High-speed force spectroscopy: microsecond force measurements using ultrashort cantilevers

Recent advances in the application of atomic force microscopy to structural biology

The application of atomic force microscopy (AFM) for (functional) imaging and manipulating biomolecules at all levels of organization has enabled great progress in the structural biology field over the last decades, contributing to the discovery of novel structural entities of biological significance across many disciplines ranging from biochemistry, biomedicine and biophysics to molecular and cell biology, up to food systems and beyond. AFM has the capability to generate high-resolution topographic images spanning from the submolecular to the (sub)cellular range and can probe biochemical and biophysical sample properties in close to native conditions with excellent temporal resolution. Instrumental developments in the past decade enable dynamical structural and conformational studies of single biomolecules and new techniques for structural and chemical modification of the AFM probe have converted the cantilever into a versatile tool to study different biological phenomena, such as the mechanical stability of biomolecular complexes or the force induced dynamic changes of mechanically stressed proteins at the nanoscopic level. To improve the functionality of AFM and approach dynamic processes of complex biological systems ex vivo, AFM is combined with complementary microscopy, nanoscopy and spectroscopy tools. These multimethodological approaches provide unprecedented possibilities of probing physical, chemical and biological properties of complex cellular systems with high spatio-temporal resolution, leading to novel applications that correlate structural results with functional biochemical, biophysical, immunological, or genetic data on the system under study.

Recent advances in sensing the inter-biomolecular interactions at the nanoscale - A comprehensive review of AFM-based force spectroscopy

Biomolecular interactions underpin most processes inside the cell. Hence, a precise and quantitative understanding of molecular association and dissociation events is crucial, not only from a fundamental perspective, but also for the rational design of biomolecular platforms for state-of-the-art biomedical and industrial applications. In this context, atomic force microscopy (AFM) appears as an invaluable experimental technique, allowing the measurement of the mechanical strength of biomolecular complexes to provide a quantitative characterization of their interaction properties from a single molecule perspective. In the present review, the most recent methodological advances in this field are presented with special focus on bioconjugation, immobilization and AFM tip functionalization, dynamic force spectroscopy measurements, molecular recognition imaging and theoretical modeling. We expect this work to significantly aid in grasping the principles of AFM-based force spectroscopy (AFM-FS) technique and provide the necessary tools to acquaint the type of data that can be achieved from this type of experiments. Furthermore, a critical assessment is done with other nanotechnology techniques to better visualize the future prospects of AFM-FS.

Novel perspective for protein-drug interaction analysis: atomic force microscope

Proteins are major drug targets, and drug-target interaction identification and analysis are important factors for drug discovery. Atomic force microscopy (AFM) is a powerful tool making it possible to image proteins with nanometric resolution and probe intermolecular forces under physiological conditions. We review recent studies conducted in the field of target protein drug discovery using AFM-based analysis technology, including drug-driven changes in nanomechanical properties of protein morphology and interactions. Underlying mechanisms (including thermodynamic and kinetic parameters) of the drug-target interaction and drug-modulating protein-protein interaction (PPI) on the surfaces of models or living cells are discussed. Furthermore, challenges and the outlook for the field are likewise discussed. Overall, this insight into the mechanical properties of protein-drug interactions provides an unprecedented information framework for rational drug discovery in the pharmaceutical field.

Interfacial Layer Breaker: A Violation of Stokes' Law in High-Speed Atomic Force Microscope Flows

Structured water near surfaces is important in nonclassical crystallization, biomineralization, and restructuring of cellular membranes. In addition to equilibrium structures, studied by atomic force microscopy (AFM), high-speed AFM (H-S AFM) can now detect piconewton forces in microseconds. With increasing speeds and decreasing tip diameters, there is a danger that continuum water models will not hold, and molecular dynamic (MD) simulations would be needed for accurate predictions. MD simulations, however, can only evolve over tens of nanoseconds due to memory and computational efficiency/speed limitations, so new methods are needed to bridge the gap. Here, we report a hybrid, multiscale simulation method, which can bridge the size and time scale gaps to existing experiments. Structured water is studied between a moving silica AFM colloidal tip and a cleaved mica surface. The computational domain includes 1,472,766 atoms. To mimic the effect of long-range hydrodynamic forces occurring in water, when moving the AFM tip at speeds from 5 × 10^-7 to 30 m/s, a hybrid multiscale method with local atomistic resolution is used, which serves as an effective open-domain boundary condition. The multiscale simulation is thus equivalent to using a macroscopically large computational domain with equilibrium boundary conditions. Quantification of the drag force shows the breaking of continuum behavior. Nonmonotonic dependence on both the tip speed and distance from the surface implies breaking of the hydration layer around the moving tip at time scales smaller than water cluster formation and strong water compressibility effects at the highest speeds.

Visualizing Intramolecular Dynamics of Membrane Proteins

Membrane proteins play important roles in biological functions, with accompanying allosteric structure changes. Understanding intramolecular dynamics helps elucidate catalytic mechanisms and develop new drugs. In contrast to the various technologies for structural analysis, methods for analyzing intramolecular dynamics are limited. Single-molecule measurements using optical microscopy have been widely used for kinetic analysis. Recently, improvements in detectors and image analysis technology have made it possible to use single-molecule determination methods using X-rays and electron beams, such as diffracted X-ray tracking (DXT), X-ray free electron laser (XFEL) imaging, and cryo-electron microscopy (cryo-EM). High-speed atomic force microscopy (HS-AFM) is a scanning probe microscope that can capture the structural dynamics of biomolecules in real time at the single-molecule level. Time-resolved techniques also facilitate an understanding of real-time intramolecular processes during chemical reactions. In this review, recent advances in membrane protein dynamics visualization techniques were presented.

The biophysics of bacterial infections: Adhesion events in the light of force spectroscopy

Bacterial infections are the most eminent public health challenge of the 21st century. The primary step leading to infection is bacterial adhesion to the surface of host cells or medical devices, which is mediated by a multitude of molecular interactions. At the interface of life sciences and physics, last years advances in atomic force microscopy (AFM)-based force spectroscopy techniques have made possible to measure the forces driving bacteria-cell and bacteria-materials interactions on a single molecule/cell basis (single molecule/cell force spectroscopy). Among the bacteria-(bio)materials surface interactions, the life-threatening infections associated to medical devices involving Staphylococcus aureus and Escherichia coli are the most eminent. On the other hand, Pseudomonas aeruginosa binding to the pulmonary and urinary tract or the Helicobacter pylori binding to the gastric mucosa, are classical examples of bacteria-host cell interactions that end in serious infections. As we approach the end of the antibiotic era, acquisition of a deeper knowledge of the fundamental forces involved in bacteria - host cells/(bio)materials surface adhesion is crucial for the identification of new ligand-binding events and its assessment as novel targets for alternative anti-infective therapies. This article aims to highlight the potential of AFM-based force spectroscopy for new targeted therapies development against bacterial infections in which adhesion plays a pivotal role and does not aim to be an extensive overview on the AFM technical capabilities and theory of single molecule force spectroscopy.

Biophysical reviews top five: atomic force microscopy in biophysics

Since its invention in the late 1980s, atomic force microscopy (AFM), in which a nanometer-sized tip is used to physically interrogate the properties of a surface at high resolution, has brought about scientific revolutions in both surface science and biological physics. In response to a request from the journal, I have prepared a top-five list of scientific papers that I feel represent truly landmark developments in the use of AFM in the biophysics field. This selection is necessarily limited by number (just five) and subjective (my opinion) and I offer my apologies to those not appearing in this list.

Determination of calibration parameters of cantilevers of arbitrary shape by finite element analysis

The use of atomic force microscopy in nanomechanical measurements requires accurate calibration of the cantilever's spring constant (k_c) and the optical lever sensitivity (OLS). The thermal method, based on the cantilever's thermal fluctuations in fluids, allows estimation of k_c in a fast, non-invasive mode. However, differences in the cantilever geometry and mounting angle require the knowledge of three correction factors to get a good estimation of k_c: the contribution of the oscillation mode to the total amplitude, the shape difference between the free and end-loaded configurations, and the tilt of the cantilever with respect to the measured surface. While the correction factors for traditional rectangular and V-shaped cantilever geometries have been reported, they must be determined for cantilevers with non-traditional geometries and large tips. Here, we develop a method based on finite element analysis to estimate the correction factors of cantilevers with arbitrary geometry and tip dimensions. The method relies on the numerical computation of the effective cantilever mass. The use of the correction factor for rectangular geometries in our model cantilever (PFQNM-LC) will lead to values underestimated by 16%. In contrast, experiments using pre-calibrated cantilevers revealed a maximum uncertainty below 5% in the estimation of the OLS, verifying our approach.

Multiswitchable photoacid-hydroxyflavylium-polyelectrolyte nano-assemblies

Light- and pH-responsive nano-assemblies with switchable size and structure are formed by the association of a photoacid, anthocyanidin, and a linear polyelectrolyte in aqueous solution. Specifically, anionic disulfonated naphthol derivatives, neutral hydroxyflavylium, and cationic poly(allylamine) are used as building blocks for the ternary electrostatic self-assembly, forming well-defined supramolecular assemblies with tunable sizes of 50 to 500 nm. Due to the network of possible chemical reactions for the anthocyanidin and the excited-state dissociation of the photoacid upon irradiation, different ways to alter the ternary system through external triggering are accessible. The structure and trigger effects can be controlled through the component ratios of the samples. Dynamic and static light scattering (DLS, SLS) and ζ-potential measurements were applied to study the size and the stability of the particles, and information on the molecular structure was gained by UV-vis spectroscopy. Isothermal titration calorimetry (ITC) provided information on the thermodynamics and interaction forces in the supramolecular assembly formation.

Biological physics by high-speed atomic force microscopy

While many fields have contributed to biological physics, nanotechnology offers a new scale of observation. High-speed atomic force microscopy (HS-AFM) provides nanometre structural information and dynamics with subsecond resolution of biological systems. Moreover, HS-AFM allows us to measure piconewton forces within microseconds giving access to unexplored, fast biophysical processes. Thus, HS-AFM provides a tool to nourish biological physics through the observation of emergent physical phenomena in biological systems. In this review, we present an overview of the contribution of HS-AFM, both in imaging and force spectroscopy modes, to the field of biological physics. We focus on examples in which HS-AFM observations on membrane remodelling, molecular motors or the unfolding of proteins have stimulated the development of novel theories or the emergence of new concepts. We finally provide expected applications and developments of HS-AFM that we believe will continue contributing to our understanding of nature, by serving to the dialogue between biology and physics. This article is part of a discussion meeting issue 'Dynamic in situ microscopy relating structure and function'.

Unfolding mechanism and free energy landscape of single, stable, alpha helices at low pull speeds

Single alpha helices (SAHs) stable in isolated form are often found in motor proteins where they bridge functional domains. Understanding the mechanical response of SAHs is thus critical to understand their function. The quasi-static force-extension relation of a small number of SAHs is known from single-molecule experiments. Unknown, or still controversial, are the molecular scale details behind those observations. We show that the deformation mechanism of SAHs pulled from the termini at pull speeds approaching the quasi-static limit differs from that of typical helices found in proteins, which are stable only when interacting with other protein domains. Using molecular dynamics simulations with atomistic resolution at low pull speeds previously inaccessible to simulation, we show that SAHs start unfolding from the termini at all pull speeds we investigated. Unfolding proceeds residue-by-residue and hydrogen bond breaking is not the main event determining the barrier to unfolding. We use the molecular simulation data to test the cooperative sticky chain model. This model yields excellent fits of the force-extension curves and quantifies the distance, xE = 0.13 nm, to the transition state, the natural frequency of bond vibration, ν0 = 0.82 ns-1, and the height, V0 = 2.9 kcal mol-1, of the free energy barrier associated with the deformation of single residues. Our results demonstrate that the sticky chain model could advantageously be used to analyze experimental force-extension curves of SAHs and other biopolymers.

Combining Experimental Data and Computational Methods for the Non-Computer Specialist

Experimental methods are indispensable for the study of the function of biological macromolecules, not just as static structures, but as dynamic systems that change conformation, bind partners, perform reactions, and respond to different stimulus. However, providing a detailed structural interpretation of the results is often a very challenging task. While experimental and computational methods are often considered as two different and separate approaches, the power and utility of combining both is undeniable. The integration of the experimental data with computational techniques can assist and enrich the interpretation, providing new detailed molecular understanding of the systems. Here, we briefly describe the basic principles of how experimental data can be combined with computational methods to obtain insights into the molecular mechanism and expand the interpretation through the generation of detailed models.

Rate-dependent force-extension models for single-molecule force spectroscopy experiments

Single-molecule force spectroscopy techniques allow for the measurement of several static and dynamic features of macromolecules of biological origin. In particular, atomic force microscopy, used with a variable pulling rate, provides valuable information on the folding/unfolding dynamics of proteins. We propose here two different models able to describe the out-of-equilibrium statistical mechanics of a chain composed of bistable units. These latter represent the protein domains, which can be either folded or unfolded. Both models are based on the Langevin approach and their implementation allows for investigating the effect of the pulling rate and of the device intrinsic elasticity on the chain unfolding response. The theoretical results (both analytical and numerical) have been compared with experimental data concerning the unfolding of the titin and filamin proteins, eventually obtaining a good agreement over a large range of the pulling rates.

Review: Cantilever-Based Sensors for High Speed Atomic Force Microscopy

This review critically summarizes the recent advances of the microcantilever-based force sensors for atomic force microscope (AFM) applications. They are one the most common mechanical spring-mass systems and are extremely sensitive to changes in the resonant frequency, thus finding numerous applications especially for molecular sensing. Specifically, we comment on the latest progress in research on the deflection detection systems, fabrication, coating and functionalization of the microcantilevers and their application as bio- and chemical sensors. A trend on the recent breakthroughs on the study of biological samples using high-speed atomic force microscope is also reported in this review.

Evaluation of intermolecular forces between lipopolysaccharides and monoclonal antibodies using atomic force microscopy

Understanding of interactions between a bacterium and an immune or non-immune host organism at the cellular and subcellular level is important in order to improve new and existing immunobiological tools for the treatment of bacterial infections (including pseudotuberculosis). The aim of this work was to quantify the interaction force between Yersinia pseudotuberculosis and monoclonal antibodies (mAbs) in the model system "lipopolysaccharide (LPS) - mAbs" by atomic force microscopy (AFM). Our research findings provided the methodical approaches to force measurements between an AFM probe, which was functionalized with Y. pseudotuberculosis LPS, and mica coated by different mAbs. Based on the criteria for force estimation there was shown a greater binding force in the system "LPS - complementary mAbs" than in the system "LPS - heterologous mAbs". In both cases binding force increase followed by increase a contact time between the functionalized AFM probe and mica from 1 to 5 s. It has been shown that single bonds between LPS and complementary mAbs molecules also included a clearly defined non-specific component along with immunochemically specific one. The evidence suggests a significant proportion of applied force exerted to unfolding of high-molecular aggregates whose length may attain many hundreds of nanometers.

Photocatalytic Nanofabrication and Intracellular Raman Imaging of Living Cells with Functionalized AFM Probes

Atomic force microscopy (AFM) is an effective platform for in vitro manipulation and analysis of living cells in medical and biological sciences. To introduce additional new features and functionalities into a conventional AFM system, we investigated the photocatalytic nanofabrication and intracellular Raman imaging of living cells by employing functionalized AFM probes. Herein, we investigated the effect of indentation speed on the cell membrane perforation of living HeLa cells based on highly localized photochemical oxidation with a catalytic titanium dioxide (TiO2)-functionalized AFM probe. On the basis of force-distance curves obtained during the indentation process, the probability of cell membrane perforation, penetration force, and cell viability was determined quantitatively. Moreover, we explored the possibility of intracellular tip-enhanced Raman spectroscopy (TERS) imaging of molecular dynamics in living cells via an AFM probe functionalized with silver nanoparticles in a homemade Raman system integrated with an inverted microscope. We successfully demonstrated that the intracellular TERS imaging has the potential to visualize distinctly different features in Raman spectra between the nucleus and the cytoplasm of a single living cell and to analyze the dynamic behavior of biomolecules inside a living cell.