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Denning D, Bennett S, Mullen T, Moyer C, Vorselen D, Wuite GJL, Nemerow G, Roos WH. Maturation of adenovirus primes the protein nano-shell for successful endosomal escape. Nanoscale 2019; 11:4015-4024. [PMID: 30768112 DOI: 10.1039/c8nr10182e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The ability of adenoviruses to infect a broad range of species has spurred a growing interest in nanomedicine to use adenovirus as a cargo delivery vehicle. While successful maturation of adenovirus and controlled disassembly are critical for efficient infection, the underlying mechanisms regulating these processes are not well understood. Here, we present Atomic Force Microscopy nanoindentation and fatigue studies of adenovirus capsids at different maturation stages to scrutinize their dynamic uncoating properties. Surprisingly, we find that the early intermediate immature (lacking DNA) capsid is mechanically indistinguishable in both break force and spring constant from the mature (containing DNA) capsid. However, mature and immature capsids do display distinct disassembly pathways, as revealed by our mechanically-induced fatigue analysis. The mature capsid first loses the pentons, followed by either long-term capsid stability or abrupt and complete disassembly. However, the immature capsid has a stable penton region and undergoes a stochastic disassembly mechanism, thought to be due to the absence of genomic pressure. Strikingly, the addition of the genome alone is not sufficient to achieve penton destabilization as indicated by the penton stability of the maturation-intermediate mutant, G33A. Full penton destabilization was achieved only when the genome was present in addition to the successful maturation-linked proteolytic cleavage of preprotein VI. Therefore these findings strongly indicate that maturation of adenovirus in concert with genomic pressure induces penton destabilization and thus, primes the capsid for controlled disassembly. This latter aspect is critical for efficient infection and successful cargo delivery.
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Affiliation(s)
- D Denning
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, The Netherlands and Natuur- en Sterrenkunde and LaserLaB, Vrije Universiteit Amsterdam, The Netherlands.
| | - S Bennett
- Department of Immunology and Microbiology, the Scripps Research Institute, La Jolla, CA 92037, USA.
| | - T Mullen
- Department of Immunology and Microbiology, the Scripps Research Institute, La Jolla, CA 92037, USA.
| | - C Moyer
- Department of Immunology and Microbiology, the Scripps Research Institute, La Jolla, CA 92037, USA.
| | - D Vorselen
- Natuur- en Sterrenkunde and LaserLaB, Vrije Universiteit Amsterdam, The Netherlands.
| | - G J L Wuite
- Natuur- en Sterrenkunde and LaserLaB, Vrije Universiteit Amsterdam, The Netherlands.
| | - G Nemerow
- Department of Immunology and Microbiology, the Scripps Research Institute, La Jolla, CA 92037, USA.
| | - W H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, The Netherlands
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Marchetti M, Malinowska A, Heller I, Wuite GJL. How to switch the motor on: RNA polymerase initiation steps at the single-molecule level. Protein Sci 2017; 26:1303-1313. [PMID: 28470684 DOI: 10.1002/pro.3183] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/26/2017] [Accepted: 04/26/2017] [Indexed: 11/06/2022]
Abstract
RNA polymerase (RNAP) is the central motor of gene expression since it governs the process of transcription. In prokaryotes, this holoenzyme is formed by the RNAP core and a sigma factor. After approaching and binding the specific promoter site on the DNA, the holoenzyme-promoter complex undergoes several conformational transitions that allow unwinding and opening of the DNA duplex. Once the first DNA basepairs (∼10 bp) are transcribed in an initial transcription process, the enzyme unbinds from the promoter and proceeds downstream along the DNA while continuously opening the helix and polymerizing the ribonucleotides in correspondence with the template DNA sequence. When the gene is transcribed into RNA, the process generally is terminated and RNAP unbinds from the DNA. The first step of transcription-initiation, is considered the rate-limiting step of the entire process. This review focuses on the single-molecule studies that try to reveal the key steps in the initiation phase of bacterial transcription. Such single-molecule studies have, for example, allowed real-time observations of the RNAP target search mechanism, a mechanism still under debate. Moreover, single-molecule studies using Förster Resonance Energy Transfer (FRET) revealed the conformational changes that the enzyme undergoes during initiation. Force-based techniques such as scanning force microscopy and magnetic tweezers allowed quantification of the energy that drives the RNAP translocation along DNA and its dynamics. In addition to these in vitro experiments, single particle tracking in vivo has provided a direct quantification of the relative populations in each phase of transcription and their locations within the cell.
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Affiliation(s)
- M Marchetti
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - I Heller
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - G J L Wuite
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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Hashemi Shabestari M, Meijering AEC, Roos WH, Wuite GJL, Peterman EJG. Recent Advances in Biological Single-Molecule Applications of Optical Tweezers and Fluorescence Microscopy. Methods Enzymol 2016; 582:85-119. [PMID: 28062046 DOI: 10.1016/bs.mie.2016.09.047] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Over the past two decades, single-molecule techniques have evolved into robust tools to study many fundamental biological processes. The combination of optical tweezers with fluorescence microscopy and microfluidics provides a powerful single-molecule manipulation and visualization technique that has found widespread application in biology. In this combined approach, the spatial (~nm) and temporal (~ms) resolution, as well as the force scale (~pN) accessible to optical tweezers is complemented with the power of fluorescence microscopy. Thereby, it provides information on the local presence, identity, spatial dynamics, and conformational dynamics of single biomolecules. Together, these techniques allow comprehensive studies of, among others, molecular motors, protein-protein and protein-DNA interactions, biomolecular conformational changes, and mechanotransduction pathways. In this chapter, recent applications of fluorescence microscopy in combination with optical trapping are discussed. After an introductory section, we provide a description of instrumentation together with the current capabilities and limitations of the approaches. Next we summarize recent studies that applied this combination of techniques in biological systems and highlight some representative biological assays to mark the exquisite opportunities that optical tweezers combined with fluorescence microscopy provide.
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Affiliation(s)
| | | | - W H Roos
- Moleculaire Biofysica, Zernike Institute, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - G J L Wuite
- Vrije Universiteit, Amsterdam, The Netherlands
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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] [What about the content of this article? (0)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 03/15/2013] [Indexed: 11/09/2022]
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Abstract
The capsids of icosahedral viruses are closed shells assembled from a hexagonal lattice of proteins with fivefold angular defects located at the icosahedral vertices. Elasticity theory predicts that these disclinations are subject to an internal compressive prestress, which provides an explanation for the link between size and shape of capsids. Using a combination of experiment and elasticity theory we investigate the question of whether macromolecular assemblies are subject to residual prestress, due to basic geometric incompatibility of the subunits. Here we report the first direct experimental test of the theory: by controlled removal of protein pentamers from the icosahedral vertices, we measure the mechanical response of so-called "whiffle ball" capsids of herpes simplex virus, and demonstrate the signature of internal prestress locked into wild-type capsids during assembly.
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Affiliation(s)
- W S Klug
- Department of Mechanical and Aerospace Engineering, and California NanoSystems Institute, UCLA, Los Angeles, California 90095, USA
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Roos WH, Gibbons MM, Arkhipov A, Uetrecht C, Watts NR, Wingfield PT, Steven AC, Heck AJR, Schulten K, Klug WS, Wuite GJL. Squeezing protein shells: how continuum elastic models, molecular dynamics simulations, and experiments coalesce at the nanoscale. Biophys J 2010; 99:1175-81. [PMID: 20713001 DOI: 10.1016/j.bpj.2010.05.033] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 05/07/2010] [Accepted: 05/20/2010] [Indexed: 01/01/2023] Open
Abstract
The current rapid growth in the use of nanosized particles is fueled in part by our increased understanding of their physical properties and ability to manipulate them, which is essential for achieving optimal functionality. Here we report detailed quantitative measurements of the mechanical response of nanosized protein shells (viral capsids) to large-scale physical deformations and compare them with theoretical descriptions from continuum elastic modeling and molecular dynamics (MD). Specifically, we used nanoindentation by atomic force microscopy to investigate the complex elastic behavior of Hepatitis B virus capsids. These capsids are hollow, approximately 30 nm in diameter, and conform to icosahedral (5-3-2) symmetry. First we show that their indentation behavior, which is symmetry-axis-dependent, cannot be reproduced by a simple model based on Föppl-von Kármán thin-shell elasticity with the fivefold vertices acting as prestressed disclinations. However, we can properly describe the measured nonlinear elastic and orientation-dependent force response with a three-dimensional, topographically detailed, finite-element model. Next, we show that coarse-grained MD simulations also yield good agreement with our nanoindentation measurements, even without any fitting of force-field parameters in the MD model. This study demonstrates that the material properties of viral nanoparticles can be correctly described by both modeling approaches. At the same time, we show that even for large deformations, it suffices to approximate the mechanical behavior of nanosized viral shells with a continuum approach, and ignore specific molecular interactions. This experimental validation of continuum elastic theory provides an example of a situation in which rules of macroscopic physics can apply to nanoscale molecular assemblies.
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Affiliation(s)
- W H Roos
- Natuur- en Sterrenkunde, Vrije Universiteit, Amsterdam, The Netherlands
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Battle C, van den Broek B, Noom MC, van Mameren J, Wuite GJL, MacKintosh FC. Unraveling DNA tori under tension. Phys Rev E Stat Nonlin Soft Matter Phys 2009; 80:031917. [PMID: 19905156 DOI: 10.1103/physreve.80.031917] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Indexed: 05/28/2023]
Abstract
Motivated by recent experiments, we develop a model for DNA toroids under external tension. We find that tori are the equilibrium states for our model up to a critical tension, above which they become only metastable. Above this tension, we find a cascade of transitions between discrete toroid states that successively lower the winding number, until the ground state (rod) is reached. In this process, this model predicts a nearly constant force plateau as a function of extension, in agreement with experiment.
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Affiliation(s)
- C Battle
- Institute for Theoretical Physics, Universiteit van Amsterdam, 1018 XE Amsterdam, The Netherlands
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Zoldesi CI, Ivanovska IL, Quilliet C, Wuite GJL, Imhof A. Elastic properties of hollow colloidal particles. Phys Rev E Stat Nonlin Soft Matter Phys 2008; 78:051401. [PMID: 19113124 DOI: 10.1103/physreve.78.051401] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Indexed: 05/27/2023]
Abstract
The elastic properties of micrometer-sized hollow colloidal particles obtained by emulsion templating are probed by nanoindentation measurements in which point forces are applied to solvent-filled particles supported on a flat substrate. We show that the shells respond linearly up to forces of 7-21 nN, where the indentation becomes of the order of the shell thickness (20-40 nm). In the linear region, the particle deformation is reversible. The measured Young's modulus (approximately 200 MPa) is comparable to values for stiff rubbers or soft polymers. At larger applied force, we observe a crossover into a nonlinear regime, where the shells assume a buckled shape. Here, the force increases approximately as the square root of the indentation, in agreement with the theory of elasticity of thin shells. We also observe permanent deformation of the shells after probing them repetitively beyond the linear regime. Finally, the measured elastic properties of the shells nicely explain their spontaneous buckling in solution and due to drying.
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Affiliation(s)
- C I Zoldesi
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Department of Physics and Astronomy, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
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Abstract
The main functions of viral capsids are to protect, transport and deliver their genome. The mechanical properties of capsids are supposed to be adapted to these tasks. Bacteriophage capsids also need to withstand the high pressures the DNA is exerting onto it as a result of the DNA packaging and its consequent confinement within the capsid. It is proposed that this pressure helps driving the genome into the host, but other mechanisms also seem to play an important role in ejection. DNA packaging and ejection strategies are obviously dependent on the mechanical properties of the capsid. This review focuses on the mechanical properties of viral capsids in general and the elucidation of the biophysical aspects of genome packaging mechanisms and genome delivery processes of double-stranded DNA bacteriophages in particular.
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Affiliation(s)
- W. H. Roos
- Fysica van complexe systemen, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - I. L. Ivanovska
- Fysica van complexe systemen, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - A. Evilevitch
- Department of Biochemistry, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - G. J. L. Wuite
- Fysica van complexe systemen, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
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Michel JP, Ivanovska IL, Gibbons MM, Klug WS, Knobler CM, Wuite GJL, Schmidt CF. Nanoindentation studies of full and empty viral capsids and the effects of capsid protein mutations on elasticity and strength. Proc Natl Acad Sci U S A 2006; 103:6184-9. [PMID: 16606825 PMCID: PMC1458852 DOI: 10.1073/pnas.0601744103] [Citation(s) in RCA: 245] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The elastic properties of capsids of the cowpea chlorotic mottle virus have been examined at pH 4.8 by nanoindentation measurements with an atomic force microscope. Studies have been carried out on WT capsids, both empty and containing the RNA genome, and on full capsids of a salt-stable mutant and empty capsids of the subE mutant. Full capsids resisted indentation more than empty capsids, but all of the capsids were highly elastic. There was an initial reversible linear regime that persisted up to indentations varying between 20% and 30% of the diameter and applied forces of 0.6-1.0 nN; it was followed by a steep drop in force that is associated with irreversible deformation. A single point mutation in the capsid protein increased the capsid stiffness. The experiments are compared with calculations by finite element analysis of the deformation of a homogeneous elastic thick shell. These calculations capture the features of the reversible indentation region and allow Young's moduli and relative strengths to be estimated for the empty capsids.
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Affiliation(s)
- J. P. Michel
- *Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569
| | - I. L. Ivanovska
- Faculty of Exact Sciences, Department of Physics and Astronomy, Vrije Universiteit, 1081 HV, Amsterdam, The Netherlands
| | - M. M. Gibbons
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA 90095-1597; and
| | - W. S. Klug
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA 90095-1597; and
| | - C. M. Knobler
- *Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569
- To whom correspondence should be addressed. E-mail:
| | - G. J. L. Wuite
- Faculty of Exact Sciences, Department of Physics and Astronomy, Vrije Universiteit, 1081 HV, Amsterdam, The Netherlands
| | - C. F. Schmidt
- Faculty of Exact Sciences, Department of Physics and Astronomy, Vrije Universiteit, 1081 HV, Amsterdam, The Netherlands
- III. Physikalisches Institut, Georg-August-Universität, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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Ivanovska IL, de Pablo PJ, Ibarra B, Sgalari G, MacKintosh FC, Carrascosa JL, Schmidt CF, Wuite GJL. Bacteriophage capsids: tough nanoshells with complex elastic properties. Proc Natl Acad Sci U S A 2004; 101:7600-5. [PMID: 15133147 PMCID: PMC419652 DOI: 10.1073/pnas.0308198101] [Citation(s) in RCA: 244] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Accepted: 03/30/2004] [Indexed: 01/28/2023] Open
Abstract
The shell of bacteriophages protects the viral DNA during host-to-host transfer and serves as a high-pressure container storing energy for DNA injection into a host bacterium. Here, we probe the mechanical properties of nanometer-sized bacteriophage phi 29 shells by applying point forces. We show that empty shells withstand nanonewton forces while being indented up to 30% of their height. The elastic response varies across the surface, reflecting the arrangement of shell proteins. The measured Young's modulus (approximately 1.8 GPa) is comparable with that of hard plastic. We also observe fatigue and breakage of capsids after probing them repetitively. These results illustrate the mechanoprotection that viral shells provide and also suggest design principles for nanotechnology.
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Affiliation(s)
- I L Ivanovska
- Faculty of Exact Sciences, Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, 1081 HV, The Netherlands
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