This first book on high-speed atomic force microscopy (HS-AFM) is intended for students and biologists who want to use HS-AFM in their research. It provides straightforward explanations of the principle and techniques of AFM and HS-AFM. Numerous examples of HS-AFM studies on proteins demonstrate how to apply this new form of microscopy to specific biological problems. Several precautions for successful imaging and the preparation of cantilever tips and substrate surfaces will greatly benefit first-time users of HS-AFM. In turn, the instrumentation techniques detailed in Chapter 4 can be skipped, but will be useful for engineers and scientists who want to develop the next generation of high-speed scanning probe microscopes for biology.
The book is intended to facilitate the first-time use of this new technique, and to inspire students and researchers to tackle their own specific biological problems by directly observing dynamic events occurring in the nanoscopic world. Microscopy in biology has recently entered a new era with the advent of high-speed atomic force microscopy (HS-AFM). Unlike optical microscopy, electron microscopy, and conventional slow AFM, it allows us to directly observe biological molecules in physiological environments. Molecular “movies” created using HS-AFM can directly reveal how molecules behave and operate, without the need for subsequent complex analyses and roundabout interpretations. It also allows us to directly monitor morphological change in live cells, and dynamic molecular events occurring on the surfaces of living bacteria and intracellular organelles. As HS-AFM instruments were recently commercialized, in the near future HS-AFM is expected to become a common tool in biology, and will enhance and accelerate our understanding of biological phenomena.
Author(s): Toshio Ando
Series: NanoScience and Technology
Publisher: Springer
Year: 2022
Language: English
Pages: 326
City: Berlin
Preface
Historical Overview
References
Contents
Part I Principle and Techniques of HS-AFM
1 Principle of AFM
1.1 Image Formation and Spatial Resolution
1.2 Configuration of AFM System
1.3 Imaging Modes
1.3.1 DC and AC Modes
1.3.2 Other AC Mode Issues
1.3.3 Phase Contrast and Energy Dissipation
1.3.4 FD Curve-Based AFM
1.3.5 Recognition Imaging
References
2 Cantilever Mechanics
2.1 Static Mechanics of Cantilever Beam
2.2 Dynamic Mechanics of Cantilever Beam
3 Feedback Control and Imaging Rate
3.1 Highest Possible Imaging Rate
3.2 PID Feedback Control and Parachuting Problem
References
4 HS-AFM System and Optimized Instrumental Components
4.1 Short Cantilevers
4.1.1 Mechanical Properties
4.1.2 Other Advantages of Short Cantilevers
4.1.3 Practical Issues for the Use of Short Cantilevers
4.1.4 Cantilever Excitation
4.2 OBD Detector for Short Cantilevers
4.3 Fast Amplitude Detector
4.4 Fast Phase Detector
4.5 Fast Scanner
4.5.1 Piezo Actuator
4.5.2 Holding Methods and Momentum Balance
4.5.3 Scanner Designs Without Displacement Amplification
4.5.4 Scanner Designs with Displacement Amplification
4.5.5 Dual Actuation for Z-Scanner
4.5.6 Piezo Driver
4.6 Dynamic PID Control to Avoid Parachuting
4.7 Measured and Theoretical Feedback Bandwidths
4.8 Compensation for Cantilever Excitation Drifts
4.9 Control Methods for Vibration Damping
4.9.1 Active Vibration Damping Method for Z-Scanner
4.9.2 Measured Effects of Q-Control on Z-Scanner Response
4.9.3 Rounding and Feedforward Vibration Damping Methods for X-Scanner
4.9.4 Measured Effects of Vibration Damping for X-Scanner
4.10 Compensation for Nonlinearity and Crosstalk in Wide-Area XY-Scanner
References
5 Tip-Scanning HS-AFM
5.1 Advantage and OBD Detectors of Tip-Scanning AFM
5.2 General Considerations for Motion Tracking
5.3 Tracking by Mirror Tilter Scanning
5.4 Tracking by Lens Scanning
5.5 Tip-Scanning HS-AFM Combined with TIRF Microscopy
References
6 Interactive HS-AFM (iHS-AFM)
6.1 Several Interactive Modes
6.2 Applications of iHS-AFM
References
7 Influence of Tip–Sample Interactions on Specimens
7.1 Quantification of Vertical Tip Force Effect
7.2 Lateral Tip Force Effect
References
8 Toward the Next Generation of HS-AFM
8.1 Speed Performance
8.2 Less Disturbing Imaging Method
8.2.1 Error Difference Between Trace and Retrace Imaging Processes
8.2.2 Only Trace Imaging (OTI) Mode
8.3 Future Prospects for Higher Imaging Rate
References
Part II Biological Applications of HS-AFM
9 Overview of Bioimaging with HS-AFM
9.1 Overview of HS-AFM Applications
9.2 Various Issues to be Considered
References
10 Substrate Surfaces
10.1 Mica Surfaces
10.2 Mica-Supported Lipid Bilayer Surfaces
10.3 Streptavidin 2D Crystal Surfaces
10.4 Tamavidin 2D Crystal Surfaces
References
11 Canonical Motor Proteins
11.1 Overview of Motor Proteins
11.2 Myosin V Walking on Actin Filaments
11.2.1 Myosin Superfamily and General Features of Myosin
11.2.2 Actomyosin ATPase Reaction and Energy Transduction
11.2.3 Visualization of Walking M5 and Lever-Arm Swing
11.2.4 Asymmetric ADP Dissociation Kinetics
11.2.5 Directional Rule
11.2.6 Unwinding of Coiled-Coil Tail, Foot Stomp and Foot Sliding
11.2.7 Flexibility of Neck-Motor Domain Junction
11.2.8 New View on Energetics in Walking M5
11.3 Rotary Motor F1-ATPase
11.3.1 Binding Change Mechanism and Rotary Catalysis
11.3.2 Physical Rotation of γ Subunit and γ-ruling Mechanism
11.3.3 HS-AFM Observation of the Stator Ring of F1-ATPase
11.3.4 Quantification of Dynamic Structural Transitions in the Stator Ring
References
12 Membrane-Remodeling Proteins
12.1 Dynamin
12.1.1 Structures of Dynamin and Its Dimers and Helical Polymer
12.1.2 Models for Membrane Fission by Dynamin
12.1.3 HS-AFM Observations of Dynamin-Coated Membrane Tubules
12.1.4 HS-AFM/EM Observations of Dynamin-Coated Membrane Tubules
12.2 ESCRT III Proteins
12.2.1 HS-AFM Observation of Snf7 Filament Dynamics
12.2.2 Vps4-Triggered Membrane Constriction and Scission
References
13 Intrinsically Disordered Proteins (IDPs)
13.1 General Remarks on IDPs
13.2 Difficulty of Structural Analysis of IDPs
13.3 First Attempt to Image IDRs Using HS-AFM
13.4 Functional Regulation of FACT by Phosphorylation
13.5 Power Law Relationship Between Molecular Dimensions and Peptide Length
13.6 Structural and Dynamics Analysis of IDPs
13.6.1 Yeast IDP Sic1
13.6.2 Measles Virus Phosphoprotein PNT
13.7 Relationship Between ⟨Rg⟩ and ⟨R2D⟩
13.8 Possible Charge Effects on the Dimensions of IDRs
13.9 Autophagy Initiation Proteins and Complexes
13.9.1 Conformational Malleability
13.9.2 Formation of Liquid Droplet-Like Condensates from Atg Proteins
References
14 Self-assembly
14.1 Amyloid Fibril Formation
14.2 Lithostathine (Reg-1)
14.3 Amyloid β (Aβ)
14.4 Coaggregation and Cross-Seeding
14.5 Yeast Prion Protein Sup35
References
15 Structural Changes of Membrane Proteins
15.1 Bacteriorhodopsin (bR)
15.1.1 bR Response to Light
15.1.2 Role of the Trimer‒Trimer Interaction in the bR Function
15.2 Ligand-Gated Ion Channels (LGICs)
15.2.1 Prokaryotic Homolog of CNG Channel, MloK1
15.2.2 Prokaryotic Homolog of CNG Channel, SthK
15.3 Pumps and Active Transporters
15.4 Membrane Protein Reconstitution Methods for HS-AFM Imaging
15.4.1 Unidirectional Reconstitution
15.4.2 Usage of Nanodiscs
15.4.3 Suspended Membranes with Asymmetric Environments
References
16 Peripheral Membrane Proteins (PMPs)
16.1 Oscillatory Reaction in the MinDE System
16.1.1 Outline of the Min System
16.1.2 HS-AFM Observation of MinDE Oscillation
16.2 Cholesterol-Dependent Cytolysins (CDCs)
16.2.1 Pioneering AFM Studies on CDCs
16.2.2 EM and AFM Studies of Suilysin
16.2.3 AFM and HS-AFM Studies of Listeriolysin O (LLO)
References
17 Molecular Chaperones
17.1 Different Classes of Molecular Chaperones
17.2 GroEL‒GroES Chaperonin System
17.2.1 Structure of GroEL‒GroES and Prevailing Model for Its Reaction Cycle
17.2.2 Opposing View
17.2.3 HS-AFM Imaging of Dynamic GroEL‒GroES Interactions
17.3 AAA+ Chaperone ClpB
17.3.1 Various Oligomer Forms of ClpB Detected by HS-AFM
17.3.2 Conformational Dynamics of ClpB
17.4 2-Cys Peroxiredoxin
17.4.1 Identification of HMW Complexes of Prx by iHS-AFM
References
18 Other Topics
18.1 Structural Fluctuations
18.2 Protein–Protein Interaction by Hydrophobic Mismatch
18.3 Antibody Walking on 2D Lattice of Epitopes
18.4 Bacterial Rotary Motor Stator MotPS
References
Index
