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E-raamat: Atomic Force Microscopy in Nanobiology

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  • Ilmumisaeg: 19-Apr-2016
  • Kirjastus: Pan Stanford Publishing Pte Ltd
  • Keel: eng
  • ISBN-13: 9789814411592
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Atomic Force Microscopy in NanobiologySuurem pilt
  • Formaat: PDF+DRM
  • Ilmumisaeg: 19-Apr-2016
  • Kirjastus: Pan Stanford Publishing Pte Ltd
  • Keel: eng
  • ISBN-13: 9789814411592
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Contributors in the biological sciences and the imaging sciences and engineering survey the use of atomic force microscopy in biology at the nanometer scale. Their topics include protocols for specimen and substrate preparation and data correction methods, the high-resolution imaging of biological molecules by frequency-modulated atomic force microscopy, real-time atomic force microscopy combined with inverted optical microscopes for wet cell/tissue imaging, genome-folding mechanisms in the three domains of life revealed by atomic force microscopy, and probing the mechanisms of mechanotransduction at the nanoscale using atomic force microscopy. Distributed in the US by CRC Press. Annotation ©2014 Ringgold, Inc., Portland, OR (protoview.com)

Recent developments in atomic force microscopy (AFM) have been accomplished through various technical and instrumental innovations, including high-resolution and recognition imaging technology under physiological conditions, fast-scanning AFM, and general methods for cantilever modification and force measurement. All these techniques are now highly powerful not only in material sciences but also in basic biological sciences. There are many nanotechnology books that focus on materials, instruments, and applications in engineering and medicine, but only a few of them are directed toward basic biological sciences. This book tries to bridge this gap.

Edited by a prominent researcher, this volume provides an overview of modern AFM technologies: the basic AFM protocols in Part I, newly developed technologies in Part II, and the most recent applications of AFM technologies in biological sciences in Parts III and IV. The chapters are contributed by some of the leading scientists in the field of nanobiology.

Arvustused

"An outstanding review of the current AFM technology and a must-read for light microscopists interested in super-resolution approaches."

Prof. Michael Tamkun, Colorado State University, USA

"In the last decade, atomic force microscope (AFM) has developed as a tool for imaging the surface of biological samples and for measuring forces at the nanoscale level. Edited by Dr. Takeyasu, this book covers many topics from basic AFM protocols to specific ones that are essential to investigate ligandreceptor binding strength, motion, and dissociation dynamics. It also discusses newly developed technologies and provides new approaches to understand the molecular mechanisms in biological sciences."

Prof. Juan C. Alonso, Centro Nacional de Biotecnologia (CSIC), Spain

Preface xv
1 A Short Story of AFM in Biology
1(12)
Aiko Hibino
Toshiro Kobori
Kunio Takeyasu
1.1 Development of Biological AFM
2(4)
1.1.1 From Contact Mode to Tapping Mode
3(1)
1.1.2 Technology Development toward High-Resolution Imaging
4(1)
1.1.3 Fast-Scanning AFM
5(1)
1.1.4 Force Measurement and Recognition Imaging
6(1)
1.2 Mapping Bio-AFM Research
6(7)
1.2.1 Blooming Activities of AFM Research Communities
6(2)
1.2.2 AFM: One of the Top Keywords in Biological Research
8(5)
2 Protocols for Specimen and Substrate Preparation and Data Correction Methods
13(20)
Toshiro Kobori
Kunio Takeyasu
2.1 Atomic Force Microscopy
14(1)
2.2 Substrate
15(3)
2.3 Cantilever
18(1)
2.4 Setup and Measurement
19(1)
2.5 Image Processing
20(2)
2.6 Specimen Preparation
22(7)
2.6.1 DNA
23(1)
2.6.2 Protein
24(2)
2.6.3 Cells
26(3)
2.7 Perspective
29(4)
3 Chemical Modification of AFM Probes and Coupling with Biomolecules
33(14)
Shige H. Yoshimura
3.1 Chemical Modification of AFM Probes and other Inorganic Materials
34(3)
3.2 Coupling Proteins to the Cantilever Surface
37(5)
3.2.1 Covalent Coupling
37(2)
3.2.2 Site-Specific Attachment
39(3)
3.3 Other Modifications
42(1)
3.4 Applications of Modified Cantilevers
42(2)
3.5 Conclusions and Outlook
44(3)
4 Single-Molecule Dissection and Isolation Based on AFM Nanomanipulation
47(14)
Yi Zhang
Bin Li
Minqian Li
Jun Hu
4.1 Introduction
47(1)
4.2 AFM Dissection and Patterning of Individual DNA Molecules
48(2)
4.3 Isolation of DNA by AFM Nanomanipulation
50(3)
4.4 Positioning Scission of Single DNA with Nonspecific Endonuclease
53(1)
4.5 Defect Repair and Guided Growth of Peptide Nanofilaments
54(3)
4.6 Future Perspective
57(4)
5 Structural Biology with Cryo-AFMs and Computational Modeling
61(24)
Daniel M. Czajkowsky
Lin Li
Jielin Sun
Jun Hu
Zhifeng Shao
5.1 Introduction
61(2)
5.2 Instrumentation
63(3)
5.3 Applications
66(6)
5.4 Combining a Cryo-AFM with Molecular Modeling
72(6)
5.5 Future Perspective
78(7)
6 High-Resolution Imaging of Biological Molecules by Frequency Modulation Atomic Force Microscopy
85(26)
Kei Kobayashi
Hirofumi Yamada
6.1 Introduction
85(1)
6.2 Instrumentation of FM-AFM
86(8)
6.2.1 Cantilever as a Force Sensor
86(2)
6.2.2 Detection of the Cantilever Resonance Frequency Shift
88(2)
6.2.3 Instrumentation of the FM Detection Method
90(2)
6.2.4 Conversion of Frequency Shift to Interaction Force
92(2)
6.3 Problems of FM-AFM in Liquids
94(4)
6.3.1 Viscous Damping of a Cantilever in Fluid
94(2)
6.3.2 Electric Double-Layer Force
96(2)
6.4 High-Resolution Imaging by FM-AFM in Liquids
98(2)
6.5 Purple Membrane Proteins
100(2)
6.6 Isolated Chaperonin Proteins
102(1)
6.7 Force Mapping Techniques Using FM-AFM in Liquids
103(5)
6.7.1 Visualization of Hydration Layers at the Mica--Water Interface
103(3)
6.7.2 Two-Dimensional Force Mapping at the Graphite--Water Interface
106(2)
6.8 Summary and Outlook
108(3)
7 Development of Recognition Imaging: From Molecules to Cells
111(32)
Lilia Chtcheglova
Michael Leitner
Andreas Ebner
Hermann J. Gruber
Peter Hinterdorfer
7.1 Introduction
111(2)
7.2 Tip Chemistry
113(3)
7.3 The Working Principle of TREC
116(8)
7.3.1 Feedback, Working Amplitude, and Frequency Optimization
117(6)
7.3.2 Specificity Proof for the Detected Interactions
123(1)
7.4 Application 1: Single-Molecule TREC on Biotinylated DNA Tetrahedra
124(6)
7.4.1 Motivation
124(1)
7.4.2 A Short Introduction to DNA Building Blocks
125(1)
7.4.3 Imaging of Single DNA Tetrahedra
126(2)
7.4.4 Single-Molecule TREC on Biotinylated DNA Tetrahedra
128(2)
7.4.5 Conclusion
130(1)
7.5 Application 2: Nanolandscape of FCγ Receptors on the Macrophage Surface
130(13)
7.5.1 Motivation
130(1)
7.5.2 Phagocytosis and Phagocytic Receptors
131(1)
7.5.3 Binding Capacity of Fcγ Receptors on the Macrophage Surface
132(2)
7.5.4 Nanomapping of Fcγ Rs
134(4)
7.5.5 Conclusion
138(5)
8 Development of High-Speed AFM and Its Biological Applications
143(34)
Takayuki Uchihashi
Noriyuki Kodera
Toshio Ando
8.1 Introduction
144(1)
8.2 Factors Limiting Scan Speed
145(2)
8.3 Instrumentation
147(12)
8.3.1 Cantilever and Tip
147(3)
8.3.2 OBD Detector
150(1)
8.3.3 Fast Amplitude Detector
151(2)
8.3.4 High-Speed Scanner
153(4)
8.3.5 High-Speed and Low-Invasive Control Methods
157(2)
8.4 Substrate Surfaces for Dynamic AFM Imaging of Biomolecules in Action
159(5)
8.4.1 Mica-Supported Planar Lipid Bilayers
161(2)
8.4.2 2D Crystals of Streptavidin
163(1)
8.5 Biological Applications
164(13)
8.5.1 Walking Mechanism of Myosin V
164(5)
8.5.2 Photoinduced Conformational Change in Bacteriorhodopsin
169(8)
9 Real-Time AFMs Combined with Inverted Optical Microscopes for Wet Cell/Tissue Imaging
177(14)
Shuichi Ito
Nobuaki Sakai
Akira Yagi
Yoshitsugu Uekusa
Koichi Karaki
Yuki Suzuki
Kunio Takeyasu
9.1 Instrumentation
178(6)
9.1.1 Setup
179(2)
9.1.2 Demonstration of the Functions of This Instrument
181(3)
9.2 Biological Application
184(3)
9.2.1 Live Cell Imaging in Solution
184(1)
9.2.2 Tissue Imaging in Solution
185(2)
9.3 Conclusion
187(4)
10 Studying the Cytoskeleton by Atomic Force Microscopy
191(28)
Clemens M. Franz
10.1 Introduction
191(5)
10.1.1 The Cytoskeleton: A Complex Scaffold Determining Cell Shape and Mechanics
192(1)
10.1.2 Actin Filaments
192(1)
10.1.3 Microtubules
193(2)
10.1.4 Intermediate Filaments
195(1)
10.2 Maging the Cytoskeleton of Living Cells
196(7)
10.2.1 Immobilizing Cells for AFM Scanning
196(1)
10.2.2 Visualizing the Cortical Actin Cytoskeleton
196(2)
10.2.3 Time-Lapse Imaging of Living Cells
198(2)
10.2.4 Investigating Intracellular Compartments in De-Roofed Cells
200(3)
10.3 Imaging Cytoskeletal Filaments in vitro
203(10)
10.3.1 Imaging Actin Filaments in vitro
203(1)
10.3.2 Immobilizing Microtubules for AFM Scanning in vitro
204(2)
10.3.3 Imaging Chemically Fixed and Unfixed Microtubules
206(2)
10.3.4 Dynamic Microtubules
208(1)
10.3.5 Imaging Single Intermediate Filaments in vitro
208(2)
10.3.6 Investigating the Mechanical Behavior of Single Intermediate Filaments
210(3)
10.4 Outlook
213(6)
11 Determination of the Architecture of Multisubunit Proteins Using AFM Imaging
219(26)
J. Michael Edwardson
Andrew P. Stewart
11.1 Introduction
219(2)
11.2 Protein Isolation
221(2)
11.3 Antibody Decoration of Epitope Tags
223(1)
11.4 AFM Imaging
224(1)
11.5 Image Analysis
224(4)
11.6 The TRPM8 Channel
228(3)
11.7 The TRPP2/TRPC1 Channel
231(2)
11.8 The Epithelial Sodium Channel
233(4)
11.9 Concluding Remarks
237(8)
12 Capturing Membrane Proteins at Work
245(14)
Yuki Suzuki
Kunio Takeyasu
12.1 AFM for the Structural Analyses of Membrane Proteins
246(1)
12.2 Conformational Changes of Ligand-Gated Ion Channels
247(5)
12.2.1 Agonist-Induced Structural Changes in the NMDA Receptor
247(3)
12.2.2 ATP-Induced Conformational Changes in the P2X4 Receptor
250(2)
12.3 Direct Visualization of the Albers--Post Scheme of P-Type ATpases
252(4)
12.4 Conclusion and Perspectives
256(3)
13 Enzymes and DNA: Molecular Motors in Action
259(16)
Robert M. Henderson
Yuki Suzuki
13.1 Atomic Force Microscopy and DNA
259(2)
13.2 Background to Restriction-Modification Systems
261(14)
13.2.1 EcoKI
262(3)
13.2.2 EcoP15I
265(3)
13.2.3 SfiI
268(3)
13.2.4 EcoRI
271(4)
14 Genome-Folding Mechanisms in the Three Domains of Life Revealed by AFM
275(36)
Hugo Maruyama
Ryosuke L. Ohniwa
Eloise Prieto
James Hejna
Kunio Takeyasu
14.1 Biophysical Properties of DNA and DNA-Binding Proteins
276(4)
14.1.1 Persistence Length and Phase Transition of DNA Conformation
276(1)
14.1.2 Principles of DNA-Protein Interaction
277(3)
14.2 Nucleosome and beyond in Eukaryotes Revealed by AFM
280(5)
14.2.1 Nucleosome Reconstitution
280(1)
14.2.2 Reconstitution of Higher-Order Structures of Chromatin
281(3)
14.2.3 Genome Architecture in vivo
284(1)
14.3 Evolutionary Aspects of Genome Architectures in Bacteria and Archaea
285(17)
14.3.1 Bacterial Nucleoid Architecture in vivo
287(3)
14.3.2 In vitro Reconstitution of the Bacterial Nucleoid
290(1)
14.3.3 In vivo Dynamics of the Bacterial Nucleoid
291(3)
14.3.4 Archaeal Chromosomal Proteins
294(1)
14.3.5 Archaeal Chromosome Architectures
295(4)
14.3.6 Archaeal Nucleoid Dynamics in vivo
299(3)
14.4 Conclusion and Perspectives
302(9)
15 Membrane Dynamics: Lipid--Protein Interactions Studied by AFM
311(18)
Hirohide Takahashi
Kunio Takeyasu
15.1 AFM as an Analytical Tool for the Study of Membrane Dynamics
312(1)
15.2 AFM Imaging of the Interaction between SNARE Proteins and Membranes
312(6)
15.2.1 Lipid Bilayers
312(1)
15.2.2 SNARE Proteins and the Lipid Bilayer
313(4)
15.2.3 Recognition ("Mapping") Imaging of Proteins Involved in Membrane Fusion
317(1)
15.3 Force Spectroscopy Addressing the Physical Mechanisms of Membrane Fusion
318(4)
15.3.1 Physical Properties of SNAREs and Synaptotagmin
318(2)
15.3.2 Physical Properties of the Synaptotagmin-Lipid Interaction
320(2)
15.4 Membrane Budding
322(1)
15.4.1 ESCRT Proteins
322(1)
15.4.2 Viral Budding
323(1)
15.5 Perspective
323(6)
16 Nanosurgery and Cytoskeletal Mechanics of a Single Cell
329(28)
Atsushi Ikai
Rehana Afrin
Shinichi Machida
Takahiro Watanabe Nakayama
Masakazu Saito
16.1 Delivery/Extraction of Nucleic Acid from a Single Cell
330(6)
16.1.1 Retrieval of DNA from Chromosomes
330(2)
16.1.2 Retrieval of mRNA from Individual Cells
332(1)
16.1.3 Insertion of DNA into Individual Cells
332(4)
16.2 Manipulation of the Red Blood Cell Cytoskeleton
336(2)
16.3 Mechanics of Fibroblast Stress Fibers with a Lateral Force
338(10)
16.4 Manipulation of Stress Fibers by FIB-Fabricated Probes
348(3)
16.5 Hole Creation on the Cell Surface
351(3)
16.6 Conclusion and Perspectives: Cellular Mechanics Probed with AFM
354(3)
17 Functional Investigations on Nuclear Pores with Atomic Force Microscopy
357(22)
Anna Meyring
Ivan Liashkovich
Hans Oberleithner
Victor Shahin
17.1 Atomic Force Microscopy
358(1)
17.2 AFM to Probe Biological Samples
359(15)
17.2.1 AFM-Based Functional Investigations on Nuclear Pore Complexes
361(1)
17.2.2 The AFM Tip as a Chemical Nanosensor to Explore the Hydrophobicity of Intact and Apoptotic NPC Channels
362(5)
17.2.3 The AFM Tip as a Nanoindentor to Study the Mechanical Properties of the NPC
367(1)
17.2.4 The Atomic Force Microscope Tip as a Surgical Nanotool to Harvest Transcripts of Early Genes from the NPC
368(6)
17.3 Conclusions and Outlook
374(5)
18 Mechanotransduction: Probing Its Mechanisms at the Nanoscale Using the Atomic Force Microscope
379(44)
Kristina M. Haase
Dominique Tremblay
Andrew E. Pelling
18.1 Cellular Mechanotransduction
379(5)
18.2 Cellular Elasticity and What It Tells Us
384(7)
18.2.1 AFM Force--Distance Curves
384(6)
18.2.2 Material Properties of the Cell
390(1)
18.3 Cellular Force Transducers
391(23)
18.3.1 Cellular Deformation
395(1)
18.3.1.1 Whole-cell deformation
396(2)
18.3.1.2 Force mapping
398(2)
18.3.1.3 Localized deformation
400(3)
18.3.2 Cytoskeletal Dynamics
403(1)
18.3.2.1 Actin dynamics
403(4)
18.3.2.2 Mitochondrial dynamics
407(1)
18.3.2.3 Inducing traction forces
408(4)
18.3.3 Inducing a Visible Biochemical Response
412(1)
18.3.3.1 Cell--cell calcium signaling
412(2)
18.4 Conclusions and Outlook
414(9)
Index 423
Kunio Takeyasu was trained as a zoologist and neuro-pharmacologist in his early career when he was a graduate student at Hiroshima University and Osaka University. After his postdoctoral research on the molecular and cell biological aspects of membrane proteins such as acetylcholine receptors and ion-motive ATPases at Cornell University and the Johns Hopkins University, he joined the University of Virginia as an assistant professor in 1988 and started to utilize atomic force microscopy (AFM) in biological studies. After four years of research and teaching at The Ohio State University, he moved to Kyoto University as a full professor in 1995. Since then, he has been developing technologies for biological application of AFM. His most recent research has been focused on single-molecule imaging of membrane proteins and chromatin at sub-second time region with nanometer space resolution. Prof. Takeyasu has been a member of the Biophysical Society and the American Society for Cell Biology.
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