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Shtykova EV, Dubrovin EV, Ksenofontov AL, Gifer PK, Petoukhov MV, Tokhtar VK, Sapozhnikova IM, Stavrianidi AN, Kordyukova LV, Batishchev OV. Structural Insights into Plant Viruses Revealed by Small-Angle X-ray Scattering and Atomic Force Microscopy. Viruses 2024; 16:427. [PMID: 38543792 PMCID: PMC10975137 DOI: 10.3390/v16030427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 05/23/2024] Open
Abstract
The structural study of plant viruses is of great importance to reduce the damage caused by these agricultural pathogens and to support their biotechnological applications. Nowadays, X-ray crystallography, NMR spectroscopy and cryo-electron microscopy are well accepted methods to obtain the 3D protein structure with the best resolution. However, for large and complex supramolecular structures such as plant viruses, especially flexible filamentous ones, there are a number of technical limitations to resolving their native structure in solution. In addition, they do not allow us to obtain structural information about dynamics and interactions with physiological partners. For these purposes, small-angle X-ray scattering (SAXS) and atomic force microscopy (AFM) are well established. In this review, we have outlined the main principles of these two methods and demonstrated their advantages for structural studies of plant viruses of different shapes with relatively high spatial resolution. In addition, we have demonstrated the ability of AFM to obtain information on the mechanical properties of the virus particles that are inaccessible to other experimental techniques. We believe that these under-appreciated approaches, especially when used in combination, are valuable tools for studying a wide variety of helical plant viruses, many of which cannot be resolved by classical structural methods.
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Affiliation(s)
- Eleonora V. Shtykova
- National Research Centre, “Kurchatov Institute”, Moscow 123098, Russia; (E.V.S.)
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
| | - Evgeniy V. Dubrovin
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
- Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander L. Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Polina K. Gifer
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
| | - Maxim V. Petoukhov
- National Research Centre, “Kurchatov Institute”, Moscow 123098, Russia; (E.V.S.)
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
| | - Valeriy K. Tokhtar
- Scientific and Educational Center, Botanical Garden of the National Research University “BelSU”, Belgorod 308033, Russia;
| | - Irina M. Sapozhnikova
- Institute of Chemical Engineering, Ural Federal University Named after the First President of Russia B. N. Yeltsin, Ekaterinburg 620002, Russia;
| | - Andrey N. Stavrianidi
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
- Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Larisa V. Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Oleg V. Batishchev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
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2
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Chakrabarti R, Verma L, Hadjiev VG, Palmer JC, Vekilov PG. The elementary reactions for incorporation into crystals. Proc Natl Acad Sci U S A 2024; 121:e2320201121. [PMID: 38315836 PMCID: PMC10873555 DOI: 10.1073/pnas.2320201121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/26/2023] [Indexed: 02/07/2024] Open
Abstract
The growth rates of crystals are largely dictated by the chemical reaction between solute and kinks, in which a solute molecule severs its bonds with the solvent and establishes new bonds with the kink. Details on this sequence of bond breaking and rebuilding remain poorly understood. To elucidate the reaction at the kinks we employ four solvents with distinct functionalities as reporters on the microscopic structures and their dynamics along the pathway into a kink. We combine time-resolved in situ atomic force microscopy and x-ray and optical methods with molecular dynamics simulations. We demonstrate that in all four solvents the solute, etioporphyrin I, molecules reach the steps directly from the solution; this finding identifies the measured rate constant for step growth as the rate constant of the reaction between a solute molecule and a kink. We show that the binding of a solute molecule to a kink divides into two elementary reactions. First, the incoming solute molecule sheds a fraction of its solvent shell and attaches to molecules from the kink by bonds distinct from those in its fully incorporated state. In the second step, the solute breaks these initial bonds and relocates to the kink. The strength of the preliminary bonds with the kink determines the free energy barrier for incorporation into a kink. The presence of an intermediate state, whose stability is controlled by solvents and additives, may illuminate how minor solution components guide the construction of elaborate crystal architectures in nature and the search for solution compositions that suppress undesirable or accelerate favored crystallization in industry.
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Affiliation(s)
- Rajshree Chakrabarti
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX77204-4004
| | - Lakshmanji Verma
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX77204-4004
| | - Viktor G. Hadjiev
- Texas Center for Superconductivity, University of Houston, Houston, TX77004-50024
| | - Jeremy C. Palmer
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX77204-4004
| | - Peter G. Vekilov
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX77204-4004
- Department of Chemistry, University of Houston, Houston, TX77204-5003
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3
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Liu Y, Liu X, Su A, Gong C, Chen S, Xia L, Zhang C, Tao X, Li Y, Li Y, Sun T, Bu M, Shao W, Zhao J, Li X, Peng Y, Guo P, Han Y, Zhu Y. Revolutionizing the structural design and determination of covalent-organic frameworks: principles, methods, and techniques. Chem Soc Rev 2024; 53:502-544. [PMID: 38099340 DOI: 10.1039/d3cs00287j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Covalent organic frameworks (COFs) represent an important class of crystalline porous materials with designable structures and functions. The interconnected organic monomers, featuring pre-designed symmetries and connectivities, dictate the structures of COFs, endowing them with high thermal and chemical stability, large surface area, and tunable micropores. Furthermore, by utilizing pre-functionalization or post-synthetic functionalization strategies, COFs can acquire multifunctionalities, leading to their versatile applications in gas separation/storage, catalysis, and optoelectronic devices. Our review provides a comprehensive account of the latest advancements in the principles, methods, and techniques for structural design and determination of COFs. These cutting-edge approaches enable the rational design and precise elucidation of COF structures, addressing fundamental physicochemical challenges associated with host-guest interactions, topological transformations, network interpenetration, and defect-mediated catalysis.
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Affiliation(s)
- Yikuan Liu
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Xiaona Liu
- National Engineering Research Center of Lower-Carbon Catalysis Technology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - An Su
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Chengtao Gong
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Shenwei Chen
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Liwei Xia
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Chengwei Zhang
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Xiaohuan Tao
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Yue Li
- Institute of Intelligent Computing, Zhejiang Lab, Hangzhou 311121, China
| | - Yonghe Li
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Tulai Sun
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Mengru Bu
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Wei Shao
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Jia Zhao
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Xiaonian Li
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Yongwu Peng
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Peng Guo
- National Engineering Research Center of Lower-Carbon Catalysis Technology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yu Han
- School of Emergent Soft Matter, South China University of Technology, Guangzhou, China.
- King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Yihan Zhu
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
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4
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Darkins R, McPherson IJ, Ford IJ, Duffy DM, Unwin PR. Critical Step Length as an Indicator of Surface Supersaturation during Crystal Growth from Solution. CRYSTAL GROWTH & DESIGN 2022; 22:982-986. [PMID: 35572167 PMCID: PMC9097158 DOI: 10.1021/acs.cgd.1c01249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/11/2022] [Indexed: 06/15/2023]
Abstract
The surface processes that control crystal growth from solution can be probed in real-time by in situ microscopy. However, when mass transport (partly) limits growth, the interfacial solution conditions are difficult to determine, precluding quantitative measurement. Here, we demonstrate the use of a thermodynamic feature of crystal surfaces-the critical step length-to convey the local supersaturation, allowing the surface-controlled kinetics to be obtained. Applying this method to atomic force microscopy measurements of calcite, which are shown to fall within the regime of mixed surface/transport control, unites calcite step velocities with the Kossel-Stranski model, resolves disparities between growth rates measured under different mass transport conditions, and reveals why the Gibbs-Thomson effect in calcite departs from classical theory. Our approach expands the scope of in situ microscopy by decoupling quantitative measurement from the influence of mass transport.
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Affiliation(s)
- Robert Darkins
- London
Centre for Nanotechnology, University College
London, 17-19 Gordon Street, London WC1H 0AH, U.K.
| | - Ian J. McPherson
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Ian J. Ford
- London
Centre for Nanotechnology, University College
London, 17-19 Gordon Street, London WC1H 0AH, U.K.
| | - Dorothy M. Duffy
- London
Centre for Nanotechnology, University College
London, 17-19 Gordon Street, London WC1H 0AH, U.K.
| | - Patrick R. Unwin
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
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5
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Akhmetova AI, Yaminsky IV. High resolution imaging of viruses: Scanning probe microscopy and related techniques. Methods 2021; 197:30-38. [PMID: 34157416 DOI: 10.1016/j.ymeth.2021.06.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 05/26/2021] [Accepted: 06/17/2021] [Indexed: 11/19/2022] Open
Abstract
Scanning probe microscopy is a group of measurements that provides 3D visualization of viruses in different environmental conditions including liquids and air. Besides 3D topography it is possible to measure the properties like mechanical rigidity and stability, adhesion, tendency to crystallization, surface charge, etc. Choosing the right substrate and scanning parameters makes it much easier to obtain reliable data. Rational interpretation of experimental results should take into account possible artifacts, proper filtering and data presentation using specially designed software packages. Animal and human virus characterization is in the focus of many intensive studies because of their potential harm to higher organisms. The article focuses on high-resolution visualization of plant viruses. Tobacco mosaic virus, potato viruses X and B and others are not dangerous for the human being and are widely used in different applications such as vaccine preparation, construction of building units in nanotechnology and material science applications, nanoparticle production and delivery, and even metrology. The methods of virus's deposition, visualization, and consequent image processing and interpretation are described in details. Specific examples of viruses imaging are illustrated using the FemtoScan Online software, which has typical and all the necessary built-in functions for constructing three-dimensional images, their processing and analysis. Despite visible progress in visualizing the viruses using probe microscopy, many unresolved problems still remain. At present time the probe microscopy data on viruses is not systemized. There is no descriptive atlas of the images and morphology as revealed by this type of high resolution microscopy. It is worth emphasizing that new virus investigation methods will appear due to the progress of science.
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Affiliation(s)
- Assel I Akhmetova
- Lomonosov Moscow State University, 1, Leninskie Gory, Moscow, 119991, GSP-1, Russia; Advanced Technologies Center, 4-5-47, Stroitelei str., Moscow, 119311, Russia
| | - Igor V Yaminsky
- Lomonosov Moscow State University, 1, Leninskie Gory, Moscow, 119991, GSP-1, Russia; Advanced Technologies Center, 4-5-47, Stroitelei str., Moscow, 119311, Russia.
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6
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Miranda A, Gómez-Varela AI, Stylianou A, Hirvonen LM, Sánchez H, De Beule PAA. How did correlative atomic force microscopy and super-resolution microscopy evolve in the quest for unravelling enigmas in biology? NANOSCALE 2021; 13:2082-2099. [PMID: 33346312 DOI: 10.1039/d0nr07203f] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With the invention of the Atomic Force Microscope (AFM) in 1986 and the subsequent developments in liquid imaging and cellular imaging it became possible to study the topography of cellular specimens under nearly physiological conditions with nanometric resolution. The application of AFM to biological research was further expanded with the technological advances in imaging modes where topographical data can be combined with nanomechanical measurements, offering the possibility to retrieve the biophysical properties of tissues, cells, fibrous components and biomolecules. Meanwhile, the quest for breaking the Abbe diffraction limit restricting microscopic resolution led to the development of super-resolution fluorescence microscopy techniques that brought the resolution of the light microscope comparable to the resolution obtained by AFM. The instrumental combination of AFM and optical microscopy techniques has evolved over the last decades from integration of AFM with bright-field and phase-contrast imaging techniques at first to correlative AFM and wide-field fluorescence systems and then further to the combination of AFM and fluorescence based super-resolution microscopy modalities. Motivated by the many developments made over the last decade, we provide here a review on AFM combined with super-resolution fluorescence microscopy techniques and how they can be applied for expanding our understanding of biological processes.
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Affiliation(s)
- Adelaide Miranda
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal.
| | - Ana I Gómez-Varela
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal. and Department of Applied Physics, University of Santiago de Compostela, E-15782, Santiago de Compostela, Spain.
| | - Andreas Stylianou
- Cancer Biophysics Laboratory, University of Cyprus, Nicosia, Cyprus and School of Sciences, European University Cyprus, Nicosia, Cyprus
| | - Liisa M Hirvonen
- Centre for Microscopy, Characterisation and Analysis (CMCA), The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Humberto Sánchez
- Faculty of Applied Sciences, Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Pieter A A De Beule
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal.
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7
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Giese CC, King HE, van den Ende MP, Plümper O, ten Kate IL, Tielens AG. In Situ Nanoscale Investigation of Step Retreat on Fluoranthene Crystal Surfaces. ACS EARTH & SPACE CHEMISTRY 2018; 2:1301-1311. [PMID: 30662975 PMCID: PMC6326534 DOI: 10.1021/acsearthspacechem.8b00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 10/25/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
Fluoranthene, a polycyclic aromatic hydrocarbon, has been detected on Earth as well as in asteroids and meteorites and may have played a role in the formation of life. Increasing the ionic strength of aqueous solutions has been observed to lower the fluoranthene solubility, but it is unclear how solution composition controls the release rate of fluoranthene to an aqueous solution. To elucidate this, we performed in situ atomic force microscopy experiments in which we characterized the sublimation and dissolution behavior of fluoranthene crystal surfaces. From this, we quantify the step retreat rate upon exposure to air, deionized water, and a 0.4 M NaCl or 0.1 M MgSO4 solution. Surface roughness is the main factor that determines the dissolution or sublimation rate. The results imply that during fluoranthene remediation or breakdown in meteorites and asteroids, ionic strength will be more important than chemical composition for controlling fluoranthene release into solution.
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Affiliation(s)
- Claudia-Corina Giese
- Leiden
Observatory, Faculty of Science, Leiden
University, 2300 RA Leiden, The Netherlands
- Department
of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CB Utrecht, The Netherlands
| | - Helen E. King
- Department
of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CB Utrecht, The Netherlands
| | - Martijn P.A. van den Ende
- Department
of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CB Utrecht, The Netherlands
- Géoazur, Université Côte
d’Azur, 06560 Valbonne, France
| | - Oliver Plümper
- Department
of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CB Utrecht, The Netherlands
| | - Inge Loes ten Kate
- Department
of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CB Utrecht, The Netherlands
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8
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Sharma S, LeClaire M, Gimzewski JK. Ascent of atomic force microscopy as a nanoanalytical tool for exosomes and other extracellular vesicles. NANOTECHNOLOGY 2018; 29:132001. [PMID: 29376505 DOI: 10.1088/1361-6528/aaab06] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Over the last 30 years, atomic force microscopy (AFM) has made several significant contributions to the field of biology and medicine. In this review, we draw our attention to the recent applications and promise of AFM as a high-resolution imaging and force sensing technology for probing subcellular vesicles: exosomes and other extracellular vesicles. Exosomes are naturally occurring nanoparticles found in several body fluids such as blood, saliva, cerebrospinal fluid, amniotic fluid and urine. Exosomes mediate cell-cell communication, transport proteins and genetic content between distant cells, and are now known to play important roles in progression of diseases such as cancers, neurodegenerative disorders and infectious diseases. Because exosomes are smaller than 100 nm (about 30-120 nm), the structural and molecular characterization of these vesicles at the individual level has been challenging. AFM has revealed a new degree of complexity in these nanosized vesicles and generated growing interest as a nanoscale tool for characterizing the abundance, morphology, biomechanics, and biomolecular make-up of exosomes. With the recent interest in exosomes for diagnostic and therapeutic applications, AFM-based characterization promises to contribute towards improved understanding of these particles at the single vesicle and sub-vesicular levels. When coupled with complementary methods like optical super resolution STED and Raman, AFM could further unlock the potential of exosomes as disease biomarkers and as therapeutic agents.
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Affiliation(s)
- S Sharma
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, United States of America
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9
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10
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Herrmann A, Sieben C. Single-virus force spectroscopy unravels molecular details of virus infection. Integr Biol (Camb) 2015; 7:620-32. [PMID: 25923471 DOI: 10.1039/c5ib00041f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Virus infection is a multistep process that has significant effects on the structure and function of both the virus and the host cell. The first steps of virus replication include cell binding, entry and release of the viral genome. Single-virus force spectroscopy (SVFS) has become a promising tool to understand the molecular details of those steps. SVFS data complemented by biochemical and biophysical, including theoretical modeling approaches provide valuable insights into molecular events that accompany virus infection. Properties of virus-cell interaction as well as structural alterations of the virus essential for infection can be investigated on a quantitative level. Here we review applications of SVFS to virus binding, structure and mechanics. We demonstrate that SVFS offers unexpected new insights not accessible by other methods.
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Affiliation(s)
- Andreas Herrmann
- Humboldt-Universität zu Berlin, Institut für Biologie, Molekulare Biophysik, Invalidenstr. 42, D-10115 Berlin, Germany.
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11
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Nguyen TTH, Hammond RB, Roberts KJ, Marziano I, Nichols G. Precision measurement of the growth rate and mechanism of ibuprofen {001} and {011} as a function of crystallization environment. CrystEngComm 2014. [DOI: 10.1039/c4ce00097h] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The growth rates of the {001} and {011} crystal faces of ibuprofen were measured as a function of the solution crystallisation environment from which the likely interfacial kinetic growth mechanisms were characterised.
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Affiliation(s)
- T. T. H. Nguyen
- Institute of Particle Science and Engineering
- Institute of Process Research and Development
- School of Process
- Environmental and Materials Engineering
- University of Leeds
| | - R. B. Hammond
- Institute of Particle Science and Engineering
- Institute of Process Research and Development
- School of Process
- Environmental and Materials Engineering
- University of Leeds
| | - K. J. Roberts
- Institute of Particle Science and Engineering
- Institute of Process Research and Development
- School of Process
- Environmental and Materials Engineering
- University of Leeds
| | - I. Marziano
- Pfizer Worldwide Research and Development
- Sandwich, UK
| | - G. Nichols
- Pfizer Worldwide Research and Development
- Sandwich, UK
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12
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Kahr B, Bullard T, Kurimoto M, De Yoreo JJ. Complex organic guests in simple crystals: potassium hydrogen phthalate as case study. CRYSTAL RESEARCH AND TECHNOLOGY 2013. [DOI: 10.1002/crat.201200710] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Bart Kahr
- Department of Chemistry; New York University, 100 Washington Square East; New York City NY 10003 USA
| | - Theresa Bullard
- Department of Chemistry; New York University, 100 Washington Square East; New York City NY 10003 USA
| | - Miki Kurimoto
- Department of Chemistry; New York University, 100 Washington Square East; New York City NY 10003 USA
| | - James J. De Yoreo
- Pacific Northwest National Laboratories; PO Box 999, MSIN: K2-01 Richland WA 99352 USA
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13
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Chung SY, Kim YM, Choi SY, Kim JG. Real-Time Observation of Crystal Evaporation in a Metal Phosphate at High Temperature. J Am Chem Soc 2013; 135:7811-4. [DOI: 10.1021/ja401753u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sung-Yoon Chung
- Graduate School
of EEWS and KAIST Institute for the Nanocentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
- Nalphates LLC, Wilmington, Delaware 19801,
United States
| | - Young-Min Kim
- Korea Basic Science Institute, Daejeon 305-333, Korea
| | - Si-Young Choi
- Korea Institute of Materials Science, Changwon 641-831, Korea
| | - Jin-Gyu Kim
- Korea Basic Science Institute, Daejeon 305-333, Korea
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14
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Chang KC, Chiang YW, Yang CH, Liou JW. Atomic force microscopy in biology and biomedicine. Tzu Chi Med J 2012. [DOI: 10.1016/j.tcmj.2012.08.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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15
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What can Mesoscopic LevelIN SITUObservations Teach us About Kinetics and Thermodynamics of Protein Crystallization? ADVANCES IN CHEMICAL PHYSICS 2012. [DOI: 10.1002/9781118309513.ch9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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Abstract
Atomic force microscopy (AFM) has proven to be a valuable approach to delineate the architectures and detailed structural features of a wide variety of viruses. These have ranged from small plant satellite viruses of only 17 nm to the giant mimivirus of 750 nm diameter, and they have included diverse morphologies such as those represented by HIV, icosahedral particles, vaccinia, and bacteriophages. Because it is a surface technique, it provides images and information that are distinct from those obtained by electron microscopy, and in some cases, at even higher resolution. By enzymatic and chemical dissection of virions, internal structures can be revealed, as well as DNA and RNA. The method is relatively rapid and can be carried out on both fixed and unfixed samples in either air or fluids, including culture media. It is nondestructive and even non-perturbing. It can be applied to individual isolated virus, as well as to infected cells. AFM is still in its early development and holds great promise for further investigation of biological systems at the nanometer scale.
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Affiliation(s)
- Alexander McPherson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.
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17
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Kuznetsov YG, McPherson A. Atomic force microscopy in imaging of viruses and virus-infected cells. Microbiol Mol Biol Rev 2011; 75:268-85. [PMID: 21646429 PMCID: PMC3122623 DOI: 10.1128/mmbr.00041-10] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Atomic force microscopy (AFM) can visualize almost everything pertinent to structural virology and at resolutions that approach those for electron microscopy (EM). Membranes have been identified, RNA and DNA have been visualized, and large protein assemblies have been resolved into component substructures. Capsids of icosahedral viruses and the icosahedral capsids of enveloped viruses have been seen at high resolution, in some cases sufficiently high to deduce the arrangement of proteins in the capsomeres as well as the triangulation number (T). Viruses have been recorded budding from infected cells and suffering the consequences of a variety of stresses. Mutant viruses have been examined and phenotypes described. Unusual structural features have appeared, and the unexpectedly great amount of structural nonconformity within populations of particles has been documented. Samples may be imaged in air or in fluids (including culture medium or buffer), in situ on cell surfaces, or after histological procedures. AFM is nonintrusive and nondestructive, and it can be applied to soft biological samples, particularly when the tapping mode is employed. In principle, only a single cell or virion need be imaged to learn of its structure, though normally images of as many as is practical are collected. While lateral resolution, limited by the width of the cantilever tip, is a few nanometers, height resolution is exceptional, at approximately 0.5 nm. AFM produces three-dimensional, topological images that accurately depict the surface features of the virus or cell under study. The images resemble common light photographic images and require little interpretation. The structures of viruses observed by AFM are consistent with models derived by X-ray crystallography and cryo-EM.
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Affiliation(s)
- Yurii G. Kuznetsov
- University of California, Irvine, Department of Molecular Biology and Biochemistry, 560 Steinhaus Hall, Irvine, California 92697-3900
| | - Alexander McPherson
- University of California, Irvine, Department of Molecular Biology and Biochemistry, 560 Steinhaus Hall, Irvine, California 92697-3900
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Lutsko JF, Basios V, Nicolis G, Kozak JJ, Sleutel M, Maes D. Kinetic rougheninglike transition with finite nucleation barrier. J Chem Phys 2010; 132:035102. [DOI: 10.1063/1.3294561] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Qiu SR, Orme CA. Dynamics of Biomineral Formation at the Near-Molecular Level. Chem Rev 2008; 108:4784-822. [DOI: 10.1021/cr800322u] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- S. Roger Qiu
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Mailstop L-367, Livermore, California 94550
| | - Christine A. Orme
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Mailstop L-367, Livermore, California 94550
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Wang X, Niu Z, Li S, Wang Q, Li X. Nanomechanical characterization of polyaniline coated tobacco mosaic virus nanotubes. J Biomed Mater Res A 2008; 87:8-14. [DOI: 10.1002/jbm.a.31617] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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21
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Guo S, Akhremitchev BB. Investigation of mechanical properties of insulin crystals by atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:880-887. [PMID: 18163652 DOI: 10.1021/la7018605] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Mechanical properties of protein crystals and aggregates depend on the conformational and structural properties of individual protein molecules as well as on the packing density and structure within solid materials. An atomic force microscopy (AFM)-based approach is developed to measure the elastic modulus of small protein crystals by nanoindentation and is applied to measure the elasticity of insulin crystals. The top face of the crystals deposited on mica substrates is identified as the (001) face. Insulin crystals exhibit a nearly elastic response during the compression cycle. The elastic modulus measured on the top face has asymmetric distribution with a significant width. This width is related to the uncertainty in the deflection sensitivity. A model that takes into account the distribution of the sensitivity values is used to correct the elastic modulus. Measurements performed in aqueous buffer on several crystals at different locations with three different AFM probes give a mean elastic modulus of 164 +/- 10 MPa. This value is close to the static elastic moduli of other protein crystals measured by different techniques that are usually measured in the range from 100 MPa to 1 GPa. The measured modulus of insulin crystals falls between the elastic modulus values of insulin amyloid fibrils measured previously at two orthogonal directions (a modulus of 14 MPa was measured by compressing the fibril in the direction perpendicular to the fibril axis, and a modulus of 3.3 GPa was measured in the direction along the fibril axis). This comparison indicates the heterogeneous structure of fibrils in the direction perpendicular to the fibril axis, with a packing density of the amyloid fibril core that is higher than the average packing density in insulin crystals. The mechanical wear of insulin crystals is detected during AFM measurements. In nanoindentation experiments on insulin crystal, the compressive load by the AFM tip ( approximately 1 nN, corresponding to a pressure of around 5 MPa) occasionally removes protein molecules from the top or the second top layer of insulin crystal in a sequential manner. The molecular model of this surface damage is proposed. In addition, the removal of the multiple layers of molecules is observed during the AC-mode imaging in aqueous buffer. The number of removed layers depends on the scan size.
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Affiliation(s)
- Senli Guo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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22
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Abstract
We present a kinetic model of crystal growth of polymers of finite molecular weight. Experiments help to classify polymer crystallization broadly into two kinetic regimes. One is observed in melts or in high molar mass polymer solutions and is dominated by nucleation control with G approximately exp(1/TDeltaT), where G is the growth rate and DeltaT is the supercooling. The other is observed in low molar mass solutions (as well as for small molecules) and is diffusion controlled with G approximately DeltaT, for small DeltaT. Our model unifies these two regimes in a single formalism. The model accounts for the accumulation of polymer chains near the growth front and invokes an entropic barrier theory to recover both limits of nucleation and diffusion control. The basic theory applies to both melts and solutions, and we numerically calculate the growth details of a single crystal in a dilute solution. The effects of molecular weight and concentration are also determined considering conventional polymer dynamics. Our theory shows that entropic considerations, in addition to the traditional energetic arguments, can capture general trends of a vast range of phenomenology. Unifying ideas on crystallization from small molecules and from flexible polymer chains emerge from our theory.
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Affiliation(s)
- Arindam Kundagrami
- Department of Polymer Science and Engineering, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, USA
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Affiliation(s)
- Peter G Vekilov
- Department of Chemical Engineering, University of Houston, Houston, Texas 77204, USA
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Reviakine I, Georgiou DK, Vekilov PG. Capillarity effects on crystallization kinetics: insulin. J Am Chem Soc 2003; 125:11684-93. [PMID: 13129373 DOI: 10.1021/ja030194t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
During layerwise growth of crystals, capillarity governs the generation of new crystal layers. Theory predicts that the line tension of the layer edge determines, via the characteristic two-dimensional capillary length L(c), the rates of generation and initial growth of the new layers. To test the correlation between L(c) and the rate of layer generation, we used in situ Tapping Mode Atomic Force Microscopy (TM-AFM) to study the generation and spreading of layers during crystallization of rhombohedral, R3, porcine insulin. We show that crystallization of this insulin form is uniquely suitable for such an investigation due to the linear kinetics of step growth it exhibits. This linear kinetics reflects the abundance of the incorporation sites along the rough steps, the lack of long-range step-step interactions, and the transport control of the growth kinetics. The kinetic coefficients are 7 x 10(-)(3) and 4 x 10(-)(2) cm s(-)(1), respectively, in the absence and presence of the cosolvent acetone-somewhat high for proteins and comparable to values for inorganic systems. We show that (i). the relevant capillary length, the size of a critical quadrangular 2D nucleus L(c), is the main scaling factor for the density of growth steps, while (ii). all steps longer than L(c) grow with a rate determined only by the supersaturation and independent of their length. We explain the divergence of (ii). from theoretical predictions with the high supersaturations typical of the growth of this protein system.
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Affiliation(s)
- Ilya Reviakine
- Department of Chemical Engineering, University of Houston, Houston, Texas 77204-4004, USA
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26
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Waizumi K, Plomp M, van Enckevort W. Atomic force microscopy studies on growing surfaces of bovine insulin crystals. Colloids Surf B Biointerfaces 2003. [DOI: 10.1016/s0927-7765(03)00037-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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27
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Petsev DN, Chen K, Gliko O, Vekilov PG. Diffusion-limited kinetics of the solution-solid phase transition of molecular substances. Proc Natl Acad Sci U S A 2003; 100:792-6. [PMID: 12552115 PMCID: PMC298680 DOI: 10.1073/pnas.0333065100] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
For critical tests of whether diffusion-limited kinetics is an option for the solution-solid phase transition of molecular substances or whether they are determined exclusively by a transition state, we performed crystallization experiments with ferritin and apoferritin, a unique pair of proteins with identical shells but different molecular masses. We find that the kinetic coefficient for crystallization is identical (accuracy <or=7%) for the pair, indicating diffusion-limited kinetics of crystallization. Data on the kinetics of this phase transition in systems ranging from small-molecule ionic to protein and viri suggest that the kinetics of solution-phase transitions for broad classes of small-molecule and protein materials are diffusion-limited.
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Affiliation(s)
- Dimiter N Petsev
- Department of Chemical Engineering, University of Houston, Houston, TX 77204, USA
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28
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Boutet S, Robinson IK, Hu ZW, Thomas BR, Chernov AA. Surface relaxation in protein crystals. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2002; 66:061914. [PMID: 12513324 DOI: 10.1103/physreve.66.061914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2002] [Indexed: 05/24/2023]
Abstract
Surface x-ray diffraction measurements were performed on (111) growth faces of crystals of the cellular iron-storage protein, horse spleen ferritin. Crystal truncation rods (CTR) were measured. A fit of the measured profile of the CTR revealed a surface roughness of 48+/-4.5 A and a top layer spacing contraction of 3.9+/-1.5%. In addition to the peak from the CTR, the rocking curves of the crystals displayed unexpected extra peaks. Multiple scattering is demonstrated to account for them. Future applications of the method could allow the exploration of hydration effects on the growth of protein crystals.
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Affiliation(s)
- S Boutet
- Department of Physics, University of Illinois, Urbana, IL 61801, USA
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29
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Malkin AJ, McPherson A. Novel Mechanisms for Defect Formation and Surface Molecular Processes in Virus Crystallization. J Phys Chem B 2002. [DOI: 10.1021/jp014580d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. J. Malkin
- Department of Molecular Biology and Biochemistry, University of California, Irvine, 560 Steinhaus Hall, Irvine, California 92697-3900
| | - A. McPherson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, 560 Steinhaus Hall, Irvine, California 92697-3900
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30
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Onuma K, Kubota T, Tanaka S, Kanzaki N, Ito A, Tsutsui K. Dynamic Light Scattering Investigation in Aqueous Solutions of bc1-Complex Membrane Protein. J Phys Chem B 2002. [DOI: 10.1021/jp0143387] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kazuo Onuma
- Tissue Engineering Research Center, National Institute of Advanced Industrial Science and Technology, Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan, Institute of Molecular and Cell Biology, National Institute of Advanced Industrial Science and Technology, Central 2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan, Special Division for Human Life Technology, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan, and Otsuka
| | - Tomomi Kubota
- Tissue Engineering Research Center, National Institute of Advanced Industrial Science and Technology, Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan, Institute of Molecular and Cell Biology, National Institute of Advanced Industrial Science and Technology, Central 2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan, Special Division for Human Life Technology, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan, and Otsuka
| | - Shinpei Tanaka
- Tissue Engineering Research Center, National Institute of Advanced Industrial Science and Technology, Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan, Institute of Molecular and Cell Biology, National Institute of Advanced Industrial Science and Technology, Central 2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan, Special Division for Human Life Technology, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan, and Otsuka
| | - Noriko Kanzaki
- Tissue Engineering Research Center, National Institute of Advanced Industrial Science and Technology, Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan, Institute of Molecular and Cell Biology, National Institute of Advanced Industrial Science and Technology, Central 2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan, Special Division for Human Life Technology, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan, and Otsuka
| | - Atsuo Ito
- Tissue Engineering Research Center, National Institute of Advanced Industrial Science and Technology, Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan, Institute of Molecular and Cell Biology, National Institute of Advanced Industrial Science and Technology, Central 2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan, Special Division for Human Life Technology, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan, and Otsuka
| | - Kazunori Tsutsui
- Tissue Engineering Research Center, National Institute of Advanced Industrial Science and Technology, Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan, Institute of Molecular and Cell Biology, National Institute of Advanced Industrial Science and Technology, Central 2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan, Special Division for Human Life Technology, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan, and Otsuka
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31
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Kuznetsov YG, Larson SB, Day J, Greenwood A, McPherson A. Structural transitions of satellite tobacco mosaic virus particles. Virology 2001; 284:223-34. [PMID: 11384222 DOI: 10.1006/viro.2000.0914] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Satellite tobacco mosaic virus (STMV) can undergo at least two physical transitions that significantly alter its mechanical and structural characteristics. At high pH the 17-nm STMV particles expand radially by about 5 A to yield particles having diameters of about 18 nm. This pH-induced transition is further promoted by aging of the virions and degradation of the RNA, so that swollen particles ultimately appear even at neutral pH. While the native 17-nm particles crystallize as orthorhombic or monoclinic crystals which diffract to high resolution (1.8 A), the enlarged 18-nm particles crystallize in a cubic form which diffracts to no better than 5 A. In the transition, not only do the capsid protein subunits move radially outward, but the helical RNA segments with which they interact do as well. This is noteworthy because it demonstrates that the RNA and the protein shell are capable of coordinated movement, and that neither structure is rigidly defined or independent of the other. Using atomic force microscopy, it can be shown that STMV particles, upon drying, lose their mechanical rigidity and undergo deformation. Virions initially 17 nm in diameter shrink to more uniform final sizes than do 18 nm, initially swollen particles. This transition appears to be irreversible, as the particles do not reassume their former size nor structural rigidity upon rehydration. Evidence is also presented that preparations of native virus and their crystals are naturally somewhat heterogeneous and contain a variety of particles of anomalous size.
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Affiliation(s)
- Y G Kuznetsov
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Room 560, Steinhaus Hall, Irvine, California 92697-3900, USA
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32
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Ward MD. Bulk crystals to surfaces: combining X-ray diffraction and atomic force microscopy to probe the structure and formation of crystal interfaces. Chem Rev 2001; 101:1697-725. [PMID: 11709996 DOI: 10.1021/cr000020j] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M D Ward
- Department of Chemical Engineering and Materials Science, University of Minnesota, Amundson Hall, 421 Washington Avenue, Southeast, Minneapolis, Minnesota 55455, USA.
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33
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McPherson A, Malkin AJ. Atomic force microscopy in the study of macromolecular crystal growth. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2001; 29:361-410. [PMID: 10940253 DOI: 10.1146/annurev.biophys.29.1.361] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Atomic force microscopy (AFM) has been used to study protein, nucleic acid, and virus crystals in situ, in their mother liquors, as they grow. From sequential AFM images taken at brief intervals over many hours, or even days, the mechanisms and kinetics of the growth process can be defined. The appearance of both two- and three-dimensional nuclei on crystal surfaces have been visualized, defect structures of crystals were clearly evident, and defect densities of crystals were also determined. The incorporation of a wide range of impurities, ranging in size from molecules to microns or larger microcrystals, and even foreign particles were visually recorded. From these observations and measurements, a more complex understanding of the detailed character of macromolecular crystals is emerging, one that reveals levels of complexity previously unsuspected. The unique features of these crystals, apparently in AFM images, undoubtedly influence the diffraction properties of the crystals and the quality of the molecular images obtained by X-ray crystallography.
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Affiliation(s)
- A McPherson
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92697-3900, USA.
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34
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Yau ST, Vekilov PG. Direct observation of nucleus structure and nucleation pathways in apoferritin crystallization. J Am Chem Soc 2001; 123:1080-9. [PMID: 11456661 DOI: 10.1021/ja003039c] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using atomic force microscopy (AFM) in situ during the crystallization of the protein apoferritin from its solution, we imaged the arrangement of the molecules in near-critical clusters, larger or smaller than the crystal nucleus, that are representative of the nucleus structure. At supersaturations Delta mu/k(B)T of 1.1 -- 1.6 -- 2.3, the nuclei contain about 50 -- 20 -- 10 molecules. The molecular arrangement within the nuclei is similar to that in the crystal bulk. Contrary to the general belief, the observed nuclei are not compact molecular clusters, but are planar arrays of several rods of 4--7 molecules set in one or two monomolecular layers. Similarly unexpected nuclei structures might be common, especially for anisotropic molecules. Hence, the nucleus structure should be considered as a variable by advanced theoretical treatments.
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Affiliation(s)
- S T Yau
- Center for Microgravity and Materials Research, University of Alabama in Huntsville, Huntsville, Alabama 35899, USA
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35
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Abstract
Biological macromolecules and particularly viruses, provide excellent systems for the study of crystallization from solution because of their relatively large size. The kinetics of their crystallization is at least an order of magnitude less than for conventional systems, and their large size permits visualization, both of crystal lattices and individual particles, by techniques such as atomic force microscopy (AFM). This technique is especially powerful for biological macromolecules because it can be utilized in situ, in the crystallization mother liquor, over long periods of time without perturbing the growing crystals. We present here observations using AFM of the nucleation and growth of crystals of satellite tobacco mosaic virus, and some recordings as well of bromegrass mosaic virus. Correlations are made, where possible, with corresponding analyses using X-ray diffraction analysis.
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36
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Plomp M, McPherson A, Larson SB, Malkin AJ. Growth Mechanisms and Kinetics of Trypsin Crystallization. J Phys Chem B 2000. [DOI: 10.1021/jp003007b] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Plomp
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900
| | - Alexander McPherson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900
| | - Steven B. Larson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900
| | - Alexander J. Malkin
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900
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37
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Thompson JB, Paloczi GT, Kindt JH, Michenfelder M, Smith BL, Stucky G, Morse DE, Hansma PK. Direct observation of the transition from calcite to aragonite growth as induced by abalone shell proteins. Biophys J 2000; 79:3307-12. [PMID: 11106633 PMCID: PMC1301204 DOI: 10.1016/s0006-3495(00)76562-3] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The mixture of EDTA-soluble proteins found in abalone nacre are known to cause the nucleation and growth of aragonite on calcite seed crystals in supersaturated solutions of calcium carbonate. Past atomic force microscope studies of the interaction of these proteins with calcite crystals did not observe this transition because no information about the crystal polymorph on the surface was obtained. Here we have used the atomic force microscope to directly observe changes in the atomic lattice on a calcite seed crystal after the introduction of abalone shell proteins. The observed changes are consistent with a transition to (001) aragonite growth on a (1014) calcite surface.
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Affiliation(s)
- J B Thompson
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA.
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38
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Abstract
First-order phase transitions of matter, such as condensation and crystallization, proceed through the formation and subsequent growth of 'critical nuclei' of the new phase. The thermodynamics and kinetics of the formation of these critical nuclei depend on their structure, which is often assumed to be a compact, three-dimensional arrangement of the constituent molecules or atoms. Recent molecular dynamics simulations have predicted compact nucleus structures for matter made up of building blocks with a spherical interaction field, whereas strongly anisotropic, dipolar molecules may form nuclei consisting of single chains of molecules. Here we show, using direct atomic force microscopy observations, that the near-critical-size clusters formed during the crystallization of apoferritin, a quasi-spherical protein, and which are representative of the critical nucleus of this system, consist of planar arrays of one or two monomolecular layers that contain 5-10 rods of up to 7 molecules each. We find that these clusters contain between 20 and 50 molecules each, and that the arrangement of the constituent molecules is identical to that found in apoferritin crystals. We anticipate that similarly unexpected critical nucleus structures may be quite common, particularly with anisotropic molecules, suggesting that advanced nucleation theories should treat the critical nucleus structure as a variable.
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Affiliation(s)
- S T Yau
- Center for Microgravity and Materials Research, University of Alabama in Huntsville, 35899, USA
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39
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Vekilov PG, Alexander JID. Dynamics of Layer Growth in Protein Crystallization. Chem Rev 2000; 100:2061-2090. [PMID: 11749284 DOI: 10.1021/cr9800558] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter G. Vekilov
- Department of Chemistry and Center for Microgravity and Materials Research, University of Alabama-Huntsville, RI Building D-29, Huntsville, Alabama 35899, and Department of Mechanical and Aerospace Engineering and National Center for Microgravity Research on Fluids and Combustion, Glennan 416, Case Western Reserve University, Cleveland, Ohio 44106-7222
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41
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Kitamura M, Onuma K. In Situ Observation of Growth Process of alpha-L-Glutamic Acid with Atomic Force Microscopy. J Colloid Interface Sci 2000; 224:311-316. [PMID: 10727341 DOI: 10.1006/jcis.1999.6686] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The growth kinetics of the (111) and (001) faces of an alpha-L-glutamic acid crystal was investigated from the measurements of the growth rates, coupling with in situ surface observation using atomic force microscopy (AFM). The data of the growth rates were examined by applying the theoretical equations of the BCF and NaN models. The results indicate that the growth mechanism is not due to the screw dislocation but to the two-dimensional nucleation, i.e., the NaN model. It was confirmed by AFM observation that both the (111) and (001) faces grew with the "nucleus above nucleus" (NaN) mechanism. However, the difference of the two-dimensional nucleation behavior was observed between the faces. The growing surface of the (111) face was also observed in the presence of L-phenylaline (L-Phe) and the pinning effect by L-Phe on the growing step on the (111) face was confirmed. This result supports the mechanism of the additive effect, which was proposed previously. Copyright 2000 Academic Press.
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Affiliation(s)
- M Kitamura
- Department of Chemical Engineering, Hiroshima University, 1-4-1, Kagamiyama, Hiroshima, 739-8527, Japan
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Yip CM, Brader ML, Frank BH, DeFelippis MR, Ward MD. Structural studies of a crystalline insulin analog complex with protamine by atomic force microscopy. Biophys J 2000; 78:466-73. [PMID: 10620310 PMCID: PMC1300654 DOI: 10.1016/s0006-3495(00)76609-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Crystallographic studies of insulin-protamine complexes, such as neutral protamine Hagedorn (NPH) insulin, have been hampered by high crystal solvent content, small crystal dimensions, and extensive disorder in the protamine molecules. We report herein in situ tapping mode atomic force microscopy (TMAFM) studies of crystalline neutral protamine Lys(B28)Pro(B29) (NPL), a complex of Lys(B28)Pro(B29) insulin, in which the C-terminal prolyl and lysyl residues of human insulin are inverted, and protamine that is used as an intermediate time-action therapy for treating insulin-dependent diabetes. Tapping mode AFM performed at 6 degrees C on bipyramidally tipped tetragonal rod-shaped NPL crystals revealed large micron-sized islands separated by 44-A tall steps. Lattice images obtained by in situ TMAFM phase and height imaging on these islands were consistent with the arrangement of individual insulin-protamine complexes on the P4(1)2(1)2 (110) crystal plane of NPH, based on a low-resolution x-ray diffraction structure of NPH, arguing that the NPH and NPL insulins are isostructural. Superposition of the height and phase images indicated that tip-sample adhesion was larger in the interstices between NPL complexes in the (110) crystal plane than over the individual complexes. These results demonstrate the utility of low-temperature TMAFM height and phase imaging for the structural characterization of biomolecular complexes.
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Affiliation(s)
- C M Yip
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, USA.
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Tanaka S, Ito K, Hayakawa R, Ataka M. Size and number density of precrystalline aggregates in lysozyme crystallization process. J Chem Phys 1999. [DOI: 10.1063/1.480381] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Malkin AJ, Kuznetsov YG, Lucas RW, McPherson A. Surface processes in the crystallization of turnip yellow mosaic virus visualized by atomic force microscopy. J Struct Biol 1999; 127:35-43. [PMID: 10479615 DOI: 10.1006/jsbi.1999.4128] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In situ atomic force microscopy (AFM) was used to investigate surface evolution during the growth of single crystals of turnip yellow mosaic virus (TYMV). Growth of the (101) face of TYMV crystals proceeded by two-dimensional nucleation. The molecular structure of the step edges and adsorption of individual virus particles and their aggregates on the crystalline surface were recorded. The surfaces of individual virions within crystals were visualized and seen to be quite distinctive with the hexameric and pentameric capsomers of the T = 3 capsids being clearly resolved. This, so far as we are aware, is the first direct visualization of the capsomere structure of a virus by AFM. In the course of recording the in situ development of the crystals, a profound restructuring of the surface arrangement was observed. This transformation was highly cooperative in nature, but the transitions were unambiguous and readily explicable in terms of an organized loss of classes of virus particles from specific lattice positions. In some cases areas of a single crystal surface were recorded in which were captured successive phases of the transition. We believe this provides the first visual record of a cooperative restructuring of the surface of a supramolecular crystal.
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Affiliation(s)
- A J Malkin
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, 92697-3900, USA.
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45
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46
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Yip CM, DeFelippis MR, Frank BH, Brader ML, Ward MD. Structural and morphological characterization of ultralente insulin crystals by atomic force microscopy: evidence of hydrophobically driven assembly. Biophys J 1998; 75:1172-9. [PMID: 9726919 PMCID: PMC1299792 DOI: 10.1016/s0006-3495(98)74036-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Although x-ray crystal structures exist for many forms of insulin, the hormone involved in glucose metabolism and used in the treatment of diabetes, x-ray structural characterization of therapeutically important long-acting crystalline ultralente insulin forms has been elusive because of small crystal size and poor diffraction characteristics. We describe tapping-mode atomic force microscopy (TMAFM) studies, performed directly in crystallization liquor, of ultralente crystals prepared from bovine, human, and porcine insulins. Lattice images obtained from direct imaging of crystal planes are consistent with R3 space group symmetry for each insulin type, but the morphology of the human and porcine crystals observed by AFM differs substantially from that of the bovine insulin crystals. Human and porcine ultralente crystals exhibited large, molecularly flat (001) faces consisting of hexagonal arrays of close packed hexamers. In contrast, bovine ultralente crystals predominantly exhibited faces with cylindrical features assignable to close-packed stacks of insulin hexamers laying in-plane, consistent with the packing motif of the (010) and (011) planes. This behavior is attributed to a twofold increase in the hydrophobic character of the upper and lower surfaces of the donut-shaped insulin hexamer in bovine insulin compared to its human and porcine counterparts that results from minor sequence differences between these insulins. The increased hydrophobicity of these surfaces can promote hexamer-hexamer stacking in precrystalline aggregates or enhance attachment of single hexamers along the c axis at the crystal surface during crystal growth. Both events lead to enhanced growth of ¿hk0¿ planes instead of (001). The insulin hexamers on the (010) and (110) faces are exposed "edge-on" to the aqueous medium, such that solvent access to the center of the hexamer and to solvent channels is reduced compared to the (001) surface, consistent with the slower dissolution and reputed unique basal activity of bovine ultralente insulin. These observations demonstrate that subtle variations in amino acid sequence can dramatically affect the interfacial structure of crystalline proteins.
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Affiliation(s)
- C M Yip
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
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47
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Yip CM, Brader ML, DeFelippis MR, Ward MD. Atomic force microscopy of crystalline insulins: the influence of sequence variation on crystallization and interfacial structure. Biophys J 1998; 74:2199-209. [PMID: 9591647 PMCID: PMC1299563 DOI: 10.1016/s0006-3495(98)77929-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The self-association of proteins is influenced by amino acid sequence, molecular conformation, and the presence of molecular additives. In the presence of phenolic additives, LysB28ProB29 insulin, in which the C-terminal prolyl and lysyl residues of wild-type human insulin have been inverted, can be crystallized into forms resembling those of wild-type insulins in which the protein exists as zinc-complexed hexamers organized into well-defined layers. We describe herein tapping-mode atomic force microscopy (TMAFM) studies of single crystals of rhombohedral (R3) LysB28ProB29 that reveal the influence of sequence variation on hexamer-hexamer association at the surface of actively growing crystals. Molecular scale lattice images of these crystals were acquired in situ under growth conditions, enabling simultaneous identification of the rhombohedral LysB28ProB29 crystal form, its orientation, and its dynamic growth characteristics. The ability to obtain crystallographic parameters on multiple crystal faces with TMAFM confirmed that bovine and porcine insulins grown under these conditions crystallized into the same space group as LysB28ProB29 (R3), enabling direct comparison of crystal growth behavior and the influence of sequence variation. Real-time TMAFM revealed hexamer vacancies on the (001) terraces of LysB28ProB29, and more rounded dislocation noses and larger terrace widths for actively growing screw dislocations compared to wild-type bovine and porcine insulin crystals under identical conditions. This behavior is consistent with weaker interhexamer attachment energies for LysB28ProB29 at active growth sites. Comparison of the single crystal x-ray structures of wild-type insulins and LysB28ProB29 suggests that differences in protein conformation at the hexamer-hexamer interface and accompanying changes in interhexamer bonding are responsible for this behavior. These studies demonstrate that subtle changes in molecular conformation due to a single sequence inversion in a region critical for insulin self-association can have a significant effect on the crystallization of proteins.
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Affiliation(s)
- C M Yip
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
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Onuma K, Ito A, Tabe I, Tateishi T. In Situ Atomic Force Microscopy Study of the Dissolution Kinetics of Dicalcium Phosphate Dihydrate Crystal in a Physiological Solution. J Phys Chem B 1997. [DOI: 10.1021/jp971863q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kazuo Onuma
- National Institute for Advanced Interdisciplinary Research, 1-1-4 Higashi, Tsukuba, Ibaraki, 305 Japan, and National Institute of Materials and Chemical Research, 1-1 Higashi, Tsukuba, Ibaraki, 305 Japan
| | - Atsuo Ito
- National Institute for Advanced Interdisciplinary Research, 1-1-4 Higashi, Tsukuba, Ibaraki, 305 Japan, and National Institute of Materials and Chemical Research, 1-1 Higashi, Tsukuba, Ibaraki, 305 Japan
| | - Ikuko Tabe
- National Institute for Advanced Interdisciplinary Research, 1-1-4 Higashi, Tsukuba, Ibaraki, 305 Japan, and National Institute of Materials and Chemical Research, 1-1 Higashi, Tsukuba, Ibaraki, 305 Japan
| | - Tetsuya Tateishi
- National Institute for Advanced Interdisciplinary Research, 1-1-4 Higashi, Tsukuba, Ibaraki, 305 Japan, and National Institute of Materials and Chemical Research, 1-1 Higashi, Tsukuba, Ibaraki, 305 Japan
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Ng JD, Kuznetsov YG, Malkin AJ, Keith G, Giegé R, McPherson A. Visualization of RNA crystal growth by atomic force microscopy. Nucleic Acids Res 1997; 25:2582-8. [PMID: 9185567 PMCID: PMC146776 DOI: 10.1093/nar/25.13.2582] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The crystallization of transfer RNA (tRNA) was investigated using atomic force microscopy (AFM) over the temperature range from 4 to 16 degrees C, and this produced the first in situ AFM images of developing nucleic acid crystals. The growth of the (110) face of hexagonal yeast tRNAPhe crystals was observed to occur at steps on vicinal hillocks generated by multiple screw dislocation sources in the temperature range of 13.5-16 degrees C. Two-dimensional nucleation begins to dominate at 13.5 degrees C, with the appearance of three-dimensional nuclei at 12 degrees C. The changes in growth mechanisms are correlated with variations in supersaturation which is higher in the low temperature range. Growth of tRNA crystals was characterized by a strong anisotropy in the tangential step movement and transformation of growth modes on single crystals were directly observed by AFM over the narrow temperature range utilized. Finally, lattice resolution images of the molecular structure of surface layers were recorded. The implications of the strong temperature dependence of tRNAPhe crystal growth are discussed in view of improving and better controlling crystallization of nucleic acids.
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Affiliation(s)
- J D Ng
- Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
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50
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Malkin AJ, Land TA, DeYoreo JJ, Barba AP, Konnert J, McPherson A. Molecular resolution imaging of macromolecular crystals by atomic force microscopy. Biophys J 1997; 72:2357-64. [PMID: 9129839 PMCID: PMC1184431 DOI: 10.1016/s0006-3495(97)78880-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Atomic force microscopy (AFM) images at the molecular level have been obtained for a number of different protein and virus crystals. They can be utilized in some special cases to obtain information useful to crystal structure analyses by x-ray diffraction. In particular, questions of space group enantiomer, the packing of molecules within a unit cell, the number of molecules per asymmetric unit, and the dispositions of multiple molecules within the asymmetric unit may be resolved. In addition, because of the increasing sensitivity and resolution of the AFM technique, some molecular features of very large asymmetric units may be within reach. We describe here high-resolution studies, using AFM, to visualize individual molecules and viruses in their crystal lattices. These investigations included fungal lipase, lysozyme, thaumatin, canavalin, and satellite tobacco mosaic virus (STMV).
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