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Abstract
Imaging of nano-sized particles and sample features is crucial in a variety of research fields. For instance in biological sciences, where it is paramount to investigate structures at the single particle level. Often two-dimensional images are not sufficient and further information such as topography and mechanical properties are required. Furthermore, to increase the biological relevance, it is desired to perform the imaging in close to physiological environments. Atomic force microscopy (AFM) meets these demands in an all-in-one instrument. It provides high-resolution images including surface height information leading to three-dimensional information on sample morphology. AFM can be operated both in air and in buffer solutions. Moreover, it has the capacity to determine protein and membrane material properties via the force spectroscopy mode. Here we discuss the principles of AFM operation and provide examples of how biomolecules can be studied. By including new approaches such as high-speed AFM (HS-AFM) we show how AFM can be used to study a variety of static and dynamic single biomolecules and biomolecular assemblies.
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Affiliation(s)
- Melissa C Piontek
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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52
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Rodriguez-Ramos J, Faulkner M, Liu LN. Nanoscale Visualization of Bacterial Microcompartments Using Atomic Force Microscopy. Methods Mol Biol 2018; 1814:373-383. [PMID: 29956244 DOI: 10.1007/978-1-4939-8591-3_22] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial microcompartments (BMCs) are polyhedral protein organelles in many prokaryotes, playing significant roles in metabolic enhancement. Due to their self-assembly and modularity nature, BMCs have gained increased interest in recent years, with the intent of constructing new nanobioreactors and scaffolding to promote cellular metabolisms and molecule delivery. In this chapter, we describe the technique of atomic force microscopy (AFM) as a method to study the self-assembly dynamics and physical properties of BMCs. We focus on the sample preparation, the measurement procedure, and the data analysis for high-speed AFM imaging and nanoindentation-based spectroscopy, which were used to determine the assembly dynamics of BMC shell proteins and the nanomechanics of intact BMC structures, respectively. The described methods could be applied to the study of other types of self-assembling biological organelles.
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Affiliation(s)
| | - Matthew Faulkner
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
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53
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Faulkner M, Rodriguez-Ramos J, Dykes GF, Owen SV, Casella S, Simpson DM, Beynon RJ, Liu LN. Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes. NANOSCALE 2017; 9:10662-10673. [PMID: 28616951 PMCID: PMC5708340 DOI: 10.1039/c7nr02524f] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Carboxysomes are proteinaceous organelles that play essential roles in enhancing carbon fixation in cyanobacteria and some proteobacteria. These self-assembling organelles encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase using a protein shell structurally resembling an icosahedral viral capsid. The protein shell serves as a physical barrier to protect enzymes from the cytosol and a selectively permeable membrane to mediate transport of enzyme substrates and products. The structural and mechanical nature of native carboxysomes remain unclear. Here, we isolate functional β-carboxysomes from the cyanobacterium Synechococcus elongatus PCC7942 and perform the first characterization of the macromolecular architecture and inherent physical mechanics of single β-carboxysomes using electron microscopy, atomic force microscopy (AFM) and proteomics. Our results illustrate that the intact β-carboxysome comprises three structural domains, a single-layered icosahedral shell, an inner layer and paracrystalline arrays of interior Rubisco. We also observe the protein organization of the shell and partial β-carboxysomes that likely serve as the β-carboxysome assembly intermediates. Furthermore, the topography and intrinsic mechanics of functional β-carboxysomes are determined in native conditions using AFM and AFM-based nanoindentation, revealing the flexible organization and soft mechanical properties of β-carboxysomes compared to rigid viruses. Our study provides new insights into the natural characteristics of β-carboxysome organization and nanomechanics, which can be extended to diverse bacterial microcompartments and are important considerations for the design and engineering of functional carboxysomes in other organisms to supercharge photosynthesis. It offers an approach for inspecting the structural and mechanical features of synthetic metabolic organelles and protein scaffolds in bioengineering.
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Affiliation(s)
- Matthew Faulkner
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | | | - Gregory F Dykes
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Siân V Owen
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Selene Casella
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Deborah M Simpson
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Robert J Beynon
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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54
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Shaheen S, Wan Z, Li Z, Chau A, Li X, Zhang S, Liu Y, Yi J, Zeng Y, Wang J, Chen X, Xu L, Chen W, Wang F, Lu Y, Zheng W, Shi Y, Sun X, Li Z, Xiong C, Liu W. Substrate stiffness governs the initiation of B cell activation by the concerted signaling of PKCβ and focal adhesion kinase. eLife 2017; 6. [PMID: 28755662 PMCID: PMC5536945 DOI: 10.7554/elife.23060] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 07/03/2017] [Indexed: 12/17/2022] Open
Abstract
The mechanosensing ability of lymphocytes regulates their activation in response to antigen stimulation, but the underlying mechanism remains unexplored. Here, we report that B cell mechanosensing-governed activation requires BCR signaling molecules. PMA-induced activation of PKCβ can bypass the Btk and PLC-γ2 signaling molecules that are usually required for B cells to discriminate substrate stiffness. Instead, PKCβ-dependent activation of FAK is required, leading to FAK-mediated potentiation of B cell spreading and adhesion responses. FAK inactivation or deficiency impaired B cell discrimination of substrate stiffness. Conversely, adhesion molecules greatly enhanced this capability of B cells. Lastly, B cells derived from rheumatoid arthritis (RA) patients exhibited an altered BCR response to substrate stiffness in comparison with healthy controls. These results provide a molecular explanation of how initiation of B cell activation discriminates substrate stiffness through a PKCβ-mediated FAK activation dependent manner.
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Affiliation(s)
- 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, China
| | - 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, China
| | - Zongyu Li
- 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, China
| | - Alicia Chau
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xinxin Li
- 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, China
| | - Shaosen Zhang
- 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, China
| | - Yang 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, China
| | - Junyang Yi
- 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, China
| | - Yingyue Zeng
- 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, China
| | - Jing Wang
- 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, China
| | - Xiangjun Chen
- 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, China
| | - Liling Xu
- 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, China
| | - Wei Chen
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Fei Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yun Lu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Wenjie Zheng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yan Shi
- Center for Life Sciences, Department of Basic Medical Sciences, Institute of Immunology, Tsinghua University, Beijing, China
| | - Xiaolin Sun
- Department of Rheumatology and Immunology, Clinical Immunology Center, Peking University People's Hospital, Beijing, China
| | - Zhanguo Li
- Department of Rheumatology and Immunology, Clinical Immunology Center, Peking University People's Hospital, Beijing, China
| | - Chunyang Xiong
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,College of Engineering, Peking University, Beijing, 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, China
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55
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AFM nanoindentation of protein shells, expanding the approach beyond viruses. Semin Cell Dev Biol 2017; 73:145-152. [PMID: 28774579 DOI: 10.1016/j.semcdb.2017.07.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/26/2017] [Accepted: 07/28/2017] [Indexed: 02/01/2023]
Abstract
The archetypical protein nanoshell is the capsid that surrounds viral genomes. These capsids protect the viral RNA or DNA and function as transport vehicle for their nucleic acid. The material properties of a variety of viral capsids have been probed by Atomic Force Microscopy. In particular nanoindentation measurements revealed the complex mechanics of these shells and the intricate interplay of the capsid with its genomic content. Furthermore, effects of capsid protein mutations, capsid maturation and the effect of environmental changes have been probed. In addition, biological questions have been addressed by AFM nanoindentation of viruses and a direct link between mechanics and infectivity has been revealed. Recently, non-viral protein nanoshells have come under intense scrutiny and now the nanoindentation approach has been expanded to such particles as well. Both natural as well as engineered non-viral protein shells have been probed by this technique. Next to the material properties of viruses, therefor also the mechanics of encapsulins, carboxysomes, vault particles, lumazine synthase and artificial protein nanoshells is discussed here.
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56
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Valbuena A, Mateu MG. Kinetics of Surface-Driven Self-Assembly and Fatigue-Induced Disassembly of a Virus-Based Nanocoating. Biophys J 2017; 112:663-673. [PMID: 28256226 DOI: 10.1016/j.bpj.2016.11.3209] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 10/19/2016] [Accepted: 11/21/2016] [Indexed: 02/02/2023] Open
Abstract
Self-assembling protein layers provide a "bottom-up" approach for precisely organizing functional elements at the nanoscale over a large solid surface area. The design of protein sheets with architecture and physical properties suitable for nanotechnological applications may be greatly facilitated by a thorough understanding of the principles that underlie their self-assembly and disassembly. In a previous study, the hexagonal lattice formed by the capsid protein (CA) of human immunodeficiency virus (HIV) was self-assembled as a monomolecular layer directly onto a solid substrate, and its mechanical properties and dynamics at equilibrium were analyzed by atomic force microscopy. Here, we use atomic force microscopy to analyze the kinetics of self-assembly of the planar CA lattice on a substrate and of its disassembly, either spontaneous or induced by materials fatigue. Both self-assembly and disassembly of the CA layer are cooperative reactions that proceed until a phase equilibrium is reached. Self-assembly requires a critical protein concentration and is initiated by formation of nucleation points on the substrate, followed by lattice growth and eventual merging of CA patches into a continuous monolayer. Disassembly of the CA layer showed hysteresis and appears to proceed only after large enough defects (nucleation points) are formed in the lattice, whose number is largely increased by inducing materials fatigue that depends on mechanical load and its frequency. Implications of the kinetic results obtained for a better understanding of self-assembly and disassembly of the HIV capsid and protein-based two-dimensional nanomaterials and the design of anti-HIV drugs targeting (dis)assembly and biocompatible nanocoatings are discussed.
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Affiliation(s)
- Alejandro Valbuena
- Centro de Biologia Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biologia Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Madrid, Spain.
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57
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Guerra P, Valbuena A, Querol-Audí J, Silva C, Castellanos M, Rodríguez-Huete A, Garriga D, Mateu MG, Verdaguer N. Structural basis for biologically relevant mechanical stiffening of a virus capsid by cavity-creating or spacefilling mutations. Sci Rep 2017; 7:4101. [PMID: 28642465 PMCID: PMC5481337 DOI: 10.1038/s41598-017-04345-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 05/12/2017] [Indexed: 11/26/2022] Open
Abstract
Recent studies reveal that the mechanical properties of virus particles may have been shaped by evolution to facilitate virus survival. Manipulation of the mechanical behavior of virus capsids is leading to a better understanding of viral infection, and to the development of virus-based nanoparticles with improved mechanical properties for nanotechnological applications. In the minute virus of mice (MVM), deleterious mutations around capsid pores involved in infection-related translocation events invariably increased local mechanical stiffness and interfered with pore-associated dynamics. To provide atomic-resolution insights into biologically relevant changes in virus capsid mechanics, we have determined by X-ray crystallography the structural effects of deleterious, mechanically stiffening mutations around the capsid pores. Data show that the cavity-creating N170A mutation at the pore wall does not induce any dramatic structural change around the pores, but instead generates subtle rearrangements that propagate throughout the capsid, resulting in a more compact, less flexible structure. Analysis of the spacefilling L172W mutation revealed the same relationship between increased stiffness and compacted capsid structure. Implications for understanding connections between virus mechanics, structure, dynamics and infectivity, and for engineering modified virus-based nanoparticles, are discussed.
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Affiliation(s)
- Pablo Guerra
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Jordi Querol-Audí
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
| | - Cristina Silva
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
| | - Milagros Castellanos
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Damià Garriga
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain.
| | - Nuria Verdaguer
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain.
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58
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Carrillo PJP, Medrano M, Valbuena A, Rodríguez-Huete A, Castellanos M, Pérez R, Mateu MG. Amino Acid Side Chains Buried along Intersubunit Interfaces in a Viral Capsid Preserve Low Mechanical Stiffness Associated with Virus Infectivity. ACS NANO 2017; 11:2194-2208. [PMID: 28117975 DOI: 10.1021/acsnano.6b08549] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Single-molecule experimental techniques and theoretical approaches reveal that important aspects of virus biology can be understood in biomechanical terms at the nanoscale. A detailed knowledge of the relationship in virus capsids between small structural changes caused by single-point mutations and changes in mechanical properties may provide further physics-based insights into virus function; it may also facilitate the engineering of viral nanoparticles with improved mechanical behavior. Here, we used the minute virus of mice to undertake a systematic experimental study on the contribution to capsid stiffness of amino acid side chains at interprotein interfaces and the specific noncovalent interactions they establish. Selected side chains were individually truncated by introducing point mutations to alanine, and the effects on local and global capsid stiffness were determined using atomic force microscopy. The results revealed that, in the natural virus capsid, multiple, mostly hydrophobic, side chains buried along the interfaces between subunits preserve a comparatively low stiffness of most (S2 and S3) regions. Virtually no point mutation tested substantially reduced stiffness, whereas most mutations increased stiffness of the S2/S3 regions. This stiffening was invariably associated with reduced virus yields during cell infection. The experimental evidence suggests that a comparatively low stiffness at S3/S2 capsid regions may have been biologically selected because it facilitates capsid assembly, increasing infectious virus yields. This study demonstrated also that knowledge of individual amino acid side chains and biological pressures that determine the physical behavior of a protein nanoparticle may be used for engineering its mechanical properties.
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Affiliation(s)
- Pablo José P Carrillo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - María Medrano
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Milagros Castellanos
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Rebeca Pérez
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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59
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Vörös Z, Csík G, Herényi L, Kellermayer MSZ. Stepwise reversible nanomechanical buckling in a viral capsid. NANOSCALE 2017; 9:1136-1143. [PMID: 28009879 DOI: 10.1039/c6nr06598h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Viruses are nanoscale infectious agents constructed of a proteinaceous capsid that protects the packaged genomic material. Nanoindentation experiments using atomic force microscopy have, in recent years, provided unprecedented insight into the elastic properties, structural stability and maturation-dependent mechanical changes in viruses. However, the dynamics of capsid behavior are still unresolved. Here we used high-resolution nanoindentation experiments on mature, DNA-filled T7 bacteriophage particles. The elastic regime of the nanoindentation force trace contained discrete, stepwise transitions that cause buckling of the T7 capsid with magnitudes that are integer multiples of ∼0.6 nm. Remarkably, the transitions are reversible and contribute to the rapid consolidation of the capsid structure against a force during cantilever retraction. The stepwise transitions were present even following the removal of the genomic DNA by heat treatment, indicating that they are related to the structure and dynamics of the capsomeric proteins. Dynamic force spectroscopy experiments revealed that the thermally activated consolidation step is ∼104 times faster than spontaneous buckling, suggesting that the capsid stability is under strong dynamic control. Capsid structural dynamics may play an important role in protecting the genomic material from harsh environmental impacts. The nanomechanics approach employed here may be used to investigate the structural dynamics of other viruses and nanoscale containers as well.
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Affiliation(s)
- Zsuzsanna Vörös
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47., Budapest H-1094, Hungary.
| | - Gabriella Csík
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47., Budapest H-1094, Hungary.
| | - Levente Herényi
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47., Budapest H-1094, Hungary.
| | - Miklós S Z Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47., Budapest H-1094, Hungary. and MTA-SE Molecular Biophysics Research Group, Semmelweis University, Tűzoltó u. 37-47., Budapest H-1094, Hungary
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60
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Medrano M, Fuertes MÁ, Valbuena A, Carrillo PJP, Rodríguez-Huete A, Mateu MG. Imaging and Quantitation of a Succession of Transient Intermediates Reveal the Reversible Self-Assembly Pathway of a Simple Icosahedral Virus Capsid. J Am Chem Soc 2016; 138:15385-15396. [PMID: 27933931 DOI: 10.1021/jacs.6b07663] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Understanding the fundamental principles underlying supramolecular self-assembly may facilitate many developments, from novel antivirals to self-organized nanodevices. Icosahedral virus particles constitute paradigms to study self-assembly using a combination of theory and experiment. Unfortunately, assembly pathways of the structurally simplest virus capsids, those more accessible to detailed theoretical studies, have been difficult to study experimentally. We have enabled the in vitro self-assembly under close to physiological conditions of one of the simplest virus particles known, the minute virus of mice (MVM) capsid, and experimentally analyzed its pathways of assembly and disassembly. A combination of electron microscopy and high-resolution atomic force microscopy was used to structurally characterize and quantify a succession of transient assembly and disassembly intermediates. The results provided an experiment-based model for the reversible self-assembly pathway of a most simple (T = 1) icosahedral protein shell. During assembly, trimeric capsid building blocks are sequentially added to the growing capsid, with pentamers of building blocks and incomplete capsids missing one building block as conspicuous intermediates. This study provided experimental verification of many features of self-assembly of a simple T = 1 capsid predicted by molecular dynamics simulations. It also demonstrated atomic force microscopy imaging and automated analysis, in combination with electron microscopy, as a powerful single-particle approach to characterize at high resolution and quantify transient intermediates during supramolecular self-assembly/disassembly reactions. Finally, the efficient in vitro self-assembly achieved for the oncotropic, cell nucleus-targeted MVM capsid may facilitate its development as a drug-encapsidating nanoparticle for anticancer targeted drug delivery.
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Affiliation(s)
- María Medrano
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Miguel Ángel Fuertes
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Pablo J P Carrillo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
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61
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Effect of bio-engineering on size, shape, composition and rigidity of bacterial microcompartments. Sci Rep 2016; 6:36899. [PMID: 27845382 PMCID: PMC5109269 DOI: 10.1038/srep36899] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 10/21/2016] [Indexed: 12/17/2022] Open
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles that are found in a broad range of bacteria and are composed of an outer shell that encases an enzyme cargo representing a specific metabolic process. The outer shell is made from a number of different proteins that form hexameric and pentameric tiles, which interact to allow the formation of a polyhedral edifice. We have previously shown that the Citrobacter freundii BMC associated with 1,2-propanediol utilization can be transferred into Escherichia coli to generate a recombinant BMC and that empty BMCs can be formed from just the shell proteins alone. Herein, a detailed structural and proteomic characterization of the wild type BMC is compared to the recombinant BMC and a number of empty BMC variants by 2D-gel electrophoresis, mass spectrometry, transmission electron microscopy (TEM) and atomic force microscopy (AFM). Specifically, it is shown that the wild type BMC and the recombinant BMC are similar in terms of composition, size, shape and mechanical properties, whereas the empty BMC variants are shown to be smaller, hollow and less malleable.
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62
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Llauró A, Schwarz B, Koliyatt R, de Pablo PJ, Douglas T. Tuning Viral Capsid Nanoparticle Stability with Symmetrical Morphogenesis. ACS NANO 2016; 10:8465-73. [PMID: 27556288 DOI: 10.1021/acsnano.6b03441] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Virus-like particles (VLPs) provide engineering platforms for the design and implementation of protein-based nanostructures. These capsids are comprised of protein subunits whose precise arrangement and mutual interactions determine their stability, responsiveness to destabilizing environments, and ability to undergo morphological transitions. The precise interplay between subunit contacts and the overall stability of the bulk capsid population remains poorly resolved. Approaching this relationship requires a combination of techniques capable of accessing nanoscale properties, such as the mechanics of individual capsids, and bulk biochemical procedures capable of interrogating the stability of the VLP ensemble. To establish such connection, a VLP system is required where the subunit interactions can be manipulated in a controlled fashion. The P22 VLP is a promising platform for the design of nanomaterials and understanding how nanomanipulation of the particle affects bulk behavior. By contrasting single-particle atomic force microscopy and bulk chemical perturbations, we have related symmetry-specific anisotropic mechanical properties to the bulk ensemble behavior of the VLPs. Our results show that the expulsion of pentons at the vertices of the VLP induces a concomitant chemical and mechanical destabilization of the capsid and implicates the capsid edges as the points of mechanical fracture. Subsequent binding of a decoration protein at these critical edge regions restores both chemical and mechanical stability. The agreement between our single molecule and bulk techniques suggests that the same structural determinants govern both destabilizing and restorative mechanisms, unveiling a phenomenological coupling between the chemical and mechanical behavior of self-assembled cages and laying a framework for the analysis and manipulation of other VLPs and symmetric self-assembled structures.
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Affiliation(s)
| | - Benjamin Schwarz
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Ranjit Koliyatt
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | | | - Trevor Douglas
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
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63
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Yang L, Yamamoto T. Quantification of Virus Particles Using Nanopore-Based Resistive-Pulse Sensing Techniques. Front Microbiol 2016; 7:1500. [PMID: 27713738 PMCID: PMC5031608 DOI: 10.3389/fmicb.2016.01500] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 09/08/2016] [Indexed: 11/13/2022] Open
Abstract
Viruses have drawn much attention in recent years due to increased recognition of their important roles in virology, immunology, clinical diagnosis, and therapy. Because the biological and physical properties of viruses significantly impact their applications, quantitative detection of individual virus particles has become a critical issue. However, due to various inherent limitations of conventional enumeration techniques such as infectious titer assays, immunological assays, and electron microscopic observation, this issue remains challenging. Thanks to significant advances in nanotechnology, nanostructure-based electrical sensors have emerged as promising platforms for real-time, sensitive detection of numerous bioanalytes. In this paper, we review recent progress in nanopore-based electrical sensing, with particular emphasis on the application of this technique to the quantification of virus particles. Our aim is to provide insights into this novel nanosensor technology, and highlight its ability to enhance current understanding of a variety of viruses.
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Affiliation(s)
| | - Takatoki Yamamoto
- Department of Mechanical Engineering, School of Engineering, Tokyo Institute of TechnologyTokyo, Japan
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64
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Korneev DV, Popova AV, Generalov VM, Zaitsev BN. Atomic force microscopy-based single virus particle spectroscopy. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916030088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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65
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Zhang L, Ru CQ. Imperfection sensitivity of pressured buckling of biopolymer spherical shells. Phys Rev E 2016; 93:062403. [PMID: 27415294 DOI: 10.1103/physreve.93.062403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Indexed: 12/18/2022]
Abstract
Imperfection sensitivity is essential for mechanical behavior of biopolymer shells [such as ultrasound contrast agents (UCAs) and spherical viruses] characterized by high geometric heterogeneity. In this work, an imperfection sensitivity analysis is conducted based on a refined shell model recently developed for spherical biopolymer shells of high structural heterogeneity and thickness nonuniformity. The influence of related parameters (including the ratio of radius to average shell thickness, the ratio of transverse shear modulus to in-plane shear modulus, and the ratio of effective bending thickness to average shell thickness) on imperfection sensitivity is examined for pressured buckling. Our results show that the ratio of effective bending thickness to average shell thickness has a major effect on the imperfection sensitivity, while the effect of the ratio of transverse shear modulus to in-plane shear modulus is usually negligible. For example, with physically realistic parameters for typical imperfect spherical biopolymer shells, the present model predicts that actual maximum external pressure could be reduced to as low as 60% of that of a perfect UCA spherical shell or 55%-65% of that of a perfect spherical virus shell, respectively. The moderate imperfection sensitivity of spherical biopolymer shells with physically realistic imperfection is largely attributed to the fact that biopolymer shells are relatively thicker (defined by smaller radius-to-thickness ratio) and therefore practically realistic imperfection amplitude normalized by thickness is very small as compared to that of classical elastic thin shells which have much larger radius-to-thickness ratio.
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Affiliation(s)
- Lei Zhang
- Department of Mechanical Engineering, University of Alberta, Edmonton, Canada T6G 2G8
| | - C Q Ru
- Department of Mechanical Engineering, University of Alberta, Edmonton, Canada T6G 2G8
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66
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Marchetti M, Wuite GJL, Roos WH. Atomic force microscopy observation and characterization of single virions and virus-like particles by nano-indentation. Curr Opin Virol 2016; 18:82-8. [DOI: 10.1016/j.coviro.2016.05.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 11/15/2022]
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67
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Heinze K, Sasaki E, King NP, Baker D, Hilvert D, Wuite GJL, Roos WH. Protein Nanocontainers from Nonviral Origin: Testing the Mechanics of Artificial and Natural Protein Cages by AFM. J Phys Chem B 2016; 120:5945-52. [DOI: 10.1021/acs.jpcb.6b01464] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- K. Heinze
- Natuur-
en Sterrenkunde and LaserLaB, Vrije Universiteit, Amsterdam 1081 HV, The Netherlands
| | - E. Sasaki
- Laboratory
of Organic Chemistry, ETH Zürich, Zurich 8093, Switzerland
| | - N. P. King
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195-7350, United States
| | - D. Baker
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195-7350, United States
| | - D. Hilvert
- Laboratory
of Organic Chemistry, ETH Zürich, Zurich 8093, Switzerland
| | - G. J. L. Wuite
- Natuur-
en Sterrenkunde and LaserLaB, Vrije Universiteit, Amsterdam 1081 HV, The Netherlands
| | - W. H. Roos
- Moleculaire
Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen 9747 AG, The Netherlands
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68
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Llauró A, Luque D, Edwards E, Trus BL, Avera J, Reguera D, Douglas T, Pablo PJD, Castón JR. Cargo-shell and cargo-cargo couplings govern the mechanics of artificially loaded virus-derived cages. NANOSCALE 2016; 8:9328-36. [PMID: 27091107 PMCID: PMC4861311 DOI: 10.1039/c6nr01007e] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nucleic acids are the natural cargo of viruses and key determinants that affect viral shell stability. In some cases the genome structurally reinforces the shell, whereas in others genome packaging causes internal pressure that can induce destabilization. Although it is possible to pack heterologous cargoes inside virus-derived shells, little is known about the physical determinants of these artificial nanocontainers' stability. Atomic force and three-dimensional cryo-electron microscopy provided mechanical and structural information about the physical mechanisms of viral cage stabilization beyond the mere presence/absence of cargos. We analyzed the effects of cargo-shell and cargo-cargo interactions on shell stability after encapsulating two types of proteinaceous payloads. While bound cargo to the inner capsid surface mechanically reinforced the capsid in a structural manner, unbound cargo diffusing freely within the shell cavity pressurized the cages up to ∼30 atm due to steric effects. Strong cargo-cargo coupling reduces the resilience of these nanocompartments in ∼20% when bound to the shell. Understanding the stability of artificially loaded nanocages will help to design more robust and durable molecular nanocontainers.
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Affiliation(s)
- Aida Llauró
- Department of Physics of the Condensed Matter, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - Daniel Luque
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain. and Centro Nacional de Microbiología/Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - Ethan Edwards
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Benes L Trus
- Imaging Sciences Laboratory, Center for Information Technology/National Institutes of Health, Bethesda, MD 20892-5624, USA
| | - John Avera
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - David Reguera
- Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Trevor Douglas
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Pedro J de Pablo
- Department of Physics of the Condensed Matter, Universidad Autónoma de Madrid, 28049 Madrid, Spain. and Solid Condensed Matter Institute IFIMAC, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain.
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del Pino P, Yang F, Pelaz B, Zhang Q, Kantner K, Hartmann R, Martinez de Baroja N, Gallego M, Möller M, Manshian BB, Soenen SJ, Riedel R, Hampp N, Parak WJ. Basic Physicochemical Properties of Polyethylene Glycol Coated Gold Nanoparticles that Determine Their Interaction with Cells. Angew Chem Int Ed Engl 2016; 55:5483-7. [DOI: 10.1002/anie.201511733] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/08/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Pablo del Pino
- Fachbereich Physik Philipps Universität Marburg Marburg Germany
- CIC biomaGUNE San Sebastian Spain
| | - Fang Yang
- Fachbereich Chemie Philipps Universität Marburg Marburg Germany
| | - Beatriz Pelaz
- Fachbereich Physik Philipps Universität Marburg Marburg Germany
| | - Qian Zhang
- Fachbereich Physik Philipps Universität Marburg Marburg Germany
| | - Karsten Kantner
- Fachbereich Physik Philipps Universität Marburg Marburg Germany
| | - Raimo Hartmann
- Fachbereich Physik Philipps Universität Marburg Marburg Germany
| | | | | | | | | | | | - René Riedel
- Fachbereich Chemie Philipps Universität Marburg Marburg Germany
| | - Norbert Hampp
- Fachbereich Chemie Philipps Universität Marburg Marburg Germany
| | - Wolfgang J. Parak
- Fachbereich Physik Philipps Universität Marburg Marburg Germany
- CIC biomaGUNE San Sebastian Spain
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70
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del Pino P, Yang F, Pelaz B, Zhang Q, Kantner K, Hartmann R, Martinez de Baroja N, Gallego M, Möller M, Manshian BB, Soenen SJ, Riedel R, Hampp N, Parak WJ. Basic Physicochemical Properties of Polyethylene Glycol Coated Gold Nanoparticles that Determine Their Interaction with Cells. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511733] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Pablo del Pino
- Fachbereich Physik Philipps Universität Marburg Marburg Germany
- CIC biomaGUNE San Sebastian Spain
| | - Fang Yang
- Fachbereich Chemie Philipps Universität Marburg Marburg Germany
| | - Beatriz Pelaz
- Fachbereich Physik Philipps Universität Marburg Marburg Germany
| | - Qian Zhang
- Fachbereich Physik Philipps Universität Marburg Marburg Germany
| | - Karsten Kantner
- Fachbereich Physik Philipps Universität Marburg Marburg Germany
| | - Raimo Hartmann
- Fachbereich Physik Philipps Universität Marburg Marburg Germany
| | | | | | | | | | | | - René Riedel
- Fachbereich Chemie Philipps Universität Marburg Marburg Germany
| | - Norbert Hampp
- Fachbereich Chemie Philipps Universität Marburg Marburg Germany
| | - Wolfgang J. Parak
- Fachbereich Physik Philipps Universität Marburg Marburg Germany
- CIC biomaGUNE San Sebastian Spain
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71
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Ramalho R, Rankovic S, Zhou J, Aiken C, Rousso I. Analysis of the mechanical properties of wild type and hyperstable mutants of the HIV-1 capsid. Retrovirology 2016; 13:17. [PMID: 26979152 PMCID: PMC4793510 DOI: 10.1186/s12977-016-0250-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/08/2016] [Indexed: 12/28/2022] Open
Abstract
Background The human immunodeficiency virus (HIV-1) capsid is a self-assembled protein shell that contains the viral genome. During the stages between viral entry into a host cell and nuclear import of the viral DNA, the capsid dissociates in a process known as uncoating, which leads to the release of the viral genetic material. Mutations that alter the stability of the capsid affect the uncoating rate and impair HIV-1 infectivity. Results To gain further insight into the role of capsid stability during uncoating, we used atomic force spectroscopy to quantify the stiffness of the capsid. Empty in vitro assemblies of wild type (WT) and mutant recombinant HIV-1 capsid protein (CA) as well as isolated WT and mutant HIV-1 cores (i.e., filled capsids) were analyzed. We find that hyperstable CA mutant assemblies (A204C, A14C/E45C, E45A and E45A/R132T) are significantly stiffer than WT assemblies. However, the hardening effect of disulfide crosslinking (A204C and A14C/E45C) is lower than that of hydrophobic interactions (E45A and E45A/R132T). Conclusions Our results demonstrate that mutations that increase the intrinsic stability of the HIV-1 capsid have an increased stiffness of their lattice.
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Affiliation(s)
- Ruben Ramalho
- Department of Physiology and Cell Biology, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Sanela Rankovic
- Department of Physiology and Cell Biology, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Jing Zhou
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Christopher Aiken
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Itay Rousso
- Department of Physiology and Cell Biology, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel.
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72
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Mateu MG. Assembly, Engineering and Applications of Virus-Based Protein Nanoparticles. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 940:83-120. [PMID: 27677510 DOI: 10.1007/978-3-319-39196-0_5] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Viruses and their protein capsids can be regarded as biologically evolved nanomachines able to perform multiple, complex biological functions through coordinated mechano-chemical actions during the infectious cycle. The advent of nanoscience and nanotechnology has opened up, in the last 10 years or so, a vast number of novel possibilities to exploit engineered viral capsids as protein-based nanoparticles for multiple biomedical, biotechnological or nanotechnological applications. This chapter attempts to provide a broad, updated overview on the self-assembly and engineering of virus capsids, and on applications of virus-based nanoparticles. Different sections provide outlines on: (i) the structure, functions and properties of virus capsids; (ii) general approaches for obtaining assembled virus particles; (iii) basic principles and events related to virus capsid self-assembly; (iv) genetic and chemical strategies for engineering virus particles; (v) some applications of engineered virus particles being developed; and (vi) some examples on the engineering of virus particles to modify their physical properties, in order to improve their suitability for different uses.
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Affiliation(s)
- Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain. .,Department of Molecular Biology, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain.
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73
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Besnard L, Fabre V, Fettig M, Gousseinov E, Kawakami Y, Laroudie N, Scanlan C, Pattnaik P. Clarification of vaccines: An overview of filter based technology trends and best practices. Biotechnol Adv 2016; 34:1-13. [DOI: 10.1016/j.biotechadv.2015.11.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 11/28/2015] [Accepted: 11/29/2015] [Indexed: 12/18/2022]
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74
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Stylianou A, Stylianopoulos T. Atomic Force Microscopy Probing of Cancer Cells and Tumor Microenvironment Components. BIONANOSCIENCE 2015. [DOI: 10.1007/s12668-015-0187-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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75
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Valbuena A, Mateu MG. Quantification and modification of the equilibrium dynamics and mechanics of a viral capsid lattice self-assembled as a protein nanocoating. NANOSCALE 2015; 7:14953-14964. [PMID: 26302823 DOI: 10.1039/c5nr04023j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Self-assembling, protein-based bidimensional lattices are being developed as functionalizable, highly ordered biocoatings for multiple applications in nanotechnology and nanomedicine. Unfortunately, protein assemblies are soft materials that may be too sensitive to mechanical disruption, and their intrinsic conformational dynamism may also influence their applicability. Thus, it may be critically important to characterize, understand and manipulate the mechanical features and dynamic behavior of protein assemblies in order to improve their suitability as nanomaterials. In this study, the capsid protein of the human immunodeficiency virus was induced to self-assemble as a continuous, single layered, ordered nanocoating onto an inorganic substrate. Atomic force microscopy (AFM) was used to quantify the mechanical behavior and the equilibrium dynamics ("breathing") of this virus-based, self-assembled protein lattice in close to physiological conditions. The results uniquely provided: (i) evidence that AFM can be used to directly visualize in real time and quantify slow breathing motions leading to dynamic disorder in protein nanocoatings and viral capsid lattices; (ii) characterization of the dynamics and mechanics of a viral capsid lattice and protein-based nanocoating, including flexibility, mechanical strength and remarkable self-repair capacity after mechanical damage; (iii) proof of principle that chemical additives can modify the dynamics and mechanics of a viral capsid lattice or protein-based nanocoating, and improve their applied potential by increasing their mechanical strength and elasticity. We discuss the implications for the development of mechanically resistant and compliant biocoatings precisely organized at the nanoscale, and of novel antiviral agents acting on fundamental physical properties of viruses.
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Affiliation(s)
- Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
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76
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Wan Z, Chen X, Chen H, Ji Q, Chen Y, Wang J, Cao Y, Wang F, Lou J, Tang Z, Liu W. The activation of IgM- or isotype-switched IgG- and IgE-BCR exhibits distinct mechanical force sensitivity and threshold. eLife 2015; 4:e06925. [PMID: 26258882 PMCID: PMC4555871 DOI: 10.7554/elife.06925] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/08/2015] [Indexed: 02/06/2023] Open
Abstract
B lymphocytes use B cell receptors (BCRs) to sense the physical features of the antigens. However, the sensitivity and threshold for the activation of BCRs resulting from the stimulation by mechanical forces are unknown. Here, we addressed this question using a double-stranded DNA-based tension gauge tether system serving as a predefined mechanical force gauge ranging from 12 to 56 pN. We observed that IgM-BCR activation is dependent on mechanical forces and exhibits a multi-threshold effect. In contrast, the activation of isotype-switched IgG- or IgE-BCR only requires a low threshold of less than 12 pN, providing an explanation for their rapid activation in response to antigen stimulation. Mechanistically, we found that the cytoplasmic tail of the IgG-BCR heavy chain is both required and sufficient to account for the low mechanical force threshold. These results defined the mechanical force sensitivity and threshold that are required to activate different isotyped BCRs.
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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, Tsinghua University, Beijing, China
| | - Xiangjun Chen
- MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haodong Chen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu, China
| | - Qinghua Ji
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yingjia Chen
- MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing Wang
- MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yiyun Cao
- MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Tsinghua University, Beijing, China
| | - Fei Wang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu, China
| | - Jizhong Lou
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu, China
| | - Wanli Liu
- MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Tsinghua University, Beijing, China
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77
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Bernaud J, Castelnovo M, Muriaux D, Faivre-Moskalenko C. [Atomic force microscopy: a tool to analyze the viral cycle]. Med Sci (Paris) 2015; 31:522-8. [PMID: 26059303 DOI: 10.1051/medsci/20153105014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Each step of the HIV-1 life cycle frequently involves a change in the morphology and/or mechanical properties of the viral particle or core. The atomic force microscope (AFM) constitutes a powerful tool for characterizing these physical changes at the scale of a single virus. Indeed, AFM enables the visualization of viral capsids in a controlled physiological environment and to probe their mechanical properties by nano-indentation. Finally, AFM force spectroscopy allows to characterize the affinities between viral envelope proteins and cell receptors at the single molecule level.
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Affiliation(s)
- Julien Bernaud
- Laboratoire de physique, CNRS UMR 5672, Ecole normale supérieure de Lyon, 46, allée d'Italie, 69364 Lyon Cedex 07, France
| | - Martin Castelnovo
- Laboratoire de physique, CNRS UMR 5672, Ecole normale supérieure de Lyon, 46, allée d'Italie, 69364 Lyon Cedex 07, France
| | - Delphine Muriaux
- Centre d'étude d'agents pathogènes et biotechnologie pour la santé, CNRS UMR 5236, 1919, route de Mende, 34 293 Montpellier Cedex 5, France
| | - Cendrine Faivre-Moskalenko
- Laboratoire de physique, CNRS UMR 5672, Ecole normale supérieure de Lyon, 46, allée d'Italie, 69364 Lyon Cedex 07, France
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78
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Zeng Y, Yi J, Wan Z, Liu K, Song P, Chau A, Wang F, Chang Z, Han W, Zheng W, Chen YH, Xiong C, Liu W. Substrate stiffness regulates B-cell activation, proliferation, class switch, and T-cell-independent antibody responses in vivo. Eur J Immunol 2015; 45:1621-34. [PMID: 25756957 DOI: 10.1002/eji.201444777] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 01/30/2015] [Accepted: 03/06/2015] [Indexed: 12/17/2022]
Abstract
B cells use B-cell receptors (BCRs) to sense antigens that are usually presented on substrates with different stiffness. However, it is not known how substrate stiffness affects B-cell proliferation, class switch, and in vivo antibody responses. We addressed these questions using polydimethylsiloxane (PDMS) substrates with different stiffness (20 or 1100 kPa). Live cell imaging experiments suggested that antigens on stiffer substrates more efficiently trigger the synaptic accumulation of BCR and phospho-Syk molecules compared with antigens on softer substrates. In vitro expansion of mouse primary B cells shows different preferences for substrate stiffness when stimulated by different expansion stimuli. LPS equally drives B-cell proliferation on stiffer or softer substrates. Anti-CD40 antibodies enhance B-cell proliferation on stiffer substrates, while antigens enhance B-cell proliferation on softer substrates through a mechanism involving the enhanced phosphorylation of PI3K, Akt, and FoxO1. In vitro class switch differentiation of B cells prefers softer substrates. Lastly, NP67-Ficoll on softer substrates accounted for an enhanced antibody response in vivo. Thus, substrate stiffness regulates B-cell activation, proliferation, class switch, and T cell independent antibody responses in vivo, suggesting its broad application in manipulating the fate of B cells in vitro and in vivo.
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Affiliation(s)
- Yingyue Zeng
- MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, China.,Collaborative Innovation Center for Infectious Diseases, Hangzhou, China
| | - Junyang Yi
- MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, China.,Collaborative Innovation Center for Infectious Diseases, Hangzhou, China
| | - Zhengpeng Wan
- MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, China
| | - Kai Liu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Ping Song
- College of Engineering, Peking University, Beijing, China
| | - Alicia Chau
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Fei Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zai Chang
- MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, China
| | - Weidong Han
- Institute of Basic Medicine, Chinese PLA General Hospital, Beijing, China
| | - Wenjie Zheng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Beijing, China
| | - Ying-Hua Chen
- MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, China
| | - Chunyang Xiong
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,College of Engineering, Peking University, Beijing, China
| | - Wanli Liu
- MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, China.,Collaborative Innovation Center for Infectious Diseases, Hangzhou, China
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79
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Castellanos M, Carrillo PJP, Mateu MG. Quantitatively probing propensity for structural transitions in engineered virus nanoparticles by single-molecule mechanical analysis. NANOSCALE 2015; 7:5654-5664. [PMID: 25744136 DOI: 10.1039/c4nr07046a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Viruses are increasingly being studied from the perspective of fundamental physics at the nanoscale as biologically evolved nanodevices with many technological applications. In viral particles of the minute virus of mice (MVM), folded segments of the single-stranded DNA genome are bound to the capsid inner wall and act as molecular buttresses that increase locally the mechanical stiffness of the particle. We have explored whether a quantitative linkage exists in MVM particles between their DNA-mediated stiffening and impairment of a heat-induced, virus-inactivating structural change. A series of structurally modified virus particles with disrupted capsid-DNA interactions and/or distorted capsid cavities close to the DNA-binding sites were engineered and characterized, both in classic kinetics assays and by single-molecule mechanical analysis using atomic force microscopy. The rate constant of the virus inactivation reaction was found to decrease exponentially with the increase in elastic constant (stiffness) of the regions closer to DNA-binding sites. The application of transition state theory suggests that the height of the free energy barrier of the virus-inactivating structural transition increases linearly with local mechanical stiffness. From a virological perspective, the results indicate that infectious MVM particles may have acquired the biological advantage of increased survival under thermal stress by evolving architectural elements that rigidify the particle and impair non-productive structural changes. From a nanotechnological perspective, this study provides proof of principle that determination of mechanical stiffness and its manipulation by protein engineering may be applied for quantitatively probing and tuning the conformational dynamics of virus-based and other protein-based nanoassemblies.
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Affiliation(s)
- Milagros Castellanos
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid 28049, Spain.
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80
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Kontomaris SV, Yova D, Stylianou A, Balogiannis G. The effects of UV irradiation on collagen D-band revealed by atomic force microscopy. SCANNING 2015; 37:101-11. [PMID: 25521598 DOI: 10.1002/sca.21185] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 11/03/2014] [Accepted: 11/14/2014] [Indexed: 05/03/2023]
Abstract
The objective of this paper was to investigate the influence of UV irradiation on collagen D-band periodicity by using the AFM imaging and nanoindentation methods. It is well known than UV irradiation is one of the main factors inducing destabilization of collagen molecules. Due to the human's skin chronic exposure to sun light, the research concerning the influence of UV radiation on collagen is of great interest. The impact of UV irradiation on collagen can be studied in nanoscale using Atomic Force Microscopy (AFM). AFM is a powerful tool as far as surface characterization is concerned, due to its ability to relate high resolution imaging with mechanical properties. Hence, high resolution images of individual collagen fibrils and load-displacement curves on the overlapping and gap regions, under various time intervals of UV exposure, were obtained. The results demonstrated that the UV rays affect the height level differences between the overlapping and gap regions. Under various time intervals of UV exposure, the height difference between overlaps and gaps reduced from ~3.7 nm to ~0.8 nm and the fibril diameters showed an average of 8-10% reduction. In addition, the irradiation influenced the mechanical properties of collagen fibrils. The Young's modulus values were reduced per 66% (overlaps) and 61% (gaps) compared to their initial values. The observed alterations on the structural and the mechanical properties of collagen fibrils are probably a consequence of the polypeptide chain scission due to the impact of the UV irradiation.
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Affiliation(s)
- Stylianos V Kontomaris
- Biomedical Optics & Applied Biophysics Lab, Division of Electromagnetics, Electrooptics & Electronic Materials, School of Electrical and Computer Engineering, National Technical University of Athens, Iroon Polytechniou, Athens, Greece; Interuniversity Postgraduate Programme on Biomedical Engineering, Faculty of Medicine of the University of Patras, School of Electrical and Computer Engineering and the School of Mechanical Engineering of the National Technical University of Athens, Athens, Greece
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81
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Greber UF. How cells tune viral mechanics--insights from biophysical measurements of influenza virus. Biophys J 2015; 106:2317-21. [PMID: 24896110 DOI: 10.1016/j.bpj.2014.04.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/10/2014] [Accepted: 04/21/2014] [Indexed: 10/25/2022] Open
Abstract
During replication, the physical state of a virus is controlled by assembly and disassembly processes, when particles are put together and dismantled by cellular cues, respectively. A fundamental question has been how a cell can assemble an infectious virus, and dismantle a virus entering an uninfected cell and thereby trigger a new round of infection. This apparent paradox might be explained by considering that infected and uninfected cells are functionally different, or that assembly and disassembly take place along different cellular pathways. A third possibility is that the physical properties of newly assembled viruses are different from the infection-ready viruses. Recent biophysical experiments measured the stiffness of single Influenza viruses and combined this with biochemical measurements and cell biological assays. Besides inducing the fusogenic state of hemagglutinin, low pH cues softened the virus and precluded aggregation of viral ribonucleoprotein particles with the matrix protein M1. The recent experiments suggest a two-step model for Influenza virus entry and uncoating involving low pH in early and late endosomes, respectively. I conclude with a short outlook into how combined biophysical and cell biological approaches might lead to the identification of new cellular cues controlling viral uncoating and infection.
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Affiliation(s)
- Urs F Greber
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
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82
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van Rosmalen MGM, Roos WH, Wuite GJL. Material properties of viral nanocages explored by atomic force microscopy. Methods Mol Biol 2015; 1252:115-137. [PMID: 25358778 DOI: 10.1007/978-1-4939-2131-7_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Single-particle nanoindentation by atomic force microscopy (AFM) is an emergent technique to characterize the material properties of nano-sized proteinaceous systems. AFM uses a very small tip attached to a cantilever to scan the surface of the substrate. As a result of the sensitive feedback loop of AFM, the force applied by the tip on the substrate during scanning can be controlled and monitored. By accurately controlling this scanning force, topographical maps of fragile substrates can be acquired to study the morphology of the substrate. In addition, mechanical properties of the substrate like stiffness and breaking point can be determined by using the force spectroscopy capability of AFM. Here we discuss basics of AFM operation and how this technique is used to determine the structure and mechanical properties of protein nanocages, in particular viral particles. Knowledge of morphology as well as mechanical properties is essential for understanding viral life cycles, including genome packaging, capsid maturation, and uncoating, but also contributes to the development of diagnostics, vaccines, imaging modalities, and targeted therapeutic devices based on viruslike particles.
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83
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Llauró A, Guerra P, Irigoyen N, Rodríguez JF, Verdaguer N, de Pablo PJ. Mechanical stability and reversible fracture of vault particles. Biophys J 2014; 106:687-95. [PMID: 24507609 DOI: 10.1016/j.bpj.2013.12.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 11/18/2013] [Accepted: 12/23/2013] [Indexed: 11/16/2022] Open
Abstract
Vaults are the largest ribonucleoprotein particles found in eukaryotic cells, with an unclear cellular function and promising applications as vehicles for drug delivery. In this article, we examine the local stiffness of individual vaults and probe their structural stability with atomic force microscopy under physiological conditions. Our data show that the barrel, the central part of the vault, governs both the stiffness and mechanical strength of these particles. In addition, we induce single-protein fractures in the barrel shell and monitor their temporal evolution. Our high-resolution atomic force microscopy topographies show that these fractures occur along the contacts between two major vault proteins and disappear over time. This unprecedented systematic self-healing mechanism, which enables these particles to reversibly adapt to certain geometric constraints, might help vaults safely pass through the nuclear pore complex and potentiate their role as self-reparable nanocontainers.
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Affiliation(s)
- Aida Llauró
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo Guerra
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - José F Rodríguez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Núria Verdaguer
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Pedro J de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain.
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84
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Ruz JJ, Tamayo J, Pini V, Kosaka PM, Calleja M. Physics of nanomechanical spectrometry of viruses. Sci Rep 2014; 4:6051. [PMID: 25116478 PMCID: PMC7365328 DOI: 10.1038/srep06051] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 07/25/2014] [Indexed: 12/26/2022] Open
Abstract
There is an emerging need of nanotools able to quantify the mechanical properties of single biological entities. A promising approach is the measurement of the shifts of the resonant frequencies of ultrathin cantilevers induced by the adsorption of the studied biological systems. Here, we present a detailed theoretical analysis to calculate the resonance frequency shift induced by the mechanical stiffness of viral nanotubes. The model accounts for the high surface-to-volume ratio featured by single biological entities, the shape anisotropy and the interfacial adhesion. The model is applied to the case in which tobacco mosaic virus is randomly delivered to a silicon nitride cantilever. The theoretical framework opens the door to a novel paradigm for biological spectrometry as well as for measuring the Young's modulus of biological systems with minimal strains.
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Affiliation(s)
- J. J. Ruz
- Institute of Microelectronics of Madrid, CSIC. Isaac Newton 8
(PTM), Madrid, Tres Cantos E-28760 Spain
| | - J. Tamayo
- Institute of Microelectronics of Madrid, CSIC. Isaac Newton 8
(PTM), Madrid, Tres Cantos E-28760 Spain
| | - V. Pini
- Institute of Microelectronics of Madrid, CSIC. Isaac Newton 8
(PTM), Madrid, Tres Cantos E-28760 Spain
| | - P. M. Kosaka
- Institute of Microelectronics of Madrid, CSIC. Isaac Newton 8
(PTM), Madrid, Tres Cantos E-28760 Spain
| | - M. Calleja
- Institute of Microelectronics of Madrid, CSIC. Isaac Newton 8
(PTM), Madrid, Tres Cantos E-28760 Spain
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85
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Sirotkin S, Mermet A, Bergoin M, Ward V, Van Etten JL. Viruses as nanoparticles: structure versus collective dynamics. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:022718. [PMID: 25215769 DOI: 10.1103/physreve.90.022718] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Indexed: 06/03/2023]
Abstract
In order to test the application of the "nanoparticle" concept to viruses in terms of low-frequency dynamics, large viruses (140-190 nm) were compared to similar-sized polymer colloids using ultra-small-angle x-ray scattering and very-low-frequency Raman or Brillouin scattering. While both viruses and polymer colloids show comparable highly defined morphologies, with comparable abilities of forming self-assembled structures, their respective abilities to confine detectable acoustic vibrations, as expected for such monodisperse systems, differed. Possible reasons for these different behaviors are discussed.
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Affiliation(s)
- S Sirotkin
- Institut Lumière Matière, Université de Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5306, 69622 Villeurbanne, France
| | - A Mermet
- Institut Lumière Matière, Université de Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5306, 69622 Villeurbanne, France
| | - M Bergoin
- Laboratoire de Virologie Comparé des Invertébrés, E.P.H.E., Université Montpellier 2, France
| | - V Ward
- University of Otago, Department of Microbology and Immunology, New Zealand
| | - J L Van Etten
- Department of Plant Pathology and the Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska USA
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86
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Bugli F, Caprettini V, Cacaci M, Martini C, Paroni Sterbini F, Torelli R, Della Longa S, Papi M, Palmieri V, Giardina B, Posteraro B, Sanguinetti M, Arcovito A. Synthesis and characterization of different immunogenic viral nanoconstructs from rotavirus VP6 inner capsid protein. Int J Nanomedicine 2014; 9:2727-39. [PMID: 24936129 PMCID: PMC4047981 DOI: 10.2147/ijn.s60014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In order to deliver low-cost viral capsomeres from a large amount of soluble viral VP6 protein from human rotavirus, we developed and optimized a biotechnological platform in Escherichia coli. Specifically, three different expression protocols were compared, differing in their genetic constructs, ie, a simple native histidine-tagged VP6 sequence, VP6 fused to thioredoxin, and VP6 obtained with the newly described small ubiquitin-like modifier (SUMO) fusion system. Our results demonstrate that the histidine-tagged protein does not escape the accumulation in the inclusion bodies, and that SUMO is largely superior to the thioredoxin-fusion tag in enhancing the expression and solubility of VP6 protein. Moreover, the VP6 protein produced according to the SUMO fusion tag displays well-known assembly properties, as observed in both transmission electron microscopy and atomic force microscopy images, giving rise to either VP6 trimers, 60 nm spherical virus-like particles, or nanotubes a few microns long. This different quaternary organization of VP6 shows a higher level of immunogenicity for the elongated structures with respect to the spheres or the protein trimers. Therefore, the expression and purification strategy presented here – providing a large amount of the viral capsid protein in the native form with relatively simple, rapid, and economical procedures – opens a new route toward large-scale production of a more efficient antigenic compound to be used as a vaccination tool or as an adjuvant, and also represents a top-quality biomaterial to be further modified for biotechnological purposes.
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Affiliation(s)
- Francesca Bugli
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Margherita Cacaci
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Cecilia Martini
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Riccardo Torelli
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Stefano Della Longa
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'Ambiente, Università dell'Aquila, L'Aquila, Italy
| | - Massimiliano Papi
- Istituto di Fisica, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Bruno Giardina
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Brunella Posteraro
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Rome, Italy
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87
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Ultrastable atomic force microscopy: improved force and positional stability. FEBS Lett 2014; 588:3621-30. [PMID: 24801176 DOI: 10.1016/j.febslet.2014.04.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/18/2014] [Accepted: 04/23/2014] [Indexed: 11/20/2022]
Abstract
Atomic force microscopy (AFM) is an exciting technique for biophysical studies of single molecules, but its usefulness is limited by instrumental drift. We dramatically reduced positional drift by adding two lasers to track and thereby actively stabilize the tip and the surface. These lasers also enabled label-free optical images that were spatially aligned to the tip position. Finally, sub-pN force stability over 100 s was achieved by removing the gold coating from soft cantilevers. These enhancements to AFM instrumentation can immediately benefit research in biophysics and nanoscience.
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88
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May ER. Recent Developments in Molecular Simulation Approaches to Study Spherical Virus Capsids. MOLECULAR SIMULATION 2014; 40:878-888. [PMID: 25197162 DOI: 10.1080/08927022.2014.907899] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Viruses are a particularly challenging systems to study via molecular simulation methods. Virus capsids typically consist of over 100 subunit proteins and reach dimensions of over 100 nm; solvated viruses capsid systems can be over 1 million atoms in size. In this review, I will present recent developments which have attempted to overcome the significant computational expense to perform simulations which can inform experimental studies, make useful predictions about biological phenomena and calculate material properties relevant to nanotechnology design efforts.
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Affiliation(s)
- Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA 06269
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89
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Calò A, Reguera D, Oncins G, Persuy MA, Sanz G, Lobasso S, Corcelli A, Pajot-Augy E, Gomila G. Force measurements on natural membrane nanovesicles reveal a composition-independent, high Young's modulus. NANOSCALE 2014; 6:2275-2285. [PMID: 24407152 DOI: 10.1039/c3nr05107b] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Mechanical properties of nano-sized vesicles made up of natural membranes are crucial to the development of stable, biocompatible nanocontainers with enhanced functional, recognition and sensing capabilities. Here we measure and compare the mechanical properties of plasma and inner membrane nanovesicles ∼80 nm in diameter obtained from disrupted yeast Saccharomyces cerevisiae cells. We provide evidence of a highly deformable behaviour for these vesicles, able to support repeated wall-to-wall compressions without irreversible deformations, accompanied by a noticeably high Young's modulus (∼300 MPa) compared to that obtained for reconstituted artificial liposomes of similar size and approaching that of some virus particles. Surprisingly enough, the results are approximately similar for plasma and inner membrane nanovesicles, in spite of their different lipid compositions, especially on what concerns the ergosterol content. These results point towards an important structural role of membrane proteins in the mechanical response of natural membrane vesicles and open the perspective to their potential use as robust nanocontainers for bioapplications.
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Affiliation(s)
- Annalisa Calò
- IBEC Institute for Bioengineering of Catalonia, C/Baldiri Reixac 10-12, 08028, Barcelona, Spain.
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90
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Tiwari PM, Eroglu E, Boyoglu-Barnum S, He Q, Willing GA, Vig K, Dennis VA, Singh SR. Atomic force microscopic investigation of respiratory syncytial virus infection in HEp-2 cells. J Microsc 2013; 253:31-41. [PMID: 24251370 DOI: 10.1111/jmi.12095] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 10/07/2013] [Indexed: 01/14/2023]
Abstract
Respiratory syncytial virus (RSV) primarily causes bronchiolitis and pneumonia in infants. In spite of intense research, no safe and effective vaccine has been developed yet. For understanding its pathogenesis and development of anti-RSV drugs/therapeutics, it is indispensable to study the RSV-host interaction. Although, there are limited studies using electron microscopy to elucidate the infection process of RSV, to our knowledge, no study has reported the morphological impact of RSV infection using atomic force microscopy. We report the cytoplasmic and nuclear changes in human epidermoid cell line type 2 using atomic force microscopy. Human epidermoid cell line type 2 cells, grown on cover slips, were infected with RSV and fixed after various time periods, processed and observed for morphological changes using atomic force microscopy. RSV infected cells showed loss of membrane integrity, with degeneration in the cellular content and cytoskeleton. Nuclear membrane was disintegrated and nuclear volume was decreased. The chromatin of the RSV infected cells was condensed, progressing towards degeneration via pyknosis and apoptosis. Membrane protrusions of ~150-200 nm diameter were observed on RSV infected cells after 6 h, suggestive of prospective RSV budding sites. To our knowledge, this is the first study of RSV infection process using atomic force microscopy. Such morphological studies could help explore viral infection process aiding the development of anti-RSV therapies.
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Affiliation(s)
- P M Tiwari
- Center for NanoBiotechnology Research, Alabama State University, Montgomery, Alabama 36101, U.S.A
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91
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Polles G, Indelicato G, Potestio R, Cermelli P, Twarock R, Micheletti C. Mechanical and assembly units of viral capsids identified via quasi-rigid domain decomposition. PLoS Comput Biol 2013; 9:e1003331. [PMID: 24244139 PMCID: PMC3828136 DOI: 10.1371/journal.pcbi.1003331] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 09/13/2013] [Indexed: 02/05/2023] Open
Abstract
Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hence well described and rationalised from a mesoscopic perspective. Accordingly, various experimental and computational efforts have been directed towards identifying the fundamental building blocks that are instrumental for the mechanical response, or constitute the assembly units, of a few specific viral shells. Motivated by these earlier studies we introduce and apply a general and efficient computational scheme for identifying the stable domains of a given viral capsid. The method is based on elastic network models and quasi-rigid domain decomposition. It is first applied to a heterogeneous set of well-characterized viruses (CCMV, MS2, STNV, STMV) for which the known mechanical or assembly domains are correctly identified. The validated method is next applied to other viral particles such as L-A, Pariacoto and polyoma viruses, whose fundamental functional domains are still unknown or debated and for which we formulate verifiable predictions. The numerical code implementing the domain decomposition strategy is made freely available. The genetic material of viruses is packaged inside capsids constituted from a few tens to thousands of proteins. The latter can organize in multimers that serve as fundamental blocks for the viral shell assembly or that control the capsid conformational transitions and response to mechanical stress. In this work, we introduce and apply a computational scheme that identifies the fundamental protein blocks from the structural fluctuations of the capsids in thermal equilibrium. These can be derived from phenomenological elastic network models with minimal computational expenditure. Accordingly, the basic functional protein units of a capsid can be obtained from the sole input of the capsid crystal structure. The method is applied to a heterogeneous set of viruses of various size and geometries. These include well-characterised instances for validation purposes, as well as debated ones for which predictions are formulated.
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Affiliation(s)
- Guido Polles
- International School for Advanced Studies (SISSA), Trieste, Italy
| | - Giuliana Indelicato
- York Centre for Complex Systems Analysis, Department of Mathematics, University of York, York, United Kingdom
| | | | - Paolo Cermelli
- Dipartimento di Matematica, Università di Torino, Torino, Italy
| | - Reidun Twarock
- York Centre for Complex Systems Analysis, Department of Mathematics, University of York, York, United Kingdom
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92
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Alonso J, Górzny M, Bittner A. The physics of tobacco mosaic virus and virus-based devices in biotechnology. Trends Biotechnol 2013; 31:530-8. [DOI: 10.1016/j.tibtech.2013.05.013] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/23/2013] [Accepted: 05/31/2013] [Indexed: 12/16/2022]
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93
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94
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Snijder J, Uetrecht C, Rose RJ, Sanchez-Eugenia R, Marti GA, Agirre J, Guérin DMA, Wuite GJL, Heck AJR, Roos WH. Probing the biophysical interplay between a viral genome and its capsid. Nat Chem 2013; 5:502-9. [DOI: 10.1038/nchem.1627] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 03/15/2013] [Indexed: 11/09/2022]
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95
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Abstract
Structural biology techniques have greatly contributed to unveil the relationships between structure, properties and functions of viruses. In recent years, classic structural approaches are being complemented by single-molecule techniques such as atomic force microscopy and optical tweezers to study physical properties and functions of viral particles that are not accessible to classic structural techniques. Among these features are mechanical properties such as stiffness, intrinsic elasticity, tensile strength and material fatigue. The field of virus mechanics is contributing to materials science by investigating some physical parameters of "soft" biological matter and biological nano-objects. Virus mechanics studies are also starting to unveil the biological implications of physical properties of viruses. Growing evidence indicate that viruses are subjected to internal and external forces, and that they may have adapted to withstand and even use those forces. This chapter describes what is known on the mechanical properties of virus particles, their structural determinants, and possible biological implications, of which several examples are provided.
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Affiliation(s)
- Pedro J de Pablo
- Department of Physics of the Condensed Matter, C03, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain,
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96
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Mateu MG. Assembly, stability and dynamics of virus capsids. Arch Biochem Biophys 2012; 531:65-79. [PMID: 23142681 DOI: 10.1016/j.abb.2012.10.015] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/18/2012] [Accepted: 10/28/2012] [Indexed: 12/13/2022]
Abstract
Most viruses use a hollow protein shell, the capsid, to enclose the viral genome. Virus capsids are large, symmetric oligomers made of many copies of one or a few types of protein subunits. Self-assembly of a viral capsid is a complex oligomerization process that proceeds along a pathway regulated by ordered interactions between the participating protein subunits, and that involves a series of (usually transient) assembly intermediates. Assembly of many virus capsids requires the assistance of scaffolding proteins or the viral nucleic acid, which interact with the capsid subunits to promote and direct the process. Once assembled, many capsids undergo a maturation reaction that involves covalent modification and/or conformational rearrangements, which may increase the stability of the particle. The final, mature capsid is a relatively robust protein complex able to protect the viral genome from physicochemical aggressions; however, it is also a metastable, dynamic structure poised to undergo controlled conformational transitions required to perform biologically critical functions during virus entry into cells, intracellular trafficking, and viral genome uncoating. This article provides an updated general overview on structural, biophysical and biochemical aspects of the assembly, stability and dynamics of virus capsids.
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Affiliation(s)
- Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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97
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Mechanical elasticity as a physical signature of conformational dynamics in a virus particle. Proc Natl Acad Sci U S A 2012; 109:12028-33. [PMID: 22797893 DOI: 10.1073/pnas.1207437109] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In this study we test the hypothesis that mechanically elastic regions in a virus particle (or large biomolecular complex) must coincide with conformationally dynamic regions, because both properties are intrinsically correlated. Hypothesis-derived predictions were subjected to verification by using 19 variants of the minute virus of mice capsid. The structural modifications in these variants reduced, preserved, or restored the conformational dynamism of regions surrounding capsid pores that are involved in molecular translocation events required for virus infectivity. The mechanical elasticity of the modified capsids was analyzed by atomic force microscopy, and the results corroborated every prediction tested: Any mutation (or chemical cross-linking) that impaired a conformational rearrangement of the pore regions increased their mechanical stiffness. On the contrary, any mutation that preserved the dynamics of the pore regions also preserved their elasticity. Moreover, any pseudo-reversion that restored the dynamics of the pore regions (lost through previous mutation) also restored their elasticity. Finally, no correlation was observed between dynamics of the pore regions and mechanical elasticity of other capsid regions. This study (i) corroborates the hypothesis that local mechanical elasticity and conformational dynamics in a viral particle are intrinsically correlated; (ii) proposes that determination by atomic force microscopy of local mechanical elasticity, combined with mutational analysis, may be used to identify and study conformationally dynamic regions in virus particles and large biomolecular complexes; (iii) supports a connection between mechanical properties and biological function in a virus; (iv) shows that viral capsids can be greatly stiffened by protein engineering for nanotechnological applications.
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