/07/2023] Open
Abstract
Reovirus attachment protein σ1 is a trimeric molecule containing tail, body, and head domains. During infection, σ1 engages sialylated glycans and junctional adhesion molecule-A (JAM-A), triggering uptake into the endocytic compartment, where virions are proteolytically converted to infectious subvirion particles (ISVPs). Further disassembly allows σ1 release and escape of transcriptionally active reovirus cores into the cytosol. Electron microscopy has revealed a distinct conformational change in σ1 from a compact form on virions to an extended form on ISVPs. To determine the importance of σ1 conformational mobility, we used reverse genetics to introduce cysteine mutations that can cross-link σ1 by establishing disulfide bonds between structurally adjacent sites in the tail, body, and head domains. We detected phenotypic differences among the engineered viruses. A mutant with a cysteine pair in the head domain replicates with enhanced kinetics, forms large plaques, and displays increased avidity for JAM-A relative to the parental virus, mimicking properties of ISVPs. However, unlike ISVPs, particles containing cysteine mutations that cross-link the head domain uncoat and transcribe viral positive-sense RNA with kinetics similar to the parental virus and are sensitive to ammonium chloride, which blocks virion-to-ISVP conversion. Together, these data suggest that σ1 conformational flexibility modulates the efficiency of reovirus host cell attachment.IMPORTANCE Nonenveloped virus entry is an incompletely understood process. For reovirus, the functional significance of conformational rearrangements in the attachment protein, σ1, that occur during entry and particle uncoating are unknown. We engineered and characterized reoviruses containing cysteine mutations that cross-link σ1 monomers in nonreducing conditions. We found that the introduction of a cysteine pair in the receptor-binding domain of σ1 yielded a virus that replicates with faster kinetics than the parental virus and forms larger plaques. Using functional assays, we found that cross-linking the σ1 receptor-binding domain modulates reovirus attachment but not uncoating or transcription. These data suggest that σ1 conformational rearrangements mediate the efficiency of reovirus host cell binding.
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29
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Grzeszczuk Z, Rosillo A, Owens Ó, Bhattacharjee S. Atomic Force Microscopy (AFM) As a Surface Mapping Tool in Microorganisms Resistant Toward Antimicrobials: A Mini-Review. Front Pharmacol 2020; 11:517165. [PMID: 33123004 PMCID: PMC7567160 DOI: 10.3389/fphar.2020.517165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 09/14/2020] [Indexed: 12/28/2022] Open
Abstract
The worldwide emergence of antimicrobial resistance (AMR) in pathogenic microorganisms, including bacteria and viruses due to a plethora of reasons, such as genetic mutation and indiscriminate use of antimicrobials, is a major challenge faced by the healthcare sector today. One of the issues at hand is to effectively screen and isolate resistant strains from sensitive ones. Utilizing the distinct nanomechanical properties (e.g., elasticity, intracellular turgor pressure, and Young’s modulus) of microbes can be an intriguing way to achieve this; while atomic force microscopy (AFM), with or without modification of the tips, presents an effective way to investigate such biophysical properties of microbial surfaces or an entire microbial cell. Additionally, advanced AFM instruments, apart from being compatible with aqueous environments—as often is the case for biological samples—can measure the adhesive forces acting between AFM tips/cantilevers (conjugated to bacterium/virion, substrates, and molecules) and target cells/surfaces to develop informative force-distance curves. Moreover, such force spectroscopies provide an idea of the nature of intercellular interactions (e.g., receptor-ligand) or propensity of microbes to aggregate into densely packed layers, that is, the formation of biofilms—a property of resistant strains (e.g., Staphylococcus aureus, Pseudomonas aeruginosa). This mini-review will revisit the use of single-cell force spectroscopy (SCFS) and single-molecule force spectroscopy (SMFS) that are emerging as powerful additions to the arsenal of researchers in the struggle against resistant microbes, identify their strengths and weakness and, finally, prioritize some future directions for research.
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Affiliation(s)
| | | | - Óisín Owens
- School of Physics, Technological University Dublin, Dublin, Ireland
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30
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Liang W, Shi H, Yang X, Wang J, Yang W, Zhang H, Liu L. Recent advances in AFM-based biological characterization and applications at multiple levels. SOFT MATTER 2020; 16:8962-8984. [PMID: 32996549 DOI: 10.1039/d0sm01106a] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Atomic force microscopy (AFM) has found a wide range of bio-applications in the past few decades due to its ability to measure biological samples in natural environments at a high spatial resolution. AFM has become a key platform in biomedical, bioengineering and drug research fields, enabling mechanical and morphological characterization of live biological systems. Hence, we provide a comprehensive review on recent advances in the use of AFM for characterizing the biomechanical properties of multi-scale biological samples, ranging from molecule, cell to tissue levels. First, we present the fundamental principles of AFM and two AFM-based models for the characterization of biomechanical properties of biological samples, covering key AFM devices and AFM bioimaging as well as theoretical models for characterizing the elasticity and viscosity of biomaterials. Then, we elaborate on a series of new experimental findings through analysis of biomechanics. Finally, we discuss the future directions and challenges. It is envisioned that the AFM technique will enable many remarkable discoveries, and will have far-reaching impacts on bio-related studies and applications in the future.
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Affiliation(s)
- Wenfeng Liang
- School of Mechanical Engineering, Shenyang Jianzhu University, Shenyang, 110168, China.
| | - Haohao Shi
- School of Mechanical Engineering, Shenyang Jianzhu University, Shenyang, 110168, China.
| | - Xieliu Yang
- School of Mechanical Engineering, Shenyang Jianzhu University, Shenyang, 110168, China.
| | - Junhai Wang
- School of Mechanical Engineering, Shenyang Jianzhu University, Shenyang, 110168, China.
| | - Wenguang Yang
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China
| | - Hemin Zhang
- Department of Neurology, The People's Hospital of Liaoning Province, Shenyang 110016, China.
| | - Lianqing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
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31
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Yang J, Petitjean SJL, Koehler M, Zhang Q, Dumitru AC, Chen W, Derclaye S, Vincent SP, Soumillion P, Alsteens D. Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor. Nat Commun 2020; 11:4541. [PMID: 32917884 PMCID: PMC7486399 DOI: 10.1038/s41467-020-18319-6] [Citation(s) in RCA: 398] [Impact Index Per Article: 99.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/18/2020] [Indexed: 12/15/2022] Open
Abstract
Study of the interactions established between the viral glycoproteins and their host receptors is of critical importance for a better understanding of virus entry into cells. The novel coronavirus SARS-CoV-2 entry into host cells is mediated by its spike glycoprotein (S-glycoprotein), and the angiotensin-converting enzyme 2 (ACE2) has been identified as a cellular receptor. Here, we use atomic force microscopy to investigate the mechanisms by which the S-glycoprotein binds to the ACE2 receptor. We demonstrate, both on model surfaces and on living cells, that the receptor binding domain (RBD) serves as the binding interface within the S-glycoprotein with the ACE2 receptor and extract the kinetic and thermodynamic properties of this binding pocket. Altogether, these results provide a picture of the established interaction on living cells. Finally, we test several binding inhibitor peptides targeting the virus early attachment stages, offering new perspectives in the treatment of the SARS-CoV-2 infection. SARS-CoV-2 spike protein binds host ACE2 for virus entry. Here, the authors determine kinetic and thermodynamic properties of this interaction using atomic force microscopy, develop peptides that inhibit binding and suggest existence of additional attachment factors.
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Affiliation(s)
- Jinsung Yang
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Simon J L Petitjean
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Qingrong Zhang
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Wenzhang Chen
- Départment de Chimie, Laboratoire de Chimie Bio-Organique, University of Namur, Namur, Belgium
| | - Sylvie Derclaye
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Stéphane P Vincent
- Départment de Chimie, Laboratoire de Chimie Bio-Organique, University of Namur, Namur, Belgium
| | - Patrice Soumillion
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium. .,Walloon Excellence in Life sciences and Biotechnology (WELBIO), 1300, Wavre, Belgium.
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32
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Alunda BO, Lee YJ. Review: Cantilever-Based Sensors for High Speed Atomic Force Microscopy. SENSORS (BASEL, SWITZERLAND) 2020; 20:E4784. [PMID: 32854193 PMCID: PMC7506678 DOI: 10.3390/s20174784] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 12/13/2022]
Abstract
This review critically summarizes the recent advances of the microcantilever-based force sensors for atomic force microscope (AFM) applications. They are one the most common mechanical spring-mass systems and are extremely sensitive to changes in the resonant frequency, thus finding numerous applications especially for molecular sensing. Specifically, we comment on the latest progress in research on the deflection detection systems, fabrication, coating and functionalization of the microcantilevers and their application as bio- and chemical sensors. A trend on the recent breakthroughs on the study of biological samples using high-speed atomic force microscope is also reported in this review.
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Affiliation(s)
- Bernard Ouma Alunda
- School of Mines and Engineering, Taita Taveta University, P.O. Box 635-80300 Voi, Kenya;
| | - Yong Joong Lee
- School of Mechanical Engineering, Kyungpook National University, Daegu 41566, Korea
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33
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Applications of atomic force microscopy in immunology. Front Med 2020; 15:43-52. [PMID: 32820379 DOI: 10.1007/s11684-020-0769-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 03/04/2020] [Indexed: 01/20/2023]
Abstract
Cellular mechanics, a major regulating factor of cellular architecture and biological functions, responds to intrinsic stresses and extrinsic forces exerted by other cells and the extracellular matrix in the microenvironment. Cellular mechanics also acts as a fundamental mediator in complicated immune responses, such as cell migration, immune cell activation, and pathogen clearance. The principle of atomic force microscopy (AFM) and its three running modes are introduced for the mechanical characterization of living cells. The peak force tapping mode provides the most delicate and desirable virtues to collect high-resolution images of morphology and force curves. For a concrete description of AFM capabilities, three AFM applications are discussed. These applications include the dynamic progress of a neutrophil-extracellular-trap release by neutrophils, the immunological functions of macrophages, and the membrane pore formation mediated by perforin, streptolysin O, gasdermin D, or membrane attack complex.
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34
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Koehler M, Lo Giudice C, Vogl P, Ebner A, Hinterdorfer P, Gruber HJ, Alsteens D. Control of Ligand-Binding Specificity Using Photocleavable Linkers in AFM Force Spectroscopy. NANO LETTERS 2020; 20:4038-4042. [PMID: 32320256 PMCID: PMC7252943 DOI: 10.1021/acs.nanolett.0c01426] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/21/2020] [Indexed: 05/26/2023]
Abstract
In recent decades, atomic force microscopy (AFM), in particular the force spectroscopy mode, has become a method of choice to study biomolecular interactions at the single-molecule level. However, grafting procedures as well as determining binding specificity remain challenging. We report here an innovative approach based on a photocleavable group that enables in situ release of the ligands bound to the AFM tip and thus allows direct assessment of the binding specificity. Applicable to a wide variety of molecules, the strategy presented here provides new opportunities to study specific interactions and deliver single molecules with high spatiotemporal resolution in a wide range of applications, including AFM-based cell biology.
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Affiliation(s)
- Melanie Koehler
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Cristina Lo Giudice
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Philipp Vogl
- Institute
of Biophysics, Johannes Kepler University, 4020 Linz, Austria
| | - Andreas Ebner
- Institute
of Biophysics, Johannes Kepler University, 4020 Linz, Austria
| | | | - Hermann J. Gruber
- Institute
of Biophysics, Johannes Kepler University, 4020 Linz, Austria
| | - David Alsteens
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
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35
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Imaging and Force Spectroscopy of Single Transmembrane Proteins with the Atomic Force Microscope. Methods Mol Biol 2020. [PMID: 31218616 DOI: 10.1007/978-1-4939-9512-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The atomic force microscope (AFM) has opened avenues and provided opportunities to investigate biological soft matter and processes ranging from nanometer (nm) to millimeter (mm). The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever-aptly termed as a "lab on a tip"-can be used as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples have convincingly established AFM as a tool to study the mechanical properties and monitor processes of single proteins and cells with high sensitivity, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of transmembrane proteins in a lipid bilayer (reconstituted or native). Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theory and practical skills.
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Simultaneous co-localized super-resolution fluorescence microscopy and atomic force microscopy: combined SIM and AFM platform for the life sciences. Sci Rep 2020; 10:1122. [PMID: 31980680 PMCID: PMC6981207 DOI: 10.1038/s41598-020-57885-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/07/2020] [Indexed: 01/05/2023] Open
Abstract
Correlating data from different microscopy techniques holds the potential to discover new facets of signaling events in cellular biology. Here we report for the first time a hardware set-up capable of achieving simultaneous co-localized imaging of spatially correlated far-field super-resolution fluorescence microscopy and atomic force microscopy, a feat only obtained until now by fluorescence microscopy set-ups with spatial resolution restricted by the Abbe diffraction limit. We detail system integration and demonstrate system performance using sub-resolution fluorescent beads and applied to a test sample consisting of human bone osteosarcoma epithelial cells, with plasma membrane transporter 1 (MCT1) tagged with an enhanced green fluorescent protein (EGFP) at the N-terminal.
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Koehler M, Aravamudhan P, Guzman-Cardozo C, Dumitru AC, Yang J, Gargiulo S, Soumillion P, Dermody TS, Alsteens D. Glycan-mediated enhancement of reovirus receptor binding. Nat Commun 2019; 10:4460. [PMID: 31575869 PMCID: PMC6773860 DOI: 10.1038/s41467-019-12411-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/06/2019] [Indexed: 01/10/2023] Open
Abstract
Viral infection is an intricate process that requires the concerted action of both viral and host cell components. Entry of viruses into cells is initiated by interactions between viral proteins and their cell surface receptors. Despite recent progress, the molecular mechanisms underlying the multistep reovirus entry process are poorly understood. Using atomic force microscopy, we investigated how the reovirus σ1 attachment protein binds to both α-linked sialic acid (α-SA) and JAM-A cell-surface receptors. We discovered that initial σ1 binding to α-SA favors a strong multivalent anchorage to JAM-A. The enhanced JAM-A binding by virions following α-SA engagement is comparable to JAM-A binding by infectious subvirion particles (ISVPs) in the absence of α-SA. Since ISVPs have an extended σ1 conformer, this finding suggests that α-SA binding triggers a conformational change in σ1. These results provide new insights into the function of viral attachment proteins in the initiation of infection and open new avenues for the use of reoviruses as oncolytic agents.
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Affiliation(s)
- Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Pavithra Aravamudhan
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Microbial Pathogenesis, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Camila Guzman-Cardozo
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Microbial Pathogenesis, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Jinsung Yang
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Serena Gargiulo
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Patrice Soumillion
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Terence S Dermody
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Center for Microbial Pathogenesis, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
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Wang H, Tang Z, Wang Y, Ma G, Tao N. Probing Single Molecule Binding and Free Energy Profile with Plasmonic Imaging of Nanoparticles. J Am Chem Soc 2019; 141:16071-16078. [DOI: 10.1021/jacs.9b08405] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hui Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhuodong Tang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yan Wang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, United States
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Guangzhong Ma
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, United States
| | - Nongjian Tao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, United States
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, United States
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Lo Giudice C, Dumitru AC, Alsteens D. Probing ligand-receptor bonds in physiologically relevant conditions using AFM. Anal Bioanal Chem 2019; 411:6549-6559. [PMID: 31410537 DOI: 10.1007/s00216-019-02077-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 12/16/2022]
Abstract
Cell surface receptors, often called transmembrane receptors, are key cellular components as they control and mediate cell communication and signalling, converting extracellular signals into intracellular signals. Elucidating the molecular details of ligand binding (cytokine, growth factors, hormones, pathogens,...) to cell surface receptors and how this binding triggers conformational changes that initiate intracellular signalling is needed to improve our understanding of cellular processes and for rational drug design. Unfortunately, the molecular complexity and high hydrophobicity of membrane proteins significantly hamper their structural and functional characterization in conditions mimicking their native environment. With its piconewton force sensitivity and (sub)nanometer spatial resolution, together with the capability of operating in liquid environment and at physiological temperature, atomic force microscopy (AFM) has proven to be one of the most powerful tools to image and quantify receptor-ligand bonds in situ under physiologically relevant conditions. In this article, a brief overview of the rapid evolution of AFM towards quantitative biological mapping will be given, followed by selected examples highlighting the main advances that AFM-based ligand-receptor studies have brought to the fields of cell biology, immunology, microbiology, and virology, along with future prospects and challenges. Graphical abstract.
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Affiliation(s)
- Cristina Lo Giudice
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du sud 4-5, 1348, Louvain-la-Neuve, Belgium.
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40
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Collett S, Torresi J, Earnest-Silveira L, Christiansen D, Elbourne A, Ramsland PA. Probing and pressing surfaces of hepatitis C virus-like particles. J Colloid Interface Sci 2019; 545:259-268. [DOI: 10.1016/j.jcis.2019.03.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/07/2019] [Accepted: 03/09/2019] [Indexed: 02/09/2023]
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41
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Wan Z, Shaheen S, Chau A, Zeng Y, Liu W. Imaging: Gear up for mechano-immunology. Cell Immunol 2019; 350:103926. [PMID: 31151736 DOI: 10.1016/j.cellimm.2019.103926] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 04/15/2019] [Accepted: 05/15/2019] [Indexed: 12/17/2022]
Abstract
Immune cells including B and T lymphocytes have a remarkable ability to sense the physical perturbations through their surface expressed receptors. At the advent of modern imaging technologies paired with biophysical methods, we have gained the understanding of mechanical forces exerted by immune cells to perform their functions. This review will go over the imaging techniques already being used to study mechanical forces in immune cells. We will also discuss the dire need for new modern technologies for future work.
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Affiliation(s)
- Zhengpeng Wan
- MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing 100084, China; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Samina Shaheen
- MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing 100084, China
| | - Alicia Chau
- MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing 100084, China
| | - Yingyue Zeng
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Wanli Liu
- MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing 100084, China; Beijing Key Lab for Immunological Research on Chronic Diseases, Beijing 100084, China.
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42
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Zhang X, He Y, Liu J, Bowden ME, Kovarik L, Mao SX, Wang C, De Yoreo JJ, Rosso KM. Accessing crystal-crystal interaction forces with oriented nanocrystal atomic force microscopy probes. Nat Protoc 2019; 13:2005-2030. [PMID: 30190550 DOI: 10.1038/s41596-018-0027-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biominerals serve as critical structures of living systems and play important roles in biochemical processes. Understanding their crystallization mechanisms is therefore central to many areas of biology, biogeoscience, and biochemistry. Some biominerals, such as bone and dentin, are hierarchical nanocomposite structures constructed by sequential addition of individual oriented nanocrystals. The driving forces that enable this oriented assembly are still poorly understood, with advances in understanding limited in part by the availability of techniques that can precisely measure the delicate interactions between nanocrystals as a function of their separation distance and mutual orientation. Here, we provide a comprehensive protocol for (i) fabricating oriented single-nanocrystal atomic force microscopy (AFM) probes using focused ion beam (FIB) milling and (ii) performing oriented nanocrystal interaction force measurements using dynamic force spectroscopy (DFS)-based AFM and environmental transmission electron microscopy (ETEM)-AFM techniques. We illustrate how to fabricate oriented nanocrystal force probes using commercial bulk crystals or nano/microcrystals of calcite, zinc oxide, and rutile. The typical protocol for fabricating one AFM crystal probe takes 2-3 h. In addition, we illustrate how to quantify the direction-specific interaction forces for a given pair of interacting oriented nanocrystal faces. The methods are fully transferrable to other minerals of interest, such as the apatites constituting bone minerals. This allows researchers across many fields to measure and understand particle-based crystallization processes.
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Affiliation(s)
- Xin Zhang
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Yang He
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jia Liu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mark E Bowden
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Libor Kovarik
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Scott X Mao
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chongmin Wang
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - James J De Yoreo
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kevin M Rosso
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
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Delguste M, Peerboom N, Le Brun G, Trybala E, Olofsson S, Bergström T, Alsteens D, Bally M. Regulatory Mechanisms of the Mucin-Like Region on Herpes Simplex Virus during Cellular Attachment. ACS Chem Biol 2019; 14:534-542. [PMID: 30735356 DOI: 10.1021/acschembio.9b00064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Mucin-like regions, characterized by a local high density of O-linked glycosylation, are found on the viral envelope glycoproteins of many viruses. Herpes simplex virus type 1 (HSV-1), for example, exhibits a mucin-like region on its glycoprotein gC, a viral protein involved in initial recruitment of the virus to the cell surface via interaction with sulfated glycosaminoglycans. So far, this mucin-like region has been proposed to play a key role in modulating the interactions with cellular glycosaminoglycans, and in particular to promote release of HSV-1 virions from infected cells. However, the molecular mechanisms and the role as a pathogenicity factor remains unclear. Using single virus particle tracking, we show that the mobility of chondroitin sulfate-bound HSV-1 virions is decreased in absence of the mucin-like region. This decrease in mobility correlates with an increase in HSV-1-chondroitin sulfate binding forces as observed using atomic force microscopy-based force spectroscopy. Our data suggest that the mucin-like region modulates virus-glycosaminoglycan interactions by regulating the affinity, type, and number of glycoproteins involved in the virus-glycosaminoglycan interaction. This study therefore presents new evidence for a role of the mucin-like region in balancing the interaction of HSV-1 with glycosaminoglycans and provides further insights into the molecular mechanisms used by the virus to ensure both successful cell entry and release from the infected cell.
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Affiliation(s)
- Martin Delguste
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348 Louvain-la-Neuve, Belgium
| | - Nadia Peerboom
- Department of Physics, Chalmers University of Technology, 41296 Göteborg, Sweden
| | - Grégoire Le Brun
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348 Louvain-la-Neuve, Belgium
| | - Edward Trybala
- Department of Infectious Diseases, University of Gothenburg, 41346 Göteborg, Sweden
| | - Sigvard Olofsson
- Department of Infectious Diseases, University of Gothenburg, 41346 Göteborg, Sweden
| | - Tomas Bergström
- Department of Infectious Diseases, University of Gothenburg, 41346 Göteborg, Sweden
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348 Louvain-la-Neuve, Belgium
| | - Marta Bally
- Department of Clinical Microbiology, Umeå University, 90185 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, 90185 Umeå, Sweden
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Rosso G, Liashkovich I, Shahin V. In Situ Investigation of Interrelationships Between Morphology and Biomechanics of Endothelial and Glial Cells and their Nuclei. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1801638. [PMID: 30643730 PMCID: PMC6325600 DOI: 10.1002/advs.201801638] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Indexed: 05/22/2023]
Abstract
Morphology and biomechanics of cells and nuclei are interlinked with one another and play key roles in fundamental physiological processes. While powerful approaches are available for performing separate morphological and biomechanical investigations on cells and nuclei, simultaneous investigations in situ are challenging. Here, an appropriate approach is presented based on the simultaneous combination of atomic force microscopy and confocal microscopy in situ. Two cell types with entirely different morphologies, physiological roles, and biomechanical environments are investigated: vascular endothelial cells (ECs) with dense cytoskeletal actin, and nervous system glial cells (Schwann cells (SCs)) with dense vimentin network. Results reveal that ECs and their nuclei show high pliability and tend to undergo deformation only at compression sites. SCs, in contrast, show greater ability to resist mechanical deformation. Likewise, SC nuclei are harder to deform than EC nuclei, despite that SC nuclei have significantly lower amounts of lamins A/C, which reportedly scale with nuclear stiffness. The morphology-biomechanics interrelationships in SCs, ECs, and their nuclei may be a key factor in ensuring their physiological functions. In adult SCs, mechanosensitivity is presumably traded for mechanical strength to protect the neurons they encase, whereas ECs maintain mechanosensitivity to ensure specific local physiological response to mechanical stimuli.
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Affiliation(s)
- Gonzalo Rosso
- Biotechnology CenterTechnische Universität DresdenTatzberg 47/4901307DresdenGermany
| | - Ivan Liashkovich
- Institute of Physiology IIUniversity of MünsterRobert‐Koch Str. 27b48149MünsterGermany
| | - Victor Shahin
- Institute of Physiology IIUniversity of MünsterRobert‐Koch Str. 27b48149MünsterGermany
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Visualization of perforin/gasdermin/complement-formed pores in real cell membranes using atomic force microscopy. Cell Mol Immunol 2018; 16:611-620. [PMID: 30283066 PMCID: PMC6804747 DOI: 10.1038/s41423-018-0165-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 08/13/2018] [Indexed: 01/05/2023] Open
Abstract
Different types of pores ubiquitously form in cell membranes, leading to various types of cell death that profoundly influence the fate of inflammation and the disease status. However, these pores have never truly been visualized to date. Atomic force microscopy (AFM), which is emerging as a powerful tool to analyze the mechanical properties of biomolecules and cells, is actually an excellent imaging platform that allows biological samples to be visualized by probing surface roughness at the level of atomic resolution. Here, membrane pore structures were clearly visualized using AFM. This visualization not only describes the aperture and depth of the pore complexes but also highlights differences among the pores formed by perforin and gasdermins in tumor cell membranes and by complement in immune cell membranes. Additionally, this type of visualization also reveals the dynamic process of pore formation, fusion, and repair.
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Delguste M, Zeippen C, Machiels B, Mast J, Gillet L, Alsteens D. Multivalent binding of herpesvirus to living cells is tightly regulated during infection. SCIENCE ADVANCES 2018; 4:eaat1273. [PMID: 30128355 PMCID: PMC6097811 DOI: 10.1126/sciadv.aat1273] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 07/11/2018] [Indexed: 05/08/2023]
Abstract
Viral infection, initiated by the landing of a virion on a cellular surface, is largely defined by the preliminary interactions established between viral particles and their receptors at the cell surface. While multiple parallel interactions would allow strong virus attachment, a low number of bonds could be preferred to allow lateral diffusion toward specific receptors and to promote efficient release of progeny virions from the cell surface. However, so far, the molecular mechanisms underlying the regulation of the multivalency in virus attachment to receptors are poorly understood. We introduce a new method to force-probe multivalent attachment directly on living cells, and we show, for the first time, direct evidence of a new mechanism by which a herpesvirus surface glycoprotein acts as a key negative regulator in the first step of herpesvirus binding. Using atomic force microscopy, we probe at the single-virion level the number and the strength of the bonds established with heparan sulfate both on model surfaces and on living cells. Our biophysical results, correlated with other techniques, show that the major envelope glycoprotein functions as a regulator of binding valency during both attachment and release steps, determining the binding, diffusion, and release potential of virions at the cellular surface.
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Affiliation(s)
- Martin Delguste
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Caroline Zeippen
- Immunology-Vaccinology, Fundamental and Applied Research for Animals and Health Center (FARAH), University of Liège, 4000 Liège, Belgium
| | - Bénédicte Machiels
- Immunology-Vaccinology, Fundamental and Applied Research for Animals and Health Center (FARAH), University of Liège, 4000 Liège, Belgium
| | - Jan Mast
- Electron Microscopy Unit, Veterinary and Agrochemical Research Centre (CODA-CERVA), Brussels, Belgium
| | - Laurent Gillet
- Immunology-Vaccinology, Fundamental and Applied Research for Animals and Health Center (FARAH), University of Liège, 4000 Liège, Belgium
- Corresponding author. (L.G.); (D.A.)
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
- Corresponding author. (L.G.); (D.A.)
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