Single-molecule recognition force spectroscopy of transmembrane transporters on living cells

High-Yield Characterization of Single Molecule Interactions with DeepTipTM Atomic Force Microscopy Probes

Single molecule interactions between biotin and streptavidin were characterized with functionalized DeepTip^TM probes and used as a model system to develop a comprehensive methodology for the high-yield identification and analysis of single molecular events. The procedure comprises the covalent binding of the target molecule to a surface and of the sensing molecule to the DeepTip^TM probe, so that the interaction between both chemical species can be characterized by obtaining force-displacement curves in an atomic force microscope. It is shown that molecular resolution is consistently attained with a percentage of successful events higher than 90% of the total number of recorded curves, and a very low level of unspecific interactions. The combination of both features is a clear indication of the robustness and versatility of the proposed methodology.

Single-Molecule Force Probing of RGD-Binding Integrins on Pancreatic Cancer Cells

Integrin-targeting arginine-glycine-aspartic acid (RGD)-based nanocarriers have been widely used for tumor imaging, monitoring of tumor development, and delivery of anticancer drugs. However, the thermodynamics of an RGD-integrin formation and dissociation associated with binding dynamics, affinity, and stability remains unclear. Here, we probed the binding strength of the binary complex to live pancreatic cancer cells using single-molecule binding force spectroscopy methods, in which RGD peptides were functionalized on a force probe tip through poly(ethylene glycol) (PEG)-based bifunctional linker molecules. While the density of integrin α_V receptors on the cell surface varies more than twofold from cell line to cell line, the individual RGD-integrin complexes exhibited a cell type-independent, monovalent bond strength. The load-dependent bond strength of multivalent RGD-integrin interactions scaled sublinearly with increasing bond number, consistent with the noncooperative, parallel bond model. Furthermore, the multivalent bonds ruptured sequentially either by one or in multiples, and the force strength was comparable to the synchronous rupture force. Comparison of energy landscapes of the bond number revealed a substantial decrease of kinetic off-rates for multivalent bonds, along with the increased width of the potential well and the increased potential barrier height between bound and unbound states, enhancing the stability of the multivalent bonds between them.

Dynamic cellular biomechanics in responses to chemotherapeutic drug in hypoxia probed by atomic force spectroscopy

The changes in cellular structure play an important role in cancer cell development, progression, and metastasis. By exploiting single-cell, force spectroscopy methods, we probed biophysical and biomechanical kinetics (stiffness, morphology, roughness, adhesion) of brain, breast, prostate, and pancreatic cancer cells with standard chemotherapeutic drugs in normoxia and hypoxia over 12–24 hours. After exposure to the drugs, we found that brain, breast, and pancreatic cancer cells became approximately 55–75% less stiff, while prostate cancer cells became more stiff, due to either drug-induced disruption or reinforcement of cytoskeletal structure. However, the rate of the stiffness change decreased up to 2-folds in hypoxia, suggesting a correlation between cellular stiffness and drug resistance of cancer cells in hypoxic tumor microenvironment. Also, we observed significant changes in the cell body height, surface roughness, and cytoadhesion of cancer cells after exposure to drugs, which followed the trend of stiffness. Our results show that a degree of chemotherapeutic drug effects on biomechanical and biophysical properties of cancer cells is distinguishable in normoxia and hypoxia, which are correlated with alteration of cytoskeletal structure and integrity during drug-induced apoptotic process.

Peak force tapping atomic force microscopy for advancing cell and molecular biology

The advent of atomic force microscopy (AFM) provides an exciting tool to detect molecular and cellular behaviors under aqueous conditions. AFM is able to not only visualize the surface topography of the specimens, but also can quantify the mechanical properties of the specimens by force spectroscopy assay. Nevertheless, integrating AFM topographic imaging with force spectroscopy assay has long been limited due to the low spatiotemporal resolution. In recent years, the appearance of a new AFM imaging mode called peak force tapping (PFT) has shattered this limit. PFT allows AFM to simultaneously acquire the topography and mechanical properties of biological samples with unprecedented spatiotemporal resolution. The practical applications of PFT in the field of life sciences in the past decade have demonstrated the excellent capabilities of PFT in characterizing the fine structures and mechanics of living biological systems in their native states, offering novel possibilities to reveal the underlying mechanisms guiding physiological/pathological activities. In this paper, the recent progress in cell and molecular biology that has been made with the utilization of PFT is summarized, and future perspectives for further progression and biomedical applications of PFT are provided.

Atomic force microscopy for revealing micro/nanoscale mechanics in tumor metastasis: from single cells to microenvironmental cues

Mechanics are intrinsic properties which appears throughout the formation, development, and aging processes of biological systems. Mechanics have been shown to play important roles in regulating the development and metastasis of tumors, and understanding tumor mechanics has emerged as a promising way to reveal the underlying mechanisms guiding tumor behaviors. In particular, tumors are highly complex diseases associated with multifaceted factors, including alterations in cancerous cells, tissues, and organs as well as microenvironmental cues, indicating that investigating tumor mechanics on multiple levels is significantly helpful for comprehensively understanding the effects of mechanics on tumor progression. Recently, diverse techniques have been developed for probing the mechanics of tumors, among which atomic force microscopy (AFM) has appeared as an excellent platform enabling simultaneously characterizing the structures and mechanical properties of living biological systems ranging from individual molecules and cells to tissue samples with unprecedented spatiotemporal resolution, offering novel possibilities for understanding tumor physics and contributing much to the studies of cancer. In this review, we survey the recent progress that has been achieved with the use of AFM for revealing micro/nanoscale mechanics in tumor development and metastasis. Challenges and future progress are also discussed.

Stiffness Tomography of Ultra-Soft Nanogels by Atomic Force Microscopy

The softness of nanohydrogels results in unique properties and recently attracted tremendous interest due to the multi-functionalization of interfaces. Herein, we study extremely soft temperature-sensitive ultra-low cross-linked (ULC) nanogels adsorbed to the solid/water interface by atomic force microscopy (AFM). The ultra-soft nanogels seem to disappear in classical imaging modes since a sharp tip fully penetrates these porous networks with very low forces in the range of steric interactions (ca. 100 pN). However, the detailed evaluation of Force Volume mode measurements allows us to resolve their overall shape and at the same time their internal structure in all three dimensions. The nanogels exhibit an extraordinary disk-like and entirely homogeneous but extremely soft structure-even softer than polymer brushes. Moreover, the temperature-sensitive nanogels can be switched on demand between the ultra-soft and a very stiff state.

Allosteric Modulation of Neurotransmitter Transporters as a Therapeutic Strategy

Neurotransmitter transporters (NTTs) are involved in the fine-tuning of brain neurotransmitter homeostasis. As such, they are implicated in a plethora of complex behaviors, including reward, movement, and cognition. During recent decades, compounds that modulate NTT functions have been developed. Some of them are in clinical use for the management of different neuropsychiatric conditions. The majority of these compounds have been found to selectively interact with the orthosteric site of NTTs. Recently, diverse allosteric sites have been described in a number of NTTs, modulating their function. A more complex NTT pharmacology may be useful in the development of novel therapeutics. Here, we summarize current knowledge on such modulatory allosteric sites, with specific focus on their pharmacological and therapeutic potential.

Investigation of Bacterial Curli Production and Adhesion Using AFM

Escherichia coli cells containing the amyloid curli protein CsgA bind to abiotic surfaces and the extracellular matrix protein fibronectin. Here we describe procedures for following bacterial attachment to glass surfaces and provide protocols for coupling bacterial cells to AFM tips. Using single microbial cell force spectroscopy in physiological environment, we show methods to probe mechanical parameters and the dissociation of curliated E. coli cells from fibronectin surfaces by quantifying Young's modulus, unbinding forces, and de-adhesion works.

Cell Topography and Its Quantitative Imaging by AFM

As a high-resolution imaging technique, AFM has been found to be a novel tool for cell topography and its quantitative imaging. This chapter is focused on the introduction of AFM cell topography and its quantitative imaging, which includes the basic principle of AFM imaging, basic operation modes of AFM imaging, AFM imaging of biological sample, critical tips for AFM cell topography and its quantitative imaging, applications of AFM cell topography and its quantitative imaging, and perspective. We believe that this work will help to promote the technological and methodological developments of AFM cell topography and its quantitative imaging, promoting further application of AFM in cell biology, immunology, and medicine.

Sensing the Ultrastructure of Bacterial Surfaces and Their Molecular Binding Forces Using AFM

In this protocol, we provide a detailed step-by-step bacterial surface imaging and molecular analysis procedure. With SPM (scanning probe microscopy)-based dynamic force microscopy (DFM) imaging, we achieved a so far unprecedented resolution of ~1 nm on the outer surface layer of Tannerella forsythia and monitored the production of curli fibers on Escherichia coli in physiological conditions. Moreover, using these immobilization methods, single-molecule force spectroscopy experiments were conducted on living bacterial cells.

Probing the Internal Heterogeneity of Responsive Microgels Adsorbed to an Interface by a Sharp SFM Tip: Comparing Core-Shell and Hollow Microgels

Microgels composed of thermoresponsive polymer poly( N-isopropylacrylamide) (PNIPAM) are interfacial active. Their adsorption leads to deformation, causing conformational changes that have profound effects on the macroscopic properties of these films. Yet, methods to quantitatively probe the local density are lacking. We introduced scanning force microscopy (SFM) to quantitatively probe the internal structure of microgels physically adsorbed on a solid (SiO₂)/water interface. Using a sharp SFM tip, we investigated the two types of microgels: (i) core-shell microgels featuring a hard silica core and a PNIPAM shell and (ii) hollow microgels obtained by dissolution of the silica core. Thus, both systems have the same polymer network as the peripheral structure but a distinctly different internal structure, that is, a rigid core versus a void. By evaluating the force-distance curves, the force profile during insertion of the tip into the polymer network enables to determine a depth-dependent contact resistance, which closely correlates with the density profiles determined in solution by small-angle neutron scattering. We found that the cavity of the swollen hollow microgels is still present when adsorbed to the solid substrate. Remarkably, while currently used techniques such as colloidal probe or reflectometry only provide an average of the z-profile, the methodology introduced herein actually probes the real three-dimensional density profile, which is ultimately important to understand the macroscopic behavior of microgel films. This will bridge the gap between the colloidal probe experiments that deform the microgel globally and the insertion in which the disturbance is located near the tip.

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.

Mechanical determination of particle–cell interactions and the associated biomedical applications

Mechanical determination of particle–cell interactions and the associated biomedical applications.

Nanoscale imaging and force probing of biomolecular systems using atomic force microscopy: from single molecules to living cells

Due to the lack of adequate tools for observation, native molecular behaviors at the nanoscale have been poorly understood. The advent of atomic force microscopy (AFM) provides an exciting instrument for investigating physiological processes on individual living cells with molecular resolution, which attracts the attention of worldwide researchers. In the past few decades, AFM has been widely utilized to investigate molecular activities on diverse biological interfaces, and the performances and functions of AFM have also been continuously improved, greatly improving our understanding of the behaviors of single molecules in action and demonstrating the important role of AFM in addressing biological issues with unprecedented spatiotemporal resolution. In this article, we review the related techniques and recent progress about applying AFM to characterize biomolecular systems in situ from single molecules to living cells. The challenges and future directions are also discussed.

Combining confocal and atomic force microscopy to quantify single-virus binding to mammalian cell surfaces

Over the past five years, atomic force microscopy (AFM)-based approaches have evolved into a powerful multiparametric tool set capable of imaging the surfaces of biological samples ranging from single receptors to membranes and tissues. One of these approaches, force-distance curve-based AFM (FD-based AFM), uses a probing tip functionalized with a ligand to image living cells at high-resolution and simultaneously localize and characterize specific ligand-receptor binding events. Analyzing data from FD-based AFM experiments using appropriate probabilistic models allows quantification of the kinetic and thermodynamic parameters that describe the free-energy landscape of the ligand-receptor bond. We have recently developed an FD-based AFM approach to quantify the binding events of single enveloped viruses to surface receptors of living animal cells while simultaneously observing them by fluorescence microscopy. This approach has provided insights into the early stages of the interaction between a virus and a cell. Applied to a model virus, we probed the specific interaction with cells expressing viral cognate receptors 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 strengthened the attachment of the virus to the cell. Here we describe detailed procedures for probing the specific interactions of viruses with living cells; these procedures cover tip preparation, cell sample preparation, step-by-step FD-based AFM imaging and data analysis. Experienced microscopists should be able to master the entire set of protocols in 1 month.

High-Resolution Imaging and Multiparametric Characterization of Native Membranes by Combining Confocal Microscopy and an Atomic Force Microscopy-Based Toolbox

To understand how membrane proteins function requires characterizing their structure, assembly, and inter- and intramolecular interactions in physiologically relevant conditions. Conventionally, such multiparametric insight is revealed by applying different biophysical methods. Here we introduce the combination of confocal microscopy, force-distance curve-based (FD-based) atomic force microscopy (AFM), and single-molecule force spectroscopy (SMFS) for the identification of native membranes and the subsequent multiparametric analysis of their membrane proteins. As a well-studied model system, we use native purple membrane from Halobacterium salinarum, whose membrane protein bacteriorhodopsin was His-tagged to bind nitrilotriacetate (NTA) ligands. First, by confocal microscopy we localize the extracellular and cytoplasmic surfaces of purple membrane. Then, we apply AFM to image single bacteriorhodopsins approaching sub-nanometer resolution. Afterwards, the binding of NTA ligands to bacteriorhodopsins is localized and quantified by FD-based AFM. Finally, we apply AFM-based SMFS to characterize the (un)folding of the membrane protein and to structurally map inter- and intramolecular interactions. The multimethodological approach is generally applicable to characterize biological membranes and membrane proteins at physiologically relevant conditions.

Single molecule force spectroscopy for in-situ probing oridonin inhibited ROS-mediated EGF-EGFR interactions in living KYSE-150 cells

As the active anticancer component of Rabdosia Rubescens, oridonin has been proved to show strong anticancer activity in cancer cells, which is also found to be closely related to its specific inhibition effects on the EGFR tyrosine kinase activity. In this study, atomic force microscopy based single molecule force spectroscopy (AFM-SMFS) was used for real-time and in-situ detection of EGF-EGFR interactions in living esophageal cancer KYSE-150 cells to evaluate the anticancer activity of oridonin for the first time. Oridonin was found to induce apoptosis and also reduce EGFR expression in KYSE-150 cells. AFM-SMFS results demonstrated that oridonin could inhibit the binding between EGF and EGFR in KYSE-150 cells by decreasing the unbinding force and binding probability for EGF-EGFR complexes, which was further proved to be closely associated with the intracellular ROS level. More precise mechanism studies based on AFM-SMFS demonstrated that oridonin treatment could decrease the energy barrier width, increase the dissociation off rate constant and decrease the activation energy of EGF-EGFR complexes in ROS dependent way, suggesting oridonin as a strong anticancer agent targeting EGF-EGFR interactions in cancer cells through ROS dependent mechanism. Our results not only suggested oridonin as a strong anticancer agent targeting EGF-EGFR interactions in ROS dependent mechanism, but also highlighted AFM-SMFS as a powerful technique for pharmacodynamic studies by detecting ligand-receptor interactions, which was also expected to be developed into a promising tool for the screening and mechanism studies of drugs.

Lipid-dependent conformational dynamics underlie the functional versatility of T-cell receptor

T-cell receptor-CD3 complex (TCR) is a versatile signaling machine that can initiate antigen-specific immune responses based on various biochemical changes of CD3 cytoplasmic domains, but the underlying structural basis remains elusive. Here we developed biophysical approaches to study the conformational dynamics of CD3ε cytoplasmic domain (CD3ε_CD). At the single-molecule level, we found that CD3ε_CD could have multiple conformational states with different openness of three functional motifs, i.e., ITAM, BRS and PRS. These conformations were generated because different regions of CD3ε_CD had heterogeneous lipid-binding properties and therefore had heterogeneous dynamics. Live-cell imaging experiments demonstrated that different antigen stimulations could stabilize CD3ε_CD at different conformations. Lipid-dependent conformational dynamics thus provide structural basis for the versatile signaling property of TCR.

Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy

The advent of atomic force microscopy (AFM) has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface) was summarized. The challenges and future directions were also discussed.

A novel approach for extracting viscoelastic parameters of living cells through combination of inverse finite element simulation and Atomic Force Microscopy

Dynamic mechanical behaviour of living cells has been described by viscoelasticity. However, quantitation of the viscoelastic parameters for living cells is far from sophisticated. In this paper, combining inverse finite element (FE) simulation with Atomic Force Microscope characterization, we attempt to develop a new method to evaluate and acquire trustworthy viscoelastic index of living cells. First, influence of the experiment parameters on stress relaxation process is assessed using FE simulation. As suggested by the simulations, cell height has negligible impact on shape of the force-time curve, i.e. the characteristic relaxation time; and the effect originates from substrate can be totally eliminated when stiff substrate (Young's modulus larger than 3 GPa) is used. Then, so as to develop an effective optimization strategy for the inverse FE simulation, the parameters sensitivity evaluation is performed for Young's modulus, Poisson's ratio, and characteristic relaxation time. With the experiment data obtained through typical stress relaxation measurement, viscoelastic parameters are extracted through the inverse FE simulation by comparing the simulation results and experimental measurements. Finally, reliability of the acquired mechanical parameters is verified with different load experiments performed on the same cell.

Magnetic domain wall tweezers: a new tool for mechanobiology studies on individual target cells

In vitro tests are of fundamental importance for investigating cell mechanisms in response to mechanical stimuli or the impact of the genotype on cell mechanical properties. In particular, the application of controlled forces to activate specific bio-pathways and investigate their effects, mimicking the role of the cellular environment, is becoming a prominent approach in the emerging field of mechanobiology. Here, we present an on-chip device based on magnetic domain wall manipulators, which allows the application of finely controlled and localized forces on target living cells. In particular, we demonstrate the application of a magnetic force in the order of hundreds of pN on the membrane of HeLa cells cultured on-chip, via manipulation of 1 μm superparamagnetic beads. Such a mechanical stimulus produces a sizable local indentation of the cellular membrane of about 2 μm. Upon evaluation of the beads' position within the magnetic field originated by the domain wall, the force applied during the experiments is accurately quantified via micromagnetic simulations. The obtained value is in good agreement with that calculated by the application of an elastic model to the cellular membrane.

The role of transporter ectodomains in drug recognition and binding: phlorizin and the sodium–glucose cotransporter

This article reviews the role of segments of SLCs located outside the plasma membrane bilayer (ectodomains) using the inhibition of SGLTs (SLC5 family) by the aromatic glucoside phlorizin as a model system.

Unraveling the complexity of the interactions of DNA nucleotides with gold by single molecule force spectroscopy

Addressing the effect of different environmental factors on the adsorption of DNA to solid supports is critical for the development of robust miniaturized devices for applications ranging from biosensors to next generation molecular technology. Most of the time, thiol-based chemistry is used to anchor DNA on gold - a substrate commonly used in nanotechnology - and little is known about the direct interaction between DNA and gold. So far there have been no systematic studies on the direct adsorption behavior of the deoxyribonucleotides (i.e., a nitrogenous base, a deoxyribose sugar, and a phosphate group) and on the factors that govern the DNA-gold bond strength. Here, using single molecule force spectroscopy, we investigated the interaction of the four individual nucleotides, adenine, guanine, cytosine, and thymine, with gold. Experiments were performed in three salinity conditions and two surface dwell times to reveal the factors that influence nucleotide-Au bond strength. Force data show that, at physiological ionic strength, adenine-Au interactions are stronger, asymmetrical and independent of surface dwell time as compared to cytosine-Au and guanine-Au interactions. We suggest that in these conditions only adenine is able to chemisorb on gold. A decrease of the ionic strength significantly increases the bond strength for all nucleotides. We show that moderate ionic strength along with longer surface dwell period suggest weak chemisorption also for cytosine and guanine.

Investigating cell mechanics with atomic force microscopy

Transmission of mechanical force is crucial for normal cell development and functioning. However, the process of mechanotransduction cannot be studied in isolation from cell mechanics. Thus, in order to understand how cells 'feel', we must first understand how they deform and recover from physical perturbations. Owing to its versatility, atomic force microscopy (AFM) has become a popular tool to study intrinsic cellular mechanical properties. Used to directly manipulate and examine whole and subcellular reactions, AFM allows for top-down and reconstitutive approaches to mechanical characterization. These studies show that the responses of cells and their components are complex, and largely depend on the magnitude and time scale of loading. In this review, we generally describe the mechanotransductive process through discussion of well-known mechanosensors. We then focus on discussion of recent examples where AFM is used to specifically probe the elastic and inelastic responses of single cells undergoing deformation. We present a brief overview of classical and current models often used to characterize observed cellular phenomena in response to force. Both simple mechanistic models and complex nonlinear models have been used to describe the observed cellular behaviours, however a unifying description of cell mechanics has not yet been resolved.

In situ single molecule imaging of cell membranes: linking basic nanotechniques to cell biology, immunology and medicine

The cell membrane, which consists of a viscous phospholipid bilayer, different kinds of proteins and various nano/micrometer-sized domains, plays a very important role in ensuring the stability of the intracellular environment and the order of cellular signal transductions. Exploring the precise cell membrane structure and detailed functions of the biomolecules in a cell membrane would be helpful to understand the underlying mechanisms involved in cell membrane signal transductions, which could further benefit research into cell biology, immunology and medicine. The detection of membrane biomolecules at the single molecule level can provide some subtle information about the molecular structure and the functions of the cell membrane. In particular, information obtained about the molecular mechanisms and other information at the single molecule level are significantly different from that detected from a large amount of biomolecules at the large-scale through traditional techniques, and can thus provide a novel perspective for the study of cell membrane structures and functions. However, the precise investigations of membrane biomolecules prompts researchers to explore cell membranes at the single molecule level by the use of in situ imaging methods, as the exact conformation and functions of biomolecules are highly controlled by the native cellular environment. Recently, the in situ single molecule imaging of cell membranes has attracted increasing attention from cell biologists and immunologists. The size of biomolecules and their clusters on the cell surface are set at the nanoscale, which makes it mandatory to use high- and super-resolution imaging techniques to realize the in situ single molecule imaging of cell membranes. In the past few decades, some amazing imaging techniques and instruments with super resolution have been widely developed for molecule imaging, which can also be further employed for the in situ single molecule imaging of cell membranes. In this review, we attempt to summarize the characteristics of these advanced techniques for use in the in situ single molecule imaging of cell membranes. We believe that this work will help to promote the technological and methodological developments of super-resolution techniques for the single molecule imaging of cell membranes and help researchers better understand which technique is most suitable for their future exploring of membrane biomolecules; ultimately promoting further developments in cell biology, immunology and medicine.

Nanoscopic polypyrrole AFM-SECM probes enabling force measurements under potential control

Conductive polymers, and in particular polypyrrole, are frequently used as biomimetic interfaces facilitating growth and/or differentiation of cells and tissues. Hence, studying forces and local interactions between such polymer interfaces and cells at the nanoscale is of particular interest. Frequently, such force interactions are not directly accessible with high spatial resolution. Consequently, we have developed nanoscopic polypyrrole electrodes, which are integrated in AFM-SECM probes. Bifunctional AFM-SECM probes were modified via ion beam-induced deposition resulting in pyramidal conductive Pt-C composite electrodes. These nanoscopic electrodes then enabled localized polypyrrole deposition, thus resulting in polymer-modified AFM probes with a well-defined geometry. Furthermore, such probes may be reversibly switched from an insulating to a conductive state. In addition, the hydrophilicity of such polymer tips is dependent on the dopant, and hence, on the oxidation state. Force studies applying different tip potentials were performed at plasma-treated glass surfaces providing localized information on the associated force interactions, which are dependent on the applied potential and the dopant.

Atomic force microscopy: a multifaceted tool to study membrane proteins and their interactions with ligands

Membrane proteins are embedded in lipid bilayers and facilitate the communication between the external environment and the interior of the cell. This communication is often mediated by the binding of ligands to the membrane protein. Understanding the nature of the interaction between a ligand and a membrane protein is required to both understand the mechanism of action of these proteins and for the development of novel pharmacological drugs. The highly hydrophobic nature of membrane proteins and the requirement of a lipid bilayer for native function have hampered the structural and molecular characterizations of these proteins under physiologically relevant conditions. Atomic force microscopy offers a solution to studying membrane proteins and their interactions with ligands under physiologically relevant conditions and can provide novel insights about the nature of these critical molecular interactions that facilitate cellular communication. In this review, we provide an overview of the atomic force microscopy technique and discuss its application in the study of a variety of questions related to the interaction between a membrane protein and a ligand. This article is part of a Special Issue entitled: Structural and biophysical characterization of membrane protein-ligand binding.

Atomic force microscopy analysis of progenitor corneal epithelial cells fractionated by a rapid centrifugation isolation technique

Purpose

To investigate the use of atomic force microscopy (AFM) to image the three groups of corneal epithelial cells fractionated by a novel rapid centrifugation isolation technique.

Methods

Epithelial cells harvested from primary cultures of rabbit limbal rings were centrifuged onto uncoated dishes, first at 1400 rpm and then at 1800 rpm. The adherent cells after centrifugation at 1400 rpm (ATC1), the adherent cells at 1800 rpm (ATC2) and the non-adherent cells at 1800 rpm (NAC) were investigated for BrdU retention and were subjected to contact mode AFM and Transmission Electron Microscopy (TEM).

Results

Compared with unfractionated cells, the ATC1 group, accounting for about 10% of the whole population, was enriched in BrdU label-retaining cells. There were dramatic overall shape, surface membrane and intra-cellular ultrastructure differences noted among ATC1, ATC2 and NAC populations. The whole cell roughness measurements were 21.1±1.5 nm, 79.5±3.4 nm and 103±4.6 nm for the ATC1, ATC2 and NAC groups, respectively. The mero-nucleus roughness measurements were 34.2±1.7 nm, 13.0±0.8 nm and 8.5±0.5 nm in the ATC1, ATC2 and NAC populations, respectively.

Conclusions

AFM was found to be a good tool for distinguishing among the three groups of cells. BrdU label retention, the AFM parameters and TEM together suggest that the ATC1, ATC2 and NAC populations may be progenitor corneal epithelial cells, transit amplifying cells and terminal differentiation cells, respectively.

Mechanistic insights into the stabilization of srcSH3 by PEGylation

Protein PEGylation (attaching PEG chains to proteins) has been widely used in pharmaceuticals and nanotechnology. Although it is widely known that PEGylation can increase the thermodynamic stability of proteins, the underlying mechanism remains elusive. In this Article, we studied the effect of PEGylation on the thermodynamic and kinetic stability of a protein, SH3. We show that the thermodynamic stability of SH3 is enhanced upon PEGylation, mainly due to the slowing of the unfolding rate. Moreover, PEGylation can decrease the solvent-accessible surface area of SH3, leading to an increase of the m-value (the change in free energy with respect to denaturant concentration, which is a measure of the transition cooperativity between corresponding states). Such an effect also causes an enhancement of the thermodynamic stability. We quantitatively measured how the physical properties of PEG, such as the molecular weight and the number of PEGylation sites, affect the stabilization effect. We found that the stabilization effect is largely dependent on the number of PEGylation sites but only has a weak correlation with the molecular weight of the attached PEG. These experimental findings inspire us to derive a physical model based on excluded volume effect, which can satisfactorily describe all experimental observations. This model allows quantitatively calculating the free energy change upon PEGylation based on the change of water excluded zone on the protein surface. Although it is still unknown whether such a mechanism can be extended to other proteins, our work represents a key step toward the understanding of the nature of protein stabilization upon PEGylation.

Sensitivity maximized near-field scanning optical microscope with dithering sample stage

We developed a new scheme for a higher sensitivity near-field scanning optical microscope (NSOM) by using a dithering sample stage rather than a dithering probe for the constant gap control between probe and sample. In a conventional NSOM, which use tip dithering feedback mechanism, the Q factor drastically decreases from 7783 to 1000 (13%) or even to 100 (1%) because harmonic oscillating characteristic is deteriorated owing to the large change of stiffness and mass of one prong of tuning fork when a probe is attached to it. In our proposed scheme, on the other hand, we use sample dithering feedback mechanism, where the probe is not attached to the tuning fork and the sample is loaded directly onto the surface of dithering tuning fork. Thus, the Q factor does not decrease significantly, from only 7783 to 7480 (96%), because the loaded sample hardly changes the stiffness and mass of tuning fork. Accordingly, gap control between the immobile fiber probe and the dithering sample is performed precisely by detecting the shear force with high sensitivity. Consequently, the extremely high Q factor enables clear observation of graphene sheets with sub-nanometer vertical resolution, which is not possible with a conventional NSOM setup.

SLC5 and SLC2 transporters in epithelia-cellular role and molecular mechanisms

Members of the SLC5 and SLC2 family are prominently involved in epithelial sugar transport. SGLT1 (sodium-glucose transporter) and SGLT2, as representatives of the former, mediate sodium-dependent uptake of sugars into intestinal and renal cells. GLUT2 (glucose transporter), as representative of the latter, facilitates the sodium-independent exit of sugars from cells. SGLT has played a major role in the formulation and experimental proof for the existence of sodium cotransport systems. Based on the sequence data and biochemical and biophysical analyses, the role of extramembranous loops in sugar and inhibitor binding can be delineated. Crystal structures and homology modeling of SGLT reveal that the sugar translocation involves operation of two hydrophobic gates and intermediate exofacial and endofacial occluded states of the carrier in an alternating access model. The same basic model is proposed for GLUT1. Studies on GLUT1 have pioneered the isolation of eukaryotic transporters by biochemical methods and the development of transport kinetics and transporter models. For GLUT1, results from extensive mutagenesis, cysteine substitution and accessibility studies can be incorporated into a homology model with a barrel-like structure in which accessibility to the extracellular and intracellular medium is altered by pinching movements of some of the helices. For SGLT1 and GLUT1, the extensive hydrophilic and hydrophobic interactions between sugars and binding sites of the various intramembrane helices occur and lead to different substrate specificities and inhibitor affinities of the two transporters. A complex network of regulatory steps adapts the transport activity to the needs of the body.