1
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Feng Y, Roos WH. Atomic Force Microscopy: An Introduction. Methods Mol Biol 2024; 2694:295-316. [PMID: 37824010 DOI: 10.1007/978-1-0716-3377-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Imaging of nano-sized particles and sample features is crucial in a variety of research fields, for instance, in biological sciences, where it is paramount to investigate structures at the single particle level. Often, two-dimensional images are not sufficient, and further information such as topography and mechanical properties are required. Furthermore, to increase the biological relevance, it is desired to perform the imaging in close to physiological environments. Atomic force microscopy (AFM) meets these demands in an all-in-one instrument. It provides high-resolution images including surface height information leading to three-dimensional information on sample morphology. AFM can be operated both in air and in buffer solutions. Moreover, it has the capacity to determine protein and membrane material properties via the force spectroscopy mode. Here we discuss the principles of AFM operation and provide examples of how biomolecules can be studied. New developments in AFM are discussed, and by including approaches such as bimodal AFM and high-speed AFM (HS-AFM), we show how AFM can be used to study a variety of static and dynamic single biomolecules and biomolecular assemblies.
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Affiliation(s)
- Yuzhen Feng
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands.
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2
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Zhekova HR, Jiang J, Wang W, Tsirulnikov K, Kayık G, Khan HM, Azimov R, Abuladze N, Kao L, Newman D, Noskov SY, Tieleman DP, Hong Zhou Z, Pushkin A, Kurtz I. CryoEM structures of anion exchanger 1 capture multiple states of inward- and outward-facing conformations. Commun Biol 2022; 5:1372. [PMID: 36517642 PMCID: PMC9751308 DOI: 10.1038/s42003-022-04306-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Anion exchanger 1 (AE1, band 3) is a major membrane protein of red blood cells and plays a key role in acid-base homeostasis, urine acidification, red blood cell shape regulation, and removal of carbon dioxide during respiration. Though structures of the transmembrane domain (TMD) of three SLC4 transporters, including AE1, have been resolved previously in their outward-facing (OF) state, no mammalian SLC4 structure has been reported in the inward-facing (IF) conformation. Here we present the cryoEM structures of full-length bovine AE1 with its TMD captured in both IF and OF conformations. Remarkably, both IF-IF homodimers and IF-OF heterodimers were detected. The IF structures feature downward movement in the core domain with significant unexpected elongation of TM11. Molecular modeling and structure guided mutagenesis confirmed the functional significance of residues involved in TM11 elongation. Our data provide direct evidence for an elevator-like mechanism of ion transport by an SLC4 family member.
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Affiliation(s)
- Hristina R Zhekova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Jiansen Jiang
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Weiguang Wang
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Kirill Tsirulnikov
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Gülru Kayık
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Hanif Muhammad Khan
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Rustam Azimov
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Natalia Abuladze
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Liyo Kao
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Debbie Newman
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Sergei Yu Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - D Peter Tieleman
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Alexander Pushkin
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Ira Kurtz
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Brain Research Institute, University of California, Los Angeles, CA, USA.
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3
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Maksudov F, Jones LK, Barsegov V. Statistical Learning from Single-Molecule Experiments: Support Vector Machines and Expectation-Maximization Approaches to Understanding Protein Unfolding Data. J Phys Chem B 2021; 125:5794-5808. [PMID: 34075752 DOI: 10.1021/acs.jpcb.1c02334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Single-molecule force spectroscopy has become a powerful tool for the exploration of dynamic processes that involve proteins; yet, meaningful interpretation of the experimental data remains challenging. Owing to low signal-to-noise ratio, experimental force-extension spectra contain force signals due to nonspecific interactions, tip or substrate detachment, and protein desorption. Unravelling of complex protein structures results in the unfolding transitions of different types. Here, we test the performance of Support Vector Machines (SVM) and Expectation Maximization (EM) approaches in statistical learning from dynamic force experiments. When the output from molecular modeling in silico (or other studies) is used as a training set, SVM and EM can be applied to understand the unfolding force data. The maximal margin or maximum likelihood classifier can be used to separate experimental test observations into the unfolding transitions of different types, and EM optimization can then be utilized to resolve the statistics of unfolding forces: weights, average forces, and standard deviations. We designed an EM-based approach, which can be directly applied to the experimental data without data classification and division into training and test observations. This approach performs well even when the sample size is small and when the unfolding transitions are characterized by overlapping force ranges.
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Bao Y, Luo Z, Cui S. Environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by atomic force microscopy-based single-molecule force spectroscopy and the implications for advanced polymer materials. Chem Soc Rev 2020; 49:2799-2827. [PMID: 32236171 DOI: 10.1039/c9cs00855a] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
"The Tao begets the One. One begets all things of the world." This quote from Tao Te Ching is still inspiring for scientists in chemistry and materials science: The "One" can refer to a single molecule. A macroscopic material is composed of numerous molecules. Although the relationship between the properties of the single molecule and macroscopic material is not well understood yet, it is expected that a deeper understanding of the single-chain mechanics of macromolecules will certainly facilitate the development of materials science. Atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) has been exploited extensively as a powerful tool to study the single-chain behaviors of macromolecules. In this review, we summarize the recent advances in the emerging field of environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by means of AFM-SMFS. First, the single-chain inherent elasticities of several typical linear macromolecules are introduced, which are also confirmed by one of three polymer models with theoretical elasticities of the corresponding macromolecules obtained from quantum mechanical (QM) calculations. Then, the effects of the external environments on the single-chain mechanics of synthetic polymers and biomacromolecules are reviewed. Finally, the impacts of single-chain mechanics of macromolecules on the development of polymer science especially polymer materials are illustrated.
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Affiliation(s)
- Yu Bao
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu 610031, China.
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5
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Dąbrowski J, Nowak W, Ptak A. How strong are hydrogen bonds in the peptide model? Phys Chem Chem Phys 2020; 22:1392-1399. [DOI: 10.1039/c9cp05564a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We provide a methodology based on the steered molecular dynamics simulations and dynamic force spectroscopy calculations to determine the kinetic and energetic characteristics of hydrogen bonds.
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Affiliation(s)
- Jakub Dąbrowski
- Institute of Physics
- Faculty of Technical Physics
- Poznan University of Technology
- PL-60965 Poznan
- Poland
| | - Wiesław Nowak
- Institute of Physics
- Faculty of Physics
- Astronomy and Informatics
- Nicolaus Copernicus University
- PL-87100 Torun
| | - Arkadiusz Ptak
- Institute of Physics
- Faculty of Technical Physics
- Poznan University of Technology
- PL-60965 Poznan
- Poland
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6
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Perego C, Potestio R. Computational methods in the study of self-entangled proteins: a critical appraisal. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:443001. [PMID: 31269476 DOI: 10.1088/1361-648x/ab2f19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The existence of self-entangled proteins, the native structure of which features a complex topology, unveils puzzling, and thus fascinating, aspects of protein biology and evolution. The discovery that a polypeptide chain can encode the capability to self-entangle in an efficient and reproducible way during folding, has raised many questions, regarding the possible function of these knots, their conservation along evolution, and their role in the folding paradigm. Understanding the function and origin of these entanglements would lead to deep implications in protein science, and this has stimulated the scientific community to investigate self-entangled proteins for decades by now. In this endeavour, advanced experimental techniques are more and more supported by computational approaches, that can provide theoretical guidelines for the interpretation of experimental results, and for the effective design of new experiments. In this review we provide an introduction to the computational study of self-entangled proteins, focusing in particular on the methodological developments related to this research field. A comprehensive collection of techniques is gathered, ranging from knot theory algorithms, that allow detection and classification of protein topology, to Monte Carlo or molecular dynamics strategies, that constitute crucial instruments for investigating thermodynamics and kinetics of this class of proteins.
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Affiliation(s)
- Claudio Perego
- Max Panck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
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7
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Barinov NA, Protopopova AD, Dubrovin EV, Klinov DV. Thermal denaturation of fibrinogen visualized by single-molecule atomic force microscopy. Colloids Surf B Biointerfaces 2018; 167:370-376. [DOI: 10.1016/j.colsurfb.2018.04.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 04/08/2018] [Accepted: 04/17/2018] [Indexed: 01/27/2023]
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8
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Zhao D, Liu S, Gao Y. Single-molecule manipulation and detection. Acta Biochim Biophys Sin (Shanghai) 2018; 50:231-237. [PMID: 29377975 DOI: 10.1093/abbs/gmx146] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/23/2017] [Indexed: 11/13/2022] Open
Abstract
Compared to conventional ensemble methods, studying macromolecules at single-molecule level can reveal extraordinary clear and even surprising views for a biological reaction. In the past 20 years, single-molecule techniques have been undergoing a very rapid development, and these cutting edge technologies have revolutionized the biological research by facilitating single-molecule manipulation and detection. Here we give a brief review about these advanced techniques, including optical tweezers, magnetic tweezers, atomic force microscopy (AFM), hydrodynamic flow-stretching assay, and single-molecule fluorescence resonance energy transfer (smFRET). We are trying to describe their basic principles and provide a few examples of applications for each technique. This review aims to give a rather introductory survey of single-molecule techniques for audiences with biological or biophysical background.
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Affiliation(s)
- Deyu Zhao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Siyun Liu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Ying Gao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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9
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Abstract
Imaging of nano-sized particles and sample features is crucial in a variety of research fields. For instance in biological sciences, where it is paramount to investigate structures at the single particle level. Often two-dimensional images are not sufficient and further information such as topography and mechanical properties are required. Furthermore, to increase the biological relevance, it is desired to perform the imaging in close to physiological environments. Atomic force microscopy (AFM) meets these demands in an all-in-one instrument. It provides high-resolution images including surface height information leading to three-dimensional information on sample morphology. AFM can be operated both in air and in buffer solutions. Moreover, it has the capacity to determine protein and membrane material properties via the force spectroscopy mode. Here we discuss the principles of AFM operation and provide examples of how biomolecules can be studied. By including new approaches such as high-speed AFM (HS-AFM) we show how AFM can be used to study a variety of static and dynamic single biomolecules and biomolecular assemblies.
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Affiliation(s)
- Melissa C Piontek
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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10
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Batchelor M, Wolny M, Kurzawa M, Dougan L, Knight PJ, Peckham M. Determining Stable Single Alpha Helical (SAH) Domain Properties by Circular Dichroism and Atomic Force Microscopy. Methods Mol Biol 2018; 1805:185-211. [PMID: 29971719 DOI: 10.1007/978-1-4939-8556-2_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Stable, single α-helical (SAH) domains exist in a number of unconventional myosin isoforms, as well as other proteins. These domains are formed from sequences rich in charged residues (Arg, Lys, and Glu), they can be hundreds of residues long, and in isolation they can tolerate significant changes in pH and salt concentration without loss in helicity. Here we describe methods for the preparation and purification of SAH domains and SAH domain-containing constructs, using the myosin 10 SAH domain as an example. We go on to describe the use of circular dichroism spectroscopy and force spectroscopy with the atomic force microscope for the elucidation of structural and mechanical properties of these unusual helical species.
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Affiliation(s)
- Matthew Batchelor
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Marcin Wolny
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Marta Kurzawa
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Lorna Dougan
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
| | - Peter J Knight
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Michelle Peckham
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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11
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da Silva M, Lenton S, Hughes M, Brockwell DJ, Dougan L. Assessing the Potential of Folded Globular Polyproteins As Hydrogel Building Blocks. Biomacromolecules 2017; 18:636-646. [PMID: 28006103 PMCID: PMC5348097 DOI: 10.1021/acs.biomac.6b01877] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 12/21/2016] [Indexed: 01/14/2023]
Abstract
The native states of proteins generally have stable well-defined folded structures endowing these biomolecules with specific functionality and molecular recognition abilities. Here we explore the potential of using folded globular polyproteins as building blocks for hydrogels. Photochemically cross-linked hydrogels were produced from polyproteins containing either five domains of I27 ((I27)5), protein L ((pL)5), or a 1:1 blend of these proteins. SAXS analysis showed that (I27)5 exists as a single rod-like structure, while (pL)5 shows signatures of self-aggregation in solution. SANS measurements showed that both polyprotein hydrogels have a similar nanoscopic structure, with protein L hydrogels being formed from smaller and more compact clusters. The polyprotein hydrogels showed small energy dissipation in a load/unload cycle, which significantly increased when the hydrogels were formed in the unfolded state. This study demonstrates the use of folded proteins as building blocks in hydrogels, and highlights the potential versatility that can be offered in tuning the mechanical, structural, and functional properties of polyproteins.
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Affiliation(s)
- Marcelo
A. da Silva
- School of Physics and Astronomy and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Samuel Lenton
- School of Physics and Astronomy and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Matthew Hughes
- School of Physics and Astronomy and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - David J. Brockwell
- School of Physics and Astronomy and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lorna Dougan
- School of Physics and Astronomy and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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12
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Kreplak L. Introduction to Atomic Force Microscopy (AFM) in Biology. ACTA ACUST UNITED AC 2016; 85:17.7.1-17.7.21. [PMID: 27479503 DOI: 10.1002/cpps.14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The atomic force microscope (AFM) has the unique capability of imaging biological samples with molecular resolution in buffer solution over a wide range of time scales from milliseconds to hours. In addition to providing topographical images of surfaces with nanometer- to angstrom-scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated from the nano-scale to the micro-scale. Importantly, the measurements are made in buffer solutions, allowing biological samples to "stay alive" within a physiological-like environment while temporal changes in structure are measured-e.g., before and after addition of chemical reagents. These qualities distinguish AFM from conventional imaging techniques of comparable resolution, e.g., electron microscopy (EM). This unit provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins, cells, and tissues. The physical principles of the technique and methodological aspects of its practical use and applications are also described. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Laurent Kreplak
- Department of Physics & Atmospheric Science, Dalhousie University, Halifax, Canada
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13
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Hughes ML, Dougan L. The physics of pulling polyproteins: a review of single molecule force spectroscopy using the AFM to study protein unfolding. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2016; 79:076601. [PMID: 27309041 DOI: 10.1088/0034-4885/79/7/076601] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
One of the most exciting developments in the field of biological physics in recent years is the ability to manipulate single molecules and probe their properties and function. Since its emergence over two decades ago, single molecule force spectroscopy has become a powerful tool to explore the response of biological molecules, including proteins, DNA, RNA and their complexes, to the application of an applied force. The force versus extension response of molecules can provide valuable insight into its mechanical stability, as well as details of the underlying energy landscape. In this review we will introduce the technique of single molecule force spectroscopy using the atomic force microscope (AFM), with particular focus on its application to study proteins. We will review the models which have been developed and employed to extract information from single molecule force spectroscopy experiments. Finally, we will end with a discussion of future directions in this field.
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Affiliation(s)
- Megan L Hughes
- School of Physics and Astronomy, University of Leeds, LS2 9JT, UK. Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, UK
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14
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Subunit unbinding mechanics of dimeric wheat germ agglutinin (WGA) studied by atomic force microscopy. FEBS Lett 2014; 588:4472-7. [DOI: 10.1016/j.febslet.2014.10.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 12/31/2022]
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15
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Interaction between pheromone and its receptor of the fission yeast Schizosaccharomyces pombe examined by a force spectroscopy study. J Biomed Biotechnol 2012; 2012:804793. [PMID: 22500108 PMCID: PMC3303674 DOI: 10.1155/2012/804793] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 11/22/2011] [Accepted: 11/26/2011] [Indexed: 11/17/2022] Open
Abstract
Interaction between P-factor, a peptide pheromone composed of 23 amino acid residues, and its pheromone receptor, Mam2, on the cell surface of the fission yeast Schizosaccharomyces pombe was examined by an atomic force microscope (AFM). An AFM tip was modified with P-factor derivatives to perform force curve measurements. The specific interaction force between P-factor and Mam2 was calculated to be around 120 pN at a probe speed of 1.74 μm/s. When the AFM tip was modified with truncated P-factor derivative lacking C-terminal Leu, the specific interaction between the tip and the cell surface was not observed. These results were also confirmed with an assay system using a green fluorescent protein (GFP) reporter gene to monitor the activation level of signal transduction following the interaction of Mam2 with P-factor.
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16
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Taniguchi Y, Kobayashi A, Kawakami M. Mechanical unfolding studies of protein molecules. Biophysics (Nagoya-shi) 2012; 8:51-58. [PMID: 27857607 PMCID: PMC5070453 DOI: 10.2142/biophysics.8.51] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 12/30/2011] [Indexed: 12/31/2022] Open
Abstract
Atomic force microscopy (AFM) enables the pick up of a single protein molecule to apply a mechanical force. This technique, called "force spectroscopy," provides unique information about the intermediates and free energy landscape of the mechanical unfolding of proteins. In this review, we introduce the AFM-based single molecule force spectroscopy of proteins and describe recent studies that answer some fundamental questions such as "is the mechanical resistance of proteins isotropic?", "what is the structure of the transition state in mechanical unfolding?", and "is mechanical unfolding related to biological functions?"
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Affiliation(s)
- Yukinori Taniguchi
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa Prefecture 923-1292, Japan
| | - Akiko Kobayashi
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa Prefecture 923-1292, Japan
| | - Masaru Kawakami
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa Prefecture 923-1292, Japan
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17
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Hoffmann T, Dougan L. Single molecule force spectroscopy using polyproteins. Chem Soc Rev 2012; 41:4781-96. [DOI: 10.1039/c2cs35033e] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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18
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Hakari T, Sekiguchi H, Osada T, Kishimoto K, Afrin R, Ikai A. Nonlinear displacement of ventral stress fibers under externally applied lateral force by an atomic force microscope. Cytoskeleton (Hoboken) 2011; 68:628-38. [PMID: 21976314 DOI: 10.1002/cm.20537] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 09/11/2011] [Accepted: 09/27/2011] [Indexed: 01/07/2023]
Abstract
Actin-based stress fibers (SFs) have fundamental importance in the maintenance of mechanical stability of living cells. Several in vitro measurements of their elastic properties have therefore been made, but direct mechanical manipulation of individual SFs in vivo for the determination of their mechanical properties has not been attempted. No less important is a search for the possible formation of a global mechanical network involving SFs and other intracellular filamentous components. In this article, we present an application of atomic force microscopy to probe into a live cell and laterally push selected SFs in a fibroblast cells (VNOf 06 fibroblast-like cells derived from rat vomeronasal tissue) transfected with a green fluorescent protein-β-actin gene. The transfected cells were transferred to a serum-depleted medium before the atomic force microscope manipulation. The lateral displacement of the SFs under a point loading condition recorded on a fluorescence microscope revealed both linear and nonlinear displacements against the contour distance from the point of force loading. The nonlinear displacements of the SFs were attributed to their association with a cortical actomyosin-cell membrane complex that effectively pulled them back as a 2D thin plate.
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Affiliation(s)
- Tomoro Hakari
- Department of Molecular Bioscience, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
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19
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Ogawa T, Kurachi S, Kageshima M, Naitoh Y, Jun Li Y, Sugawara Y. Step response measurement of AFM cantilever for analysis of frequency-resolved viscoelasticity. Ultramicroscopy 2010; 110:612-7. [DOI: 10.1016/j.ultramic.2010.02.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Phang IY, Aldred N, Ling XY, Huskens J, Clare AS, Vancso GJ. Atomic force microscopy of the morphology and mechanical behaviour of barnacle cyprid footprint proteins at the nanoscale. J R Soc Interface 2010; 7:285-96. [PMID: 19570797 PMCID: PMC2842607 DOI: 10.1098/rsif.2009.0127] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 05/26/2009] [Indexed: 11/12/2022] Open
Abstract
Barnacles are a major biofouler of man-made underwater structures. Prior to settlement, cypris larvae explore surfaces by reversible attachment effected by a 'temporary adhesive'. During this exploratory behaviour, cyprids deposit proteinaceous 'footprints' of a putatively adhesive material. In this study, footprints deposited by Balanus amphitrite cyprids were probed by atomic force microscopy (AFM) in artificial sea water (ASW) on silane-modified glass surfaces. AFM images obtained in air yielded better resolution than in ASW and revealed the fibrillar nature of the secretion, suggesting that the deposits were composed of single proteinaceous nanofibrils, or bundles of fibrils. The force curves generated in pull-off force experiments in sea water consisted of regions of gradually increasing force, separated by sharp drops in extension force manifesting a characteristic saw-tooth appearance. Following the relaxation of fibrils stretched to high strains, force-distance curves in reverse stretching experiments could be described by the entropic elasticity model of a polymer chain. When subjected to relaxation exceeding 500 ms, extended footprint proteins refolded, and again showed saw-tooth unfolding peaks in subsequent force cycles. Observed rupture and hysteresis behaviour were explained by the 'sacrificial bond' model. Longer durations of relaxation (>5 s) allowed more sacrificial bond reformation and contributed to enhanced energy dissipation (higher toughness). The persistence length for the protein chains (L(P)) was obtained. At high elongation, following repeated stretching up to increasing upper strain limits, footprint proteins detached at total stretched length of 10 microm.
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Affiliation(s)
- In Yee Phang
- Department of Materials Science and Technology of Polymers, MESA Institute for Nanotechnology, PO Box 217, 7500 AE Enschede, The Netherlands
- Dutch Polymer Institute, PO Box 902, 5600 Eindhoven, The Netherlands
| | - Nick Aldred
- School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Xing Yi Ling
- Molecular Nanofabrication Group, MESA Institute for Nanotechnology, University of Twente, PO Box 217, 7500 Enschede, The Netherlands
| | - Jurriaan Huskens
- Molecular Nanofabrication Group, MESA Institute for Nanotechnology, University of Twente, PO Box 217, 7500 Enschede, The Netherlands
| | - Anthony S. Clare
- School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - G. Julius Vancso
- Department of Materials Science and Technology of Polymers, MESA Institute for Nanotechnology, PO Box 217, 7500 AE Enschede, The Netherlands
- Dutch Polymer Institute, PO Box 902, 5600 Eindhoven, The Netherlands
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21
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Kawakami M, Taniguchi Y, Hiratsuka Y, Shimoike M, Smith DA. Reduction of the damping on an AFM cantilever in fluid by the use of micropillars. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:1002-1007. [PMID: 19785459 DOI: 10.1021/la902472h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In single molecule force measurements with soft atomic force microscope (AFM) cantilevers, the force sensitivity is limited by the Brownian motion of the cantilever. When a cantilever is close to the surface, the hydrodynamic interaction between the cantilever beam and the surface, called the "squeezing effect", becomes significant, and the resonance peak of the thermal oscillation of the cantilever is heavily broadened and shifted to lower frequency which makes it difficult to eliminate the thermal noise by low-pass filtering. In this study, we propose an easy and low-cost method to improve the force sensitivity. We demonstrate that by bringing a tip of a cantilever onto the edge of a micropillar structure a significant reduction of the damping and an enhancement of force sensitivity are achieved.
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Affiliation(s)
- Masaru Kawakami
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan.
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22
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Ikai A. A review on: atomic force microscopy applied to nano-mechanics of the cell. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010; 119:47-61. [PMID: 19343307 DOI: 10.1007/10_2008_41] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Since its introduction in 1986, AFM has been applied to biological studies along with its widespread use in physics, chemistry and engineering fields. Due to its dual capabilities of imaging nano-materials with an atomic level resolution and of directly manipulating samples with high precision, AFM is now considered an indispensable instrument for nano-technological researchers especially in physically oriented fields. In biology in general, however, and in biotechnology in particular, its usefulness must be critically examined and, if necessary as it certainly is, further explored from a practical point of view. In this review, a new trend of applying AFM based technology to elucidate the mechanical basis of the cellular structure and its interaction with the extracellular matrix including cell to cell interaction is reviewed. Some of the recent studies done by using other force measuring or force exerting methods are also covered in the hope that all the nano-mechanical work on the cellular level will eventually contribute to the emergence of the mechano-chemical view of the cell in a unified manner.
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Affiliation(s)
- Atsushi Ikai
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan,
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23
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Tensile Mechanics of α-Helical Coil Springs. Biopolymers 2010. [DOI: 10.1007/12_2009_41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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Goldsbury CS, Scheuring S, Kreplak L. Introduction to Atomic Force Microscopy (AFM) in Biology. ACTA ACUST UNITED AC 2009; Chapter 17:17.7.1-17.7.19. [DOI: 10.1002/0471140864.ps1707s58] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | - Laurent Kreplak
- Dalhousie University, Department of Physics & Atmospheric Science Halifax Canada
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25
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Markelov DA, Neelov IM, Neelov AI, Gotlib YY, Darinskii AA. The theory of viscoelastic characteristics of a highly stretched macromolecule in single molecule AFM. POLYMER SCIENCE SERIES A 2009. [DOI: 10.1134/s0965545x09080148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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26
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Afrin R, Zohora US, Uehara H, Watanabe-Nakayama T, Ikai A. Atomic force microscopy for cellular level manipulation: imaging intracellular structures and DNA delivery through a membrane hole. J Mol Recognit 2009; 22:363-72. [DOI: 10.1002/jmr.971] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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High-sensitivity detection of proteins using gel electrophoresis and atomic force microscopy. Ultramicroscopy 2009; 109:916-22. [DOI: 10.1016/j.ultramic.2009.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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28
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Afrin R, Takahashi I, Shiga K, Ikai A. Tensile mechanics of alanine-based helical polypeptide: force spectroscopy versus computer simulations. Biophys J 2009; 96:1105-14. [PMID: 19186146 DOI: 10.1016/j.bpj.2008.10.046] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Accepted: 10/27/2008] [Indexed: 11/16/2022] Open
Abstract
In nature, an alpha-helix is commonly used to build thermodynamically stable and mechanically rigid protein conformations. In view of growing interest in the mechanical rigidity of proteins, we measured the tensile profile of an alanine-based alpha-helical polypeptide on an atomic-force microscope to investigate the basic mechanics of helix extension with minimal interference from side-chain interactions. The peptide was extended to its maximum contour length with much less force than in reported cases of poly-L-Glu or poly-L-Lys, indicating that chain stiffness strongly depended on the physicochemical properties of side chains, such as their bulkiness. The low tensile-force extension originated presumably in locally unfolded parts because of spontaneous structural fluctuations. In 50% trifluoroethanol, the well-known helix-promoting agent, the rigidity of the sample polypeptide was markedly increased. Computer simulations of the peptide-stretching process showed that a majority of constituent residues underwent a transition from an alpha-helical to an extended conformation by overcoming an energy barrier around psi approximately 0 degrees on the Ramachandran plot. The observed lability of an isolated helix signified the biological importance of the lateral bundling of helices to maintain a rigid protein structure.
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Affiliation(s)
- Rehana Afrin
- Biofrontier Center, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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29
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Sakane I, Hongo K, Mizobata T, Kawata Y. Mechanical unfolding of covalently linked GroES: evidence of structural subunit intermediates. Protein Sci 2009; 18:252-7. [PMID: 19177369 DOI: 10.1002/pro.7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It is difficult to determine the structural stability of the individual subunits or protomers of many proteins in the cell that exist in an oligomeric or complexed state. In this study, we used single-molecule force spectroscopy on seven subunits of covalently linked cochaperonin GroES (ESC7) to evaluate the structural stability of the subunit. A modified form of ESC7 was immobilized on a mica surface. The force-extension profile obtained from the mechanical unfolding of this ESC7 showed a distinctive sawtooth pattern that is typical for multimodular proteins. When analyzed according to the worm-like chain model, the contour lengths calculated from the peaks in the profile suggested that linked-GroES subunits unfold in distinct steps after the oligomeric ring structure of ESC7 is disrupted. The evidence that structured subunits of ESC7 withstand external force to some extent even after the perturbation of the oligomeric ring structure suggests that a stable monomeric intermediate is an important component of the equilibrium unfolding reaction of GroES.
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Affiliation(s)
- Isao Sakane
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Japan
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30
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Kawakami M, Smith DA. A new atomic force microscope force ramp technique using digital force feedback control reveals mechanically weak protein unfolding events. NANOTECHNOLOGY 2008; 19:495704. [PMID: 21730684 DOI: 10.1088/0957-4484/19/49/495704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We have developed a new force ramp modification of the atomic force microscope (AFM) which can control multiple unfolding events of a multi-modular protein using software-based digital force feedback control. With this feedback the force loading rate can be kept constant regardless the length of soft elastic linkage or number of unfolded polypeptide domains. An unfolding event is detected as a sudden drop in force, immediately after which the feedback control reduces the applied force to a low value of a few pN by lowering the force set point. Hence the remaining folded domains can relax and the subsequent force ramp is applied to relaxed protein domains identically in each case. We have applied this technique to determine the kinetic parameters x(u), which is the distance between the native state and transition state, and α(0), which is the unfolding rate constant at zero force, for the mechanical unfolding of a pentamer of I27 domains of titin. In each force ramp the unfolding probability depends on the number of folded domains remaining in the system and we had to take account of this effect in the analysis of unfolding force data. We obtained values of x(u) and α(0) to be 0.28 nm and 1.02 × 10(-3) s(-1), which are in good agreement with those obtained from conventional constant velocity experiments. This method reveals unfolding data at low forces that are not seen in constant velocity experiments and corrects for the change in stiffness that occurs with most mechanical systems throughout the unfolding process to allow constant force ramp experiments to be carried out. In addition, a mechanically weak structure was detected, which formed from the fully extended polypeptide chain during a force quench. This indicates that the new technique will allow studies of the folding kinetics of previously hidden, mechanically weak species.
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Affiliation(s)
- M Kawakami
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan
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31
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Abstract
A review of the work done in the Laboratory of Biodynamics of Tokyo Institute of Technology in the last decade has been summarized in this article in relation to the results reported from other laboratories. The emphasis here is the application of nanomechanics based on the force mode of atomic force microscopy (AFM) to proteins and protein-based biological structures. Globular proteins were stretched in various ways to detect the localized rigidity inside of the molecule. When studied by this method, bovine carbonic anhydrase II (BCA II), calmodulin and OspA protein all showed the presence of localized rigid structures inside the molecules. Protein compression experiments were done on BCA II to obtain an estimate of the Young modulus and its change in the process of denaturation. Then, the AFM probe method was turned on to cell membranes and cytoplasmic components. Force curves accompanying the extraction process of membrane proteins from intact cells were analysed in relation to their interaction with the cytoskeletal components. By pushing the AFM probe further into the cytoplasm, mRNAs were recovered from a live cell with minimal damage, and multiplied using PCR technology for their identification. Altogether, the work introduced here forms the basis of nanomechanics of protein and protein-based biostructures and application of the nanomechanical technology to cell biology.
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Affiliation(s)
- Atsushi Ikai
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
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32
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Goldsbury C, Scheuring S. Introduction to atomic force microscopy (AFM) in biology. ACTA ACUST UNITED AC 2008; Chapter 17:17.7.1-17.7.17. [PMID: 18429225 DOI: 10.1002/0471140864.ps1707s29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The atomic force microscope has the unique capability of imaging biological samples with molecular resolution in buffer solution. In addition to providing topographical images of surfaces with nanometer- to angstrom-scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated. Importantly, the measurements are made in buffer solutions, allowing biological samples to stay alive within a physiological-like environment while temporal changes in structure are measured. This overview provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins. The physical principles of the technique and methodological aspects of its practical use and applications are also described.
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Affiliation(s)
- Claire Goldsbury
- Cytoskeleton Group, Max Planck Unit for Structural Molecular Biology, Hamburg, Germany
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33
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Probing the mechanical stability of proteins using the atomic force microscope. Biochem Soc Trans 2008; 35:1564-8. [PMID: 18031267 DOI: 10.1042/bst0351564] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mechanical strength of single protein molecules can be investigated by using the atomic force microscope. By applying this technique to a wide range of proteins, it appears that the type of secondary structure and its orientation relative to the extension points are important determinants of mechanical strength. Unlike chemical denaturants, force acts locally and the mechanical strength of a protein may thus appear to be mechanically weak or strong by simply varying the region of the landscape through which the protein is unfolded. Similarly, the effect of ligand binding on the mechanical resistance of a protein may also depend on the relative locations of the binding site and force application. Mechanical deformation may thus facilitate the degradation or remodelling of thermodynamically stable proteins and their complexes in vivo.
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34
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Giannotti MI, Vancso GJ. Interrogation of Single Synthetic Polymer Chains and Polysaccharides by AFM-Based Force Spectroscopy. Chemphyschem 2007; 8:2290-307. [PMID: 17847140 DOI: 10.1002/cphc.200700175] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
This contribution reviews selected mechanical experiments on individual flexible macromolecules using single-molecule force spectroscopy (SMFS) based on atomic force microscopy. Focus is placed on the analysis of elasticity and conformational changes in single polymer chains upon variation of the external environment, as well as on conformational changes induced by the mechanical stress applied to individual macromolecular chains. Various experimental strategies regarding single-molecule manipulation and SMFS testing are discussed, as is theoretical analysis through single-chain elasticity models derived from statistical mechanics. Moreover, a complete record, reported to date, of the parameters obtained when applying the models to fit experimental results on synthetic polymers and polysaccharides is presented.
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Affiliation(s)
- Marina I Giannotti
- Department of Materials Science and Technology of Polymers, MESA+Research Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
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35
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Voïtchovsky K, Contera SA, Ryan JF. Electrostatic and steric interactions determine bacteriorhodopsin single-molecule biomechanics. Biophys J 2007; 93:2024-37. [PMID: 17513362 PMCID: PMC1959538 DOI: 10.1529/biophysj.106.101469] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Bacteriorhodopsin (bR) is a haloarchaeal membrane protein that converts the energy of single photons into large structural changes to directionally pump protons across purple membrane. This is achieved by a complex combination of local dynamic interactions controlling bR biomechanics at the submolecular level, producing efficient amplification of the retinal photoisomerization. Using single molecule force spectroscopy at different salt concentrations, we show that tryptophan (Trp) residues use steric specific interactions to create a rigid scaffold in bR extracellular region and are responsible for the main unfolding barriers. This scaffold, which encloses the retinal, controls bR local mechanical properties and anchors the protein into the membrane. Furthermore, the stable Trp-based network allows ion binding to two specific sites on the extracellular loops (BC and FG), which are involved in proton release and lateral transport. In contrast, the cytoplasmic side of bR is mainly governed by relatively weak nonspecific electrostatic interactions that provide the flexibility necessary for large cytoplasmic structural rearrangements during the photocycle. The presence of an extracellular Trp-based network tightly enclosing the retinal seems common to most haloarchaeal rhodopsins, and could be relevant to their exceptional efficiency.
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Affiliation(s)
- Kislon Voïtchovsky
- Bionanotechnology Interdisciplinary Research Collaboration, Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, United Kingdom
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36
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Watabe H, Nakajima K, Sakai Y, Nishi T. Dynamic Force Spectroscopy on a Single Polymer Chain. Macromolecules 2006. [DOI: 10.1021/ma060724g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiroyuki Watabe
- Department of Organic and Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan, and Department of Advanced Materials Science, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Japan
| | - Ken Nakajima
- Department of Organic and Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan, and Department of Advanced Materials Science, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Japan
| | - Yasuhiro Sakai
- Department of Organic and Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan, and Department of Advanced Materials Science, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Japan
| | - Toshio Nishi
- Department of Organic and Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan, and Department of Advanced Materials Science, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Japan
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37
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Kawakami M, Byrne K, Brockwell DJ, Radford SE, Smith DA. Viscoelastic study of the mechanical unfolding of a protein by AFM. Biophys J 2006; 91:L16-8. [PMID: 16698787 PMCID: PMC1483103 DOI: 10.1529/biophysj.106.085019] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have applied a dynamic force modulation technique to the mechanical unfolding of a homopolymer of immunoglobulin (Ig) domains from titin, (C47S C63S I27)5, [(I27)5] to determine the viscoelastic response of single protein molecules as a function of extension. Both the stiffness and the friction of the homopolymer system show a sudden decrease when a protein domain unfolds. The decrease in measured friction suggests that the system is dominated by the internal friction of the (I27)5 molecule and not solvent friction. In the stiffness-extension spectrum we detected an abrupt feature before each unfolding event, the amplitude of which decreased with each consecutive unfolding event. We propose that these features are a clear indication of the formation of the known unfolding intermediate of I27, which has been observed previously in constant velocity unfolding experiments. This simple force modulation AFM technique promises to be a very useful addition to constant velocity experiments providing detailed viscoelastic characterization of single molecules under extension.
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38
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Nakajima K, Watabe H, Nishi T. Single polymer chain rubber elasticity investigated by atomic force microscopy. POLYMER 2006. [DOI: 10.1016/j.polymer.2005.12.092] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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39
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Abstract
The invention of atomic force microscopy (AFM) enabled us to study the statistical properties of single polymer chains by a method called "nanofishing," which stretches a single polymer chain adsorbed on a substrate with its one end by picking it at the other end. A force-extension curve obtained for a single polystyrene chain in a Theta solvent (cyclohexane) shows good agreement with a worm-like chain model and, therefore, gives microscopic information about entropic elasticity. Furthermore, the nanofishing technique can be used for dynamic viscoelastic measurement of single polymer chains. An AFM cantilever is mechanically oscillated at its resonant frequency during the stretching process. This technique enables the estimation of quantitative and simultaneous elongation-dependent changes of stiffness and viscosity of a single chain with the use of a phenomenological model. In this study, the effect of solvent on viscosity in low extension regions reveals that the viscosity is attributed to monomer-solvent friction. Thus, static and dynamic nanofishing techniques are shown to give powerful experimental proofs for several basic questions in polymer physics. The techniques are expected to reveal hidden properties of polymer chains or polymer solutions by any types of macroscopic measurements in the future.
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Affiliation(s)
- Ken Nakajima
- Department of Organic and Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552, Japan.
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40
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Kodama T, Ohtani H, Arakawa H, Ikai A. Observation of the destruction of biomolecules under compression force. Ultramicroscopy 2005. [DOI: 10.1016/j.ultramic.2005.06.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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41
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Ikai A. Local rigidity of a protein molecule. Biophys Chem 2005; 116:187-91. [PMID: 15882923 DOI: 10.1016/j.bpc.2005.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2004] [Revised: 04/04/2005] [Accepted: 04/05/2005] [Indexed: 11/16/2022]
Abstract
Distribution of soft and rigid substructures within a protein molecule has been implicated in several occasions and most recently from the imaging and indentation experiments using an atomic force microscope. In this paper, previously reported result of mechanical extension experiments on the recombinant bovine carbonic anhydrase II, Q253C, is re-analyzed to estimate the distribution of Young's modulus, Y, in this protein. The force vs. extension curve of the enzymatically active, type I conformer gave an estimate of Y increasing from 40 to 220 MPa as the polypeptide chain was extended from 10 to 75 nm indicating the presence of a rigid core structure. The enzymatically inactive type II, in contrast, gave an almost constant modulus of 55+/-15 MPa in the same extension range in agreement with the previous proposal that it lacked a core structure.
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Affiliation(s)
- Atsushi Ikai
- Laboratory of Biodynamics, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta Midoriku, Yokohama 226-8501, Japan.
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42
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Forman JR, Qamar S, Paci E, Sandford RN, Clarke J. The remarkable mechanical strength of polycystin-1 supports a direct role in mechanotransduction. J Mol Biol 2005; 349:861-71. [PMID: 15894330 DOI: 10.1016/j.jmb.2005.04.008] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2004] [Revised: 03/24/2005] [Accepted: 04/05/2005] [Indexed: 11/20/2022]
Abstract
Polycystin-1 is a large membrane-associated protein that interacts with polycystin-2 in the primary cilia of renal epithelial cells to form a mechanosensitive ion channel. Bending of the cilia induces calcium flow into the cells, mediated by the polycystin complex. Antibodies to polycystin-1 and polycystin-2 abolish this activation. Based on this, it has been suggested that the extracellular region of polycystin-1, which has a number of putative binding domains, may act as a mechanosensor. A large proportion of the extracellular region of polycystin-1 consists of beta-sandwich PKD domains in tandem array. We use atomic force microscopy to investigate the mechanical properties of the PKD domains of polycystin-1. We show that these domains, despite having a low thermodynamic stability, exhibit a remarkable mechanical strength, similar to that of immunoglobulin domains in the giant muscle protein titin. In agreement with the experimental results molecular dynamics simulations performed at low constant force show that the first PKD domain of polycystin (PKDd1) has a similar unfolding time as titin I27, under the same conditions. The simulations suggest that the basis for this mechanical stability is the formation of a force-stabilised intermediate. Our results suggest that these domains will remain folded under external force supporting the hypothesis that polycystin-1 could act as a mechanosensor, detecting changes in fluid flow in the kidney tubule.
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Affiliation(s)
- Julia R Forman
- Cambridge University Chemical Laboratory, MRC Centre for Protein Engineering, Lensfield Road, Cambridge CB2 1EW, UK
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43
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Afrin R, Alam MT, Ikai A. Pretransition and progressive softening of bovine carbonic anhydrase II as probed by single molecule atomic force microscopy. Protein Sci 2005; 14:1447-57. [PMID: 15929995 PMCID: PMC2253376 DOI: 10.1110/ps.041282305] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 03/06/2005] [Accepted: 03/11/2005] [Indexed: 10/25/2022]
Abstract
To develop a simple method for probing the physical state of surface adsorbed proteins, we adopted the force curve mode of an atomic force microscope (AFM) to extract information on the mechanical properties of surface immobilized bovine carbonic anhydrase II under native conditions and in the course of guanidinium chloride-induced denaturation. A progressive increase in the population of individually softened molecules was probed under mildly to fully denaturing conditions. The use of the approach regime of force curves gave information regarding the height and rigidity of the molecule under compressive stress, whereas use of the retracting regime of the curves gave information about the tensile characteristics of the protein. The results showed that protein molecules at the beginning of the transition region possessed slightly more flattened and significantly more softened conformations compared with that of native molecules, but were still not fully denatured, in agreement with results based on solution studies. Thus the force curve mode of an AFM was shown to be sensitive enough to provide information concerning the different physical states of single molecules of globular proteins.
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Affiliation(s)
- Rehana Afrin
- Laboratory of Biodynamics, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuka, Midori-ku, Yokohama, 226-8501, Japan
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Kawakami M, Byrne K, Khatri BS, Mcleish TCB, Radford SE, Smith DA. Viscoelastic measurements of single molecules on a millisecond time scale by magnetically driven oscillation of an atomic force microscope cantilever. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:4765-72. [PMID: 16032901 DOI: 10.1021/la0469699] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The dynamical nature of biomolecular systems means that knowledge of their viscoelastic behavior is important in fully understanding function. The linear viscoelastic response can be derived from an analysis of Brownian motion. However, this is a slow measurement and technically demanding for many molecular systems of interest. To address this issue, we have developed a simple method for measuring the full linear viscoelastic response of single molecules based on magnetically driven oscillations of an atomic force microscope cantilever. The cantilever oscillation frequency is periodically swept through the system resonance in less than 200 ms allowing the power spectrum to be obtained rapidly and analyzed with a suitable model. The technique has been evaluated using dextran, a polysaccharide commonly used as a test system for single molecule mechanical manipulation experiments. The monomer stiffness and friction constants were compared with those derived from other methods. Excellent agreement is obtained indicating that the new method accurately and, most importantly, rapidly provides the viscoelastic response of a single molecule between the tip and substrate. The method will be a useful tool for studying systems that change their structure and dynamic response on a time scale of 100-200 ms, such as protein folding and unfolding under applied force.
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Affiliation(s)
- Masaru Kawakami
- Institute of Molecular Biophysics, Astbury Centre for Structural Molecular Biology, School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
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Brockwell DJ, Beddard GS, Paci E, West DK, Olmsted PD, Smith DA, Radford SE. Mechanically unfolding the small, topologically simple protein L. Biophys J 2005; 89:506-19. [PMID: 15863479 PMCID: PMC1366550 DOI: 10.1529/biophysj.105.061465] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
beta-sheet proteins are generally more able to resist mechanical deformation than alpha-helical proteins. Experiments measuring the mechanical resistance of beta-sheet proteins extended by their termini led to the hypothesis that parallel, directly hydrogen-bonded terminal beta-strands provide the greatest mechanical strength. Here we test this hypothesis by measuring the mechanical properties of protein L, a domain with a topology predicted to be mechanically strong, but with no known mechanical function. A pentamer of this small, topologically simple protein is resistant to mechanical deformation over a wide range of extension rates. Molecular dynamics simulations show the energy landscape for protein L is highly restricted for mechanical unfolding and that this protein unfolds by the shearing apart of two structural units in a mechanism similar to that proposed for ubiquitin, which belongs to the same structural class as protein L, but unfolds at a significantly higher force. These data suggest that the mechanism of mechanical unfolding is conserved in proteins within the same fold family and demonstrate that although the topology and presence of a hydrogen-bonded clamp are of central importance in determining mechanical strength, hydrophobic interactions also play an important role in modulating the mechanical resistance of these similar proteins.
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Affiliation(s)
- David J Brockwell
- School of Biochemistry and Microbiology, Institute of Molecular Biophysics, Centre for Chemical Dynamics, University of Leeds, Leeds, United Kingdom.
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Wang T, Sakai Y, Nakajima K, Miyawaki A, Ito K, Hara M. Nanorheology measurement on single circularly permuted green fluorescent protein molecule. Colloids Surf B Biointerfaces 2005; 40:183-7. [PMID: 15708511 DOI: 10.1016/j.colsurfb.2004.10.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The force measurement mode of an atomic force microscope (AFM) has enabled us to measure the mechanical properties of biological materials at the single molecular level. In a conventional quasi-static force measurement on a single circularly permuted green fluorescent protein (cpGFP), we could unfold it by unraveling several sub-domains in a distinct sawtooth pattern at a slow stretching speed. In order to elucidate more detailed conformational changes at each extension length, we further measured dynamic relax-stress response of cpGFP molecules. In this measurement, several cycles of sinusoidal movement were applied to the sample during the stretching process. We found the protein molecule showed in-phase response to the sinusoidal input in most case of measurements.
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Affiliation(s)
- Tong Wang
- Local Spatio-Temporal Functions Laboratory, Frontier Research System, RIKEN, Wako, Saitama 351-0198, Japan
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Janovjak H, Müller DJ, Humphris ADL. Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins. Biophys J 2004; 88:1423-31. [PMID: 15574708 PMCID: PMC1305144 DOI: 10.1529/biophysj.104.052746] [Citation(s) in RCA: 55] [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
Recent advances in atomic force microscopy allowed globular and membrane proteins to be mechanically unfolded on a single-molecule level. Presented is an extension to the existing force spectroscopy experiments. While unfolding single bacteriorhodopsins from native purple membranes, small oscillation amplitudes (6-9 nm) were supplied to the vertical displacement of the cantilever at a frequency of 3 kHz. The phase and amplitude response of the cantilever-protein system was converted to reveal the elastic (conservative) and viscous (dissipative) contributions to the unfolding process. The elastic response (stiffness) of the extended parts of the protein were in the range of a few tens pN/nm and could be well described by the derivative of the wormlike chain model. Discrete events in the viscous response coincided with the unfolding of single secondary structure elements and were in the range of 1 microNs/m. In addition, these force modulation spectroscopy experiments revealed novel mechanical unfolding intermediates of bacteriorhodopsin. We found that kinks result in a loss of unfolding cooperativity in transmembrane helices. Reconstructing force-distance spectra by the integration of amplitude-distance spectra verified their position, offering a novel approach to detect intermediates during the forced unfolding of single proteins.
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Affiliation(s)
- Harald Janovjak
- BioTechnological Center, University of Technology, Dresden, Germany
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Atomic force microscope equipped with confocal laser scanning microscope for the spectroscopic measurement of the contact area in liquid. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.01.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Nakamura C, Takeda S, Kageshima M, Ito M, Sugimoto N, Sekizawa K, Miyake J. Mechanical force analysis of peptide interactions using atomic force microscopy. Biopolymers 2004; 76:48-54. [PMID: 14997474 DOI: 10.1002/bip.10572] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Some peptides have previously been reported to bind low molecular weight chemicals. One such peptide with the amino acid sequence His-Ala-Ser-Tyr-Ser was selectively screened from a phage library and bound to a cationic porphyrin, 5,10,15,20-tetrakis(N-methylpyridinium-4-yl)-21H,23H-porphine (TMpyP), with a binding constant of 10(5) M(-1) (J. Kawakami, T. Kitano, and N. Sugimoto, Chemical Communications, 1999, pp. 1765-1766). The proposed binding was due to pi-electron stacking from two aromatic amino acids of histidine and tyrosine. In this study, the weak interactions between TMpyP and the peptide were further investigated by force curve analysis using atomic force microscopy (AFM). The mechanical force required to unbind the peptide-porphyrin complex was measured by vertical movement of the AFM tip. Peptide self-assembled monolayers were formed on both a gold-coated mica substrate and a gold-coated AFM tip. The TMpyPs could bind between the two peptide layers when the peptide-immobilized AFM tip contacted the peptide-immobilized substrate in solution containing TMpyP. In the retracting process a force that ruptured the interaction between TMpyPs and peptides was observed. The unbinding force values correlated to the concentration of TMpyP. A detection limit of 100 ng/mL porphyrin was obtained for the force measurement, and was similar to surface plasmon resonance sensor detection limits. Furthermore, we calculated the product of the observed force and the length of the molecular elongation to determine the work required to unbind the complexes. The obtained values of unbinding work were in a reasonable range compared to the binding energy of porphyrin-peptide.
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Affiliation(s)
- Chikashi Nakamura
- Tissue Engineering Research Center, National Institute of Advanced Industrial Science and Technology, 3-11-46 Nakoji, Amagasaki, Hyogo 661-0974, Japan.
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Okajima T, Arakawa H, Alam MT, Sekiguchi H, Ikai A. Dynamics of a partially stretched protein molecule studied using an atomic force microscope. Biophys Chem 2004; 107:51-61. [PMID: 14871600 DOI: 10.1016/j.bpc.2003.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2003] [Revised: 08/11/2003] [Accepted: 08/13/2003] [Indexed: 10/27/2022]
Abstract
The dynamics of a single protein molecule subjected to forced mechanical unfolding was investigated in a millisecond time domain using a custom-made atomic force microscope (AFM) apparatus, which allows simultaneous measurements of an average tensile force applied to a single molecule and its mechanical response with respect to an external oscillation. Our target protein was genetically engineered bovine carbonic anhydrase II (BCA) which is a monomeric globular protein, and it has been shown that the as-expressed BCA from Escherichia coli contains two conformational isomers, one with enzymatic activity (type I) and the other without (type II). An interesting feature observed from the dynamic measurements was that when the type I BCA conformer was extended, it often exhibited a clear out-of-phase response against an external oscillation. The type II BCA conformer, however, always exhibited an in-phase response to the external oscillation. This relationship between different types of BCA and their dynamical behaviors was evidently observed around the discontinuous transition point from type I to II.
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Affiliation(s)
- Takaharu Okajima
- Laboratory of Biodynamics, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
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