Visualization of single proteins from stripped native cell membranes: A protocol for high‐resolution atomic force microscopy

Atomic force microscopy (AFM) proved to be able to obtain high‐resolution three‐dimensional images of single‐membrane proteins, isolated, crystallized, or included in reconstructed model membranes. The extension of this technique to native systems, such as the protein immersed in a cell membrane, needs a careful manipulation of the biological sample to meet the experimental constraints for high‐resolution AFM imaging. In this article, a general protocol for sample preparation is presented, based on the mechanical stretch of the cell membrane. The effectiveness for AFM imaging has been tested on the basis of an integrated optical and AFM approach and the proposed method has been applied to cells expressing cystic fibrosis transmembrane conductance regulator, a channel involved in cystic fibrosis, showing the possibility to identify and analyze single proteins in the plasma membrane. Microsc. Res. Tech. 76:723–732, 2013. © 2013 Wiley Periodicals, Inc.     

Kinetics of interaction of HIV fusion protein (gp41) with lipid membranes studied by real-time AFM imaging

One of the most important steps in the process of viral infection is a fusion between cell membrane and virus, which is mediated by the viral envelope glycoprotein. The study of activity of the glycoprotein in the post-fusion state is important for understanding the progression of infection. Here we present a first real-time kinetic study of the activity of gp41 (the viral envelope glycoprotein of human immunodeficiency virus—HIV) and its two mutants in the post-fusion state with nanometer resolution by atomic force microscopy (AFM). Tracking the changes in the phosphatidylcholine (PC) and phosphatidylcholine–phosphatidylserine (PC:PS) membrane integrity over one hour by a set of AFM images revealed differences in the interaction of the three types of protein with zwitterionic and negatively charged membranes. A quantitative analysis of the slow kinetics of hole formation in the negatively charged lipid bilayer is presented. Specifically, analysis of the rate of roughness change for the three types of proteins suggests that they exhibit different types of kinetic behavior.     

Temperature-dependent imaging of living cells by AFM

Characterization of lateral organization of plasma membranes is a prerequisite to the understanding of membrane structure-function relationships in living cells. Lipid-lipid and lipid-protein interactions are responsible for the existence of various membrane microdomains involved in cell signalization and in numerous pathologies. Developing approaches for characterizing microdomains associate identification tools like recognition imaging with high-resolution topographical imaging. Membrane properties are markedly dependent on temperature. However, mesoscopic scale topographical information of cell surface in a temperature range covering most of cell biology experimentation is still lacking. In this work we have examined the possibility of imaging the temperature-dependent behavior of eukaryotic cells by atomic force microscopy (AFM). Our results establish that the surface of living CV1 kidney cells can be imaged by AFM, between 5 and 37 degrees C, both in contact and tapping modes. These first temperature-dependent data show that large cell structures appeared essentially stable at a microscopic scale. On the other hand, as shown by contact mode AFM, the surface was highly dynamic at a mesoscopic scale, with marked changes in apparent topography, friction, and deflection signals. When keeping the scanning conditions constant, a progressive loss in the image contrast was however observed, using tapping mode, on decreasing the temperature.     

Nano-wear of the diamond AFM probing tip under scratching of silicon, studied by AFM

In order to improve such a widely used microtribological testing procedure as surface scratching by an AFM diamond tip, an experimental study has been carried out using single-crystalline silicon as the tested material. Wear of the AFM diamond tip under scratching was observed by a decrease in the scratch depth with increasing wear cycles and by the direct imaging of the diamond tip shape using a Si₃N₄ AFM tip. It was shown that the current widely used experimental method, which assumes the diamond tip to be non-wearable, introduces uncontrollable error into the obtained values for the tested material's wear rate. The harder the tested material, the larger may be the tip wear, and, therefore, the bigger may be its effect on the obtained wear rate values. The specific wear rates for the diamond tip and a silicon wafer were estimated to be 1.4 × 10^-9 and 4.5 × 10^-4 mm³/(N m), respectively.     

Real-Time analysis of exosome secretion of single cells with single molecule imaging

The exosome-mediated response can promote or restrain the diseases by regulating the intracellular pathways, making the exosome become an effective marker for diagnosis and therapeutic control at the single-cell level. However, real-time analysis is hard to be achieved with traditional approaches because the exosomes usually need to be enriched by ultracentrifugation for a measurable signal-to-noise ratio. Recently developed label-free single-molecule imaging approaches may become an real-time quantitative tool for the analysis of single exosomes and related secretion behaviors of single living cells owing to their extreme sensitivity.     

High resolution imaging of surface patterns of single bacterial cells

We systematically studied the origin of surface patterns observed on single Sinorhizobium meliloti bacterial cells by comparing the complementary techniques atomic force microscopy (AFM) and scanning electron microscopy (SEM). Conditions ranged from living bacteria in liquid to fixed bacteria in high vacuum. Stepwise, we applied different sample modifications (fixation, drying, metal coating, etc.) and characterized the observed surface patterns. A detailed analysis revealed that the surface structure with wrinkled protrusions in SEM images were not generated de novo but most likely evolved from similar and naturally present structures on the surface of living bacteria. The influence of osmotic stress to the surface structure of living cells was evaluated and also the contribution of exopolysaccharide and lipopolysaccharide (LPS) by imaging two mutant strains of the bacterium under native conditions. AFM images of living bacteria in culture medium exhibited surface structures of the size of single proteins emphasizing the usefulness of AFM for high resolution cell imaging.     

Optimized hand fabricated AFM probes for simultaneous topographical and electrochemical tapping mode imaging

In this work hybrid AFM-electrochemical (SECM) probes to be used in dynamic atomic force microscopy are presented. These nanosensors are hand fabricated from gold microwires using a simple benchtop method. They display proportions close to commercially available silicon and silicon nitride cantilevers giving comparable performance in terms of resolution and imaging stability. The remarkable characteristic of these hybrid nanosensors is that they allow the coupling of 3D imaging ability and versatility of atomic force microscopy with the power of electrochemical methods. Local measurement of electrochemical-activity of a test sample consisting of gold bands functionalized by redox-labeled nanometer-sized polyethylene glycol chains has been achieved with simultaneous imaging of the 3D surface topography at high resolution. These hybrid AFM-SECM tips are capable of sensing local electrochemical currents down to ∼10 fA emphasizing the sensitivity and resolution of this technique.     

Combining AFM and FRET for high resolution fluorescence microscopy

Here we demonstrate a new microscopic method that combines atomic force microscopy (AFM) with fluorescence resonance energy transfer (FRET). This method takes advantage of the strong distance dependence in Förster energy transfer between dyes with the appropriate donor/acceptor properties to couple an optical dimension with conventional AFM. This is achieved by attaching an acceptor dye to the end of an AFM tip and exciting a sample bound donor dye through far-field illumination. Energy transfer from the excited donor to the tip immobilized acceptor dye leads to emission in the red whenever there is sufficient overlap between the two dyes. Because of the highly exponential distance dependence in this process, only those dyes located at the apex of the AFM tip, nearest the sample, interact strongly. This limited and highly specific interaction provides a mechanism for obtaining fluorescence contrast with high spatial resolution. Initial results in which 400 nm resolution is obtained through this AFM/FRET imaging technique are reported. Future modifications in the probe design are discussed to further improve both the fluorescence resolution and imaging capabilities of this new technique.     

Phase imaging quality improvement by modification of AFM probes’ cantilever

Imaging of the surface of materials by atomic force microscopy under tapping and phase imaging mode, with use of modified probes is addressed. In this study, the circularly shaped holes located in varying distance from the probe base, were cut out by focused ion beam. Such modification was a consequence of the results of the previous experiments (probe tip sharpening and cantilever thinning) where significant improvement of image quality in tapping and phase imaging mode has been revealed. The solution proposed herein gives similar results, but is much simpler from the technological point of view. Shorter exposition time of the tip onto gallium ions during FIB processing allows to reduce material degradation. The aim of this modification was to change harmonic oscillators’ properties in the simplest and fastest way, to obtain stronger signal for higher resonant frequencies, which can be advantageous for improving the quality of imaging in PI mode. Probes shaped in that way were used for AFM investigations with Bruker AFM nanoscope 8. As a testing material, titanium roughness standard sample, supplied by Bruker, was used. The results have shown that the modifications performed within these studies influence the oscillation of the probes, which in some cases may result in deterioration of the imaging quality under tapping mode for one or both self‐resonant frequencies. However, phase imaging results obtained using modified probes are of higher quality. The numerical simulations performed by application of finite element method were used to explain the results obtained experimentally. Phenomenon described within this study allows to apply developed modelling methodology for prediction of effects of various modifications on the probes' tip, and as a result, to predict how proposed modifications will affect AFM imaging quality.     

基于单片机的AFM纳米机械性能测试系统

摘要：目的：为解决采用AFM系统进行纳米机械性能测试中存在的不能够直接获得载荷——压深曲线以及不能够随意改变加载、保载、卸载时间等问题,对AFM系统进行改造。方法：开发了一套基于单片机的信号输入输出模块。将该模块与AFM控制系统相联,形成新的纳米机械性能测试系统。结果：该系统可以实现动态改变垂直载荷,并依据相应算法,可以实现载荷——压深曲线的实时获得。通过单片机设置模拟信号的输出速率可以实现加载、保载和卸载速率的改变。并结合二维微动精密工作台,可以实现较大范围内点阵的压痕测试。结论：通过在聚碳酸酯、聚二甲基硅氧烷等材料表面进行试验测试表明：该系统可以进行高速高精度的测量样品的纳米机械性能参数,包括对样品进行纳米压痕测试和对样品的纯弹性变形过程进行检测如聚二甲基硅氧烷或者各种微梁等微小构件。     

Instrumental requirements for high resolution imaging

The resolution of modern transmission electron microscopes reaches the physical limits imposed by lens aberrations and energy width. One of the many conditions to be fulfilled, the alignment of illuminating and imaging beam onto the coma-free objective axis, is particularly discussed here since axial coma cannot be detected by the usual resolution-checking methods. Space consumption of specimen stages prevents the full utilization of the magnetic saturation limit only in the 100 keV range. With higher energies, this handicap is obviated, and some additional advantages can be gained which promote material investigations at atomic resolution, and which are presently utilized in instrumental research projects. High resolution with biological specimens has up to now been unsuccessful because of radiation damage. Optimum utilization of all electrons scattered at the specimen must thus be given priority over optical resolution. Important instrumental requirements are minimum exposure beam control, imaging modes with high collection efficiency, and recording devices with high detection quantum efficiency connected on-line to image processors. A remarkable decrease in beam sensitivity of organic crystals, by more than one order, has been found by cooling the specimen down to 4 K which, by the use of superconducting lenses, can be combined with both ultra high vacuum and the stability requirements for high resolution. Yet up to now, such protection has not been achieved with He cryostates in conventional lenses, perhaps because a temperature increase even of only a few degree K is harmful. Purely magnetic imaging energy filters are about to be developed to a high optical quality but have been employed so far in only a few high resolution instruments. Such filters allow removal of the inelastic background and thus improvement of contrast of images of low-Z specimens, particularly in the dark field mode. Finally, some ‘non-conventional’ projects have made progress. Correction of spherical and chromatic aberration by multipole lenses offers a chance to improve remarkably the resolution in the 100 keV range, to extend the bandwidth of phase contrast transfer and to obtain highly resolved information about inelastic images when an energy filter is also applied. Electron holography provides possibly useful large area phase contrast, particularly if the electron energy is decreased, which may be of great benefit in investigations of unstained specimens.     

Application of AFM from microbial cell to biofilm

Atomic Force Microscopy (AFM) has proven itself over recent years as an essential tool for the analysis of microbial systems. This article will review how AFM has been used to study microbial systems to provide unique insight into their behavior and relationship with their environment. Immobilization of live cells has enabled AFM imaging and force measurement to provide understanding of the structure and function of numerous microbial cells. At the macromolecular level AFM investigation into the properties of surface macromolecules and the energies associated with their mechanical conformation and functionality has helped unravel the complex interactions of microbial cells. At the level of the whole cell AFM has provided an integrated analysis of how the microbial cell exploits its environment through its selective, adaptable interface, the cell surface. In addition to these areas of study the AFM investigation of microbial biofilms has been vital for industrial and medical process analysis. There exists a tremendous potential for the future application of AFM to microbial systems and this has been strengthened by the trend to use AFM in combination with other characterization methods, such as confocal microscopy and Raman spectroscopy, to elucidate dynamic cellular processes. SCANNING 32: 134–149, 2010. © 2010 Wiley Periodicals, Inc.     

Artesunate induced morphological and mechanical changes of Jurkat cell studied by AFM

In this study, we have used atomic force microscopy (AFM) to study the morphology and mechanical property changes of Jurkat cells exposed to different concentrations of Artesunate (ART) for 24 h at single cellular level. Cell viability and proliferation assays were performed by using the Cell Counting Kit‐8. The concentration of ART, which resulted in the inhibition rate >50% was selected. The AFM images revealed that the cell membrane changed and the ultrastructure also became complex. Mechanical properties of individual cell were tracked with AFM‐based force spectroscopy. The force curves revealed that when a cell was exposed to the ART, the mechanical properties changed obviously. Treated cells had a lower adhesion force of 416.8±37.9 pN, whereas control group had a higher adhesion force of 1064.2±97.0 pN. The Young's modulus decreased to nearly one‐third, from control group of 0.648±0.037 kPa to treated group of 0.254±0.035 kPa and the stiffness increased to nearly 1.5 times, from control group of 1.231±0.084 mN/m to treated group of 1.917±0.137 mN/m. These results suggest that ART can inhibit the proliferation of Jurkat and induce changes in the morphological structure and mechanical properties of Jurkat cells. The high resolution and high sensitivity of AFM can be used to detect morphological and mechanical properties of cells exposed to ART. The AFM may be developed to be a useful tool for detecting the cell death and evaluating the anti‐carcinogen efficacy against tumor cell. SCANNING 31: 83–89, 2009. © 2009 Wiley Periodicals, Inc.     

Mapping of enzyme activity by detection of enzymatic products during AFM imaging with integrated SECM-AFM probes

With the integration of submicro- and nanoelectrodes into atomic force microscopy (AFM) probes using microfabrication techniques, an elegant approach combining scanning electrochemical microscopy (SECM) with AFM has recently been introduced. Simultaneous contact mode imaging of a micropatterned sample with immobilized enzyme spots and imaging of enzyme activity is shown. In contrast to force spectroscopy the conversion of an enzymatic byproduct is directly detected during AFM imaging and correlated to the activity of the enzyme.     

Lateral Displacement of an AFM Tip Observed by In-Situ TEM/AFM Combined Microscopy: The Effect of the Friction in AFM

When the lateral displacement of an AFM tip due to friction is comparable to or larger than the scan size, for example during atomic-scale friction measurement, the interpretation of the friction image is different from the situation where the scan size is much larger than the lateral displacement of the tip and the image is a simple direct mapping of the friction value. This is because, due to the lateral displacement of the tip, the tip is not at the position where the scan indicates, as can be clearly observed by an in-situ TEM/AFM combined microscopy and atomic-scale friction analysis. This lateral displacement of the tip at the nanometer scale affects the shape of the force-distance curve. We discuss the effect of the tip lateral displacement in AFM data and its normal load dependence.     

AFM工作台扫描控制电路的设计

在现有理论的基础上,设计出一种新型的AFM工作台扫描控制电路。介绍了该电路的设计思想,与现有的AFM控制系统相比,X、Y方向的运动采用闭环控制,提高了控制精度。文中还介绍了一种简单实用的PI调节电路,该电路具有结构简单、成本低、功耗小和控制精度高等优点。     

High accuracy FIONA-AFM hybrid imaging

Multi-protein complexes are ubiquitous and play essential roles in many biological mechanisms. Single molecule imaging techniques such as electron microscopy (EM) and atomic force microscopy (AFM) are powerful methods for characterizing the structural properties of multi-protein and multi-protein-DNA complexes. However, a significant limitation to these techniques is the ability to distinguish different proteins from one another. Here, we combine high resolution fluorescence microscopy and AFM (FIONA-AFM) to allow the identification of different proteins in such complexes. Using quantum dots as fiducial markers in addition to fluorescently labeled proteins, we are able to align fluorescence and AFM information to ≥8 nm accuracy. This accuracy is sufficient to identify individual fluorescently labeled proteins in most multi-protein complexes. We investigate the limitations of localization precision and accuracy in fluorescence and AFM images separately and their effects on the overall registration accuracy of FIONA-AFM hybrid images. This combination of the two orthogonal techniques (FIONA and AFM) opens a wide spectrum of possible applications to the study of protein interactions, because AFM can yield high resolution (5-10 nm) information about the conformational properties of multi-protein complexes and the fluorescence can indicate spatial relationships of the proteins in the complexes.     

AFM picking-up manipulation of the metaphase chromosome fragment by using the tweezers-type probe

We have studied the development of a new procedure based on atomic force microscopy (AFM) for the analysis of metaphase chromosome. The aim of this study was to obtain detailed information about the specific locations of genes on the metaphase chromosome. In this research, we performed the manipulation of the metaphase chromosome by using novel AFM probes to obtain chromosome fragments of a smaller size than the ones obtained using the conventional methods, such as glass microneedles. We could pick up the fragment of the metaphase chromosome dissected by the knife-edged probe by using our tweezers-type probe.