Dynamics of bacteriorhodopsin 2D crystal observed by high-speed atomic force microscopy

Artificial organelles for sustainable chemical energy conversion and production in artificial cells: Artificial mitochondrion and chloroplasts

Sustainable energy conversion modules are the main challenges for building complex reaction cascades in artificial cells. Recent advances in biotechnology have enabled this sustainable energy supply, especially the adenosine triphosphate (ATP), by mimicking the organelles, which are the core structures for energy conversion in living cells. Three components are mainly shared by the artificial organelles: the membrane compartment separating the inner and outer parts, membrane proteins for proton translocation, and the molecular rotary machine for ATP synthesis. Depending on the initiation factors, they are further categorized into artificial mitochondrion and artificial chloroplasts, which use chemical nutrients for oxidative phosphorylation and light for photosynthesis, respectively. In this review, we summarize the essential components needed for artificial organelles and then review the recent progress on two different artificial organelles. Recent strategies, purified and identified proteins, and working principles are discussed. With more study on the artificial mitochondrion and artificial chloroplasts, they are expected to be very powerful tools, allowing us to achieve complex cascading reactions in artificial cells, like the ones that happen in real cells.

Single molecule kinetics of bacteriorhodopsin by HS-AFM

Bacteriorhodopsin is a seven-helix light-driven proton-pump that was structurally and functionally extensively studied. Despite a wealth of data, the single molecule kinetics of the reaction cycle remain unknown. Here, we use high-speed atomic force microscopy methods to characterize the single molecule kinetics of wild-type bR exposed to continuous light and short pulses. Monitoring bR conformational changes with millisecond temporal resolution, we determine that the cytoplasmic gate opens 2.9 ms after photon absorption, and stays open for proton capture for 13.2 ms. Surprisingly, a previously active protomer cannot be reactivated for another 37.6 ms, even under excess continuous light, giving a single molecule reaction cycle of ~20 s⁻¹. The reaction cycle slows at low light where the closed state is prolonged, and at basic or acidic pH where the open state is extended.

Here, the authors use high-speed atomic force microscopy (HS-AFM) methods to characterize the single molecule kinetics of wild-type bacteriorhodopsin (bR) with millisecond temporal resolution, providing new insights into the bR conformational cycle.

Development of a flexure-based nano-actuator for high-frequency high-resolution directional sensing with atomic force microscopy

Scanning probe microscopies typically rely on the high-precision positioning of a nanoscale probe in order to gain local information about the properties of a sample. At a given location, the probe is used to interrogate a minute region of the sample, often relying on dynamical sensing for improved accuracy. This is the case for most force-based measurements in atomic force microscopy (AFM) where sensing occurs with a tip oscillating vertically, typically in the kHz to MHz frequency regime. While this approach is ideal for many applications, restricting dynamical sensing to only one direction (vertical) can become a serious limitation when aiming to quantify the properties of inherently three-dimensional systems, such as a liquid near a wall. Here, we present the design, fabrication, and calibration of a miniature high-speed scanner able to apply controlled fast and directional in-plane vibrations with sub-nanometer precision. The scanner has a resonance frequency of ∼35 kHz and is used in conjunction with a traditional AFM to augment the measurement capabilities. We illustrate its capabilities at a solid-liquid interface where we use it to quantify the preferred lateral flow direction of the liquid around every sample location. The AFM can simultaneously acquire high-resolution images of the interface, which can be superimposed with the directional measurements. Examples of sub-nanometer measurements conducted with the new scanner are also presented.

TopoStats - A program for automated tracing of biomolecules from AFM images

We present TopoStats, a Python toolkit for automated editing and analysis of Atomic Force Microscopy images. The program automates identification and tracing of individual molecules in circular and linear conformations without user input. TopoStats was able to identify and trace a range of molecules within AFM images, finding, on average, ~90% of all individual molecules and molecular assemblies within a wide field of view, and without the need for prior processing. DNA minicircles of varying size, DNA origami rings and pore forming proteins were identified and accurately traced with contour lengths of traces typically within 10 nm of the predicted contour length. TopoStats was also able to reliably identify and trace linear and enclosed circular molecules within a mixed population. The program is freely available via GitHub (https://github.com/afm-spm/TopoStats) and is intended to be modified and adapted for use if required.

Measuring interactions of DNA with nanoporous protein crystals by atomic force microscopy

Crosslinked porous protein crystals are a new biomaterial that can be engineered to encapsulate, stabilize, and organize guest molecules, nanoparticles, and biological moieties. In this study, for the first time, the combined interactions of DNA strands with porous protein crystals are quantitatively measured by high-resolution atomic force microscopy (AFM) and chemical force microscopy. The surface structure of protein crystals with unusually large pores was observed in liquid via high-resolution AFM. Force-distance (F-D) curves were also obtained using AFM tips modified to present or capture DNA. The modification of AFM tips allowed the tips to covalently bind DNA that was pre-loaded in the protein crystal nanopores. The modified tips enabled the interactions of DNA molecules with protein crystals to be quantitatively studied while revealing the morphology of the buffer-immersed protein crystal surface in detail, thereby preserving the structure and properties of protein crystals that could be disrupted or destroyed by drying. The hexagonal space group was manifest at the crystal surface, as were the strong interactions between DNA and the porous protein crystals in question. In sum, this study furthered our understanding of how a new protein-based biomaterial can be used to bind guest DNA assemblies.

Structural dynamics of channels and transporters by high-speed atomic force microscopy

Channels and transporters are vital for transmembrane transport of ions and solutes, and also of larger compounds such as lipids and macromolecules. Therefore, they are crucial in many biological processes such as sensing, signal transduction, and the regulation of the distribution of molecules. Dysfunctions of these membrane proteins are associated to numerous diseases, and their interaction with drugs is critical in medicine. Understanding the behavior of channels and transporters requires structural and dynamic information to decipher the molecular mechanisms underlying their function. High-Speed Atomic Force Microscopy (HS-AFM) now allows the study of single transmembrane channels and transporters in action under physiological conditions, i.e., at ambient temperature and pressure, in physiological buffer and in a membrane, and in a most direct, label-free manner. In this chapter, we discuss the HS-AFM sample preparation, application, and data analysis protocols to study the structural and conformational dynamics of membrane-embedded channels and transporters.

Fake It 'Till You Make It-The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics

Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.

Unfolding pathway and intermolecular interactions of the cytochrome subunit in the bacterial photosynthetic reaction center

Precise folding of photosynthetic proteins and organization of multicomponent assemblies to form functional entities are fundamental to efficient photosynthetic electron transfer. The bacteriochlorophyll b-producing purple bacterium Blastochloris viridis possesses a simplified photosynthetic apparatus. The light-harvesting (LH) antenna complex surrounds the photosynthetic reaction center (RC) to form the RC-LH1 complex. A non-membranous tetraheme cytochrome (4Hcyt) subunit is anchored at the periplasmic surface of the RC, functioning as the electron donor to transfer electrons from mobile electron carriers to the RC. Here, we use atomic force microscopy (AFM) and single-molecule force spectroscopy (SMFS) to probe the long-range organization of the photosynthetic apparatus from Blc. viridis and the unfolding pathway of the 4Hcyt subunit in its native supramolecular assembly with its functional partners. AFM images reveal that the RC-LH1 complexes are densely organized in the photosynthetic membranes, with restricted lateral protein diffusion. Unfolding of the 4Hcyt subunit represents a multi-step process and the unfolding forces of the 4Hcyt α-helices are approximately 121 picoNewtons. Pulling of 4Hcyt could also result in the unfolding of the RC L subunit that binds with the N-terminus of 4Hcyt, suggesting strong interactions between RC subunits. This study provides new insights into the protein folding and interactions of photosynthetic multicomponent complexes, which are essential for their structural and functional integrity to conduct photosynthetic electron flow.

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AFM and single-molecule force spectroscopy reveal the membrane organization and unfolding process of Blastochloris viridis RC

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RC-light-harvesting 1 complexes are densely organized in photosynthetic membranes, with restricted lateral diffusion

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Unfolding of the non-membranous cytochrome (4Hcyt) subunit represents a multi-step process;

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The average unfolding forces of the 4Hcyt α-helices are ~121 pN;

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Pulling of 4Hcyt from the RC suggests strong interactions (> 150 pN) between 4Hcyt and L subunits in the RC structure.

Imaging and Force Spectroscopy of Single Transmembrane Proteins with the Atomic Force Microscope

The atomic force microscope (AFM) has opened avenues and provided opportunities to investigate biological soft matter and processes ranging from nanometer (nm) to millimeter (mm). The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever-aptly termed as a "lab on a tip"-can be used as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples have convincingly established AFM as a tool to study the mechanical properties and monitor processes of single proteins and cells with high sensitivity, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of transmembrane proteins in a lipid bilayer (reconstituted or native). Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theory and practical skills.

The emerging science of electrosynbionics

Dramatic changes in electricity generation, use and storage are needed to keep pace with increasing demand while reducing carbon dioxide emissions. There is great potential for application of bioengineering in this area. We have the tools to re-engineer biological molecules and systems, and a significant amount of research and development is being carried out on technologies such as biophotovoltaics, biocapacitors, biofuel cells and biobatteries. However, there does not seem to be a satisfactory overarching term to describe this area, and I propose a new word-'electrosynbionics'. This is to be defined as: the creation of engineered devices that use components derived from or inspired by biology to perform a useful electrical function. Here, the phrase 'electrical function' is taken to mean the generation, use and storage of electricity, where the primary charge carriers may be either electrons or ions. 'Electrosynbionics' is distinct from 'bioelectronics', which normally relates to applications in sensing, computing or electroceuticals. Electrosynbionic devices have the potential to solve challenges in electricity generation, use and storage by exploiting or mimicking some of the desirable attributes of biological systems, including high efficiency, benign operating conditions and intricate molecular structures.

Advances in high-speed atomic force microscopy (HS-AFM) reveal dynamics of transmembrane channels and transporters

Recent advances in high-speed atomic force microscopy (HS-AFM) have made it possible to study the conformational dynamics of single unlabeled transmembrane channels and transporters. Improving environmental control with the integration of a non-disturbing buffer exchange system, which in turn allows the gradual change of conditions during HS-AFM operation, has provided a breakthrough toward the performance of structural titration experiments. Further advancements in temporal resolution with the use of line scanning and height spectroscopy techniques show how high-speed atomic force microscopy can measure millisecond to microsecond dynamics, pushing this method beyond current spatial and temporal limits offered by less direct techniques.

Long-lived ionic nano-domains can modulate the stiffness of soft interfaces

Metal ions underpin countless processes at bio-interfaces, including maintaining electroneutrality, modifying mechanical properties and driving bioenergetic activity. These processes are typically described by ions behaving as independently diffusing point charges. Here we show that Na+ and K+ ions instead spontaneously form correlated nanoscale networks that evolve over seconds at the interface with an anionic bilayer in solution. Combining single-ion level atomic force microscopy and molecular dynamic simulations we investigate the configuration and dynamics of Na+, K+, and Rb+ at the lipid surface. We identify two distinct ionic states: the well-known direct electrostatic interaction with lipid headgroups and a water-mediated interaction that can drive the formation of remarkably long-lived ionic networks which evolve over many seconds. We show that this second state induces ionic network formation via correlative ion-ion interactions that generate an effective energy well of -0.4kBT/ion. These networks locally reduce the stiffness of the membrane, providing a spontaneous mechanism for tuning its mechanical properties with nanoscale precision. The ubiquity of water-mediated interactions suggest that our results have far-reaching implications for controlling the properties of soft interfaces.

Disulfide-mediated reversible two-dimensional self-assembly of protein nanocages

Disulfide-mediated 2D protein self-assembly was achieved by single point mutation of hot spots at the C₄ interface of ferritin.

[Progress in the applications of high-speed atomic force microscopy in cell biology]

Without losing its high resolution, high-speed atomic force microscope (HS-AFM) represents a perfect combinationof scanning speed and precision and allows real-time and in situ observation of the dynamic processes in a biological system atboth the cellular and molecular levels. By combining the extremely high temporal resolution with the spatial resolution andcoupling with other advanced technologies, HS-AFM shows promising prospects for applications in life sciences such as cellbiology. In this review, we summarize the latest progress of HS-AFM in the field of cell biology, and discuss the impact ofenvironmental factors on conformation dynamics of DNA, the binding processes between DNA and protein, the domainchanges of membrane proteins, motility of myosin, and surface structure changes of living cells.

Reversible Cation-Selective Attachment and Self-Assembly of Human Tau on Supported Brain Lipid Membranes

Misfolding and aggregation of the neuronal, microtubule-associated protein tau is involved in the pathogenesis of Alzheimer's disease and tauopathies. It has been proposed that neuronal membranes could play a role in tau release, internalization, and aggregation and that tau aggregates could exert toxicity via membrane permeabilization. Whether and how tau interacts with lipid membranes remains a matter of discussion. Here, we characterize the interaction of full-length human tau (htau40) with supported lipid membranes (SLMs) made from brain total lipid extract by time-lapse high-resolution atomic force microscopy (AFM). We observe that tau attaches to brain lipid membranes where it self-assembles in a cation-dependent manner. Sodium triggers the attachment, self-assembly, and growth, whereas potassium inhibits these processes. Moreover, tau assemblies are stable in the presence of sodium and lithium but disassemble in the presence of potassium and rubidium. Whereas the pseudorepeat domains (R1-R4) of htau40 promote the sodium-dependent attachment to the membrane and stabilize the tau assemblies, the N-terminal region promotes tau self-assembly and growth.

Optimum Substrates for Imaging Biological Molecules with High-Speed Atomic Force Microscopy

Recent progresses in high-speed atomic force microscopy (HS-AFM) have enabled us to directly visualize dynamic processes of various proteins in liquid conditions. One of the key factors leading to successful HS-AFM observations is the selection of an appropriate substrate depending on molecules to be observed. For the HS-AFM imaging, a target molecule must be absorbed on a substrate by controlling its orientation without impairing the dynamics or physiological function of the molecule. In this chapter, we describe protocols for preparation of substrates that have been used for HS-AFM and then introduce observation examples on dynamic processes of biological molecules.

Tuning membrane protein mobility by confinement into nanodomains

High-speed atomic force microscopy (HS-AFM) can be used to visualize function-related conformational changes of single soluble proteins. Similar studies of single membrane proteins are, however, hampered by a lack of suitable flat, non-interacting membrane supports and by high protein mobility. Here we show that streptavidin crystals grown on mica-supported lipid bilayers can be used as porous supports for membranes containing biotinylated lipids. Using SecYEG (protein translocation channel) and GlpF (aquaglyceroporin), we demonstrate that the platform can be used to tune the lateral mobility of transmembrane proteins to any value within the dynamic range accessible to HS-AFM imaging through glutaraldehyde-cross-linking of the streptavidin. This allows HS-AFM to study the conformation or docking of spatially confined proteins, which we illustrate by imaging GlpF at sub-molecular resolution and by observing the motor protein SecA binding to SecYEG.

High resolution atomic force microscopy of double-stranded RNA

Double-stranded (ds) RNA mediates the suppression of specific gene expression, it is the genetic material of a number of viruses, and a key activator of the innate immune response against viral infections. The ever increasing list of roles played by dsRNA in the cell and its potential biotechnological applications over the last decade has raised an interest for the characterization of its mechanical properties and structure, and that includes approaches using Atomic Force Microscopy (AFM) and other single-molecule techniques. Recent reports have resolved the structure of dsDNA with AFM at unprecedented resolution. However, an equivalent study with dsRNA is still lacking. Here, we have visualized the double helix of dsRNA under near-physiological conditions and at sufficient resolution to resolve the A-form sub-helical pitch periodicity. We have employed different high-sensitive force-detection methods and obtained images with similar spatial resolution. Therefore, we show here that the limiting factors for high-resolution AFM imaging of soft materials in liquid medium are, rather than the imaging mode, the force between the tip and the sample and the sharpness of the tip apex.

Assemblies of pore-forming toxins visualized by atomic force microscopy

A number of pore-forming toxins (PFTs) can assemble on lipid membranes through their specific interactions with lipids. The oligomeric assemblies of some PFTs have been successfully revealed either by electron microscopy (EM) and/or atomic force microscopy (AFM). Unlike EM, AFM imaging can be performed under physiological conditions, enabling the real-time visualization of PFT assembly and the transition from the prepore state, in which the toxin does not span the membrane, to the pore state. In addition to characterizing PFT oligomers, AFM has also been used to examine toxin-induced alterations in membrane organization. In this review, we summarize the contributions of AFM to the understanding of both PFT assembly and PFT-induced membrane reorganization. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.

High-resolution atomic force microscopy imaging of rhodopsin in rod outer segment disk membranes

Atomic force microscopy (AFM) is a powerful imaging technique that allows recording topographical information of membrane proteins under near-physiological conditions. Remarkable results have been obtained on membrane proteins that were reconstituted into lipid bilayers. High-resolution AFM imaging of native disk membranes from vertebrate rod outer segments has unveiled the higher-order oligomeric state of the G protein-coupled receptor rhodopsin, which is highly expressed in disk membranes. Based on AFM imaging, it has been demonstrated that rhodopsin assembles in rows of dimers and paracrystals and that the rhodopsin dimer is the fundamental building block of higher-order structures.

Real-time visualization of assembling of a sphingomyelin-specific toxin on planar lipid membranes

Pore-forming toxins (PFTs) are soluble proteins that can oligomerize on the cell membrane and induce cell death by membrane insertion. PFT oligomers sometimes form hexagonal close-packed (hcp) structures on the membrane. Here, we show the assembling of the sphingomyelin (SM)-binding PFT, lysenin, into an hcp structure after oligomerization on SM/cholesterol membrane. This process was monitored by high-speed atomic force microscopy. Hcp assembly was driven by reorganization of lysenin oligomers such as association/dissociation and rapid diffusion along the membrane. Besides rapid association/dissociation of oligomers, the height change for some oligomers, possibly resulting from conformational changes in lysenin, could also be visualized. After the entire membrane surface was covered with a well-ordered oligomer lattice, the lysenin molecules were firmly bound on the membrane and the oligomers neither dissociated nor diffused. Our results reveal the dynamic nature of the oligomers of a lipid-binding toxin during the formation of an hcp structure. Visualization of this dynamic process is essential for the elucidation of the assembling mechanism of some PFTs that can form ordered structures on the membrane.

Opportunities in high-speed atomic force microscopy

The atomic force microscope (AFM) has become integrated into standard characterisation procedures in many different areas of research. Nonetheless, typical imaging rates of commercial microscopes are still very slow, much to the frustration of the user. Developments in instrumentation for "high-speed AFM" (HSAFM) have been ongoing since the 1990s, and now nanometer resolution imaging at video rate is readily achievable. Despite thorough investigation of samples of a biological nature, use of HSAFM instruments to image samples of interest to materials scientists, or to carry out AFM lithography, has been minimal. This review gives a summary of different approaches to and advances in the development of high-speed AFMs, highlights important discoveries made with new instruments, and briefly discusses new possibilities for HSAFM in materials science.

High-speed AFM and applications to biomolecular systems

Directly observing individual protein molecules in action at high spatiotemporal resolution has long been a holy grail for biological science. This is because we long have had to infer how proteins function from the static snapshots of their structures and dynamic behavior of optical makers attached to the molecules. This limitation has recently been removed to a large extent by the materialization of high-speed atomic force microscopy (HS-AFM). HS-AFM allows us to directly visualize the structure dynamics and dynamic processes of biological molecules in physiological solutions, at subsecond to sub-100-ms temporal resolution, without disturbing their function. In fact, dynamically acting molecules such as myosin V walking on an actin filament and bacteriorhodopsin in response to light are successfully visualized. In this review, we first describe theoretical considerations for the highest possible imaging rate of this new microscope, and then highlight recent imaging studies. Finally, the current limitation and future challenges to explore are described.

Wide-area scanner for high-speed atomic force microscopy

High-speed atomic force microscopy (HS-AFM) has recently been established. The dynamic processes and structural dynamics of protein molecules in action have been successfully visualized using HS-AFM. However, its maximum scan ranges in the X- and Y-directions have been limited to ~1 μm and ~4 μm, respectively, making it infeasible to observe the dynamics of much larger samples, including live cells. Here, we develop a wide-area scanner with a maximum XY scan range of ~46 × 46 μm(2) by magnifying the displacements of stack piezoelectric actuators using a leverage mechanism. Mechanical vibrations produced by fast displacement of the X-scanner are suppressed by a combination of feed-forward inverse compensation and the use of triangular scan signals with rounded vertices. As a result, the scan speed in the X-direction reaches 6.3 mm/s even for a scan size as large as ~40 μm. The nonlinearity of the X- and Y-piezoelectric actuators' displacements that arises from their hysteresis is eliminated by polynomial-approximation-based open-loop control. The interference between the X- and Y-scanners is also eliminated by the same technique. The usefulness of this wide-area scanner is demonstrated by video imaging of dynamic processes in live bacterial and eukaryotic cells.

Nanomechanical properties of proteins and membranes depend on loading rate and electrostatic interactions

Knowing the dynamic mechanical response of tissue, cells, membranes, proteins, nucleic acids, and carbohydrates to external perturbations is important to understand various biological and biotechnological problems. Atomic force microscopy (AFM)-based approaches are the most frequently used nanotechnologies to determine the mechanical properties of biological samples that range in size from microscopic to (sub)nanoscopic. However, the dynamic nature of biomechanical properties has barely been addressed by AFM imaging. In this work, we characterizethe viscoelastic properties of the native light-driven proton pump bacteriorhodopsin of the purple membrane of Halobacterium salinarum. Using force-distance curve (F-D)-based AFM we imaged purple membranes while force probing their mechanical response over a wide range of loading rates (from ∼0.5 to 100 μN/s). Our results show that the mechanical stiffness of protein and membrane increases with the loading rate up to a factor of 10 (from ∼0.3 to 3.2 N/m). In addition, the electrostatic repulsion between AFM tip and sample can alter the mechanical stiffness measured by AFM up to ∼60% (from ∼0.8 to 1.3 N/m).These findings indicate that the mechanical response of membranes and proteins and probably of other biomolecular systems should be determined at different loading rates to fully understand their properties.

Role of trimer-trimer interaction of bacteriorhodopsin studied by optical spectroscopy and high-speed atomic force microscopy

Bacteriorhodopsin (bR) trimers form a two-dimensional hexagonal lattice in the purple membrane of Halobacterium salinarum. However, the physiological significance of forming the lattice has long been elusive. Here, we study this issue by comparing properties of assembled and non-assembled bR trimers using directed mutagenesis, high-speed atomic force microscopy (HS-AFM), optical spectroscopy, and a proton pumping assay. First, we show that the bonds formed between W12 and F135 amino acid residues are responsible for trimer-trimer association that leads to lattice assembly; the lattice is completely disrupted in both W12I and F135I mutants. HS-AFM imaging reveals that both crystallized D96N and non-crystallized D96N/W12I mutants undergo a large conformational change (i.e., outward E-F loop displacement) upon light-activation. However, lattice disruption significantly reduces the rate of conformational change under continuous light illumination. Nevertheless, the quantum yield of M-state formation, measured by low-temperature UV-visible spectroscopy, and proton pumping efficiency are unaffected by lattice disruption. From these results, we conclude that trimer-trimer association plays essential roles in providing bound retinal with an appropriate environment to maintain its full photo-reactivity and in maintaining the natural photo-reaction pathway.

Molecular machines directly observed by high-speed atomic force microscopy

Molecular machines made of proteins are highly dynamic and carry out sophisticated biological functions. The direct and dynamic high-resolution visualization of molecular machines in action is considered to be the most straightforward approach to understanding how they function but this has long been infeasible until recently. High-speed atomic force microscopy has recently been realized, making such visualization possible. The captured images of myosin V, F1-ATPase, and bacteriorhodopsin have enabled their dynamic processes and structure dynamics to be revealed in great detail, giving unique and deep insights into their functional mechanisms.

High-speed atomic force microscopy

High-speed atomic force microscopy (HS-AFM) has been developed as a nano-dynamics visualization technique. This microscopy permits direct observation of structure dynamics and dynamic processes of biological molecules in physiological solutions, at a subsecond to sub-100 ms temporal resolution and an ∼2 nm lateral and a 0.1 nm vertical resolution. Importantly, tip-sample interactions do not disturb the biomolecules' functions. Various functioning proteins including myosin V walking on an actin filament and bacteriorhodopsin responding to light have been successfully visualized with HS-AFM. In the quest for understanding the functional mechanisms of proteins, inferences no longer have to be made from static snapshots of molecular structures and dynamic behavior of optical markers attached to proteins. High-resolution molecular movies obtained from HS-AFM observations reveal the details of molecules' dynamic behavior in action, without the need for intricate analyses and interpretations. In this review, I first describe the fundamentals behind the achieved high imaging rate and low invasiveness to samples, and then highlight recent imaging studies. Finally, future studies are briefly described.

Atomic force microscopy and spectroscopy to probe single membrane proteins in lipid bilayers

The atomic force microscope (AFM) has opened vast avenues hitherto inaccessible to the biological scientist. The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever stylus is aptly termed as a "lab on a tip" owing to its versatility as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples assert that the AFM can be used to study the mechanical properties and monitor processes of single proteins and single cells, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of membrane proteins. Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theoretical, and practical skills.

Atomic force microscopy: a versatile tool to probe the physical and chemical properties of supported membranes at the nanoscale

Atomic force microscopy (AFM) was developed in the 1980s following the invention of its precursor, scanning tunneling microscopy (STM), earlier in the decade. Several modes of operation have evolved, demonstrating the extreme versatility of this method for measuring the physicochemical properties of samples at the nanoscopic scale. AFM has proved an invaluable technique for visualizing the topographic characteristics of phospholipid monolayers and bilayers, such as roughness, height or laterally segregated domains. Implemented modes such as phase imaging have also provided criteria for discriminating the viscoelastic properties of different supported lipid bilayer (SLB) regions. In this review, we focus on the AFM force spectroscopy (FS) mode, which enables determination of the nanomechanical properties of membrane models. The interpretation of force curves is presented, together with newly emerging techniques that provide complementary information on physicochemical properties that may contribute to our understanding of the structure and function of biomembranes. Since AFM is an imaging technique, some basic indications on how real-time AFM imaging is evolving are also presented at the end of this paper.

High-speed atomic force microscopy: cooperative adhesion and dynamic equilibrium of junctional microdomain membrane proteins

Junctional microdomains, paradigm for membrane protein segregation in functional assemblies, in eye lens fiber cell membranes are constituted of lens-specific aquaporin-0 tetramers (AQP0(4)) and connexin (Cx) hexamers, termed connexons. Both proteins have double function to assure nutrition and mediate adhesion of lens cells. Here we use high-speed atomic force microscopy to examine microdomain protein dynamics at the single-molecule level. We found that the adhesion function of head-to-head associated AQP0(4) and Cx is cooperative. This finding provides first experimental evidence for the mechanistic importance for junctional microdomain formation. From the observation of lateral association-dissociation events of AQP0(4), we determine that the enthalpic energy gain of a single AQP0(4)-AQP0(4) interaction in the membrane plane is -2.7 k(B)T, sufficient to drive formation of microdomains. Connexon association is stronger as dynamics are rarely observed, explaining their rim localization in junctional microdomains.

High-speed atomic force microscopy coming of age

High-speed atomic force microscopy (HS-AFM) is now materialized. It allows direct visualization of dynamic structural changes and dynamic processes of functioning biological molecules in physiological solutions, at high spatiotemporal resolution. Dynamic molecular events unselectively appear in detail in an AFM movie, facilitating our understanding of how biological molecules operate to function. This review describes a historical overview of technical development towards HS-AFM, summarizes elementary devices and techniques used in the current HS-AFM, and then highlights recent imaging studies. Finally, future challenges of HS-AFM studies are briefly discussed.

Visualization of mobility by atomic force microscopy

Intrinsically disordered regions (IDRs) of proteins are very thin and hence hard to be visualized by electron microscopy. Thus far, only high-speed atomic force microscopy (HS-AFM) can visualize them. The molecular movies identify the alignment of IDRs and ordered regions in an intrinsically disordered protein (IDP) and show undulation motion of the IDRs. The visualized tail-like structures contain the information of mechanical properties of the IDRs. Here, we describe methods of HS-AFM visualization of IDPs and methods of analyzing the obtained images to characterize IDRs.

Gating of the MlotiK1 potassium channel involves large rearrangements of the cyclic nucleotide-binding domains

Cyclic nucleotide-regulated ion channels are present in bacteria, plants, vertebrates, and humans. In higher organisms, they are closely involved in signaling networks of vision and olfaction. Binding of cAMP or cGMP favors the activation of these ion channels. Despite a wealth of structural and studies, there is a lack of structural data describing the gating process in a full-length cyclic nucleotide-regulated channel. We used high-resolution atomic force microscopy (AFM) to directly observe the conformational change of the membrane embedded bacterial cyclic nucleotide-regulated channel MlotiK1. In the nucleotide-bound conformation, the cytoplasmic cyclic nucleotide-binding (CNB) domains of MlotiK1 are disposed in a fourfold symmetric arrangement forming a pore-like vestibule. Upon nucleotide-unbinding, the four CNB domains undergo a large rearrangement, stand up by ∼1.7 nm, and adopt a structurally variable grouped conformation that closes the cytoplasmic vestibule. This fully reversible conformational change provides insight into how CNB domains rearrange when regulating the potassium channel.

High-speed atomic force microscopy: Structure and dynamics of single proteins

For surface analysis of biological molecules, atomic force microscopy (AFM) is an appealing technique combining data acquisition under physiological conditions, for example buffer solution, room temperature and ambient pressure, and high resolution. However, a key feature of life, dynamics, could not be assessed until recently because of the slowness of conventional AFM setups. Thus, for observing bio-molecular processes, the gain of image acquisition speed signifies a key progress. Here, we review the development and recent achievements using high-speed atomic force microscopy (HS-AFM). The HS-AFM is now the only technique to assess structure and dynamics of single molecules, revealing molecular motor action and diffusion dynamics. From this imaging data, watching molecules at work, novel and direct insights could be gained concerning the structure, dynamics and function relationship at the single bio-molecule level.