High-speed AFM and applications to biomolecular systems

Design and Fabrication of a High-Speed Atomic Force Microscope Scan-Head

A high-speed atomic force microscope (HS-AFM) requires a specialized set of hardware and software and therefore improving video-rate HS-AFMs for general applications is an ongoing process. To improve the imaging rate of an AFM, all components have to be carefully redesigned since the slowest component determines the overall bandwidth of the instrument. In this work, we present a design of a compact HS-AFM scan-head featuring minimal loading on the Z-scanner. Using a custom-programmed controller and a high-speed lateral scanner, we demonstrate its working by obtaining topographic images of Blu-ray disk data tracks in contact- and tapping-modes. Images acquired using a contact-mode cantilever with a natural frequency of 60 kHz in constant deflection mode show good tracking of topography at 400 Hz. In constant height mode, tracking of topography is demonstrated at rates up to 1.9 kHz for the scan size of 1μm×1μm with 100×100 pixels.

Direct visualization of translational GTPase factor pool formed around the archaeal ribosomal P-stalk by high-speed AFM

Translation of genetic information by the ribosome is a core biological process in all organisms. The ribosomal stalk is a multimeric ribosomal protein complex which plays an essential role in translation elongation. However, the working mechanism of the ribosomal stalk still remains unclear. In this study, we applied HS-AFM to investigate the working mechanism of the archaeal ribosomal P-stalk. HS-AFM movies demonstrate that the P-stalk collects two translational GTPase factors (trGTPases), aEF1A and aEF2, and increases their local concentration near the ribosome. These direct visual evidences show that the multiple arms of the ribosomal P-stalk catch the trGTPases for efficient protein synthesis in the crowded intracellular environment.

In translation elongation, two translational guanosine triphosphatase (trGTPase) factors EF1A and EF2 alternately bind to the ribosome and promote polypeptide elongation. The ribosomal stalk is a multimeric ribosomal protein complex which plays an essential role in the recruitment of EF1A and EF2 to the ribosome and their GTP hydrolysis for efficient and accurate translation elongation. However, due to the flexible nature of the ribosomal stalk, its structural dynamics and mechanism of action remain unclear. Here, we applied high-speed atomic force microscopy (HS-AFM) to directly visualize the action of the archaeal ribosomal heptameric stalk complex, aP0•(aP1•aP1)₃ (P-stalk). HS-AFM movies clearly demonstrated the wobbling motion of the P-stalk on the large ribosomal subunit where the stalk base adopted two conformational states, a predicted canonical state, and a newly identified flipped state. Moreover, we showed that up to seven molecules of archaeal EF1A (aEF1A) and archaeal EF2 (aEF2) assembled around the ribosomal P-stalk, corresponding to the copy number of the common C-terminal factor-binding site of the P-stalk. These results provide visual evidence for the factor-pooling mechanism by the P-stalk within the ribosome and reveal that the ribosomal P-stalk promotes translation elongation by increasing the local concentration of translational GTPase factors.

Digital Polymerase Chain Reaction Paired with High-Speed Atomic Force Microscopy for Quantitation and Length Analysis of DNA Length Polymorphisms

DNA length polymorphisms are found in many serious diseases, and assessment of their length and abundance is often critical for accurate diagnosis. However, measuring their length and frequency in a mostly wild-type background, as occurs in many situations, remains challenging due to their variable and repetitive nature. To overcome these hurdles, we combined two powerful techniques, digital polymerase chain reaction (dPCR) and high-speed atomic force microscopy (HSAFM), to create a simple, rapid, and flexible method for quantifying both the size and proportion of DNA length polymorphisms. In our approach, individual amplicons from each dPCR partition are imaged and sized directly. We focused on internal tandem duplications (ITDs) located within the FLT3 gene, which are associated with acute myeloid leukemia and often indicative of a poor prognosis. In an analysis of over 1.5 million HSAFM-imaged amplicons from cell line and clinical samples containing FLT3-ITDs, dPCR-HSAFM returned the expected variant length and variant allele frequency, down to 5% variant samples. As a high-throughput method with single-molecule resolution, dPCR-HSAFM thus represents an advance in HSAFM analysis and a powerful tool for the diagnosis of length polymorphisms.

BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics

We provide a stand-alone software, the BioAFMviewer, which transforms biomolecular structures into the graphical representation corresponding to the outcome of atomic force microscopy (AFM) experiments. The AFM graphics is obtained by performing simulated scanning over the molecular structure encoded in the corresponding PDB file. A versatile molecular viewer integrates the visualization of PDB structures and control over their orientation, while synchronized simulated scanning with variable spatial resolution and tip-shape geometry produces the corresponding AFM graphics. We demonstrate the applicability of the BioAFMviewer by comparing simulated AFM graphics to high-speed AFM observations of proteins. The software can furthermore process molecular movies of conformational motions, e.g. those obtained from servers which model functional transitions within a protein, and produce the corresponding simulated AFM movie. The BioAFMviewer software provides the platform to employ the plethora of structural and dynamical data of proteins in order to help in the interpretation of biomolecular AFM experiments.

Nowadays nanotechnology allows to observe single proteins at work. Under atomic force microscopy (AFM), e.g., their surface can be rapidly scanned and functional motions monitored, which is of great importance for applications in all fields of Life science. The analysis and interpretation of experimental results remains however challenging, because the resolution of obtained images or molecular movies is far from perfect. On the other side, high-resolution static structures of most proteins are known and their conformational dynamics can be computed in molecular simulations. This enormous amount of available data offers a great opportunity to better understand the outcome of resolution-limited scanning experiments. Our software provides the computational package towards this goal. The BioAFMviewer computationally emulates the scanning of any biomolecular structure to produce graphical images that mimic the outcome of AFM experiments. This makes the comparison of all available structural data and computational molecular movies to AFM results possible. We demonstrate that simulated AFM images are of great value to facilitate the interpretation of high-speed AFM observations. With its versatile interactive interface and rich functionality, the BioAFMviewer provides a convenient platform for the broad Bio-AFM community to better understand experiments.

Resolving the data asynchronicity in high-speed atomic force microscopy measurement via the Kalman Smoother

High-speed atomic force microscopy (HS-AFM) is a scanning probe microscopy that can capture structural dynamics of biomolecules in real time at single molecule level near physiological condition. Albeit much improvement, while scanning one frame of HS-AFM movies, biomolecules often change their conformations largely. Thus, the obtained frame images can be hampered by the time-difference, the asynchronicity, in the data acquisition. Here, to resolve this data asynchronicity in the HS-AFM movie, we developed Kalman filter and smoother methods, some of the sequential Bayesian filtering approaches. The Kalman filter/smoother methods use alternative steps of a short time-propagation by a linear dynamical system and a correction by the likelihood of AFM data acquired pixel by pixel. We first tested the method using a toy model of a diffusing cone, showing that the Kalman smoother method outperforms to reproduce the ground-truth movie. We then applied the Kalman smoother to a synthetic movie for conformational change dynamics of a motor protein, i.e., dynein, confirming the superiority of the Kalman smoother. Finally, we applied the Kalman smoother to two real HS-AFM movies, FlhA_C and centralspindlin, reducing distortion and noise in the AFM movies. The method is general and can be applied to any HS-AFM movies.

How fast are the motions of tertiary-structure elements in proteins?

Protein motions occur on multiple time and distance scales. Large-scale motions of protein tertiary-structure elements, i.e., domains, are particularly intriguing as they are essential for the catalytic activity of many enzymes and for the functional cycles of protein machines and motors. Theoretical estimates suggest that domain motions should be very fast, occurring on the nanosecond or microsecond time scales. Indeed, free-energy barriers for domain motions are likely to involve salt bridges, which can break in microseconds. Experimental methods that can directly probe domain motions on fast time scales have appeared only in recent years. This Perspective discusses briefly some of these techniques, including nuclear magnetic resonance and single-molecule fluorescence spectroscopies. We introduce a few recent studies that demonstrate ultrafast domain motions and discuss their potential roles. Particularly surprising is the observation of tertiary-structure element dynamics that are much faster than the functional cycles in some protein machines. These swift motions can be rationalized on a case-by-case basis. For example, fast domain closure in multi-substrate enzymes may be utilized to optimize relative substrate orientation. Whether a large mismatch in time scales of conformational dynamics vs functional cycles is a general design principle in proteins remains to be determined.

High-Speed AFM Reveals Molecular Dynamics of Human Influenza A Hemagglutinin and Its Interaction with Exosomes

Influenza A hemagglutinin (HA) is one of the crucial virulence factors that mediate host tropism and viral infectivity. Presently, the mechanism of the fusogenic transition of HA remains elusive. Here, we used high-speed atomic force microscopy (HS-AFM) to decipher the molecular dynamics of HA and its interaction with exosomes. Our data reveal that the native conformation of HA in the neutral buffer is ellipsoidal, and HA undergoes a conformational change in an acidic buffer. Real-time visualization of the fusogenic transition by HS-AFM suggests that the mechanism is possibly fit to the "uncaging" model, and HA intermediate appears as Y-shaped. A firm interaction between the HA and exosome in an acidic buffer indicates the insertion of a fusion peptide into the exosomal layer and subsequently destabilizes the layer, resulting in the deformation or rupture of exosomes, releasing exosomal contents. In contrast, the HA-exosome interaction is weak in a neutral buffer because the interaction is mediated by weak bonds between the HA receptor-binding site and receptors on the exosome.

Particle Filter Method to Integrate High-Speed Atomic Force Microscopy Measurements with Biomolecular Simulations

High-speed atomic force microscopy (HS-AFM) can be used to observe the structural dynamics of biomolecules at the single-molecule level in real time under near-physiological conditions; however, its spatiotemporal resolution is limited. Complementarily, molecular dynamics (MD) simulations have higher spatiotemporal resolutions, albeit with some artifacts. Here, to integrate HS-AFM data and coarse-grained molecular dynamics (CG-MD) simulations, we develop a particle filter method that implements a sequential Bayesian data assimilation approach. We test the method in a twin experiment. First, we generate a reference HS-AFM movie from the CG-MD trajectory of a test molecule, a nucleosome; this serves as the "experimental measurement". Then, we perform a particle filter simulation with 512 particles, which captures the large-scale nucleosome structural dynamics compatible with the AFM movie. Comparing particle filter simulations with 8-8192 particles, we find that using greater numbers of particles consistently increases the likelihood of the whole AFM movie. By comparing the likelihoods for different ionic concentrations and time scale mappings, we find that the "true" concentration and time scale mapping can be inferred as the largest likelihood of the whole AFM movie but not that of each AFM image. The particle filter method provides a general approach for integrating HS-AFM data with MD simulations.

Quantitative Assessment of Tip Effects in Single-Molecule High-Speed Atomic Force Microscopy Using DNA Origami Substrates

High-speed atomic force microscopy (HS-AFM) is widely employed in the investigation of dynamic biomolecular processes at a single-molecule level. However, it remains an open and somewhat controversial question, how these processes are affected by the rapidly scanned AFM tip. While tip effects are commonly believed to be of minor importance in strongly binding systems, weaker interactions may significantly be disturbed. Herein, we quantitatively assess the role of tip effects in a strongly binding system using a DNA origami-based single-molecule assay. Despite its femtomolar dissociation constant, we find that HS-AFM imaging can disrupt monodentate binding of streptavidin (SAv) to biotin (Bt) even under gentle scanning conditions. To a lesser extent, this is also observed for the much stronger bidentate SAv-Bt complex. The presented DNA origami-based assay can be universally employed to quantify tip effects in strongly and weakly binding systems and to optimize the experimental settings for their reliable HS-AFM imaging.

Plasmonic Nanosensors for the Label-Free Imaging of Dynamic Protein Patterns

We introduce a new approach to monitor the dynamics and spatial patterns of biological molecular assemblies. Our molecular imaging method relies on plasmonic gold nanoparticles as point-like detectors and requires no labeling of the molecules. We show spatial resolution of up to 5 μm and 30 ms temporal resolution, which is comparable to wide-field fluorescence microscopy, while requiring only readily available gold nanoparticles and a dark-field optical microscope. We demonstrate the method on MinDE proteins attaching to and detaching from lipid membranes of different composition for 24 h. We foresee our new imaging method as an indispensable tool in advanced molecular biology and biophysics laboratories around the world.

Surface analysis tools for characterizing biological materials

Surfaces represent a unique state of matter that typically have significantly different compositions and structures from the bulk of a material. Since surfaces are the interface between a material and its environment, they play an important role in how a material interacts with its environment. Thus, it is essential to characterize, in as much detail as possible, the surface structure and composition of a material. However, this can be challenging since the surface region typically is only minute portion of the entire material, requiring specialized techniques to selectively probe the surface region. This tutorial will provide a brief review of several techniques used to characterize the surface and interface regions of biological materials. For each technique we provide a description of the key underlying physics and chemistry principles, the information provided, strengths and weaknesses, the types of samples that can be analyzed, and an example application. Given the surface analysis challenges for biological materials, typically there is never just one technique that can provide a complete surface characterization. Thus, a multi-technique approach to biological surface analysis is always required.

Single-Molecule Biophysical Techniques to Study Actomyosin Force Transduction

Inside the cellular environment, molecular motors can work in concert to conduct a variety of important physiological functions and processes that are vital for the survival of a cell. However, in order to decipher the mechanism of how these molecular motors work, single-molecule microscopy techniques have been popular methods to understand the molecular basis of the emerging ensemble behavior of these motor proteins.In this chapter, we discuss various single-molecule biophysical imaging techniques that have been used to expose the mechanics and kinetics of myosins. The chapter should be taken as a general overview and introductory guide to the many existing techniques; however, since other chapters will discuss some of these techniques more thoroughly, the readership should refer to those chapters for further details and discussions. In particular, we will focus on scattering-based single-molecule microscopy methods, some of which have become more popular in the recent years and around which the work in our laboratories has been centered.

High-Speed Atomic Force Microscopy to Study Myosin Motility

High-speed atomic force microscopy (HS-AFM) is a unique tool that enables imaging of protein molecules during their functional activity at sub-100 ms temporal and submolecular spatial resolution. HS-AFM is suited for the study of highly dynamic proteins, including myosin motors. HS-AFM images of myosin V walking on actin filaments provide irrefutable evidence for the swinging lever arm motion propelling the molecule forward. Moreover, molecular behaviors that have not been noticed before are also displayed on the AFM movies. This chapter describes the principle, underlying techniques and performance of HS-AFM, filmed images of myosin V, and mechanistic insights into myosin motility provided from the filmed images.

Initial Step of Virus Entry: Virion Binding to Cell-Surface Glycans

Virus infection is an intricate process that requires the concerted action of both viral and host cell components. Entry of viruses into cells is initiated by interactions between viral proteins and cell-surface receptors. Various cell-surface glycans function as initial, usually low-affinity attachment factors, providing a first anchor of the virus to the cell surface, and further facilitate high-affinity binding to virus-specific cell-surface receptors, while other glycans function as specific entry receptors themselves. It is now possible to rapidly identify specific glycan receptors using different techniques, define atomic-level structures of virus-glycan complexes, and study these interactions at the single-virion level. This review provides a detailed overview of the role of glycans in viral infection and highlights experimental approaches to study virus-glycan binding along with specific examples. In particular, we highlight the development of the atomic force microscope to investigate interactions with glycans at the single-virion level directly on living mammalian cells, which offers new perspectives to better understand virus-glycan interactions in physiologically relevant conditions.

Atomic Force Microscopy in Mechanoimmunology Analysis: A New Perspective for Cancer Immunotherapy

Immunotherapy has remarkable success outcomes against hematological malignancies with high rates of complete remission. To date, many studies have been conducted to increase its effectiveness in other types of cancer. However, it still yields unsatisfying results in solid tumor therapy. This limitation is partly attributed to the lack of understanding of how immunotherapy works in cancer from other perspectives. The traditional studies focus on the biological and chemical perspectives to determine which molecular substrates are involved in the immune system that can eradicate cancer cells. In the last decades, accumulating evidence has shown that physical properties also play important roles in the immune system to combat cancer, which is studied in mechanoimmunology. Mechanoimmunology analysis requires special tools; and herein, atomic force microscopy (AFM) appears as a versatile tool to determine and quantify the mechanical properties of a sample in nanometer precisions. Owing to its multifunctional capabilities, AFM can be used to explore immune system function from the physical perspective. This review paper explains the mechanoimmunology of how immune systems work through AFM, which includes mechanosignaling, mechanosensing, and mechanotransduction, with the aim to deepen the understanding of the mechanistic role of immunotherapy for further development in cancer treatment.

Intrinsically disordered proteins of viruses: Involvement in the mechanism of cell regulation and pathogenesis

Intrinsically disordered proteins (IDPs) possess the property of inherent flexibility and can be distinguished from other proteins in terms of lack of any fixed structure. Such dynamic behavior of IDPs earned the name "Dancing Proteins." The exploration of these dancing proteins in viruses has just started and crucial details such as correlation of rapid evolution, high rate of mutation and accumulation of disordered contents in viral proteome at least understood partially. In order to gain a complete understanding of this correlation, there is a need to decipher the complexity of viral mediated cell hijacking and pathogenesis in the host organism. Further there is necessity to identify the specific patterns within viral and host IDPs such as aggregation; Molecular recognition features (MoRFs) and their association to virulence, host range and rate of evolution of viruses in order to tackle the viral-mediated diseases. The current book chapter summarizes the aforementioned details and suggests the novel opportunities for further research of IDPs senses in viruses.

Biological phase separation: cell biology meets biophysics

Progress in development of biophysical analytic approaches has recently crossed paths with macromolecule condensates in cells. These cell condensates, typically termed liquid-like droplets, are formed by liquid-liquid phase separation (LLPS). More and more cell biologists now recognize that many of the membrane-less organelles observed in cells are formed by LLPS caused by interactions between proteins and nucleic acids. However, the detailed biophysical processes within the cell that lead to these assemblies remain largely unexplored. In this review, we evaluate recent discoveries related to biological phase separation including stress granule formation, chromatin regulation, and processes in the origin and evolution of life. We also discuss the potential issues and technical advancements required to properly study biological phase separation.

Dynamics of oligomer and amyloid fibril formation by yeast prion Sup35 observed by high-speed atomic force microscopy

The yeast prion protein Sup35, which contains intrinsically disordered regions, forms amyloid fibrils responsible for a prion phenotype [PSI ⁺]. Using high-speed atomic force microscopy (HS-AFM), we directly visualized the prion determinant domain (Sup35NM) and the formation of its oligomers and fibrils at subsecond and submolecular resolutions. Monomers with freely moving tail-like regions initially appeared in the images, and subsequently oligomers with distinct sizes of ∼1.7 and 3 to 4 nm progressively accumulated. Nevertheless, these oligomers did not form fibrils, even after an incubation for 2 h in the presence of monomers. Fibrils appeared after much longer monomer incubation. The fibril elongation occurred smoothly without discrete steps, suggesting gradual conversions of the incorporated monomers into cross-β structures. The individual oligomers were separated from each other and also from the fibrils by respective, identical lengths on the mica surface, probably due to repulsion caused by the freely moving disordered regions. Based on these HS-AFM observations, we propose that the freely moving tails of the monomers are incorporated into the fibril ends, and then the structural conversions to cross-β structures gradually occur.

Scratching the Surface: Bacterial Cell Envelopes at the Nanoscale

The bacterial cell envelope is essential for viability, the environmental gatekeeper and first line of defense against external stresses. For most bacteria, the envelope biosynthesis is also the site of action of some of the most important groups of antibiotics. It is a complex, often multicomponent structure, able to withstand the internally generated turgor pressure. Thus, elucidating the architecture and dynamics of the cell envelope is important, to unravel not only the complexities of cell morphology and maintenance of integrity but also how interventions such as antibiotics lead to death. To address these questions requires the capacity to visualize the cell envelope in situ via high-spatial resolution approaches. In recent years, atomic force microscopy (AFM) has brought novel molecular insights into the assembly, dynamics, and functions of bacterial cell envelopes. The ultrafine resolution and physical sensitivity of the technique have revealed a wealth of ultrastructural features that are invisible to traditional optical microscopy techniques or imperceptible in their true physiological state by electron microscopy. Here, we discuss recent progress in our use of AFM imaging for understanding the architecture and dynamics of the bacterial envelope. We survey recent studies that demonstrate the power of the technique to observe isolated membranes and live cells at (sub)nanometer resolution and under physiological conditions and to track in vitro structural dynamics in response to growth or to drugs.

Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations

High-speed (HS) atomic force microscopy (AFM) is a prominent imaging technology that observes large-scale structural dynamics of biomolecules near the physiological condition, but the AFM data are limited to the surface shape of specimens. Rigid-body fitting methods were developed to obtain molecular structures that fit to an AFM image, without accounting for conformational changes. Here, we developed a method to fit flexibly a three-dimensional (3D) biomolecular structure into an AFM image. First, we describe a method to produce a pseudo-AFM image from a given 3D structure in a differentiable form. Then, using a correlation function between the experimental AFM image and the computational pseudo-AFM image, we developed a flexible fitting molecular dynamics (MD) simulation method by which we obtain protein structures that well fit to the given AFM image. We first test it with a twin experiment; using an AFM image produced from a protein structure different from its native conformation as a reference, we performed the flexible fitting MD simulations to sample conformations that fit well the reference AFM image, and the method was confirmed to work well. Then, parameter dependence in the protocol was discussed. Finally, we applied the method to a real experimental HS-AFM image for a flagellar protein FlhA, demonstrating its applicability. We also test the rigid-body fitting of a molecular structure to an AFM image. Our method will be a general tool for dynamic structure modeling based on HS-AFM images and is publicly available through the CafeMol software.

Advances in Atomic Force Microscopy: Weakly Perturbative Imaging of the Interfacial Water

The structure and dynamics of interfacial water, determined by the water-interface interactions, are important for a wide range of applied fields and natural processes, such as water diffusion (Kim et al., 2013), electrochemistry (Markovic, 2013), heterogeneous catalysis (Over et al., 2000), and lubrication (Zilibotti et al., 2013). The precise understanding of water-interface interactions largely relies on the development of atomic-scale experimental techniques (Guo et al., 2014) and computational methods (Hapala et al., 2014b). Scanning probe microscopy has been extensively applied to probe interfacial water in many interdisciplinary fields (Ichii et al., 2012; Shiotari and Sugimoto, 2017; Peng et al., 2018a). In this perspective, we review the recent progress in the noncontact atomic force microscopy (nc-AFM) imaging and AFM simulation techniques and discuss how the newly developed techniques are applied to study the properties of interfacial water. The nc-AFM with the quadrupole-like CO-terminated tip can achieve ultrahigh-resolution imaging of the interfacial water on different surfaces, trace the reconstruction of H-bonding network and determine the intrinsic structures of the weakly bonded water clusters and even their metastable states. In the end, we present an outlook on the directions of future AFM studies of interfacial water as well as the challenges faced by this field.

Statistical physics and mesoscopic modeling to interpret tethered particle motion experiments

Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques provide raw data such as the tracked particle amplitude of movement, from which relevant information about DNA conformations or states must be recovered. Solving this inverse problem appeals to specific theoretical tools that have been designed in the two last decades, together with the data pre-processing procedures that ought to be implemented to avoid biases inherent to these experimental techniques. These statistical tools and models are reviewed in this paper.

OBSERVER-BASED CONTROL OF A DUAL-STAGE PIEZOELECTRIC SCANNER

Despite its proven success in a wide variety of applications, the atomic force microscope (AFM) remains limited by its slow imaging rate. One approach to overcome this challenge is to rely on algorithmic approaches that reduce the imaging time not by scanning faster but by scanning less. Such schemes are particularly useful on older instruments as they can provide significant gains despite the existing (slow) hardware. At the same time, algorithms for sub-sampling can yield even greater improvements in imaging rate when combined with advanced scanners that can be retrofitted into the system. In this work, we focus on the use of a dual-stage piezoelectric scanner coupled with a particular scanning algorithm known as Local Circular Scan (LCS). LCS drives the tip of the AFM along a circular trajectory while using feedback to center that circle on a sample edge and to move the circle along the feature, thus reducing imaging time by concentrating the samples to the region of interest. Dual-stage systems are well-suited to LCS as the algorithm is naturally described in terms of a high-frequency, short range path (the scanning circle) and a slower, long range path (the track along the sample). However, control of the scanner is not straightforward as the system is multi-input, single-output. Here we establish controllability and observability of the scanning stage, allowing us to develop individual controllers for the long-range and short-range actuators through the principle of separation. We then use an internal model controller for the short range actuator to track a sinusoidal input (to generate the circular motion) and a state-space set-point tracking controller for the long range actuator. The results are demonstrated through simulation.

Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images

BACKGROUND

Atomic Force Microscopy (AFM) is an experimental technique to study structure-function relationship of biomolecules. AFM provides images of biomolecules at nanometer resolution. High-speed AFM experiments produce a series of images following dynamics of biomolecules. To further understand biomolecular functions, information on three-dimensional (3D) structures is beneficial.

METHOD

We aim to recover 3D information from an AFM image by computational modeling. The AFM image includes only low-resolution representation of a molecule; therefore we represent the structures by a coarse grained model (Gaussian mixture model). Using Monte-Carlo sampling, candidate models are generated to increase similarity between AFM images simulated from the models and target AFM image.

RESULTS

The algorithm was tested on two proteins to model their conformational transitions. Using a simulated AFM image as reference, the algorithm can produce a low-resolution 3D model of the target molecule. Effect of molecular orientations captured in AFM images on the 3D modeling performance was also examined and it is shown that similar accuracy can be obtained for many orientations.

CONCLUSIONS

The proposed algorithm can generate 3D low-resolution protein models, from which conformational transitions observed in AFM images can be interpreted in more detail.

GENERAL SIGNIFICANCE

High-speed AFM experiments allow us to directly observe biomolecules in action, which provides insights on biomolecular function through dynamics. However, as only partial structural information can be obtained from AFM data, this new AFM based hybrid modeling method would be useful to retrieve 3D information of the entire biomolecule.

In-cell single-molecule FRET measurements reveal three conformational state changes in RAF protein

BACKGROUND

The structures of proteins are intimately related to their functions. Significant efforts have been dedicated to the structural investigation of proteins, mainly those of purified proteins in in vitro environments. Proteins function in living cells and thus protein structures must be regulated by interactions with various molecules, some of which participate in reaction networks, depending on the states, conditions, or actions of the cell. Therefore, it is very important to understand the structural behavior of proteins in living cells.

METHODS

Single-molecule Förster resonance energy transfer (smFRET) measurements were conducted using the alternative laser excitation (ALEX) technique. smFRET distributions of cytosolic Rapidly Accelerated Fibrosarcoma (RAF) proteins in living HeLa cells were obtained with exclusion of the negative effects of photobleached fluorophores and incompletely labeled proteins on smFRET.

RESULTS

smFRET histograms of wildtype (wt) RAF in live cells exhibited two major peaks, whereas that of the S621A mutant, which has been thought to have an expanded structure, was almost single-peaked. A population shift involving the peaks for wt RAF was detected upon epidermal growth factor stimulation. Spontaneous transitions between the conformational states corresponding to the two peaks were also detected using the FRET-two-channel kernel-based density distribution estimator method in comparison to static double-stranded DNA samples.

CONCLUSIONS

Cytosolic CRAF has at least three conformational states; in addition to the closed and open forms, the fully-open form was distinctly specified. Based on the results, we propose a speculative structural model for CRAF.

GENERAL SIGNIFICANCE

Structural distribution and changes to proteins in live cells as a result of intracellular interactions were successfully identified. smFRET using ALEX is applicable to any other cytosolic proteins.

Imaging DNA Equilibrated onto Mica in Liquid Using Biochemically Relevant Deposition Conditions

For over 25 years, imaging of DNA by atomic force microscopy has been intensely pursued. Ideally, such images are then used to probe the physical properties of DNA and characterize protein-DNA interactions. The atomic flatness of mica makes it the preferred substrate for high signal-to-noise ratio (SNR) imaging, but the negative charge of mica and DNA hinders deposition. Traditional methods for imaging DNA and protein-DNA complexes in liquid have drawbacks: DNA conformations with an anomalous persistence length ( p), low SNR, and/or ionic deposition conditions detrimental to preserving protein-DNA interactions. Here, we developed a process to bind DNA to mica in a buffer containing both MgCl₂ and KCl that resulted in high SNR images of equilibrated DNA in liquid. Achieving an equilibrated 2D configuration ( i. e., p = 50 nm) not only implied a minimally perturbative binding process but also improved data quality and quantity because the DNA's configuration was more extended. In comparison to a purely NiCl₂-based protocol, we showed that an 8-fold larger fraction (90%) of 680-nm-long DNA molecules could be quantified. High-resolution images of select equilibrated molecules revealed the right-handed structure of DNA with a helical pitch of 3.5 nm. Deposition and imaging of DNA was achieved over a wide range of monovalent and divalent ionic conditions, including a buffer containing 50 mM KCl and 3 mM MgCl₂. Finally, we imaged two protein-DNA complexes using this protocol: a restriction enzyme bound to DNA and a small three-nucleosome array. We expect such deposition of protein-DNA complexes at biochemically relevant ionic conditions will facilitate biophysical insights derived from imaging diverse protein-DNA complexes.

The Protein Disulfide Isomerase Family: from proteostasis to pathogenesis

In mammalian cells, nearly one-third of proteins are inserted into the endoplasmic reticulum (ER), where they undergo oxidative folding and chaperoning assisted by approximately 20 members of the protein disulfide isomerase family (PDIs). PDIs consist of multiple thioredoxin-like domains and recognize a wide variety of proteins via highly conserved interdomain flexibility. Although PDIs have been studied intensely for almost 50 years, exactly how they maintain protein homeostasis in the ER remains unknown, and is important not only for fundamental biological understanding but also for protein misfolding- and aggregation-related pathophysiology. Herein, we review recent advances in structural biology and biophysical approaches that explore the underlying mechanism by which PDIs fulfil their distinct functions to promote productive protein folding and scavenge misfolded proteins in the ER, the primary factory for efficient production of the secretome.

Inner lumen proteins stabilize doublet microtubules in cilia and flagella

Motile cilia are microtubule-based organelles that play important roles in most eukaryotes. Although axonemal microtubules are sufficiently stable to withstand their beating motion, it remains unknown how they are stabilized while serving as tracks for axonemal dyneins. To address this question, we have identified two uncharacterized proteins, FAP45 and FAP52, as microtubule inner proteins (MIPs) in Chlamydomonas. These proteins are conserved among eukaryotes with motile cilia. Using cryo-electron tomography (cryo-ET) and high-speed atomic force microscopy (HS-AFM), we show that lack of these proteins leads to a loss of inner protrusions in B-tubules and less stable microtubules. These protrusions are located near the inner junctions of doublet microtubules and lack of both FAP52 and a known inner junction protein FAP20 results in detachment of the B-tubule from the A-tubule, as well as flagellar shortening. These results demonstrate that FAP45 and FAP52 bind to the inside of microtubules and stabilize ciliary axonemes.

Monitoring Fast, Voxel-Scale Cure Kinetics via Sample-Coupled-Resonance Photorheology

Photopolymerizable materials are the focus of extensive research across a variety of fields ranging from additive manufacturing to regenerative medicine. However, poorly understood material mechanical and rheological properties during polymerization at the relevant exposure powers and single-voxel length-scales limit advancements in part performance and throughput. Here, a novel atomic force microscopy (AFM) technique, sample-coupled-resonance photorheology (SCRPR), to locally characterize the mechano-rheological properties of photopolymerized materials on the relevant reaction kinetic timescales, is demonstrated. By coupling an AFM tip to a photopolymer and exposing the coupled region to a laser, two fundamental photopolymerization phenomena: (1) timescales of photopolymerization at high laser power and (2) reciprocity between photodose and material properties are studied. The ability to capture rapid kinetic changes occurring during polymerization with SCRPR is demonstrated. It is found that reciprocity is only valid for a finite range of exposure powers in the verification material and polymerization is highly localized in a low-diffusion system. After polymerization, in situ imaging of a single polymerized voxel is performed using material-appropriate topographic and nanomechanical modalities of the AFM while still in the as-printed environment.

Atomic Force Microscopy Meets Biophysics, Bioengineering, Chemistry, and Materials Science

Briefly, herein the use of atomic force microscopy (AFM) in the characterization of molecules and (bioengineered) materials related to chemistry, materials science, chemical engineering, and environmental science and biotechnology is reviewed. First, the basic operations of standard AFM, Kelvin probe force microscopy, electrochemical AFM, and tip-enhanced Raman microscopy are described. Second, several applications of these techniques to the characterization of single molecules, polymers, biological membranes, films, cells, hydrogels, catalytic processes, and semiconductors are provided and discussed.

Length computation of irradiated plasmid DNA molecules

Compromised detection of short DNA fragments can result in underestimation of radiation-induced clustered DNA damage. The fragments can be detected with atomic force microscopy (AFM), followed by image analysis to compute the length of plasmid molecules. Plasmid molecules imaged with AFM are represented by open or closed curves, possibly with crossings. For the analysis of such objects, a dedicated algorithm was developed, and its usability was demonstrated on the AFM images of plasmid pBR322 irradiated with ⁶⁰Co gamma rays. The analysis of the set of the acquired AFM images revealed the presence of DNA fragments with lengths shorter than 300 base pairs that would have been neglected by a conventional detection method.

Cryptic binding sites become accessible through surface reconstruction of the type I collagen fibril

Collagen fibril interactions with cells and macromolecules in the extracellular matrix drive numerous cellular functions. Binding motifs for dozens of collagen-binding proteins have been determined on fully exposed collagen triple helical monomers. However, when the monomers are assembled into the functional collagen fibril, many binding motifs become inaccessible, and yet critical cellular processes occur. Here, we have developed an early stage atomic model of the smallest repeating unit of the type I collagen fibril at the fibril surface that provides a novel framework to address questions about these functionally necessary yet seemingly obstructed interactions. We use an integrative approach by combining molecular dynamics (MD) simulations with atomic force microscopy (AFM) experiments and show that reconstruction of the collagen monomers within the complex fibril play a critical role in collagen interactions. In particular, the fibril surface shows three major conformational changes, which allow cryptic binding sites, including an integrin motif involved in platelet aggregation, to be exposed. The observed dynamics and reconstruction of the fibril surface promote its role as a “smart fibril” to keep certain binding sites cryptic, and to allow accessibility of recognition domains when appropriate.

Time-frequency analysis of the tip motion in liquids using the wavelet transform in dynamic atomic force microscopy

The tip motion of the dynamic atomic force microscope in liquids shows complex transient behaviors when using a low stiffness cantilever. The second flexural mode of the cantilever is momentarily excited. Multiple impacts between the tip and the sample might occur in one oscillation cycle. However, the commonly used Fourier transform method cannot provide time-related information about these transient features. To overcome this limitation, we apply the wavelet transform to perform the time-frequency analysis of the tip motion in liquids. The momentary excitation of the second mode and the phenomenon of multiple impacts are clearly shown in the time-frequency plane of the wavelet scalogram. The instantaneous frequencies and magnitudes of the second mode are extracted by the wavelet ridge analysis, which can provide quantitative estimations of the tip motion in the second mode. Moreover, the relations of the maximum instantaneous magnitude (MIM) to the amplitude setpoint and the Young's modulus of the sample surface are investigated. The results suggest that the MIM can be used to characterize the nanomechanical property of the sample surface at high amplitude setpoints.

Algal Viruses: The (Atomic) Shape of Things to Come

Visualization of algal viruses has been paramount to their study and understanding. The direct observation of the morphological dynamics of infection is a highly desired capability and the focus of instrument development across a variety of microscopy technologies. However, the high temporal (ms) and spatial resolution (nm) required, combined with the need to operate in physiologically relevant conditions presents a significant challenge. Here we present a short history of virus structure study and its relation to algal viruses and highlight current work, concentrating on electron microscopy and atomic force microscopy, towards the direct observation of individual algae⁻virus interactions. Finally, we make predictions towards future algal virus study direction with particular focus on the exciting opportunities offered by modern high-speed atomic force microscopy methods and instrumentation.

Simple and Robust Study of Backbone Dynamics of Crystalline Proteins Employing 1H-15N Dipolar Coupling Dispersion

We report a new solid-state multidimensional NMR approach based on the cross-polarization with variable-contact pulse sequence [ Paluch , P. ; Pawlak , T. ; Amoureux , J.-P. ; Potrzebowski , M. J. J. Magn. Reson. 233 , 2013 , 56 ], with ¹H inverse detection and very fast magic angle spinning (ν_R = 60 kHz), dedicated to the measurement of local molecular motions of ¹H-¹⁵N vectors. The introduced three-dimensional experiments, ¹H-¹⁵N-¹H and hCA(N)H, are particularly useful for the study of molecular dynamics of proteins and other complex structures. The applicability and power of this methodology have been revealed by employing as a model sample the GB-1 small protein doped with Na₂CuEDTA. The results clearly prove that the dispersion of ¹H-¹⁵N dipolar coupling constants well correlates with higher order structure of the protein. Our approach complements the conventional studies and offers a fast and reasonably simple method.

Revealing circadian mechanisms of integration and resilience by visualizing clock proteins working in real time

The circadian clock proteins KaiA, KaiB, and KaiC reconstitute a remarkable circa-24 h oscillation of KaiC phosphorylation that persists for many days in vitro. Here we use high-speed atomic force microscopy (HS-AFM) to visualize in real time and quantify the dynamic interactions of KaiA with KaiC on sub-second timescales. KaiA transiently interacts with KaiC, thereby stimulating KaiC autokinase activity. As KaiC becomes progressively more phosphorylated, KaiA's affinity for KaiC weakens, revealing a feedback of KaiC phosphostatus back onto the KaiA-binding events. These non-equilibrium interactions integrate high-frequency binding and unbinding events, thereby refining the period of the longer term oscillations. Moreover, this differential affinity phenomenon broadens the range of Kai protein stoichiometries that allow rhythmicity, explaining how the oscillation is resilient in an in vivo milieu that includes noise. Therefore, robustness of rhythmicity on a 24-h scale is explainable by molecular events occurring on a scale of sub-seconds.

Microfluidics for mechanobiology of model organisms

Mechanical stimuli play a critical role in organ development, tissue homeostasis, and disease. Understanding how mechanical signals are processed in multicellular model systems is critical for connecting cellular processes to tissue- and organism-level responses. However, progress in the field that studies these phenomena, mechanobiology, has been limited by lack of appropriate experimental techniques for applying repeatable mechanical stimuli to intact organs and model organisms. Microfluidic platforms, a subgroup of microsystems that use liquid flow for manipulation of objects, are a promising tool for studying mechanobiology of small model organisms due to their size scale and ease of customization. In this work, we describe design considerations involved in developing a microfluidic device for studying mechanobiology. Then, focusing on worms, fruit flies, and zebrafish, we review current microfluidic platforms for mechanobiology of multicellular model organisms and their tissues and highlight research opportunities in this developing field.

Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments

In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.

Single-molecule techniques in biophysics: a review of the progress in methods and applications

Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k _B T, where k _B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.

Dynamic clustering of dynamin-amphiphysin helices regulates membrane constriction and fission coupled with GTP hydrolysis

Dynamin is a mechanochemical GTPase essential for membrane fission during clathrin-mediated endocytosis. Dynamin forms helical complexes at the neck of clathrin-coated pits and their structural changes coupled with GTP hydrolysis drive membrane fission. Dynamin and its binding protein amphiphysin cooperatively regulate membrane remodeling during the fission, but its precise mechanism remains elusive. In this study, we analyzed structural changes of dynamin-amphiphysin complexes during the membrane fission using electron microscopy (EM) and high-speed atomic force microscopy (HS-AFM). Interestingly, HS-AFM analyses show that the dynamin-amphiphysin helices are rearranged to form clusters upon GTP hydrolysis and membrane constriction occurs at protein-uncoated regions flanking the clusters. We also show a novel function of amphiphysin in size control of the clusters to enhance biogenesis of endocytic vesicles. Our approaches using combination of EM and HS-AFM clearly demonstrate new mechanistic insights into the dynamics of dynamin-amphiphysin complexes during membrane fission.

The nerve cells that make up a nervous system connect at junctions known as synapses. When a nerve impulse reaches the end of the cell, membrane-bound packages called vesicles fuse with the surface membrane and release their contents to the outside. The contents, namely chemicals called neurotransmitters, then travels across the synapse, relaying the signal to the next cell.

Nerve cells can fire many times per second. The membrane from fused vesicles must be retrieved from the surface membrane and recycled to make new vesicles, ready to transmit more signals across the synapse. Many proteins at these sites are involved in folding the fused membrane back into the cell, constricting the opening, and eventually pinching off the new vesicles – a process known as endocytosis. Two proteins named dynamin and amphiphysin cooperate in this process, but their precise mechanism remained elusive. Dynamin is a protein that acts like a motor; it breaks down a molecule called GTP to release energy. Previous studies have seen that dynamin-amphiphysin complexes join end to end to form long helical structures.

Takeda et al. have now looked at how the structure of the helices changes during endocytosis. This revealed that the dynamin-amphiphysin helices rearrange to form clusters when the GTP is broken down. Further analysis showed that the folded membrane becomes constricted at regions that are not coated with the clusters of dynamin-amphiphysin helices. Takeda et al. also discovered that amphiphysin controls the size of the clusters to help make the new vesicles more uniform.

The gene for dynamin is altered in a number of disorders affecting the nervous system and muscles, including epileptic encephalopathy, Charcot-Marie-Tooth disease and congenital myopathy. Moreover, a neurological disorder characterized by muscle stiffness (known as Stiff-person syndrome) occurs when an individual’s immune system mistakenly attacks the amphiphysin protein. As such, these new findings will not only help scientists to better understand the process of endocytosis, but they will also give new insight into a number of human diseases.

Probing Single Virus Binding Sites on Living Mammalian Cells Using AFM

In the last years, atomic force microscopy (AFM)-based approaches have evolved into a powerful multiparametric tool that allows biological samples ranging from single receptors to membranes and tissues to be probed. Force-distance curve-based AFM (FD-based AFM) nowadays enables to image living cells at high resolution and simultaneously localize and characterize specific ligand-receptor binding events. In this chapter, we present how FD-based AFM permits to investigate virus binding to living mammalian cells and quantify the kinetic and thermodynamic parameters that describe the free-energy landscape of the single virus-receptor-mediated binding. Using a model virus, we probed the specific interaction with cells expressing its cognate receptor and measured the affinity of the interaction. Furthermore, we observed that the virus rapidly established specific multivalent interactions and found that each bond formed in sequence strengthens the attachment of the virus to the cell.

High-Resolution and High-Speed Atomic Force Microscope Imaging

The advent of high-speed atomic force microscopy (HS-AFM) over the recent years has opened up new horizons for the study of structure, function and dynamics of biological molecules. HS-AFM is capable of 1000 times faster imaging than conventional AFM. This circumstance uniquely enables the observation of the dynamics of all the molecules present in the imaging area. Over the last 10 years, the HS-AFM has gone from a prototype-state technology that only a few labs in the world had access to (including ours) to an established commercialized technology that is present in tens of labs around the world. In this protocol chapter we share with the readers our practical know-how on high resolution HS-AFM imaging.